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Willige BC, Yoo CY, Saldierna Guzmán JP. What is going on inside of phytochrome B photobodies? THE PLANT CELL 2024; 36:2065-2085. [PMID: 38511271 PMCID: PMC11132900 DOI: 10.1093/plcell/koae084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 12/20/2023] [Accepted: 01/08/2024] [Indexed: 03/22/2024]
Abstract
Plants exhibit an enormous phenotypic plasticity to adjust to changing environmental conditions. For this purpose, they have evolved mechanisms to detect and measure biotic and abiotic factors in their surroundings. Phytochrome B exhibits a dual function, since it serves as a photoreceptor for red and far-red light as well as a thermosensor. In 1999, it was first reported that phytochromes not only translocate into the nucleus but also form subnuclear foci upon irradiation by red light. It took more than 10 years until these phytochrome speckles received their name; these foci were coined photobodies to describe unique phytochrome-containing subnuclear domains that are regulated by light. Since their initial discovery, there has been much speculation about the significance and function of photobodies. Their presumed roles range from pure experimental artifacts to waste deposits or signaling hubs. In this review, we summarize the newest findings about the meaning of phyB photobodies for light and temperature signaling. Recent studies have established that phyB photobodies are formed by liquid-liquid phase separation via multivalent interactions and that they provide diverse functions as biochemical hotspots to regulate gene expression on multiple levels.
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Affiliation(s)
- Björn Christopher Willige
- Department of Soil and Crop Sciences, College of Agricultural Sciences, Colorado State University, Fort Collins, CO 80521, USA
| | - Chan Yul Yoo
- School of Biological Sciences, University of Utah, UT 84112, USA
| | - Jessica Paola Saldierna Guzmán
- Department of Soil and Crop Sciences, College of Agricultural Sciences, Colorado State University, Fort Collins, CO 80521, USA
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2
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Zhan ML, Zhao X, Li XD, Tan ZZ, Xu QZ, Zhou M, Zhao KH. Photoreversible Aggregation of the Biliprotein Containing the First and Second GAF Domains of a Cyanobacteriochrome All2699 in Nostoc sp. PCC7120. Biochemistry 2024; 63:1225-1233. [PMID: 38682295 DOI: 10.1021/acs.biochem.4c00058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2024]
Abstract
As plant photoreceptors, phytochromes are capable of detecting red light and far-red light, thereby governing plant growth. All2699 is a photoreceptor found in Nostoc sp. PCC7120 that specifically responds to red light and far-red light. All2699g1g2 is a truncated protein carrying the first and second GAF (cGMP phosphodiesterase/adenylyl cyclase/FhlA) domains of All2699. In this study, we found that, upon exposure to red light, the protein underwent aggregation, resulting in the formation of protein aggregates. Conversely, under far-red light irradiation, these protein aggregates dissociated. We delved into the factors that impact the aggregation of All2699g1g2, focusing on the protein structure. Our findings showed that the GAF2 domain contains a low-complexity (LC) loop region, which plays a crucial role in mediating protein aggregation. Specifically, phenylalanine at position 239 within the LC loop region was identified as a key site for the aggregation process. Furthermore, our research revealed that various factors, including irradiation time, temperature, concentration, NaCl concentration, and pH value, can impact the aggregation of All2699g1g2. The aggregation led to variations in Pfr concentration depending on temperature, NaCl concentration, and pH value. In contrast, ΔLC did not aggregate and therefore lacked responses to these factors. Consequently, the LC loop region of All2699g1g2 extended and enhanced sensory properties.
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Affiliation(s)
- Min-Li Zhan
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, P. R. China
| | - Xi Zhao
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, P. R. China
| | - Xiao-Dan Li
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, P. R. China
| | - Zi-Zhu Tan
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, P. R. China
| | - Qian-Zhao Xu
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, P. R. China
| | - Ming Zhou
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, P. R. China
| | - Kai-Hong Zhao
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, P. R. China
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Huerta-Venegas PI, Raya-González J, Ruíz-Herrera LF, López-Bucio J. PHYTOCHROME A controls the DNA damage response and cell death tolerance within the Arabidopsis root meristem. PLANT, CELL & ENVIRONMENT 2024; 47:1513-1525. [PMID: 38251425 DOI: 10.1111/pce.14831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 11/21/2023] [Accepted: 01/11/2024] [Indexed: 01/23/2024]
Abstract
The DNA damage response avoids mutations into dividing cells. Here, we analysed the role of photoreceptors on the restriction of root growth imposed by genotoxic agents and its relationship with cell viability and performance of meristems. Comparison of root growth of Arabidopsis WT, phyA-211, phyB-9, and phyA-211phyB-9 double mutants unveiled a critical role for phytochrome A (PhyA) in protecting roots from genotoxic stress, regeneration and cell replenishment in the meristematic zone. PhyA was located on primary root tips, where it influences genes related to the repair of DNA, including ERF115 and RAD51. Interestingly, phyA-211 mutants treated with zeocin failed to induce the expression of the repressor of cell cycle MYB3R3, which correlated with expression of the mitotic cyclin CycB1, suggesting that PhyA is required for safeguarding the DNA integrity during cell division. Moreover, the growth of the primary roots of PhyA downstream component HY5 and root growth analyses in darkness suggest that cell viability and DNA damage responses within root meristems may act independently from light and photomorphogenesis. These data support novel roles for PhyA as a key player for stem cell niche maintenance and DNA damage responses, which are critical for proper root growth.
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Affiliation(s)
- Pedro Iván Huerta-Venegas
- Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Michoacán, México
| | - Javier Raya-González
- Facultad de Químico Farmacobiología, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Michoacán, México
| | - León Francisco Ruíz-Herrera
- Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Michoacán, México
| | - José López-Bucio
- Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Michoacán, México
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Fu Y, Zhu W, Zhou Y, Su Y, Li Z, Zhang D, Zhang D, Shen J, Liang J. RACK1A promotes hypocotyl elongation by scaffolding light signaling components in Arabidopsis. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024; 66:956-972. [PMID: 38558526 DOI: 10.1111/jipb.13651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Accepted: 03/07/2024] [Indexed: 04/04/2024]
Abstract
Plants deploy versatile scaffold proteins to intricately modulate complex cell signaling. Among these, RACK1A (Receptors for Activated C Kinase 1A) stands out as a multifaceted scaffold protein functioning as a central integrative hub for diverse signaling pathways. However, the precise mechanisms by which RACK1A orchestrates signal transduction to optimize seedling development remain largely unclear. Here, we demonstrate that RACK1A facilitates hypocotyl elongation by functioning as a flexible platform that connects multiple key components of light signaling pathways. RACK1A interacts with PHYTOCHROME INTERACTING FACTOR (PIF)3, enhances PIF3 binding to the promoter of BBX11 and down-regulates its transcription. Furthermore, RACK1A associates with ELONGATED HYPOCOTYL 5 (HY5) to repress HY5 biochemical activity toward target genes, ultimately contributing to hypocotyl elongation. In darkness, RACK1A is targeted by CONSTITUTIVELY PHOTOMORPHOGENIC (COP)1 upon phosphorylation and subjected to COP1-mediated degradation via the 26 S proteasome system. Our findings provide new insights into how plants utilize scaffold proteins to regulate hypocotyl elongation, ensuring proper skoto- and photo-morphogenic development.
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Affiliation(s)
- Yajuan Fu
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Department of Biology, School of Life Sciences, Institute of Plant and Food Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Wei Zhu
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Department of Biology, School of Life Sciences, Institute of Plant and Food Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Yeling Zhou
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Department of Biology, School of Life Sciences, Institute of Plant and Food Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Yujing Su
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Department of Biology, School of Life Sciences, Institute of Plant and Food Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Zhiyong Li
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Department of Biology, School of Life Sciences, Institute of Plant and Food Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Dayan Zhang
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Department of Biology, School of Life Sciences, Institute of Plant and Food Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Dong Zhang
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Department of Biology, School of Life Sciences, Institute of Plant and Food Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Jinyu Shen
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Department of Biology, School of Life Sciences, Institute of Plant and Food Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Jiansheng Liang
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Department of Biology, School of Life Sciences, Institute of Plant and Food Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
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Feng Z, Wang M, Liu Y, Li C, Zhang S, Duan J, Chen J, Qi L, Liu Y, Li H, Wu J, Liu Y, Terzaghi W, Tian F, Zhong B, Fang X, Qian W, Guo Y, Deng XW, Li J. Liquid-liquid phase separation of TZP promotes PPK-mediated phosphorylation of the phytochrome A photoreceptor. NATURE PLANTS 2024; 10:798-814. [PMID: 38714768 DOI: 10.1038/s41477-024-01679-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 03/28/2024] [Indexed: 05/10/2024]
Abstract
Phytochrome A (phyA) is the plant far-red (FR) light photoreceptor and plays an essential role in regulating photomorphogenic development in FR-rich conditions, such as canopy shade. It has long been observed that phyA is a phosphoprotein in vivo; however, the protein kinases that could phosphorylate phyA remain largely unknown. Here we show that a small protein kinase family, consisting of four members named PHOTOREGULATORY PROTEIN KINASES (PPKs) (also known as MUT9-LIKE KINASES), directly phosphorylate phyA in vitro and in vivo. In addition, TANDEM ZINC-FINGER/PLUS3 (TZP), a recently characterized phyA-interacting protein required for in vivo phosphorylation of phyA, is also directly phosphorylated by PPKs. We reveal that TZP contains two intrinsically disordered regions in its amino-terminal domain that undergo liquid-liquid phase separation (LLPS) upon light exposure. The LLPS of TZP promotes colocalization and interaction between PPKs and phyA, thus facilitating PPK-mediated phosphorylation of phyA in FR light. Our study identifies PPKs as a class of protein kinases mediating the phosphorylation of phyA and demonstrates that the LLPS of TZP contributes significantly to more production of the phosphorylated phyA form in FR light.
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Affiliation(s)
- Ziyi Feng
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, Frontiers Science Center for Molecular Design Breeding (MOE), China Agricultural University, Beijing, China
| | - Meijiao Wang
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, Frontiers Science Center for Molecular Design Breeding (MOE), China Agricultural University, Beijing, China
| | - Yan Liu
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, Frontiers Science Center for Molecular Design Breeding (MOE), China Agricultural University, Beijing, China
| | - Cong Li
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, Frontiers Science Center for Molecular Design Breeding (MOE), China Agricultural University, Beijing, China
| | - Shaoman Zhang
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, Frontiers Science Center for Molecular Design Breeding (MOE), China Agricultural University, Beijing, China
| | - Jie Duan
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, Frontiers Science Center for Molecular Design Breeding (MOE), China Agricultural University, Beijing, China
| | - Jiaqi Chen
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, Frontiers Science Center for Molecular Design Breeding (MOE), China Agricultural University, Beijing, China
| | - Lijuan Qi
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, Frontiers Science Center for Molecular Design Breeding (MOE), China Agricultural University, Beijing, China
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Yanru Liu
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, Frontiers Science Center for Molecular Design Breeding (MOE), China Agricultural University, Beijing, China
| | - Hong Li
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, Frontiers Science Center for Molecular Design Breeding (MOE), China Agricultural University, Beijing, China
| | - Jie Wu
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Yannan Liu
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | | | - Feng Tian
- State Key Laboratory of Plant Environmental Resilience, Frontiers Science Center for Molecular Design Breeding (MOE), China Agricultural University, Beijing, China
| | - Bojian Zhong
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Xiaofeng Fang
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Weiqiang Qian
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
- State Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, China
| | - Yan Guo
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, Frontiers Science Center for Molecular Design Breeding (MOE), China Agricultural University, Beijing, China
| | - Xing Wang Deng
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
- State Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, China
| | - Jigang Li
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, Frontiers Science Center for Molecular Design Breeding (MOE), China Agricultural University, Beijing, China.
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Li J, Song Y. Plant thermosensors. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 342:112025. [PMID: 38354752 DOI: 10.1016/j.plantsci.2024.112025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 01/02/2024] [Accepted: 02/06/2024] [Indexed: 02/16/2024]
Abstract
Plants dynamically regulate their genes expression and physiological outputs to adapt to changing temperatures. The underlying molecular mechanisms have been extensively studied in diverse plants and in multiple dimensions. However, the question of exactly how temperature is detected at molecular level to transform the physical information into recognizable intracellular signals remains continues to be one of the undetermined occurrences in plant science. Recent studies have provided the physical and biochemical mechanistic breakthrough of how temperature changes can influence molecular thermodynamically stability, thus changing molecular structures, activities, interaction and signaling transduction. In this review, we focus on the thermosensing mechanisms of recognized and potential plant thermosensors, to describe the multi-level thermal input system in plants. We also consider the attributes of a thermosensor on the basis of thermal-triggered changes in function, structure, and physical parameters. This study thus provides a reference for discovering more plant thermosensors and elucidating plant thermal adaptive mechanisms.
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Affiliation(s)
- Jihong Li
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Yuan Song
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, School of Life Sciences, Lanzhou University, Lanzhou, China; Gansu Province Key Laboratory of Gene Editing for Breeding, Lanzhou, China.
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7
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Kwon Y, Kim C, Choi G. Phytochrome B photobody components. THE NEW PHYTOLOGIST 2024; 242:909-915. [PMID: 38477037 DOI: 10.1111/nph.19675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 03/01/2024] [Indexed: 03/14/2024]
Abstract
Phytochrome B (phyB) is a red and far-red photoreceptor that promotes light responses. Upon photoactivation, phyB enters the nucleus and forms a molecular condensate called a photobody through liquid-liquid phase separation. Phytochrome B photobody comprises phyB, the main scaffold molecule, and at least 37 client proteins. These clients belong to diverse functional categories enriched with transcription regulators, encompassing both positive and negative light signaling factors, with the functional bias toward the negative factors. The functionally diverse clients suggest that phyB photobody acts either as a trap to capture proteins, including negatively acting transcription regulators, for processes such as sequestration, modification, or degradation or as a hub where proteins are brought into close proximity for interaction in a light-dependent manner.
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Affiliation(s)
- Yongmin Kwon
- Department of Biological Sciences, KAIST, Daejeon, 34141, Korea
| | - Chanhee Kim
- Department of Biological Sciences, KAIST, Daejeon, 34141, Korea
| | - Giltsu Choi
- Department of Biological Sciences, KAIST, Daejeon, 34141, Korea
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Park YJ, Nam BE, Park CM. Environmentally adaptive reshaping of plant photomorphogenesis by karrikin and strigolactone signaling. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024; 66:865-882. [PMID: 38116738 DOI: 10.1111/jipb.13602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Revised: 12/09/2023] [Accepted: 12/18/2023] [Indexed: 12/21/2023]
Abstract
Coordinated morphogenic adaptation of growing plants is critical for their survival and propagation under fluctuating environments. Plant morphogenic responses to light and warm temperatures, termed photomorphogenesis and thermomorphogenesis, respectively, have been extensively studied in recent decades. During photomorphogenesis, plants actively reshape their growth and developmental patterns to cope with changes in light regimes. Accordingly, photomorphogenesis is closely associated with diverse growth hormonal cues. Notably, accumulating evidence indicates that light-directed morphogenesis is profoundly affected by two recently identified phytochemicals, karrikins (KARs) and strigolactones (SLs). KARs and SLs are structurally related butenolides acting as signaling molecules during a variety of developmental steps, including seed germination. Their receptors and signaling mediators have been identified, and associated working mechanisms have been explored using gene-deficient mutants in various plant species. Of particular interest is that the KAR and SL signaling pathways play important roles in environmental responses, among which their linkages with photomorphogenesis are most comprehensively studied during seedling establishment. In this review, we focus on how the phytochemical and light signals converge on the optimization of morphogenic fitness. We also discuss molecular mechanisms underlying the signaling crosstalks with an aim of developing potential ways to improve crop productivity under climate changes.
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Affiliation(s)
- Young-Joon Park
- Department of Smart Farm Science, Kyung Hee University, Yongin, 17104, Korea
| | - Bo Eun Nam
- Department of Biological Sciences, Seoul National University, Seoul, 08826, Korea
| | - Chung-Mo Park
- Department of Chemistry, Seoul National University, Seoul, 08826, Korea
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Du J, Kim K, Chen M. Distinguishing individual photobodies using Oligopaints reveals thermo-sensitive and -insensitive phytochrome B condensation at distinct subnuclear locations. Nat Commun 2024; 15:3620. [PMID: 38684657 PMCID: PMC11058242 DOI: 10.1038/s41467-024-47789-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 04/10/2024] [Indexed: 05/02/2024] Open
Abstract
Photobodies (PBs) are membraneless subnuclear organelles that self-assemble via concentration-dependent liquid-liquid phase separation (LLPS) of the plant photoreceptor and thermosensor phytochrome B (PHYB). The current PHYB LLPS model posits that PHYB phase separates randomly in the nucleoplasm regardless of the cellular or nuclear context. Here, we established a robust Oligopaints method in Arabidopsis to determine the positioning of individual PBs. We show surprisingly that even in PHYB overexpression lines - where PHYB condensation would be more likely to occur randomly - PBs positioned at twelve distinct subnuclear locations distinguishable by chromocenter and nucleolus landmarks, suggesting that PHYB condensation occurs nonrandomly at preferred seeding sites. Intriguingly, warm temperatures reduce PB number by inducing the disappearance of specific thermo-sensitive PBs, demonstrating that individual PBs possess different thermosensitivities. These results reveal a nonrandom PB nucleation model, which provides the framework for the biogenesis of spatially distinct individual PBs with diverse environmental sensitivities within a single plant nucleus.
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Affiliation(s)
- Juan Du
- Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, CA, 92521, USA
| | - Keunhwa Kim
- Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, CA, 92521, USA
- Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, 52828, Republic of Korea
| | - Meng Chen
- Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, CA, 92521, USA.
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Kim RJA, Fan D, He J, Kim K, Du J, Chen M. Photobody formation spatially segregates two opposing phytochrome B signaling actions of PIF5 degradation and stabilization. Nat Commun 2024; 15:3519. [PMID: 38664420 PMCID: PMC11045832 DOI: 10.1038/s41467-024-47790-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 04/10/2024] [Indexed: 04/28/2024] Open
Abstract
Photoactivation of the plant photoreceptor and thermosensor phytochrome B (PHYB) triggers its condensation into subnuclear membraneless organelles named photobodies (PBs). However, the function of PBs in PHYB signaling remains frustratingly elusive. Here, we found that PHYB recruits PHYTOCHROME-INTERACTING FACTOR 5 (PIF5) to PBs. Surprisingly, PHYB exerts opposing roles in degrading and stabilizing PIF5. Perturbing PB size by overproducing PHYB provoked a biphasic PIF5 response: while a moderate increase in PHYB enhanced PIF5 degradation, further elevating the PHYB level stabilized PIF5 by retaining more of it in enlarged PBs. Conversely, reducing PB size by dim light, which enhanced PB dynamics and nucleoplasmic PHYB and PIF5, switched the balance towards PIF5 degradation. Together, these results reveal that PB formation spatially segregates two antagonistic PHYB signaling actions - PIF5 stabilization in PBs and PIF5 degradation in the surrounding nucleoplasm - which could enable an environmentally sensitive, counterbalancing mechanism to titrate nucleoplasmic PIF5 and environmental responses.
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Affiliation(s)
- Ruth Jean Ae Kim
- Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, CA, 92521, USA
| | - De Fan
- Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, CA, 92521, USA
| | - Jiangman He
- Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, CA, 92521, USA
| | - Keunhwa Kim
- Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, CA, 92521, USA
- Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, 52828, Republic of Korea
| | - Juan Du
- Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, CA, 92521, USA
| | - Meng Chen
- Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, CA, 92521, USA.
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11
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Kimura I, Kanegae T. A phytochrome/phototropin chimeric photoreceptor promotes growth of fern gametophytes under limited light conditions. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:2403-2416. [PMID: 38189579 DOI: 10.1093/jxb/erae003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 01/06/2024] [Indexed: 01/09/2024]
Abstract
Many ferns thrive even in low-light niches such as under an angiosperm forest canopy. However, the shade adaptation strategy of ferns is not well understood. Phytochrome 3/neochrome (phy3/neo) is an unconventional photoreceptor, found in the fern Adiantum capillus-veneris, that controls both red and blue light-dependent phototropism and chloroplast photorelocation, which are considered to improve photosynthetic efficiency in ferns. Here we show that phy3/neo localizes not only at the plasma membrane but also in the nucleus. Since both phototropism and chloroplast photorelocation are mediated by membrane-associated phototropin photoreceptors, we speculated that nucleus-localized phy3/neo possesses a previously undescribed biological function. We reveal that phy3/neo directly interacts with Adiantum cryptochrome 3 (cry3) in the nucleus. Plant cryptochromes are blue light receptors that transcriptionally regulate photomorphogenesis; therefore, phy3/neo may function via cry3 to synchronize light-mediated development with phototropism and chloroplast photorelocation to promote fern growth under low-light conditions. Furthermore, we demonstrate that phy3/neo regulates the expression of the Cyclin-like gene AcCyc1 and promotes prothallium expansion growth. These findings provide insight into the shade adaptation strategy of ferns and suggest that phy3/neo plays a substantial role in the survival and growth of ferns during the tiny gametophytic stage under low-light conditions, such as those on the forest floor.
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Affiliation(s)
- Izumi Kimura
- Department of Biological Sciences, Graduate School of Science and Technology, Tokyo Metropolitan University, Hachioji, Tokyo 192-0397, Japan
| | - Takeshi Kanegae
- Department of Biological Sciences, Graduate School of Science and Technology, Tokyo Metropolitan University, Hachioji, Tokyo 192-0397, Japan
- Department of Biological Sciences, Graduate School of Science, Tokyo Metropolitan University, Hachioji, Tokyo 192-0397, Japan
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12
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Qu L, Zhong M, Duan F, Li X, Yang J, Zhou Q, Tang D, He R, Liu X, Zhao X. The PHYB-FOF2-VOZ2 module functions to fine-tune flowering in response to changes in light quality by modulating FLC expression in Arabidopsis. PLANT COMMUNICATIONS 2024:100922. [PMID: 38616490 DOI: 10.1016/j.xplc.2024.100922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 02/06/2024] [Accepted: 04/11/2024] [Indexed: 04/16/2024]
Abstract
Proper timing of flowering under different environmental conditions is critical for plant propagation. Light quality is a pivotal environmental cue that plays a critical role in flowering regulation. Plants tend to flower late under light with a high red (R)/far-red (FR) light ratio but early under light with a low R/FR light ratio. However, how plants fine-tune flowering in response to changes in light quality is not well understood. Here, we demonstrate that F-box of Flowering 2 (FOF2), an autonomous pathway-related regulator, physically interacts with VASCULAR PLANT ONE-ZINC FINGER 1 and 2 (VOZ1 and VOZ2), which are direct downstream factors of the R/FR light receptor phytochrome B (PHYB). We show that PHYB physically interacts with FOF2, mediates stabilization of the FOF2 protein under FR light and end-of-day FR light, and enhances FOF2 binding to VOZ2, which leads to degradation of VOZ2 by SCFFOF2 E3 ligase. By contrast, PHYB mediates degradation of FOF2 protein under R light and end-of-day R light. Genetic interaction studies demonstrated that FOF2 functions downstream of PHYB to promote FLC expression and inhibit flowering under both high R/FR light and simulated shade conditions, processes that are partially dependent on VOZ proteins. Taken together, our findings suggest a novel mechanism whereby plants fine-tune flowering time through a PHYB-FOF2-VOZ2 module that modulates FLC expression in response to changes in light quality.
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Affiliation(s)
- Lina Qu
- College of Biology, Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan Engineering and Technology Research Center of Hybrid Rapeseed, Hunan University, Changsha 410082, China; Shenzhen Institute, Hunan University, Shenzhen 518057, China
| | - Ming Zhong
- College of Biology, Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan Engineering and Technology Research Center of Hybrid Rapeseed, Hunan University, Changsha 410082, China; Shenzhen Institute, Hunan University, Shenzhen 518057, China
| | - Feifei Duan
- College of Biology, Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan Engineering and Technology Research Center of Hybrid Rapeseed, Hunan University, Changsha 410082, China; Shenzhen Institute, Hunan University, Shenzhen 518057, China
| | - Xinmei Li
- College of Biology, Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan Engineering and Technology Research Center of Hybrid Rapeseed, Hunan University, Changsha 410082, China; Shenzhen Institute, Hunan University, Shenzhen 518057, China
| | - Jiaxin Yang
- College of Biology, Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan Engineering and Technology Research Center of Hybrid Rapeseed, Hunan University, Changsha 410082, China; Shenzhen Institute, Hunan University, Shenzhen 518057, China
| | - Quanyu Zhou
- College of Biology, Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan Engineering and Technology Research Center of Hybrid Rapeseed, Hunan University, Changsha 410082, China; Shenzhen Institute, Hunan University, Shenzhen 518057, China
| | - Dongying Tang
- College of Biology, Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan Engineering and Technology Research Center of Hybrid Rapeseed, Hunan University, Changsha 410082, China
| | - Reqing He
- College of Biology, Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan Engineering and Technology Research Center of Hybrid Rapeseed, Hunan University, Changsha 410082, China
| | - Xuanming Liu
- College of Biology, Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan Engineering and Technology Research Center of Hybrid Rapeseed, Hunan University, Changsha 410082, China.
| | - Xiaoying Zhao
- College of Biology, Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan Engineering and Technology Research Center of Hybrid Rapeseed, Hunan University, Changsha 410082, China; Shenzhen Institute, Hunan University, Shenzhen 518057, China.
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13
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Sénéchal F, Robinson S, Van Schaik E, Trévisan M, Saxena P, Reinhardt D, Fankhauser C. Pectin methylesterification state and cell wall mechanical properties contribute to neighbor proximity-induced hypocotyl growth in Arabidopsis. PLANT DIRECT 2024; 8:e584. [PMID: 38646567 PMCID: PMC11033045 DOI: 10.1002/pld3.584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 01/25/2024] [Accepted: 03/24/2024] [Indexed: 04/23/2024]
Abstract
Plants growing with neighbors compete for light and consequently increase the growth of their vegetative organs to enhance access to sunlight. This response, called shade avoidance syndrome (SAS), involves photoreceptors such as phytochromes as well as phytochrome interacting factors (PIFs), which regulate the expression of growth-mediating genes. Numerous cell wall-related genes belong to the putative targets of PIFs, and the importance of cell wall modifications for enabling growth was extensively shown in developmental models such as dark-grown hypocotyl. However, the contribution of the cell wall in the growth of de-etiolated seedlings regulated by shade cues remains poorly established. Through analyses of mechanical and biochemical properties of the cell wall coupled with transcriptomic analysis of cell wall-related genes from previously published data, we provide evidence suggesting that cell wall modifications are important for neighbor proximity-induced elongation. Further analysis using loss-of-function mutants impaired in the synthesis and remodeling of the main cell wall polymers corroborated this. We focused on the cgr2cgr3 double mutant that is defective in methylesterification of homogalacturonan (HG)-type pectins. By following hypocotyl growth kinetically and spatially and analyzing the mechanical and biochemical properties of cell walls, we found that methylesterification of HG-type pectins was required to enable global cell wall modifications underlying neighbor proximity-induced hypocotyl growth. Collectively, our work suggests that plant competition for light induces changes in the expression of numerous cell wall genes to enable modifications in biochemical and mechanical properties of cell walls that contribute to neighbor proximity-induced growth.
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Affiliation(s)
- Fabien Sénéchal
- Centre for Integrative Genomics, Faculty of Biology and Medicine, Génopode BuildingUniversity of LausanneLausanneSwitzerland
- Present address:
UMR INRAE 1158 BioEcoAgro, Plant Biology and InnovationUniversity of Picardie Jules VerneAmiensFrance
| | - Sarah Robinson
- Institute of Plant SciencesUniversity of BernBernSwitzerland
- Present address:
The Sainsbury LaboratoryUniversity of CambridgeCambridgeUK
| | - Evert Van Schaik
- Department of BiologyUniversity of FribourgFribourgSwitzerland
- Present address:
University of Applied Sciences LeidenLeidenNetherlands
| | - Martine Trévisan
- Centre for Integrative Genomics, Faculty of Biology and Medicine, Génopode BuildingUniversity of LausanneLausanneSwitzerland
| | - Prashant Saxena
- Centre for Integrative Genomics, Faculty of Biology and Medicine, Génopode BuildingUniversity of LausanneLausanneSwitzerland
- Present address:
James Watt School of EngineeringUniversity of GlasgowGlasgowUK
| | | | - Christian Fankhauser
- Centre for Integrative Genomics, Faculty of Biology and Medicine, Génopode BuildingUniversity of LausanneLausanneSwitzerland
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14
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Han R, Ma L, Terzaghi W, Guo Y, Li J. Molecular mechanisms underlying coordinated responses of plants to shade and environmental stresses. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:1893-1913. [PMID: 38289877 DOI: 10.1111/tpj.16653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Revised: 01/09/2024] [Accepted: 01/17/2024] [Indexed: 02/01/2024]
Abstract
Shade avoidance syndrome (SAS) is triggered by a low ratio of red (R) to far-red (FR) light (R/FR ratio), which is caused by neighbor detection and/or canopy shade. In order to compete for the limited light, plants elongate hypocotyls and petioles by deactivating phytochrome B (phyB), a major R light photoreceptor, thus releasing its inhibition of the growth-promoting transcription factors PHYTOCHROME-INTERACTING FACTORs. Under natural conditions, plants must cope with abiotic stresses such as drought, soil salinity, and extreme temperatures, and biotic stresses such as pathogens and pests. Plants have evolved sophisticated mechanisms to simultaneously deal with multiple environmental stresses. In this review, we will summarize recent major advances in our understanding of how plants coordinately respond to shade and environmental stresses, and will also discuss the important questions for future research. A deep understanding of how plants synergistically respond to shade together with abiotic and biotic stresses will facilitate the design and breeding of new crop varieties with enhanced tolerance to high-density planting and environmental stresses.
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Affiliation(s)
- Run Han
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, Frontiers Science Center for Molecular Design Breeding (MOE), China Agricultural University, Beijing, 100193, China
| | - Liang Ma
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, Frontiers Science Center for Molecular Design Breeding (MOE), China Agricultural University, Beijing, 100193, China
| | - William Terzaghi
- Department of Biology, Wilkes University, Wilkes-Barre, Pennsylvania, 18766, USA
| | - Yan Guo
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, Frontiers Science Center for Molecular Design Breeding (MOE), China Agricultural University, Beijing, 100193, China
| | - Jigang Li
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, Frontiers Science Center for Molecular Design Breeding (MOE), China Agricultural University, Beijing, 100193, China
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15
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Sineshchekov VA. Applications of fluorescence spectroscopy in the investigation of plant phytochrome invivo. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 208:108434. [PMID: 38412703 DOI: 10.1016/j.plaphy.2024.108434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 02/08/2024] [Accepted: 02/10/2024] [Indexed: 02/29/2024]
Abstract
Fluorometry is an effective research tool in biology and medicine; it is widely used in the study of the photosynthetic pigment apparatus in vivo. This method can be applied to the key plant photoreceptor phytochrome (phy). The fluorescence of phytochrome in plants was recorded for the first time in the group of the author, and a spectrofluorometric technique for its in vivo study was developed. The photophysical and photochemical properties of the pigment were described, and the photoreceptor was shown to be present in plants as two phenomenological types-active (at cryogenic temperatures) and water-soluble (Pr') and inactive and amphiphilic (Pr″). The scheme of the photoreaction explaining their photochemical distinctions was proposed. Phytochrome A was shown to comprise both types (phyA' and phyA″), whereas phytochrome B was only the second type. For phyA', distinct conformers have been detected. phyA' and phyA″ differ by the N-terminus of the molecule, possibly by serine phosphorylation. They mediate, respectively, the very low fluence and high irradiance photoresponses. Light, internal factors (kinase/phosphatase balance, pH), and hormones (jasmonate) were shown to affect the content and functions of the two phyA pools. All this points to the effectiveness of the developed method for invivo investigations of the phytochrome system. The data obtained can be applied in practical terms in agrobiology and light culture, as well as in the use of phytochrome as a new nanotool and a fluorescent probe.
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Affiliation(s)
- V A Sineshchekov
- Biology Department, M. V. Lomonosov Moscow State University, Moscow, 119234, Russia.
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16
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Wu S, Gao Y, Zhang Q, Liu F, Hu W. Application of Multi-Omics Technologies to the Study of Phytochromes in Plants. Antioxidants (Basel) 2024; 13:99. [PMID: 38247523 PMCID: PMC10812741 DOI: 10.3390/antiox13010099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 01/10/2024] [Accepted: 01/12/2024] [Indexed: 01/23/2024] Open
Abstract
Phytochromes (phy) are distributed in various plant organs, and their physiological effects influence plant germination, flowering, fruiting, and senescence, as well as regulate morphogenesis throughout the plant life cycle. Reactive oxygen species (ROS) are a key regulatory factor in plant systemic responses to environmental stimuli, with an attractive regulatory relationship with phytochromes. With the development of high-throughput sequencing technology, omics techniques have become powerful tools, and researchers have used omics techniques to facilitate the big data revolution. For an in-depth analysis of phytochrome-mediated signaling pathways, integrated multi-omics (transcriptomics, proteomics, and metabolomics) approaches may provide the answer from a global perspective. This article comprehensively elaborates on applying multi-omics techniques in studying phytochromes. We describe the current research status and future directions on transcriptome-, proteome-, and metabolome-related network components mediated by phytochromes when cells are subjected to various stimulation. We emphasize the importance of multi-omics technologies in exploring the effects of phytochromes on cells and their molecular mechanisms. Additionally, we provide methods and ideas for future crop improvement.
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Affiliation(s)
- Shumei Wu
- Basic Medical Experiment Center, School of Traditional Chinese Medicine, Jiangxi University of Chinese Medicine, Nanchang 330004, China; (S.W.); (Y.G.); (Q.Z.)
- Lushan Botanical Garden, Jiangxi Province and Chinese Academy of Sciences, Jiujiang 332000, China
| | - Yue Gao
- Basic Medical Experiment Center, School of Traditional Chinese Medicine, Jiangxi University of Chinese Medicine, Nanchang 330004, China; (S.W.); (Y.G.); (Q.Z.)
| | - Qi Zhang
- Basic Medical Experiment Center, School of Traditional Chinese Medicine, Jiangxi University of Chinese Medicine, Nanchang 330004, China; (S.W.); (Y.G.); (Q.Z.)
| | - Fen Liu
- Lushan Botanical Garden, Jiangxi Province and Chinese Academy of Sciences, Jiujiang 332000, China
| | - Weiming Hu
- Lushan Botanical Garden, Jiangxi Province and Chinese Academy of Sciences, Jiujiang 332000, China
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17
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Kim RJA, Fan D, He J, Kim K, Du J, Chen M. Photobody formation spatially segregates two opposing phytochrome B signaling actions to titrate plant environmental responses. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.12.566724. [PMID: 38014306 PMCID: PMC10680666 DOI: 10.1101/2023.11.12.566724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Photoactivation of the plant photoreceptor and thermosensor phytochrome B (PHYB) triggers its condensation into subnuclear photobodies (PBs). However, the function of PBs remains frustratingly elusive. Here, we found that PHYB recruits PHYTOCHROME-INTERACTING FACTOR5 (PIF5) to PBs. Surprisingly, PHYB exerts opposing roles in degrading and stabilizing PIF5. Perturbing PB size by overproducing PHYB provoked a biphasic PIF5 response: while a moderate increase in PHYB enhanced PIF5 degradation, further elevating the PHYB level stabilized PIF5 by retaining more of it in enlarged PBs. These results reveal a PB-mediated light and temperature sensing mechanism, in which PHYB condensation confers the co-occurrence and competition of two antagonistic phase-separated PHYB signaling actions-PIF5 stabilization in PBs and PIF5 degradation in the surrounding nucleoplasm-thereby enabling an environmentally-sensitive counterbalancing mechanism to titrate nucleoplasmic PIF5 and its transcriptional output. This PB-enabled signaling mechanism provides a framework for regulating a plethora of PHYB-interacting signaling molecules in diverse plant environmental responses.
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Affiliation(s)
- Ruth Jean Ae Kim
- Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, CA 92521, USA
- These authors contributed equally
| | - De Fan
- Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, CA 92521, USA
- These authors contributed equally
| | - Jiangman He
- Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, CA 92521, USA
- These authors contributed equally
| | - Keunhwa Kim
- Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, CA 92521, USA
- Current address: Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Juan Du
- Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, CA 92521, USA
| | - Meng Chen
- Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, CA 92521, USA
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18
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Yao X, Fang K, Qiao K, Xiong J, Lan J, Chen J, Tian Y, Kang X, Lei W, Zhang D, Lin H. Cooperative transcriptional regulation by ATAF1 and HY5 promotes light-induced cotyledon opening in Arabidopsis thaliana. Sci Signal 2024; 17:eadf7318. [PMID: 38166030 DOI: 10.1126/scisignal.adf7318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 11/17/2023] [Indexed: 01/04/2024]
Abstract
The opening of the embryonic leaves (cotyledons) as seedlings emerge from the dark soil into the light is crucial to ensure the survival of the plant. Seedlings that sprout in the dark elongate rapidly to reach light but keep their cotyledons closed. During de-etiolation, the transition from dark to light growth, elongation slows and the cotyledons open. Here, we report that the transcription factor ACTIVATING FACTOR1 (ATAF1) participates in de-etiolation and facilitates light-induced cotyledon opening. The transition from dark to light rapidly induced ATAF1 expression and ATAF1 accumulation in cotyledons. Seedlings lacking or overexpressing ATAF1 exhibited reduced or enhanced cotyledon opening, respectively, and transcriptomic analysis indicated that ATAF1 repressed the expression of genes associated with growth and cotyledon closure. The activation of the photoreceptor phytochrome A (phyA) by far-red light induced its association with the ATAF1 promoter and stimulation of ATAF1 expression. The transcription factor ELONGATED HYPOCOTYL5 (HY5), which is also activated in response far-red light, cooperated with phyA to induce ATAF1 expression. ATAF1 and HY5 interacted with one another and cooperatively repressed the expression of growth-promoting and cotyledon closure genes. Together, our study reveals a mechanism through which far-red light promotes cotyledon opening.
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Affiliation(s)
- Xiuhong Yao
- Ministry of Education Key Laboratory for Bio-Resource and Eco-Environment, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610064, China
- Solid-State Fermentation Resource Utilization Key Laboratory of Sichuan Province, Department of Agriculture Forestry and Food Engineering, Yibin University, Yibin 644000, China
| | - Ke Fang
- Ministry of Education Key Laboratory for Bio-Resource and Eco-Environment, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610064, China
| | - Kang Qiao
- Ministry of Education Key Laboratory for Bio-Resource and Eco-Environment, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610064, China
| | - Jiawei Xiong
- Ministry of Education Key Laboratory for Bio-Resource and Eco-Environment, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610064, China
| | - Jiayi Lan
- Ministry of Education Key Laboratory for Bio-Resource and Eco-Environment, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610064, China
| | - Juan Chen
- Ministry of Education Key Laboratory for Bio-Resource and Eco-Environment, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610064, China
| | - Yuang Tian
- Ministry of Education Key Laboratory for Bio-Resource and Eco-Environment, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610064, China
| | - Xinke Kang
- Ministry of Education Key Laboratory for Bio-Resource and Eco-Environment, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610064, China
| | - Wei Lei
- Ministry of Education Key Laboratory for Bio-Resource and Eco-Environment, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610064, China
| | - Dawei Zhang
- Ministry of Education Key Laboratory for Bio-Resource and Eco-Environment, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610064, China
| | - Honghui Lin
- Ministry of Education Key Laboratory for Bio-Resource and Eco-Environment, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610064, China
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19
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Kim H, Kang HW, Hwang DY, Lee N, Kubota A, Imaizumi T, Song YH. Low temperature-mediated repression and far-red light-mediated induction determine morning FLOWERING LOCUS T expression levels. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024; 66:103-120. [PMID: 38088490 PMCID: PMC10829767 DOI: 10.1111/jipb.13595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 12/12/2023] [Indexed: 01/24/2024]
Abstract
In order to flower in the appropriate season, plants monitor light and temperature changes and alter downstream pathways that regulate florigen genes such as Arabidopsis (Arabidopsis thaliana) FLOWERING LOCUS T (FT). In Arabidopsis, FT messenger RNA levels peak in the morning and evening under natural long-day conditions (LDs). However, the regulatory mechanisms governing morning FT induction remain poorly understood. The morning FT peak is absent in typical laboratory LDs characterized by high red:far-red light (R:FR) ratios and constant temperatures. Here, we demonstrate that ZEITLUPE (ZTL) interacts with the FT repressors TARGET OF EATs (TOEs), thereby repressing morning FT expression in natural environments. Under LDs with simulated sunlight (R:FR = 1.0) and daily temperature cycles, which are natural LD-mimicking environmental conditions, FT transcript levels in the ztl mutant were high specifically in the morning, a pattern that was mirrored in the toe1 toe2 double mutant. Low night-to-morning temperatures increased the inhibitory effect of ZTL on morning FT expression by increasing ZTL protein levels early in the morning. Far-red light counteracted ZTL activity by decreasing its abundance (possibly via phytochrome A (phyA)) while increasing GIGANTEA (GI) levels and negatively affecting the formation of the ZTL-GI complex in the morning. Therefore, the phyA-mediated high-irradiance response and GI play pivotal roles in morning FT induction. Our findings suggest that the delicate balance between low temperature-mediated ZTL activity and the far-red light-mediated functions of phyA and GI offers plants flexibility in fine-tuning their flowering time by controlling FT expression in the morning.
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Affiliation(s)
- Hayeon Kim
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Korea
| | - Hye Won Kang
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Korea
| | | | - Nayoung Lee
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, Korea
| | - Akane Kubota
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara, Japan
| | - Takato Imaizumi
- Department of Biology, University of Washington, Seattle, WA, USA
| | - Young Hun Song
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, Korea
- Institute of Agricultural Life Sciences, Seoul National University, Seoul, Korea
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20
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Kwon Y, Kim C, Choi G. Isolation of Phytochrome B Photobodies. Methods Mol Biol 2024; 2795:113-122. [PMID: 38594533 DOI: 10.1007/978-1-0716-3814-9_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2024]
Abstract
Phytochrome B (phyB), a plant photoreceptor, forms a membraneless organelle known as a photobody. Here, we present a protocol for the isolation of phyB photobodies through fluorescence-activated particle sorting from mature transgenic Arabidopsis leaves expressing phyB-GFP. This protocol involves the isolation of nuclei from frozen ground leaves using sucrose gradient centrifugation, the disruption of nuclear envelopes by sonication, and the subsequent isolation of phyB photobodies through fluorescence-activated particle sorting. We include experimental tips and notes for each step.
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Affiliation(s)
- Yongmin Kwon
- Department of Biological Sciences, KAIST, Daejeon, South Korea
| | - Chanhee Kim
- Department of Biological Sciences, KAIST, Daejeon, South Korea
| | - Giltsu Choi
- Department of Biological Sciences, KAIST, Daejeon, South Korea.
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21
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Peng J, Dong X, Yang S, Li J. Assessing the Function of CBF1 in Modulating the Interaction Between Phytochrome B and PIF4. Methods Mol Biol 2024; 2795:183-194. [PMID: 38594539 DOI: 10.1007/978-1-0716-3814-9_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2024]
Abstract
Phytochromes are red (R) and far-red (FR) light photoreceptors in plants. Upon light exposure, photoactivated phytochromes translocate into the nucleus, where they interact with their partner proteins to transduce light signals. The yeast two-hybrid (Y2H) system is a powerful technique for rapidly identifying and verifying protein-protein interactions, and PHYTOCHROME-INTERACTING FACTOR3 (PIF3), the founding member of the PIF proteins, was initially identified in a Y2H screen for phytochrome B (phyB)-interacting proteins. Recently, we developed a yeast three-hybrid (Y3H) system by introducing an additional vector into this Y2H system, and thus a new regulator could be co-expressed and its role in modulating the interactions between phytochromes and their signaling partners could be examined. By employing this Y3H system, we recently showed that both MYB30 and CBF1, two negative regulators of seedlings photomorphogenesis, act to inhibit the interactions between phyB and PIF4/PIF5. In this chapter, we will use the CBF1-phyB-PIF4 module as an example and describe the detailed procedure for performing this Y3H assay. It will be intriguing and exciting to explore the potential usage of this Y3H system in future research.
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Affiliation(s)
- Jing Peng
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Xiaojing Dong
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Shuhua Yang
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Jigang Li
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing, China.
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22
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Mu XR, Wang YB, Bao QX, Wei YT, Zhao ST, Tao WZ, Liu YX, Wang WN, Yu FH, Tong C, Wang JW, Gu CY, Wang QM, Liu XR, Sai N, Zhu JL, Zhang J, Loake GJ, Meng LS. Glucose status within dark-grown etiolated cotyledons determines seedling de-etiolation upon light irradiation. PLANT PHYSIOLOGY 2023; 194:391-407. [PMID: 37738410 DOI: 10.1093/plphys/kiad508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 09/06/2023] [Accepted: 09/08/2023] [Indexed: 09/24/2023]
Abstract
Exposure of dark-grown etiolated seedlings to light triggers the transition from skotomorphogenesis/etiolation to photomorphogenesis/de-etiolation. In the life cycle of plants, de-etiolation is essential for seedling development and plant survival. The mobilization of soluble sugars (glucose [Glc], sucrose, and fructose) derived from stored carbohydrates and lipids to target organs, including cotyledons, hypocotyls, and radicles, underpins de-etiolation. Therefore, dynamic carbohydrate biochemistry is a key feature of this phase transition. However, the molecular mechanisms coordinating carbohydrate status with the cellular machinery orchestrating de-etiolation remain largely opaque. Here, we show that the Glc sensor HEXOKINASE 1 (HXK1) interacts with GROWTH REGULATOR FACTOR5 (GRF5), a transcriptional activator and key plant growth regulator, in Arabidopsis (Arabidopsis thaliana). Subsequently, GRF5 directly binds to the promoter of phytochrome A (phyA), encoding a far-red light (FR) sensor/cotyledon greening inhibitor. We demonstrate that the status of Glc within dark-grown etiolated cotyledons determines the de-etiolation of seedlings when exposed to light irradiation by the HXK1-GRF5-phyA molecular module. Thus, following seed germination, accumulating Glc within dark-grown etiolated cotyledons stimulates a HXK1-dependent increase of GRF5 and an associated decrease of phyA, triggering the perception, amplification, and relay of HXK1-dependent Glc signaling, thereby facilitating the de-etiolation of seedlings following light irradiation. Our findings, therefore, establish how cotyledon carbohydrate signaling under subterranean darkness is sensed, amplified, and relayed, determining the phase transition from skotomorphogenesis to photomorphogenesis on exposure to light irradiation.
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Affiliation(s)
- Xin-Rong Mu
- The Key Laboratory of Biotechnology for Medicinal Plants of Jiangsu Province, School of Life Science, Jiangsu Normal University, Xuzhou 221116, People's Republic of China
- State Key Laboratory of Pharmaceutical Biotechnology, Institute of Plant Molecular Biology, School of Life Sciences, Nanjing University, Nanjing 210023, People's Republic of China
| | - Yi-Bo Wang
- College of Bioengineering and Biotechnology, Tianshui Normal University, Tianshui 741600, People's Republic of China
| | - Qin-Xin Bao
- The Key Laboratory of Biotechnology for Medicinal Plants of Jiangsu Province, School of Life Science, Jiangsu Normal University, Xuzhou 221116, People's Republic of China
| | - Yu-Ting Wei
- The Key Laboratory of Biotechnology for Medicinal Plants of Jiangsu Province, School of Life Science, Jiangsu Normal University, Xuzhou 221116, People's Republic of China
| | - Sheng-Ting Zhao
- The Key Laboratory of Biotechnology for Medicinal Plants of Jiangsu Province, School of Life Science, Jiangsu Normal University, Xuzhou 221116, People's Republic of China
| | - Wen-Zhe Tao
- The Key Laboratory of Biotechnology for Medicinal Plants of Jiangsu Province, School of Life Science, Jiangsu Normal University, Xuzhou 221116, People's Republic of China
| | - Yu-Xin Liu
- The Key Laboratory of Biotechnology for Medicinal Plants of Jiangsu Province, School of Life Science, Jiangsu Normal University, Xuzhou 221116, People's Republic of China
| | - Wan-Ni Wang
- The Key Laboratory of Biotechnology for Medicinal Plants of Jiangsu Province, School of Life Science, Jiangsu Normal University, Xuzhou 221116, People's Republic of China
| | - Fu-Huan Yu
- The Key Laboratory of Biotechnology for Medicinal Plants of Jiangsu Province, School of Life Science, Jiangsu Normal University, Xuzhou 221116, People's Republic of China
| | - Chen Tong
- The Key Laboratory of Biotechnology for Medicinal Plants of Jiangsu Province, School of Life Science, Jiangsu Normal University, Xuzhou 221116, People's Republic of China
| | - Jing-Wen Wang
- The Key Laboratory of Biotechnology for Medicinal Plants of Jiangsu Province, School of Life Science, Jiangsu Normal University, Xuzhou 221116, People's Republic of China
| | - Cheng-Yue Gu
- The Key Laboratory of Biotechnology for Medicinal Plants of Jiangsu Province, School of Life Science, Jiangsu Normal University, Xuzhou 221116, People's Republic of China
| | - Qi-Meng Wang
- The Key Laboratory of Biotechnology for Medicinal Plants of Jiangsu Province, School of Life Science, Jiangsu Normal University, Xuzhou 221116, People's Republic of China
| | - Xin-Ran Liu
- The Key Laboratory of Biotechnology for Medicinal Plants of Jiangsu Province, School of Life Science, Jiangsu Normal University, Xuzhou 221116, People's Republic of China
| | - Na Sai
- The Key Laboratory of Biotechnology for Medicinal Plants of Jiangsu Province, School of Life Science, Jiangsu Normal University, Xuzhou 221116, People's Republic of China
| | - Jin-Lei Zhu
- The Key Laboratory of Biotechnology for Medicinal Plants of Jiangsu Province, School of Life Science, Jiangsu Normal University, Xuzhou 221116, People's Republic of China
| | - Jian Zhang
- The Key Laboratory of Biotechnology for Medicinal Plants of Jiangsu Province, School of Life Science, Jiangsu Normal University, Xuzhou 221116, People's Republic of China
| | - Gary J Loake
- Centre for Transformative Biotechnology of Medicinal and Food Plants, Jiangsu Normal University-Edinburgh University, Jiangsu Normal University, Xuzhou 221116, People's Republic of China
- Institute of Molecular Plant Sciences, School of Biological Sciences, Edinburgh University, Edinburgh EH9 3JR, UK
| | - Lai-Sheng Meng
- The Key Laboratory of Biotechnology for Medicinal Plants of Jiangsu Province, School of Life Science, Jiangsu Normal University, Xuzhou 221116, People's Republic of China
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23
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Staudt AM, Kretsch T, Hiltbrunner A. EID1 promotes the response to canopy shade in Arabidopsis thaliana by repressing the action of phytochrome A. MICROPUBLICATION BIOLOGY 2023; 2023:10.17912/micropub.biology.001015. [PMID: 38152059 PMCID: PMC10751583 DOI: 10.17912/micropub.biology.001015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 11/29/2023] [Accepted: 12/05/2023] [Indexed: 12/29/2023]
Abstract
The phytochrome (phy) system enables plants to adapt to canopy shade. By sensing the reduction of the red:far-red light ratio in shade, phyA and phyB trigger downstream signalling cascades which eventually lead to enhanced elongation growth. In this study, we show that the F-box protein EID1 takes on an essential function within the shade avoidance response in Arabidopsis thaliana by repressing phyA action and thereby allowing seedlings to elongate in shade. Thus, altering EID1 activity provides a means to adapt the shade response without affecting phyB action and could have played a role in the evolution of shade tolerance.
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Affiliation(s)
| | - Thomas Kretsch
- Institute of Biology II, University of Freiburg, Germany
| | - Andreas Hiltbrunner
- Institute of Biology II, University of Freiburg, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg
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24
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Mammarella MF, Lucero L, Hussain N, Muñoz‐Lopez A, Huang Y, Ferrero L, Fernandez‐Milmanda GL, Manavella P, Benhamed M, Crespi M, Ballare CL, Gutiérrez Marcos J, Cubas P, Ariel F. Long noncoding RNA-mediated epigenetic regulation of auxin-related genes controls shade avoidance syndrome in Arabidopsis. EMBO J 2023; 42:e113941. [PMID: 38054357 PMCID: PMC10711646 DOI: 10.15252/embj.2023113941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 10/04/2023] [Accepted: 10/18/2023] [Indexed: 12/07/2023] Open
Abstract
The long noncoding RNA (lncRNA) AUXIN-REGULATED PROMOTER LOOP (APOLO) recognizes a subset of target loci across the Arabidopsis thaliana genome by forming RNA-DNA hybrids (R-loops) and modulating local three-dimensional chromatin conformation. Here, we show that APOLO regulates shade avoidance syndrome by dynamically modulating expression of key factors. In response to far-red (FR) light, expression of APOLO anti-correlates with that of its target BRANCHED1 (BRC1), a master regulator of shoot branching in Arabidopsis thaliana. APOLO deregulation results in BRC1 transcriptional repression and an increase in the number of branches. Accumulation of APOLO transcription fine-tunes the formation of a repressive chromatin loop encompassing the BRC1 promoter, which normally occurs only in leaves and in a late response to far-red light treatment in axillary buds. In addition, our data reveal that APOLO participates in leaf hyponasty, in agreement with its previously reported role in the control of auxin homeostasis through direct modulation of auxin synthesis gene YUCCA2, and auxin efflux genes PID and WAG2. We show that direct application of APOLO RNA to leaves results in a rapid increase in auxin signaling that is associated with changes in the plant response to far-red light. Collectively, our data support the view that lncRNAs coordinate shade avoidance syndrome in A. thaliana, and reveal their potential as exogenous bioactive molecules. Deploying exogenous RNAs that modulate plant-environment interactions may therefore become a new tool for sustainable agriculture.
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Affiliation(s)
| | - Leandro Lucero
- Instituto de Agrobiotecnología del Litoral, CONICETUniversidad Nacional del LitoralSanta FeArgentina
| | | | - Aitor Muñoz‐Lopez
- Plant Molecular Genetics Department, Centro Nacional de Biotecnología‐CSICCampus Universidad Autónoma de MadridMadridSpain
| | - Ying Huang
- Institute of Plant Sciences Paris Saclay IPS2, CNRS, INRAUniversité Evry, Université Paris‐SaclayOrsayFrance
- Institute of Plant Sciences Paris‐Saclay IPS2Université de ParisOrsayFrance
| | - Lucia Ferrero
- Instituto de Agrobiotecnología del Litoral, CONICETUniversidad Nacional del LitoralSanta FeArgentina
| | - Guadalupe L Fernandez‐Milmanda
- Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura (IFEVA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)Universidad de Buenos AiresBuenos AiresArgentina
| | - Pablo Manavella
- Instituto de Agrobiotecnología del Litoral, CONICETUniversidad Nacional del LitoralSanta FeArgentina
| | - Moussa Benhamed
- Institute of Plant Sciences Paris Saclay IPS2, CNRS, INRAUniversité Evry, Université Paris‐SaclayOrsayFrance
- Institute of Plant Sciences Paris‐Saclay IPS2Université de ParisOrsayFrance
| | - Martin Crespi
- Institute of Plant Sciences Paris Saclay IPS2, CNRS, INRAUniversité Evry, Université Paris‐SaclayOrsayFrance
- Institute of Plant Sciences Paris‐Saclay IPS2Université de ParisOrsayFrance
| | - Carlos L Ballare
- Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura (IFEVA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)Universidad de Buenos AiresBuenos AiresArgentina
- Instituto de Investigaciones Biotecnológicas (IIBIO), CONICETUniversidad Nacional de San MartínBuenos AiresArgentina
| | | | - Pilar Cubas
- Plant Molecular Genetics Department, Centro Nacional de Biotecnología‐CSICCampus Universidad Autónoma de MadridMadridSpain
| | - Federico Ariel
- Instituto de Agrobiotecnología del Litoral, CONICETUniversidad Nacional del LitoralSanta FeArgentina
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25
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Ince YÇ, Sugimoto K. Illuminating the path to shoot meristem regeneration: Molecular insights into reprogramming cells into stem cells. CURRENT OPINION IN PLANT BIOLOGY 2023; 76:102452. [PMID: 37709567 DOI: 10.1016/j.pbi.2023.102452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 08/08/2023] [Accepted: 08/23/2023] [Indexed: 09/16/2023]
Abstract
Plant cells possess the ability to dedifferentiate and reprogram into stem cell-like populations, enabling the regeneration of new organs. However, the maintenance of stem cells relies on specialized microenvironments composed of distinct cell populations with specific functions. Consequently, the regeneration process necessitates the orchestrated regulation of multiple pathways across diverse cellular populations. One crucial pathway involves the transcription factor WUSCHEL HOMEOBOX 5 (WOX5), which plays a pivotal role in reprogramming cells into stem cells and promoting their conversion into shoot meristems through WUSCHEL (WUS). Additionally, cell and tissue mechanics, including cell wall modifications and mechanical stress, critically contribute to de novo shoot organogenesis by regulating polar auxin transport. Furthermore, light signaling emerges as a key regulator of plant regeneration, directly influencing expression of meristem genes and potentially influencing aforementioned pathways as well.
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Affiliation(s)
- Yetkin Çaka Ince
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehirocho, Tsurumi, Yokohama, Kanagawa, 230-0045 Japan.
| | - Keiko Sugimoto
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehirocho, Tsurumi, Yokohama, Kanagawa, 230-0045 Japan; Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo, 113-0033 Japan.
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26
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Legris M. Light and temperature regulation of leaf morphogenesis in Arabidopsis. THE NEW PHYTOLOGIST 2023; 240:2191-2196. [PMID: 37715490 DOI: 10.1111/nph.19258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 07/31/2023] [Indexed: 09/17/2023]
Abstract
Leaves are the main photosynthetic organs in plants, and their anatomy is optimized for light interception and gas exchange. Although each species has a characteristic leaf anatomy, which depends on the genotype, leaves also show a large degree of developmental plasticity. Light and temperature regulate leaf development from primordia differentiation to late stages of blade expansion. While the molecular mechanisms of light and temperature signaling have been mostly studied in seedlings, in the latest years, research has focused on leaf development. Here, I will describe the latest work carried out in the environmental regulation of Arabidopsis leaf development, comparing signaling mechanisms between leaves and seedlings, highlighting the new discoveries, and pointing out the most exciting open questions.
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Affiliation(s)
- Martina Legris
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, Genopode Building, 1015, Lausanne, Switzerland
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27
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Gao Q, Hu S, Wang X, Han F, Luo H, Liu Z, Kang C. The red/far-red light photoreceptor FvePhyB regulates tissue elongation and anthocyanin accumulation in woodland strawberry. HORTICULTURE RESEARCH 2023; 10:uhad232. [PMID: 38143485 PMCID: PMC10745270 DOI: 10.1093/hr/uhad232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 11/01/2023] [Indexed: 12/26/2023]
Abstract
Light is an important environmental signal that influences plant growth and development. Among the photoreceptors, phytochromes can sense red/far-red light to coordinate various biological processes. However, their functions in strawberry are not yet known. In this study, we identified an EMS mutant, named P8, in woodland strawberry (Fragaria vesca) that showed greatly increased plant height and reduced anthocyanin content. Mapping-by-sequencing revealed that the causal mutation in FvePhyB leads to premature termination of translation. The light treatment assay revealed that FvePhyB is a bona fide red/far-red light photoreceptor, as it specifically inhibits hypocotyl length under red light. Transcriptome analysis showed that the FvePhyB mutation affects the expression levels of genes involved in hormone synthesis and signaling and anthocyanin biosynthesis in petioles and fruits. The srl mutant with a longer internode is caused by a mutation in the DELLA gene FveRGA1 (Repressor of GA1) in the gibberellin pathway. We found that the P8 srl double mutant has much longer internodes than srl, suggesting a synergistic role of FvePhyB and FveRGA1 in this process. Taken together, these results demonstrate the important role of FvePhyB in regulating plant architecture and anthocyanin content in woodland strawberry.
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Affiliation(s)
- Qi Gao
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Shaoqiang Hu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Xiaoli Wang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Fu Han
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Huifeng Luo
- Institute of Horticulture, Hangzhou Academy of Agricultural Sciences, Hangzhou, 310024, China
| | - Zhongchi Liu
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, 20742, USA
| | - Chunying Kang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
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28
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Diao R, Zhao M, Liu Y, Zhang Z, Zhong B. The advantages of crosstalk during the evolution of the BZR1-ARF6-PIF4 (BAP) module. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:2631-2644. [PMID: 37552560 DOI: 10.1111/jipb.13554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 08/07/2023] [Indexed: 08/10/2023]
Abstract
The BAP module, comprising BRASSINAZOLE RESISTANT 1 (BZR1), AUXIN RESPONSE FACTOR 6 (ARF6), and PHYTOCHROME-INTERACTING FACTOR 4 (PIF4), functions as a molecular hub to orchestrate plant growth and development. In Arabidopsis thaliana, components of the BAP module physically interact to form a complex system that integrates light, brassinosteroid (BR), and auxin signals. Little is known about the origin and evolution of the BAP module. Here, we conducted comparative genomic and transcriptomic analyses to investigate the evolution and functional diversification of the BAP module. Our results suggest that the BAP module originated in land plants and that the ζ, ε, and γ whole-genome duplication/triplication events contributed to the expansion of BAP module components in seed plants. Comparative transcriptomic analysis suggested that the prototype BAP module arose in Marchantia polymorpha, experienced stepwise evolution, and became established as a mature regulatory system in seed plants. We developed a formula to calculate the signal transduction productivity of the BAP module and demonstrate that more crosstalk among components enables higher signal transduction efficiency. Our results reveal the evolutionary history of the BAP module and provide insights into the evolution of plant signaling networks and the strategies employed by plants to integrate environmental and endogenous signals.
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Affiliation(s)
- Runjie Diao
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Mengru Zhao
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Yannan Liu
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Zhenhua Zhang
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Bojian Zhong
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
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29
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Liu Y, Singh SK, Pattanaik S, Wang H, Yuan L. Light regulation of the biosynthesis of phenolics, terpenoids, and alkaloids in plants. Commun Biol 2023; 6:1055. [PMID: 37853112 PMCID: PMC10584869 DOI: 10.1038/s42003-023-05435-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 10/09/2023] [Indexed: 10/20/2023] Open
Abstract
Biosynthesis of specialized metabolites (SM), including phenolics, terpenoids, and alkaloids, is stimulated by many environmental factors including light. In recent years, significant progress has been made in understanding the regulatory mechanisms involved in light-stimulated SM biosynthesis at the transcriptional, posttranscriptional, and posttranslational levels of regulation. While several excellent recent reviews have primarily focused on the impacts of general environmental factors, including light, on biosynthesis of an individual class of SM, here we highlight the regulation of three major SM biosynthesis pathways by light-responsive gene expression, microRNA regulation, and posttranslational modification of regulatory proteins. In addition, we present our future perspectives on this topic.
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Affiliation(s)
- Yongliang Liu
- Department of Plant and Soil Sciences and Kentucky Tobacco Research and Development Center, University of Kentucky, Lexington, KY, 40546, USA
| | - Sanjay K Singh
- Department of Plant and Soil Sciences and Kentucky Tobacco Research and Development Center, University of Kentucky, Lexington, KY, 40546, USA
| | - Sitakanta Pattanaik
- Department of Plant and Soil Sciences and Kentucky Tobacco Research and Development Center, University of Kentucky, Lexington, KY, 40546, USA.
| | - Hongxia Wang
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences Chenshan Botanical Garden, 3888 Chenhua Road, 201602, Songjiang, Shanghai, China.
| | - Ling Yuan
- Department of Plant and Soil Sciences and Kentucky Tobacco Research and Development Center, University of Kentucky, Lexington, KY, 40546, USA.
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30
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Careno DA, Assaf CH, Eggermont EDC, Canelo M, Cerdán PD, Yanovsky MJ. Role of Phytochromes in Red Light-Regulated Alternative Splicing in Arabidopsis thaliana: Impactful but Not Indispensable. Cells 2023; 12:2447. [PMID: 37887291 PMCID: PMC10605401 DOI: 10.3390/cells12202447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 10/04/2023] [Accepted: 10/10/2023] [Indexed: 10/28/2023] Open
Abstract
Light is both the main source of energy and a key environmental signal for plants. It regulates not only gene expression but also the tightly related processes of splicing and alternative splicing (AS). Two main pathways have been proposed to link light sensing with the splicing machinery. One occurs through a photosynthesis-related signal, and the other is mediated by photosensory proteins, such as red light-sensing phytochromes. Here, we evaluated the relative contribution of each of these pathways by performing a transcriptome-wide analysis of light regulation of AS in plants that do not express any functional phytochrome (phyQ). We found that an acute 2-h red-light pulse in the middle of the night induces changes in the splicing patterns of 483 genes in wild-type plants. Approximately 30% of these genes also showed strong light regulation of splicing patterns in phyQ mutant plants, revealing that phytochromes are important but not essential for the regulation of AS by R light. We then performed a meta-analysis of related transcriptomic datasets and found that different light regulatory pathways can have overlapping targets in terms of AS regulation. All the evidence suggests that AS is regulated simultaneously by various light signaling pathways, and the relative contribution of each pathway is highly dependent on the plant developmental stage.
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Affiliation(s)
- Daniel Alejandro Careno
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires–Consejo Nacional de Investigaciones Científicas y Técnicas (IIBBA-CONICET), Buenos Aires C1405BWE, Argentina; (C.H.A.); (E.D.C.E.); (M.C.); (P.D.C.)
- Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires C1428EGA, Argentina
| | - Constanza Helena Assaf
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires–Consejo Nacional de Investigaciones Científicas y Técnicas (IIBBA-CONICET), Buenos Aires C1405BWE, Argentina; (C.H.A.); (E.D.C.E.); (M.C.); (P.D.C.)
- Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires C1428EGA, Argentina
| | - Eline Dieuwerke Catharina Eggermont
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires–Consejo Nacional de Investigaciones Científicas y Técnicas (IIBBA-CONICET), Buenos Aires C1405BWE, Argentina; (C.H.A.); (E.D.C.E.); (M.C.); (P.D.C.)
- Plant-Environment Signaling Group, Department of Biology, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Micaela Canelo
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires–Consejo Nacional de Investigaciones Científicas y Técnicas (IIBBA-CONICET), Buenos Aires C1405BWE, Argentina; (C.H.A.); (E.D.C.E.); (M.C.); (P.D.C.)
- Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires C1428EGA, Argentina
| | - Pablo Diego Cerdán
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires–Consejo Nacional de Investigaciones Científicas y Técnicas (IIBBA-CONICET), Buenos Aires C1405BWE, Argentina; (C.H.A.); (E.D.C.E.); (M.C.); (P.D.C.)
- Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires C1428EGA, Argentina
| | - Marcelo Javier Yanovsky
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires–Consejo Nacional de Investigaciones Científicas y Técnicas (IIBBA-CONICET), Buenos Aires C1405BWE, Argentina; (C.H.A.); (E.D.C.E.); (M.C.); (P.D.C.)
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31
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Wang J, Zhou C, Guan Z, Wang Q, Zhao J, Wang L, Zhang L, Zhang D, Deng XW, Ma L, Yin P. Plant phytochrome A in the Pr state assembles as an asymmetric dimer. Cell Res 2023; 33:802-805. [PMID: 37402899 PMCID: PMC10542778 DOI: 10.1038/s41422-023-00847-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Accepted: 06/24/2023] [Indexed: 07/06/2023] Open
Affiliation(s)
- Jiao Wang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Chen Zhou
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Zeyuan Guan
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Qiang Wang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Jun Zhao
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang, Shandong, China
| | - Lixia Wang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Liuqing Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Delin Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Xing Wang Deng
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang, Shandong, China
| | - Ling Ma
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei, China.
| | - Ping Yin
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei, China.
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Zhang Y, Lin X, Ma C, Zhao J, Shang X, Wang Z, Xu B, Gao N, Deng XW, Wang J. Structural insights into plant phytochrome A as a highly sensitized photoreceptor. Cell Res 2023; 33:806-809. [PMID: 37491602 PMCID: PMC10542756 DOI: 10.1038/s41422-023-00858-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 07/16/2023] [Indexed: 07/27/2023] Open
Affiliation(s)
- Yuxuan Zhang
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences at Weifang, Weifang, Shandong, China
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing, China
| | - Xiaoli Lin
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences at Weifang, Weifang, Shandong, China
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing, China
| | - Chengying Ma
- Peking-Tsinghua Joint Center for Life Sciences, Peking University, Beijing, China
- State Key Laboratory of Membrane Biology, School of Life Sciences, Peking University, Beijing, China
| | - Jun Zhao
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences at Weifang, Weifang, Shandong, China
| | - Xiaojin Shang
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences at Weifang, Weifang, Shandong, China
| | - Zhengdong Wang
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences at Weifang, Weifang, Shandong, China
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing, China
- Peking-Tsinghua Joint Center for Life Sciences, Peking University, Beijing, China
| | - Bin Xu
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences at Weifang, Weifang, Shandong, China
| | - Ning Gao
- Peking-Tsinghua Joint Center for Life Sciences, Peking University, Beijing, China
- State Key Laboratory of Membrane Biology, School of Life Sciences, Peking University, Beijing, China
| | - Xing Wang Deng
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences at Weifang, Weifang, Shandong, China.
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing, China.
- Peking-Tsinghua Joint Center for Life Sciences, Peking University, Beijing, China.
| | - Jizong Wang
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences at Weifang, Weifang, Shandong, China.
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing, China.
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33
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Li H, Zhou Y, Qin X, Peng J, Han R, Lv Y, Li C, Qi L, Qu GP, Yang L, Li Y, Terzaghi W, Li Z, Qin F, Gong Z, Deng XW, Li J. Reconstitution of phytochrome A-mediated light modulation of the ABA signaling pathways in yeast. Proc Natl Acad Sci U S A 2023; 120:e2302901120. [PMID: 37590408 PMCID: PMC10450666 DOI: 10.1073/pnas.2302901120] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 07/06/2023] [Indexed: 08/19/2023] Open
Abstract
Abscisic acid (ABA), a classical plant hormone, plays an essential role in plant adaptation to environmental stresses. The ABA signaling mechanisms have been extensively investigated, and it was shown that the PYR1 (PYRABACTIN RESISTANCE1)/PYL (PYR1-LIKE)/RCAR (REGULATORY COMPONENT OF ABA RECEPTOR) ABA receptors, the PP2C coreceptors, and the SnRK2 protein kinases constitute the core ABA signaling module responsible for ABA perception and initiation of downstream responses. We recently showed that ABA signaling is modulated by light signals, but the underlying molecular mechanisms remain largely obscure. In this study, we established a system in yeast cells that was not only successful in reconstituting a complete ABA signaling pathway, from hormone perception to ABA-responsive gene expression, but also suitable for functionally characterizing the regulatory roles of additional factors of ABA signaling. Using this system, we analyzed the roles of several light signaling components, including the red and far-red light photoreceptors phytochrome A (phyA) and phyB, and the photomorphogenic central repressor COP1, in the regulation of ABA signaling. Our results showed that both phyA and phyB negatively regulated ABA signaling, whereas COP1 positively regulated ABA signaling in yeast cells. Further analyses showed that photoactivated phyA interacted with the ABA coreceptors ABI1 and ABI2 to decrease their interactions with the ABA receptor PYR1. Together, data from our reconstituted yeast ABA signaling system provide evidence that photoactivated photoreceptors attenuate ABA signaling by directly interacting with the key components of the core ABA signaling module, thus conferring enhanced ABA tolerance to light-grown plants.
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Affiliation(s)
- Hong Li
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, Frontiers Science Center for Molecular Design Breeding, China Agricultural University, Beijing100193, China
| | - Yangyang Zhou
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, Frontiers Science Center for Molecular Design Breeding, China Agricultural University, Beijing100193, China
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing100871, China
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, Shandong261325, China
| | - Xinyan Qin
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, Frontiers Science Center for Molecular Design Breeding, China Agricultural University, Beijing100193, China
| | - Jing Peng
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, Frontiers Science Center for Molecular Design Breeding, China Agricultural University, Beijing100193, China
| | - Run Han
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, Frontiers Science Center for Molecular Design Breeding, China Agricultural University, Beijing100193, China
| | - Yang Lv
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, Frontiers Science Center for Molecular Design Breeding, China Agricultural University, Beijing100193, China
| | - Cong Li
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, Frontiers Science Center for Molecular Design Breeding, China Agricultural University, Beijing100193, China
| | - Lijuan Qi
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, Frontiers Science Center for Molecular Design Breeding, China Agricultural University, Beijing100193, China
| | - Gao-Ping Qu
- Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou350002, China
| | - Li Yang
- Department of Plant Pathology, China Agricultural University, Beijing100193, China
| | - Yanjie Li
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT06520
| | | | - Zhen Li
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, Frontiers Science Center for Molecular Design Breeding, China Agricultural University, Beijing100193, China
| | - Feng Qin
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, Frontiers Science Center for Molecular Design Breeding, China Agricultural University, Beijing100193, China
| | - Zhizhong Gong
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, Frontiers Science Center for Molecular Design Breeding, China Agricultural University, Beijing100193, China
| | - Xing Wang Deng
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing100871, China
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, Shandong261325, China
| | - Jigang Li
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, Frontiers Science Center for Molecular Design Breeding, China Agricultural University, Beijing100193, China
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Zhao J, Bo K, Pan Y, Li Y, Yu D, Li C, Chang J, Wu S, Wang Z, Zhang X, Gu X, Weng Y. Phytochrome-interacting factor PIF3 integrates phytochrome B and UV-B signaling pathways to regulate gibberellin- and auxin-dependent growth in cucumber hypocotyls. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:4520-4539. [PMID: 37201922 DOI: 10.1093/jxb/erad181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 05/11/2023] [Indexed: 05/20/2023]
Abstract
In Arabidopsis, the photoreceptors phytochrome B (PhyB) and UV-B resistance 8 (UVR8) mediate light responses that play a major role in regulating photomorphogenic hypocotyl growth, but how they crosstalk to coordinate this process is not well understood. Here we report map-based cloning and functional characterization of an ultraviolet (UV)-B-insensitive, long-hypocotyl mutant, lh1, and a wild-type-like mutant, lh2, in cucumber (Cucumis sativus), which show defective CsPhyB and GA oxidase2 (CsGA20ox-2), a key gibberellic acid (GA) biosynthesis enzyme, respectively. The lh2 mutation was epistatic to lh1 and partly suppressed the long-hypocotyl phenotype in the lh1lh2 double mutant. We identified phytochrome interacting factor (PIF) CsPIF3 as playing a critical role in integrating the red/far-red and UV-B light responses for hypocotyl growth. We show that two modules, CsPhyB-CsPIF3-CsGA20ox-2-DELLA and CsPIF3-auxin response factor 18 (CsARF18), mediate CsPhyB-regulated hypocotyl elongation through GA and auxin pathways, respectively, in which CsPIF3 binds to the G/E-box motifs in the promoters of CsGA20ox-2 and CsARF18 to regulate their expression. We also identified a new physical interaction between CsPIF3 and CsUVR8 mediating CsPhyB-dependent, UV-B-induced hypocotyl growth inhibition. Our work suggests that hypocotyl growth in cucumber involves a complex interplay of multiple photoreceptor- and phytohormone-mediated signaling pathways that show both conservation with and divergence from those in Arabidopsis.
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Affiliation(s)
- Jianyu Zhao
- Horticulture Department, University of Wisconsin, Madison WI 53706, USA
| | - Kailiang Bo
- Horticulture Department, University of Wisconsin, Madison WI 53706, USA
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yupeng Pan
- Horticulture Department, University of Wisconsin, Madison WI 53706, USA
- College of Horticulture, Northwest A& F University, Yangling 712100, China
| | - Yuhong Li
- College of Horticulture, Northwest A& F University, Yangling 712100, China
| | - Daoliang Yu
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Chuang Li
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jiang Chang
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Shuang Wu
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zhongyi Wang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xiaolan Zhang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xingfang Gu
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yiqun Weng
- Horticulture Department, University of Wisconsin, Madison WI 53706, USA
- USDA-ARS Vegetable Crops Research Unit, Madison, WI 53705, USA
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Rodríguez-Bolaños M, Martínez T, Juárez S, Quiroz S, Domínguez A, Garay-Arroyo A, Sanchez MDLP, Álvarez-Buylla ER, García-Ponce B. XAANTAL1 Reveals an Additional Level of Flowering Regulation in the Shoot Apical Meristem in Response to Light and Increased Temperature in Arabidopsis. Int J Mol Sci 2023; 24:12773. [PMID: 37628953 PMCID: PMC10454237 DOI: 10.3390/ijms241612773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 08/03/2023] [Accepted: 08/09/2023] [Indexed: 08/27/2023] Open
Abstract
Light and photoperiod are environmental signals that regulate flowering transition. In plants like Arabidopsis thaliana, this regulation relies on CONSTANS, a transcription factor that is negatively posttranslational regulated by phytochrome B during the morning, while it is stabilized by PHYA and cryptochromes 1/2 at the end of daylight hours. CO induces the expression of FT, whose protein travels from the leaves to the apical meristem, where it binds to FD to regulate some flowering genes. Although PHYB delays flowering, we show that light and PHYB positively regulate XAANTAL1 and other flowering genes in the shoot apices. Also, the genetic data indicate that XAL1 and FD participate in the same signaling pathway in flowering promotion when plants are grown under a long-day photoperiod at 22 °C. By contrast, XAL1 functions independently of FD or PIF4 to induce flowering at higher temperatures (27 °C), even under long days. Furthermore, XAL1 directly binds to FD, SOC1, LFY, and AP1 promoters. Our findings lead us to propose that light and temperature influence the floral network at the meristem level in a partially independent way of the signaling generated from the leaves.
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Affiliation(s)
- Mónica Rodríguez-Bolaños
- Instituto de Ecologίa, Departamento de Ecologίa Funcional, Universidad Nacional Autónoma de México, Circuito ext. s/no. Ciudad Universitaria, Coyoacán 04510, CDMX, Mexico
| | - Tania Martínez
- Instituto de Ecologίa, Departamento de Ecologίa Funcional, Universidad Nacional Autónoma de México, Circuito ext. s/no. Ciudad Universitaria, Coyoacán 04510, CDMX, Mexico
| | - Saray Juárez
- Instituto de Ecologίa, Departamento de Ecologίa Funcional, Universidad Nacional Autónoma de México, Circuito ext. s/no. Ciudad Universitaria, Coyoacán 04510, CDMX, Mexico
| | - Stella Quiroz
- Instituto de Ecologίa, Departamento de Ecologίa Funcional, Universidad Nacional Autónoma de México, Circuito ext. s/no. Ciudad Universitaria, Coyoacán 04510, CDMX, Mexico
- Laboratory of Pathogens and Host Immunity, University of Montpellier, 34 090 Montpellier, France
| | - Andrea Domínguez
- Instituto de Ecologίa, Departamento de Ecologίa Funcional, Universidad Nacional Autónoma de México, Circuito ext. s/no. Ciudad Universitaria, Coyoacán 04510, CDMX, Mexico
| | - Adriana Garay-Arroyo
- Instituto de Ecologίa, Departamento de Ecologίa Funcional, Universidad Nacional Autónoma de México, Circuito ext. s/no. Ciudad Universitaria, Coyoacán 04510, CDMX, Mexico
| | - María de la Paz Sanchez
- Instituto de Ecologίa, Departamento de Ecologίa Funcional, Universidad Nacional Autónoma de México, Circuito ext. s/no. Ciudad Universitaria, Coyoacán 04510, CDMX, Mexico
| | - Elena R. Álvarez-Buylla
- Instituto de Ecologίa, Departamento de Ecologίa Funcional, Universidad Nacional Autónoma de México, Circuito ext. s/no. Ciudad Universitaria, Coyoacán 04510, CDMX, Mexico
| | - Berenice García-Ponce
- Instituto de Ecologίa, Departamento de Ecologίa Funcional, Universidad Nacional Autónoma de México, Circuito ext. s/no. Ciudad Universitaria, Coyoacán 04510, CDMX, Mexico
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Han R, Ma L, Lv Y, Qi L, Peng J, Li H, Zhou Y, Song P, Duan J, Li J, Li Z, Terzaghi W, Guo Y, Li J. SALT OVERLY SENSITIVE2 stabilizes phytochrome-interacting factors PIF4 and PIF5 to promote Arabidopsis shade avoidance. THE PLANT CELL 2023; 35:2972-2996. [PMID: 37119311 PMCID: PMC10396385 DOI: 10.1093/plcell/koad119] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 03/08/2023] [Accepted: 04/10/2023] [Indexed: 06/19/2023]
Abstract
Sun-loving plants trigger the shade avoidance syndrome (SAS) to compete against their neighbors for sunlight. Phytochromes are plant red (R) and far-red (FR) light photoreceptors that play a major role in perceiving the shading signals and triggering SAS. Shade induces a reduction in the level of active phytochrome B (phyB), thus increasing the abundance of PHYTOCHROME-INTERACTING FACTORS (PIFs), a group of growth-promoting transcription factors. However, whether other factors are involved in modulating PIF activity in the shade remains largely obscure. Here, we show that SALT OVERLY SENSITIVE2 (SOS2), a protein kinase essential for salt tolerance, positively regulates SAS in Arabidopsis thaliana. SOS2 directly phosphorylates PIF4 and PIF5 at a serine residue close to their conserved motif for binding to active phyB. This phosphorylation thus decreases their interaction with phyB and posttranslationally promotes PIF4 and PIF5 protein accumulation. Notably, the role of SOS2 in regulating PIF4 and PIF5 protein abundance and SAS is more prominent under salt stress. Moreover, phyA and phyB physically interact with SOS2 and promote SOS2 kinase activity in the light. Collectively, our study uncovers an unexpected role of salt-activated SOS2 in promoting SAS by modulating the phyB-PIF module, providing insight into the coordinated response of plants to salt stress and shade.
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Affiliation(s)
- Run Han
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Liang Ma
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Yang Lv
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Lijuan Qi
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Jing Peng
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Hong Li
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Yangyang Zhou
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Pengyu Song
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Jie Duan
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Jianfang Li
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Zhen Li
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - William Terzaghi
- Department of Biology, Wilkes University, Wilkes-Barre, PA 18766, USA
| | - Yan Guo
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Jigang Li
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing 100193, China
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Ma L, Han R, Yang Y, Liu X, Li H, Zhao X, Li J, Fu H, Huo Y, Sun L, Yan Y, Zhang H, Li Z, Tian F, Li J, Guo Y. Phytochromes enhance SOS2-mediated PIF1 and PIF3 phosphorylation and degradation to promote Arabidopsis salt tolerance. THE PLANT CELL 2023; 35:2997-3020. [PMID: 37119239 PMCID: PMC10396371 DOI: 10.1093/plcell/koad117] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 03/08/2023] [Accepted: 04/10/2023] [Indexed: 06/19/2023]
Abstract
Soil salinity is one of the most detrimental abiotic stresses affecting plant survival, and light is a core environmental signal regulating plant growth and responses to abiotic stress. However, how light modulates the plant's response to salt stress remains largely obscure. Here, we show that Arabidopsis (Arabidopsis thaliana) seedlings are more tolerant to salt stress in the light than in the dark, and that the photoreceptors phytochrome A (phyA) and phyB are involved in this tolerance mechanism. We further show that phyA and phyB physically interact with the salt tolerance regulator SALT OVERLY SENSITIVE2 (SOS2) in the cytosol and nucleus, and enhance salt-activated SOS2 kinase activity in the light. Moreover, SOS2 directly interacts with and phosphorylates PHYTOCHROME-INTERACTING FACTORS PIF1 and PIF3 in the nucleus. Accordingly, PIFs act as negative regulators of plant salt tolerance, and SOS2 phosphorylation of PIF1 and PIF3 decreases their stability and relieves their repressive effect on plant salt tolerance in both light and dark conditions. Together, our study demonstrates that photoactivated phyA and phyB promote plant salt tolerance by increasing SOS2-mediated phosphorylation and degradation of PIF1 and PIF3, thus broadening our understanding of how plants adapt to salt stress according to their dynamic light environment.
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Affiliation(s)
- Liang Ma
- State Key Laboratory of Plant Environmental Resilience (SKLPER), College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Run Han
- State Key Laboratory of Plant Environmental Resilience (SKLPER), College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Yongqing Yang
- State Key Laboratory of Plant Environmental Resilience (SKLPER), College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Xiangning Liu
- State Key Laboratory of Plant Environmental Resilience (SKLPER), College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Hong Li
- State Key Laboratory of Plant Environmental Resilience (SKLPER), College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Xiaoyun Zhao
- State Key Laboratory of Plant Environmental Resilience (SKLPER), College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Jianfang Li
- State Key Laboratory of Plant Environmental Resilience (SKLPER), College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Haiqi Fu
- State Key Laboratory of Plant Environmental Resilience (SKLPER), College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Yandan Huo
- State Key Laboratory of Plant Environmental Resilience (SKLPER), College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Liping Sun
- State Key Laboratory of Plant Environmental Resilience (SKLPER), College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Yan Yan
- State Key Laboratory of Plant Environmental Resilience (SKLPER), College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Hongyan Zhang
- State Key Laboratory of Plant Environmental Resilience (SKLPER), College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Zhen Li
- State Key Laboratory of Plant Environmental Resilience (SKLPER), College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Feng Tian
- National Maize Improvement Center, Key Laboratory of Biology and Genetic Improvement of Maize (MOA), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Jigang Li
- State Key Laboratory of Plant Environmental Resilience (SKLPER), College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Yan Guo
- State Key Laboratory of Plant Environmental Resilience (SKLPER), College of Biological Sciences, China Agricultural University, Beijing 100193, China
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38
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Zhu Y, Zhang Q, Li Y, Pan Z, Liu C, Lin D, Gao J, Tang Z, Li Z, Wang R, Sun J. Role of Soil and Foliar-Applied Carbon Dots in Plant Iron Biofortification and Cadmium Mitigation by Triggering Opposite Iron Signaling in Roots. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2301137. [PMID: 37119405 DOI: 10.1002/smll.202301137] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 04/17/2023] [Indexed: 06/19/2023]
Abstract
In China, iron (Fe) availability is low in most soils but cadmium (Cd) generally exceeds regulatory soil pollution limits. Thus, biofortification of Fe along with mitigation of Cd in edible plant parts is important for human nutrition and health. Carbon dots (CDs) are considered as potential nanomaterials for agricultural applications. Here, Salvia miltiorrhiza-derived CDs are an efficient modulator of Fe, manganese (Mn), zinc (Zn), and Cd accumulation in plants. CDs irrigation (1 mg mL-1 , performed every week starting at the jointing stage for 12 weeks) increased Fe content by 18% but mitigated Cd accumulation by 20% in wheat grains. This finding was associated with the Fe3+ -mobilizing properties of CDs from the soil and root cell wall, as well as endocytosis-dependent internalization in roots. The resulting excess Fe signaling mitigated Cd uptake via inhibiting TaNRAMP5 expression. Foliar spraying of CDs enhanced Fe (44%), Mn (30%), and Zn (19%) content with an unchanged Cd accumulation in wheat grains. This result is attributed to CDs-enhanced light signaling, which triggered shoot-to-root Fe deficiency response. This study not only reveals the molecular mechanism underlying CDs modulation of Fe signaling in plants but also provides useful strategies for concurrent Fe biofortification and Cd mitigation in plant-based foods.
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Affiliation(s)
- Yixia Zhu
- Department of Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, Jiangsu Province, 221116, China
| | - Qian Zhang
- Agro-Environmental Pollution Remediation Research Center, Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, 300191, China
| | - Yanjuan Li
- Department of Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, Jiangsu Province, 221116, China
| | - Zhiyuan Pan
- Department of Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, Jiangsu Province, 221116, China
| | - Chong Liu
- Department of Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, Jiangsu Province, 221116, China
| | - Dasong Lin
- Agro-Environmental Pollution Remediation Research Center, Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, 300191, China
| | - Jia Gao
- Department of Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, Jiangsu Province, 221116, China
| | - Zhonghou Tang
- Department of Sweetpotato Physiology Cultivation, Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District, Xuzhou, Jiangsu Province, 221122, China
| | - Zongyun Li
- Department of Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, Jiangsu Province, 221116, China
| | - Ruigang Wang
- Agro-Environmental Pollution Remediation Research Center, Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, 300191, China
| | - Jian Sun
- Department of Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, Jiangsu Province, 221116, China
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Chen L, Li Q, Wang M, Xiao F, Li K, Yang R, Sun M, Zhang H, Guo J, Chen J, Jiao F. ZmCOP1 Regulates Maize Mesocotyl Length and Plant Height through the Phytohormone Pathways. Life (Basel) 2023; 13:1522. [PMID: 37511897 PMCID: PMC10381158 DOI: 10.3390/life13071522] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 06/27/2023] [Accepted: 06/30/2023] [Indexed: 07/30/2023] Open
Abstract
The morphogenesis of crops is critical to their yield performance. COP1 (constitutively photomorphogenic1) is one of the core regulators in plant morphogenesis and has been deeply studied in Arabidopsis thaliana. However, the function of COP1 in maize is still unclear. Here, we found that the mesocotyl lengths of zmcop1 loss-of-function mutants were shorter than those of wild-type B73 in darkness, while the mesocotyl lengths of lines with ZmCOP1 overexpression were longer than those of wild-type B104. The plant height with zmcop1 was shorter than that of B73 in both short- and long-day photoperiods. Using transcriptome RNA sequencing technology, we identified 33 DEGs (differentially expressed genes) between B73's etiolated seedlings and those featuring zmcop1, both in darkness. The DEGs were mainly enriched in the plant phytohormone pathways. Our results provide direct evidence that ZmCOP1 functions in the elongation of etiolated seedlings in darkness and affects plant height in light. Our data can be applied in the improvement of maize plant architecture.
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Affiliation(s)
- Liping Chen
- College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China
- The Characteristic Laboratory of Crop Germplasm Innovation and Application, Provincial Department of Education, College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China
| | - Qiuhua Li
- College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China
- The Characteristic Laboratory of Crop Germplasm Innovation and Application, Provincial Department of Education, College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China
| | - Ming Wang
- College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China
- The Characteristic Laboratory of Crop Germplasm Innovation and Application, Provincial Department of Education, College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China
| | - Feng Xiao
- College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China
- The Characteristic Laboratory of Crop Germplasm Innovation and Application, Provincial Department of Education, College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China
| | - Kangshi Li
- College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China
- The Characteristic Laboratory of Crop Germplasm Innovation and Application, Provincial Department of Education, College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China
| | - Ran Yang
- College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China
- The Characteristic Laboratory of Crop Germplasm Innovation and Application, Provincial Department of Education, College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China
| | - Meng Sun
- College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China
- The Characteristic Laboratory of Crop Germplasm Innovation and Application, Provincial Department of Education, College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China
| | - Haiyan Zhang
- College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China
- The Characteristic Laboratory of Crop Germplasm Innovation and Application, Provincial Department of Education, College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China
| | - Jinjie Guo
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Sub-Center for National Maize Improvement Center, College of Agronomy, Hebei Agricultural University, Baoding 071001, China
| | - Jingtang Chen
- College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China
- The Characteristic Laboratory of Crop Germplasm Innovation and Application, Provincial Department of Education, College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China
| | - Fuchao Jiao
- College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China
- The Characteristic Laboratory of Crop Germplasm Innovation and Application, Provincial Department of Education, College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China
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Burgie ES, Li H, Gannam ZTK, McLoughlin KE, Vierstra RD, Li H. The structure of Arabidopsis phytochrome A reveals topological and functional diversification among the plant photoreceptor isoforms. NATURE PLANTS 2023; 9:1116-1129. [PMID: 37291396 PMCID: PMC10546791 DOI: 10.1038/s41477-023-01435-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 05/10/2023] [Indexed: 06/10/2023]
Abstract
Plants employ a divergent cohort of phytochrome (Phy) photoreceptors to govern many aspects of morphogenesis through reversible photointerconversion between inactive Pr and active Pfr conformers. The two most influential are PhyA whose retention of Pfr enables sensation of dim light, while the relative instability of Pfr for PhyB makes it better suited for detecting full sun and temperature. To better understand these contrasts, we solved, by cryo-electron microscopy, the three-dimensional structure of full-length PhyA as Pr. Like PhyB, PhyA dimerizes through head-to-head assembly of its C-terminal histidine kinase-related domains (HKRDs), while the remainder assembles as a head-to-tail light-responsive platform. Whereas the platform and HKRDs associate asymmetrically in PhyB dimers, these lopsided connections are absent in PhyA. Analysis of truncation and site-directed mutants revealed that this decoupling and altered platform assembly have functional consequences for Pfr stability of PhyA and highlights how plant Phy structural diversification has extended light and temperature perception.
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Affiliation(s)
- E Sethe Burgie
- Department of Biology, Washington University in St. Louis, St. Louis, MO, USA
| | - Hua Li
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, USA
| | - Zira T K Gannam
- Department of Biology, Washington University in St. Louis, St. Louis, MO, USA
| | - Katrice E McLoughlin
- Department of Biology, Washington University in St. Louis, St. Louis, MO, USA
- Burning Rock Dx, Irvine, CA, USA
| | - Richard D Vierstra
- Department of Biology, Washington University in St. Louis, St. Louis, MO, USA.
| | - Huilin Li
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, USA.
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Kusuma P, Bugbee B. On the contrasting morphological response to far-red at high and low photon fluxes. FRONTIERS IN PLANT SCIENCE 2023; 14:1185622. [PMID: 37332690 PMCID: PMC10274578 DOI: 10.3389/fpls.2023.1185622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 05/10/2023] [Indexed: 06/20/2023]
Abstract
Plants compete for sunlight and have evolved to perceive shade through both relative increases in the flux of far-red photons (FR; 700 to 750 nm) and decreases in the flux of all photons (intensity). These two signals interact to control stem elongation and leaf expansion. Although the interacting effects on stem elongation are well quantified, responses for leaf expansion are poorly characterized. Here we report a significant interaction between far-red fraction and total photon flux. Extended photosynthetic photon flux density (ePPFD; 400 to 750 nm) was maintained at three levels (50/100, 200 and 500 µmol m-2 s-1), each with a range of 2 to 33% FR. Increasing FR increased leaf expansion in three cultivars of lettuce at the highest ePPFD but decreased expansion at the lowest ePPFD. This interaction was attributed to differences in biomass partitioning between leaves and stems. Increased FR favored stem elongation and biomass partitioning to stems at low ePPFD and favored leaf expansion at high ePPFD. In cucumber, leaf expansion was increased with increasing percent FR under all ePPFD levels showing minimal interaction. The interactions (and lack thereof) have important implications for horticulture and warrant further study for plant ecology.
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Affiliation(s)
- Paul Kusuma
- Department of Plant Sciences, Horticulture and Product Physiology, Wageningen University and Research, Wageningen, Netherlands
- Crop Physiology Laboratory, Department of Plants Soils and Climate, Utah State University, Logan, UT, United States
| | - Bruce Bugbee
- Crop Physiology Laboratory, Department of Plants Soils and Climate, Utah State University, Logan, UT, United States
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Cannon AE, Sabharwal T, Salmi ML, Chittari GK, Annamalai V, Leggett L, Morris H, Slife C, Clark G, Roux SJ. Two distinct light-induced reactions are needed to promote germination in spores of Ceratopteris richardii. FRONTIERS IN PLANT SCIENCE 2023; 14:1150199. [PMID: 37332704 PMCID: PMC10272463 DOI: 10.3389/fpls.2023.1150199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 05/18/2023] [Indexed: 06/20/2023]
Abstract
Germination of Ceratopteris richardii spores is initiated by light and terminates 3-4 days later with the emergence of a rhizoid. Early studies documented that the photoreceptor for initiating this response is phytochrome. However, completion of germination requires additional light input. If no further light stimulus is given after phytochrome photoactivation, the spores do not germinate. Here we show that a crucial second light reaction is required, and its function is to activate and sustain photosynthesis. Even in the presence of light, blocking photosynthesis with DCMU after phytochrome photoactivation blocks germination. In addition, RT-PCR showed that transcripts for different phytochromes are expressed in spores in darkness, and the photoactivation of these phytochromes results in the increased transcription of messages encoding chlorophyll a/b binding proteins. The lack of chlorophyll-binding protein transcripts in unirradiated spores and their slow accumulation makes it unlikely that photosynthesis is required for the initial light reaction. This conclusion is supported by the observation that the transient presence of DCMU, only during the initial light reaction, had no effect on germination. Additionally, the [ATP] in Ceratopteris richardii spores increased coincidentally with the length of light treatment during germination. Overall, these results support the conclusion that two distinct light reactions are required for the germination of Ceratopteris richardii spores.
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Sineshchekov VA. Two Distinct Molecular Types of Phytochrome A in Plants: Evidence of Existence and Implications for Functioning. Int J Mol Sci 2023; 24:ijms24098139. [PMID: 37175844 PMCID: PMC10179679 DOI: 10.3390/ijms24098139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 04/24/2023] [Accepted: 04/28/2023] [Indexed: 05/15/2023] Open
Abstract
Phytochrome (phy) system in plants comprising a small number of phytochromes with phyA and phyB as major ones is responsible for acquiring light information in the red-far-red region of the solar spectrum. It provides optimal strategy for plant development under changing light conditions throughout all its life cycle beginning from seed germination and seedling establishment to fruiting and plant senescence. The phyA was shown to participate in the regulation of this cycle which is especially evident at its early stages. It mediates three modes of reactions-the very low and low fluence responses (VLFR and LFR) and the high irradiance responses (HIR). The phyA is the sole light receptor in the far-red spectral region responsible for plant's survival under a dense plant canopy where light is enriched with the far-red component. Its appearance is believed to be one of the main factors of plants' successful evolution. So far, it is widely accepted that one molecular phyA species is responsible for its complex functional manifestations. In this review, the evidence of the existence of two distinct phyA types-major, light-labile and soluble phyA' and minor, relatively light-stable and amphiphilic phyA″-is presented as what may account for the diverse modes of phyA action.
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Sineshchekov VA. Two Distinct Molecular Types of Phytochrome A in Plants: Evidence of Existence and Implications for Functioning. Int J Mol Sci 2023; 24:8139. [DOI: https:/doi.org/10.3390/ijms24098139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2023] Open
Abstract
Phytochrome (phy) system in plants comprising a small number of phytochromes with phyA and phyB as major ones is responsible for acquiring light information in the red—far-red region of the solar spectrum. It provides optimal strategy for plant development under changing light conditions throughout all its life cycle beginning from seed germination and seedling establishment to fruiting and plant senescence. The phyA was shown to participate in the regulation of this cycle which is especially evident at its early stages. It mediates three modes of reactions—the very low and low fluence responses (VLFR and LFR) and the high irradiance responses (HIR). The phyA is the sole light receptor in the far-red spectral region responsible for plant’s survival under a dense plant canopy where light is enriched with the far-red component. Its appearance is believed to be one of the main factors of plants′ successful evolution. So far, it is widely accepted that one molecular phyA species is responsible for its complex functional manifestations. In this review, the evidence of the existence of two distinct phyA types—major, light-labile and soluble phyA′ and minor, relatively light-stable and amphiphilic phyA″—is presented as what may account for the diverse modes of phyA action.
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45
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Rahman A, Tajti J, Majláth I, Janda T, Prerostova S, Ahres M, Pál M. Influence of a phyA Mutation on Polyamine Metabolism in Arabidopsis Depends on Light Spectral Conditions. PLANTS (BASEL, SWITZERLAND) 2023; 12:1689. [PMID: 37111912 PMCID: PMC10146636 DOI: 10.3390/plants12081689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 04/13/2023] [Accepted: 04/15/2023] [Indexed: 06/19/2023]
Abstract
The aim of the study was to reveal the influence of phyA mutations on polyamine metabolism in Arabidopsis under different spectral compositions. Polyamine metabolism was also provoked with exogenous spermine. The polyamine metabolism-related gene expression of the wild type and phyA plants responded similarly under white and far-red light conditions but not at blue light. Blue light influences rather the synthesis side, while far red had more pronounced effects on the catabolism and back-conversion of the polyamines. The observed changes under elevated far-red light were less dependent on PhyA than the blue light responses. The polyamine contents were similar under all light conditions in the two genotypes without spermine application, suggesting that a stable polyamine pool is important for normal plant growth conditions even under different spectral conditions. However, after spermine treatment, the blue regime had more similar effects on synthesis/catabolism and back-conversion to the white light than the far-red light conditions. The additive effects of differences observed on the synthesis, back-conversion and catabolism side of metabolism may be responsible for the similar putrescine content pattern under all light conditions, even in the presence of an excess of spermine. Our results demonstrated that both light spectrum and phyA mutation influence polyamine metabolism.
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Affiliation(s)
- Altafur Rahman
- Agricultural Institute, Centre for Agricultural Research, Eötvös Loránd Research Network, 2462 Martonvásár, Hungary
| | - Judit Tajti
- Agricultural Institute, Centre for Agricultural Research, Eötvös Loránd Research Network, 2462 Martonvásár, Hungary
| | - Imre Majláth
- Agricultural Institute, Centre for Agricultural Research, Eötvös Loránd Research Network, 2462 Martonvásár, Hungary
| | - Tibor Janda
- Agricultural Institute, Centre for Agricultural Research, Eötvös Loránd Research Network, 2462 Martonvásár, Hungary
| | - Sylva Prerostova
- Laboratory of Hormonal Regulations in Plants, Institute of Experimental Botany, Czech Academy of Sciences, 11720 Prague, Czech Republic
| | - Mohamed Ahres
- Agricultural Institute, Centre for Agricultural Research, Eötvös Loránd Research Network, 2462 Martonvásár, Hungary
| | - Magda Pál
- Agricultural Institute, Centre for Agricultural Research, Eötvös Loránd Research Network, 2462 Martonvásár, Hungary
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Balderrama D, Barnwell S, Carlson KD, Salido E, Guevara R, Nguyen C, Madlung A. Phytochrome F mediates red light responsiveness additively with phytochromes B1 and B2 in tomato. PLANT PHYSIOLOGY 2023; 191:2353-2366. [PMID: 36670526 PMCID: PMC10069882 DOI: 10.1093/plphys/kiad028] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 01/04/2023] [Indexed: 06/17/2023]
Abstract
Phytochromes are red light and far-red light sensitive, plant-specific light receptors that allow plants to orient themselves in space and time. Tomato (Solanum lycopersicum) contains a small family of five phytochrome genes, for which to date stable knockout mutants are only available for three of them. Using CRISPR technology, we created multiple alleles of SlPHYTOCHROME F (phyF) mutants to determine the function of this understudied phytochrome. We report that SlphyF acts as a red/far-red light reversible low fluence sensor, likely through the formation of heterodimers with SlphyB1 and SlphyB2. During photomorphogenesis, phyF functions additively with phyB1 and phyB2. Our data further suggest that phyB2 requires the presence of either phyB1 or phyF during seedling de-etiolation in red light, probably via heterodimerization, while phyB1 homodimers are required and sufficient to suppress hypocotyl elongation in red light. During the end-of-day far-red response, phyF works additively with phyB1 and phyB2. In addition, phyF plays a redundant role with phyB1 in photoperiod detection and acts additively with phyA in root patterning. Taken together, our results demonstrate various roles for SlphyF during seedling establishment, sometimes acting additively, other times acting redundantly with the other phytochromes in tomato.
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Kim H, Kim J, Choi G. Epidermal phyB requires RRC1 to promote light responses by activating the circadian rhythm. THE NEW PHYTOLOGIST 2023; 238:705-723. [PMID: 36651061 DOI: 10.1111/nph.18746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 12/30/2022] [Indexed: 06/17/2023]
Abstract
Phytochrome B (phyB) expressed in the epidermis is sufficient to promote red light responses, including the inhibition of hypocotyl elongation and hypocotyl negative gravitropism. Nonetheless, the downstream mechanism of epidermal phyB in promoting light responses had been elusive. Here, we mutagenized the epidermis-specific phyB-expressing line (MLB) using ethyl methanesulfonate (EMS) and characterized a novel mutant allele of RRC1 (rrc1-689), which causes reduced epidermal phyB-mediated red light responses. The rrc1-689 mutation increases the alternative splicing of major clock gene transcripts, including PRR7 and TOC1, disrupting the rhythmic expression of the entire clock and clock-controlled genes. Combined with the result that MLB/prr7 exhibits the same red-hyposensitive phenotypes as MLB/rrc1-689, our data support that the circadian clock is required for the ability of epidermal phyB to promote light responses. We also found that, unlike phyB, RRC1 preferentially acts in the endodermis to maintain the circadian rhythm by suppressing the alternative splicing of core clock genes. Together, our results suggest that epidermal phyB requires RRC1 to promote light responses by activating the circadian rhythm in Arabidopsis thaliana.
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Affiliation(s)
- Hanim Kim
- Department of Biological Sciences, KAIST, Daejeon, 34141, Korea
| | - Jaewook Kim
- Department of Biological Sciences, KAIST, Daejeon, 34141, Korea
| | - Giltsu Choi
- Department of Biological Sciences, KAIST, Daejeon, 34141, Korea
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48
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Liu LY, Jia MZ, Wang SN, Han S, Jiang J. Identification and characterization of cotton PHYTOCHROME-INTERACTING FACTORs in temperature-dependent flowering. JOURNAL OF EXPERIMENTAL BOTANY 2023:erad119. [PMID: 36988239 DOI: 10.1093/jxb/erad119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Indexed: 06/19/2023]
Abstract
PHYTOCHROME INTERACTING FACTORs (PIFs) assimilate with light and temperature signs to control plant growth and development. However, little is known about PIFs in crop plants such as cotton. Here, we identified 68 PIF proteins and their coding genes from an allotetraploid and three diploid ancestors. Cotton PIFs contain typical APA and APB motifs by means of which they bind to phytochrome phyA and phyB, respectively, and have a bHLH domain and a nuclear localization sequence necessary for bHLH-type transcription factors. Bioinformatics analysis showed that the promoter of each PIF gene contains multiple cis-acting elements and that the evolution of cotton genomes likely underwent loss, recombination, and tandem replication. Further observations indicated that the sensitivity of cotton PIF expression to low or high temperature was significantly different, of which allotetraploid Gossypium hirsutum PIF4a (GhPIF4a) was induced by high temperature. GhPIF4a promotes flowering in cotton and Arabidopsis and binds to the promoter of GhFT (FLOWERING LOCUS T) increasing with temperature rise. In conclusion, our work identifies the evolutionary and structural characteristics and functions of PIF family members in cotton.
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Affiliation(s)
- Ling-Yun Liu
- State Key Laboratory of Cotton Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, College of Life Sciences, Henan University, Kaifeng 475004, Henan Province, China
| | - Ming-Zhu Jia
- State Key Laboratory of Cotton Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, College of Life Sciences, Henan University, Kaifeng 475004, Henan Province, China
| | - Sheng-Nan Wang
- State Key Laboratory of Cotton Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, College of Life Sciences, Henan University, Kaifeng 475004, Henan Province, China
| | - Shuan Han
- State Key Laboratory of Cotton Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, College of Life Sciences, Henan University, Kaifeng 475004, Henan Province, China
| | - Jing Jiang
- State Key Laboratory of Cotton Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, College of Life Sciences, Henan University, Kaifeng 475004, Henan Province, China
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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] [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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50
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Sahu S, Gupta P, Gowtham TP, Yogesh KS, Sanjay TD, Singh A, Duong HV, Pradhan SK, Bisht DS, Singh NK, Baig MJ, Rai R, Dash PK. Generation of High-Value Genomic Resource in Rice: A “Subgenomic Library” of Low-Light Tolerant Rice Cultivar Swarnaprabha. BIOLOGY 2023; 12:biology12030428. [PMID: 36979120 PMCID: PMC10044706 DOI: 10.3390/biology12030428] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 02/09/2023] [Accepted: 02/14/2023] [Indexed: 03/16/2023]
Abstract
Rice is the major staple food crop for more than 50% of the world’s total population, and its production is of immense importance for global food security. As a photophilic plant, its yield is governed by the quality and duration of light. Like all photosynthesizing plants, rice perceives the changes in the intensity of environmental light using phytochromes as photoreceptors, and it initiates a morphological response that is termed as the shade-avoidance response (SAR). Phytochromes (PHYs) are the most important photoreceptor family, and they are primarily responsible for the absorption of the red (R) and far-red (FR) spectra of light. In our endeavor, we identified the morphological differences between two contrasting cultivars of rice: IR-64 (low-light susceptible) and Swarnaprabha (low-light tolerant), and we observed the phenological differences in their growth in response to the reduced light conditions. In order to create genomic resources for low-light tolerant rice, we constructed a subgenomic library of Swarnaprabha that expedited our efforts to isolate light-responsive photoreceptors. The titer of the library was found to be 3.22 × 105 cfu/mL, and the constructed library comprised clones of 4–9 kb in length. The library was found to be highly efficient as per the number of recombinant clones. The subgenomic library will serve as a genomic resource for the Gramineae community to isolate photoreceptors and other genes from rice.
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Affiliation(s)
- Sovanlal Sahu
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi 110001, India
| | - Payal Gupta
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi 110001, India
| | | | - Kumar Shiva Yogesh
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi 110001, India
| | | | - Ayushi Singh
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi 110001, India
| | - Hay Van Duong
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi 110001, India
- Institute of Agricultural Sciences for Southern Vietnam, Ho Chi Minh City 71007, Vietnam
| | - Sharat Kumar Pradhan
- ICAR-National Rice Research Institute, Cuttack 753006, India
- Indian Council of Agriculture Research, Krishi Bhawan, New Delhi 110001, India
| | - Deepak Singh Bisht
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi 110001, India
| | - Nagendra Kumar Singh
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi 110001, India
| | - Mirza J. Baig
- ICAR-National Rice Research Institute, Cuttack 753006, India
| | - Rhitu Rai
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi 110001, India
- Correspondence: (R.R.); (P.K.D.); Tel.: +91-1125841787 (R.R. & P.K.D.); Fax: +91-1125843984 (R.R. & P.K.D.)
| | - Prasanta K. Dash
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi 110001, India
- Correspondence: (R.R.); (P.K.D.); Tel.: +91-1125841787 (R.R. & P.K.D.); Fax: +91-1125843984 (R.R. & P.K.D.)
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