1
|
Huq E, Lin C, Quail PH. Light signaling in plants-a selective history. PLANT PHYSIOLOGY 2024; 195:213-231. [PMID: 38431282 PMCID: PMC11060691 DOI: 10.1093/plphys/kiae110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 12/15/2023] [Accepted: 02/16/2024] [Indexed: 03/05/2024]
Abstract
In addition to providing the radiant energy that drives photosynthesis, sunlight carries signals that enable plants to grow, develop and adapt optimally to the prevailing environment. Here we trace the path of research that has led to our current understanding of the cellular and molecular mechanisms underlying the plant's capacity to perceive and transduce these signals into appropriate growth and developmental responses. Because a fully comprehensive review was not possible, we have restricted our coverage to the phytochrome and cryptochrome classes of photosensory receptors, while recognizing that the phototropin and UV classes also contribute importantly to the full scope of light-signal monitoring by the plant.
Collapse
Affiliation(s)
- Enamul Huq
- Department of Molecular Biosciences and The Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Chentao Lin
- Basic Forestry and Plant Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Peter H Quail
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA
- Plant Gene Expression Center, Agricultural Research Service, US Department of Agriculture, Albany, CA 94710, USA
| |
Collapse
|
2
|
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.
Collapse
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.
| |
Collapse
|
3
|
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.
Collapse
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.
| |
Collapse
|
4
|
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.
Collapse
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
| |
Collapse
|
5
|
Chen D, Zhong S. Phase Separation of Phytochrome B in HEK293T Cells. Methods Mol Biol 2024; 2795:105-111. [PMID: 38594532 DOI: 10.1007/978-1-0716-3814-9_11] [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
In this method, we employed HEK293T cells to express the plant photoreceptor phytochrome B (phyB). Through the application of various treatments such as phycocyanobilin (PCB) supplementation, red light exposure, and temperature adjustments, the phyB proteins exhibited liquid-liquid phase separation, leading to the formation of biomolecular condensates. Here, we present a comprehensive description of the protein expression, cell treatment, and imaging capture procedures. This detailed guide provides step-by-step instructions on how to induce phase separation of phyB proteins in HEK293T cells. By utilizing this approach, researchers can investigate the physicochemical characteristics and dynamic formation process of phyB photobodies with precision.
Collapse
Affiliation(s)
- Di Chen
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, China
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Shangwei Zhong
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, China.
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China.
| |
Collapse
|
6
|
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.
Collapse
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.
| |
Collapse
|
7
|
Field S, Jang GJ, Dean C, Strader LC, Rhee SY. Plants use molecular mechanisms mediated by biomolecular condensates to integrate environmental cues with development. THE PLANT CELL 2023; 35:3173-3186. [PMID: 36879427 PMCID: PMC10473230 DOI: 10.1093/plcell/koad062] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 02/01/2023] [Accepted: 02/09/2023] [Indexed: 06/18/2023]
Abstract
This review highlights recent literature on biomolecular condensates in plant development and discusses challenges for fully dissecting their functional roles. Plant developmental biology has been inundated with descriptive examples of biomolecular condensate formation, but it is only recently that mechanistic understanding has been forthcoming. Here, we discuss recent examples of potential roles biomolecular condensates play at different stages of the plant life cycle. We group these examples based on putative molecular functions, including sequestering interacting components, enhancing dwell time, and interacting with cytoplasmic biophysical properties in response to environmental change. We explore how these mechanisms could modulate plant development in response to environmental inputs and discuss challenges and opportunities for further research into deciphering molecular mechanisms to better understand the diverse roles that biomolecular condensates exert on life.
Collapse
Affiliation(s)
- Sterling Field
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA
| | - Geng-Jen Jang
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Caroline Dean
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Lucia C Strader
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Seung Y Rhee
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA
| |
Collapse
|
8
|
Huang J, Qiu ZY, He J, Xu HS, Wang K, Du HY, Gao D, Zhao WN, Sun QG, Wang YS, Wen PZ, Li Q, Dong XO, Xie XZ, Jiang L, Wang HY, Liu YQ, Wan JM. Phytochrome B mediates dim-light-reduced insect resistance by promoting the ethylene pathway in rice. PLANT PHYSIOLOGY 2023; 191:1272-1287. [PMID: 36437699 PMCID: PMC9922401 DOI: 10.1093/plphys/kiac518] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 09/08/2022] [Indexed: 06/16/2023]
Abstract
Increasing planting density is one of the most effective ways to improve crop yield. However, one major factor that limits crop planting density is the weakened immunity of plants to pathogens and insects caused by dim light (DL) under shade conditions. The molecular mechanism underlying how DL compromises plant immunity remains unclear. Here, we report that DL reduces rice (Oryza sativa) resistance against brown planthopper (BPH; Nilaparvata lugens) by elevating ethylene (ET) biosynthesis and signaling in a Phytochrome B (OsPHYB)-dependent manner. The DL-reduced BPH resistance is relieved in osphyB mutants, but aggravated in OsPHYB overexpressing plants. Further, we found that DL reduces the nuclear accumulation of OsphyB, thus alleviating Phytochrome Interacting Factor Like14 (OsPIL14) degradation, consequently leading to the up-regulation of 1-Aminocyclopropane-1-Carboxylate Oxidase1 (OsACO1) and an increase in ET levels. In addition, we found that nuclear OsphyB stabilizes Ethylene Insensitive Like2 (OsEIL2) by competitively interacting with EIN3 Binding F-Box Protein (OsEBF1) to enhance ET signaling in rice, which contrasts with previous findings that phyB blocks ET signaling by facilitating Ethylene Insensitive3 (EIN3) degradation in other plant species. Thus, enhanced ET biosynthesis and signaling reduces BPH resistance under DL conditions. Our findings provide insights into the molecular mechanism of the light-regulated ET pathway and host-insect interactions and potential strategies for sustainable insect management.
Collapse
Affiliation(s)
- Jie Huang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Province and Ministry Co-sponsored Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
| | - Ze-Yu Qiu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Province and Ministry Co-sponsored Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
| | - Jun He
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Province and Ministry Co-sponsored Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
| | - Hao-Sen Xu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Province and Ministry Co-sponsored Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
| | - Kan Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Province and Ministry Co-sponsored Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
| | - Hua-Ying Du
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Province and Ministry Co-sponsored Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
| | - Dong Gao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Province and Ministry Co-sponsored Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
| | - Wei-Ning Zhao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Province and Ministry Co-sponsored Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
| | - Quan-Guang Sun
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Province and Ministry Co-sponsored Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
| | - Yong-Sheng Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Province and Ministry Co-sponsored Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
| | - Pei-Zheng Wen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Province and Ministry Co-sponsored Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
| | - Qi Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Province and Ministry Co-sponsored Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiao-Ou Dong
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Province and Ministry Co-sponsored Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
| | - Xian-Zhi Xie
- Shandong Rice Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Ling Jiang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Province and Ministry Co-sponsored Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
| | - Hai-Yang Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yu-Qiang Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Province and Ministry Co-sponsored Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
| | - Jian-Min Wan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Province and Ministry Co-sponsored Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| |
Collapse
|
9
|
Muñoz-Díaz E, Sáez-Vásquez J. Nuclear dynamics: Formation of bodies and trafficking in plant nuclei. FRONTIERS IN PLANT SCIENCE 2022; 13:984163. [PMID: 36082296 PMCID: PMC9445803 DOI: 10.3389/fpls.2022.984163] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 08/04/2022] [Indexed: 06/01/2023]
Abstract
The existence of the nucleus distinguishes prokaryotes and eukaryotes. Apart from containing most of the genetic material, the nucleus possesses several nuclear bodies composed of protein and RNA molecules. The nucleus is separated from the cytoplasm by a double membrane, regulating the trafficking of molecules in- and outwards. Here, we investigate the composition and function of the different plant nuclear bodies and molecular clues involved in nuclear trafficking. The behavior of the nucleolus, Cajal bodies, dicing bodies, nuclear speckles, cyclophilin-containing bodies, photobodies and DNA damage foci is analyzed in response to different abiotic stresses. Furthermore, we research the literature to collect the different protein localization signals that rule nucleocytoplasmic trafficking. These signals include the different types of nuclear localization signals (NLSs) for nuclear import, and the nuclear export signals (NESs) for nuclear export. In contrast to these unidirectional-movement signals, the existence of nucleocytoplasmic shuttling signals (NSSs) allows bidirectional movement through the nuclear envelope. Likewise, nucleolar signals are also described, which mainly include the nucleolar localization signals (NoLSs) controlling nucleolar import. In contrast, few examples of nucleolar export signals, called nucleoplasmic localization signals (NpLSs) or nucleolar export signals (NoESs), have been reported. The existence of consensus sequences for these localization signals led to the generation of prediction tools, allowing the detection of these signals from an amino acid sequence. Additionally, the effect of high temperatures as well as different post-translational modifications in nuclear and nucleolar import and export is discussed.
Collapse
Affiliation(s)
- Eduardo Muñoz-Díaz
- Centre National de la Recherche Scientifique (CNRS), Laboratoire Génome et Développement des Plantes, UMR 5096, Perpignan, France
- Univ. Perpignan Via Domitia, Laboratoire Génome et Développement des Plantes, UMR 5096, Perpignan, France
| | - Julio Sáez-Vásquez
- Centre National de la Recherche Scientifique (CNRS), Laboratoire Génome et Développement des Plantes, UMR 5096, Perpignan, France
- Univ. Perpignan Via Domitia, Laboratoire Génome et Développement des Plantes, UMR 5096, Perpignan, France
| |
Collapse
|
10
|
Wang Y, Su C, Yu Y, He Y, Wei H, Li N, Li H, Duan J, Li B, Li J, Davis SJ, Wang L. TIME FOR COFFEE regulates phytochrome A-mediated hypocotyl growth through dawn-phased signaling. THE PLANT CELL 2022; 34:2907-2924. [PMID: 35543486 PMCID: PMC9338810 DOI: 10.1093/plcell/koac138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 04/24/2022] [Indexed: 05/14/2023]
Abstract
To enhance plant fitness under natural conditions, the circadian clock is synchronized and entrained by light via photoreceptors. In turn, the circadian clock exquisitely regulates the abundance and activity of photoreceptors via largely uncharacterized mechanisms. Here we show that the clock regulator TIME FOR COFFEE (TIC) controls the activity of the far-red light photoreceptor phytochrome A (phyA) at multiple levels in Arabidopsis thaliana. Null mutants of TIC displayed dramatically increased sensitivity to light irradiation with respect to hypocotyl growth, especially to far-red light. RNA-sequencing demonstrated that TIC and phyA play largely opposing roles in controlling light-regulated gene expression at dawn. Additionally, TIC physically interacts with the transcriptional repressor TOPLESS (TPL), which was associated with the significantly increased PHYA transcript levels in the tic-2 and tpl-1 mutants. Moreover, TIC interacts with phyA in the nucleus, thereby affecting phyA protein turnover and the formation of phyA nuclear speckles following light irradiation. Genetically, phyA was found to act downstream of TIC in regulating far red light-inhibited growth. Taken together, these findings indicate that TIC acts as a major negative regulator of phyA by integrating transcriptional and post-translational mechanisms at multiple levels.
Collapse
Affiliation(s)
| | | | | | - Yuqing He
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing 10093, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hua Wei
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing 10093, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Na Li
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing 10093, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hong Li
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Jie Duan
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Bin Li
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing 10093, People’s Republic of China
| | - Jigang Li
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Seth J Davis
- Department of Biology, University of York, Heslington, York YO10 5DD, UK
- State Key Laboratory of Crop Stress Biology, School of Life Sciences, Henan University, Kaifeng 475004, China
| | | |
Collapse
|
11
|
Liu Y, Sun Y, Yao H, Zheng Y, Cao S, Wang H. Arabidopsis Circadian Clock Repress Phytochrome a Signaling. FRONTIERS IN PLANT SCIENCE 2022; 13:809563. [PMID: 35645991 PMCID: PMC9131076 DOI: 10.3389/fpls.2022.809563] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 04/04/2022] [Indexed: 06/15/2023]
Abstract
The plants' internal circadian clock can strongly influence phytochrome signaling in response to the changes in the external light environment. Phytochrome A (phyA) is the photoreceptor that mediates various far-red (FR) light responses. phyA signaling is modulated by FHY3 and FAR1, which directly activate the transcription of FHY1 and FHL, whose products are essential for light-induced phyA nuclear accumulation and subsequent light responses. However, the mechanisms by which the clock regulates phyA signaling are poorly understood. Here, we discovered that FHY1 expression is diurnally regulated, peaking in the middle of the day. Two Arabidopsis core clock components, CIRCADIAN CLOCK ASSOCIATED1 (CCA1) and TIMING OF CAB EXPRESSION1 (TOC1), repress FHY3/FAR1-mediated FHY1/FHL activation. Consistently, the specific expression pattern of FHY1 under diurnal conditions is altered in cca1-1, toc1-101, CCA1, and TOC1 overexpression plants. Furthermore, far-red induced gene expression and particularly nuclear accumulation of phyA are compromised in TOC1 and CCA1 overexpression seedlings. Our results therefore revealed a previously unidentified FHY1 expression pattern in diurnal cycles, which is negatively regulated by CCA1 and TOC1.
Collapse
Affiliation(s)
- Yang Liu
- College of Horticulture, China Agricultural University, Beijing, China
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing, China
| | - Yanzhao Sun
- College of Horticulture, China Agricultural University, Beijing, China
| | - Heng Yao
- College of Horticulture, China Agricultural University, Beijing, China
| | - Yanyan Zheng
- College of Horticulture, China Agricultural University, Beijing, China
| | - Shuyuan Cao
- College of Horticulture, China Agricultural University, Beijing, China
| | - Haiyang Wang
- College of Life Sciences, South China Agricultural University, Guangzhou, China
| |
Collapse
|
12
|
Zhao J, Yang G, Jiang L, Zhang S, Miao L, Xu P, Chen H, Chen L, Mao Z, Guo T, Kou S, Yang HQ, Wang W. Phytochromes A and B Mediate Light Stabilization of BIN2 to Regulate Brassinosteroid Signaling and Photomorphogenesis in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2022; 13:865019. [PMID: 35432407 PMCID: PMC9005995 DOI: 10.3389/fpls.2022.865019] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 03/07/2022] [Indexed: 06/14/2023]
Abstract
Phytochromes A and B (phyA and phyB) are the far-red and red lights photoreceptors mediating many light responses in Arabidopsis thaliana. Brassinosteroid (BR) is a pivotal phytohormone regulating a variety of plant developmental processes including photomorphogenesis. It is known that phyB interacts with BES1 to inhibit its DNA-binding activity and repress BR signaling. Here, we show that far-red and red lights modulate BR signaling through phyA and phyB regulation of the stability of BIN2, a glycogen synthase kinase 3 (GSK3)-like kinase that phosphorylates BES1/BZR1 to inhibit BR signaling. The BIN2 gain-of-function mutant bin2-1 displays an enhanced photomorphogenic phenotype in both far-red and red lights. phyA-enhanced accumulation of BIN2 promotes the phosphorylation of BES1 in far-red light. BIN2 acts genetically downstream from PHYA to regulate photomorphogenesis under far-red light. Both phyA and phyB interact directly with BIN2, which may promote the interaction of BIN2 with BES1 and induce the phosphorylation of BES1. Our results suggest that far-red and red lights inhibit BR signaling through phyA and phyB stabilization of BIN2 and promotion of BES1 phosphorylation, which defines a new layer of the regulatory mechanism that allows plants to coordinate light and BR signaling pathways to optimize photomorphogenesis.
Collapse
Affiliation(s)
- Jiachen Zhao
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Guangqiong Yang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Lu Jiang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Shilong Zhang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Langxi Miao
- School of Life Sciences, Fudan University, Shanghai, China
| | - Peng Xu
- School of Life Sciences, Fudan University, Shanghai, China
| | - Huiru Chen
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Li Chen
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Zhilei Mao
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Tongtong Guo
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Shuang Kou
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Hong-Quan Yang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Wenxiu Wang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| |
Collapse
|
13
|
von Horsten S, Essen LO. Conformational Change of Tetratricopeptide Repeats Region Triggers Activation of Phytochrome-Associated Protein Phosphatase 5. FRONTIERS IN PLANT SCIENCE 2021; 12:733069. [PMID: 34721460 PMCID: PMC8551457 DOI: 10.3389/fpls.2021.733069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 09/21/2021] [Indexed: 06/13/2023]
Abstract
Phytochrome activity is not only controlled by light but also by post-translational modifications, e. g. phosphorylation. One of the phosphatases responsible for plant phytochrome dephosphorylation and thereby increased activity is the phytochrome-associated protein phosphatase 5 (PAPP5). We show that PAPP5 recognizes phospho-site mimicking mutants of phytochrome B, when being activated by arachidonic acid (AA). Addition of AA to PAPP5 decreases the α-helical content as tracked by CD-spectroscopy. These changes correspond to conformational changes of the regulatory tetratricopeptide repeats (TPR) region as shown by mapping data from hydrogen deuterium exchange mass spectrometry onto a 3.0 Å crystal structure of PAPP5. Surprisingly, parts of the linker between the TPR and PP2A domains and of the so-called C-terminal inhibitory motif exhibit reduced deuterium uptake upon AA-binding. Molecular dynamics analyses of PAPP5 complexed to a phyB phosphopeptide show that this C-terminal motif remains associated with the TPR region in the substrate bound state, suggesting that this motif merely serves for restricting the orientations of the TPR region relative to the catalytic PP2A domain. Given the high similarity to mammalian PP5 these data from a plant ortholog show that the activation mode of these PPP-type protein phosphatases is highly conserved.
Collapse
Affiliation(s)
- Silke von Horsten
- Department of Biochemistry, Faculty of Chemistry, Philipps-University, Marburg, Germany
| | - Lars-Oliver Essen
- Department of Biochemistry, Faculty of Chemistry, Philipps-University, Marburg, Germany
- Center for Synthetic Microbiology, Philipps-University, Marburg, Germany
| |
Collapse
|
14
|
Affiliation(s)
- Peter H Quail
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA.
- USDA/ARS Plant Gene Expression Center, Albany, CA, USA.
| |
Collapse
|
15
|
Santin M, Ranieri A, Castagna A. Anything New under the Sun? An Update on Modulation of Bioactive Compounds by Different Wavelengths in Agricultural Plants. PLANTS (BASEL, SWITZERLAND) 2021; 10:1485. [PMID: 34371687 PMCID: PMC8309429 DOI: 10.3390/plants10071485] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 07/17/2021] [Accepted: 07/18/2021] [Indexed: 12/15/2022]
Abstract
Plants continuously rely on light as an energy source and as the driver of many processes in their lifetimes. The ability to perceive different light radiations involves several photoreceptors, which in turn activate complex signalling cascades that ultimately lead to a rearrangement in plant metabolism as an adaptation strategy towards specific light conditions. This review, after a brief summary of the structure and mode of action of the different photoreceptors, introduces the main classes of secondary metabolites and specifically focuses on the influence played by the different wavelengths on the content of these compounds in agricultural plants, because of their recognised roles as nutraceuticals.
Collapse
Affiliation(s)
- Marco Santin
- Department of Agriculture, Food and Environment, University of Pisa, I-56124 Pisa, Italy; (M.S.); (A.R.)
| | - Annamaria Ranieri
- Department of Agriculture, Food and Environment, University of Pisa, I-56124 Pisa, Italy; (M.S.); (A.R.)
- Interdepartmental Research Center “Nutraceuticals and Food for Health”, University of Pisa, Via del Borghetto 80, I-56124 Pisa, Italy
| | - Antonella Castagna
- Department of Agriculture, Food and Environment, University of Pisa, I-56124 Pisa, Italy; (M.S.); (A.R.)
- Interdepartmental Research Center “Nutraceuticals and Food for Health”, University of Pisa, Via del Borghetto 80, I-56124 Pisa, Italy
| |
Collapse
|
16
|
Sun J, Lu J, Bai M, Chen Y, Wang W, Fan C, Liu J, Ning G, Wang C. Phytochrome-interacting factors interact with transcription factor CONSTANS to suppress flowering in rose. PLANT PHYSIOLOGY 2021; 186:1186-1201. [PMID: 33693800 PMCID: PMC8195524 DOI: 10.1093/plphys/kiab109] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 02/15/2021] [Indexed: 05/05/2023]
Abstract
As day-neutral (DN) woody perennial plants, the flowering time of roses (Rosa spp.) is assumed to be independent of the photoperiodic conditions; however, light responses of rose plants are not well understood. Chinese rose (Rosa chinensis) plants were grown under two light intensities (low light [LL], 92 μmol·m-2·s-1; or high light [HL], 278 μmol·m-2·s-1), and either with or without an end-of-day far-red (EOD-FR) treatment. Flowering was significantly delayed in the LL condition compared with the HL, but was not affected by EOD-FR treatment. The time until flowering positively corresponded with the mRNA and protein levels of phytochrome-interacting factors (PIFs; RcPIFs). The heterologous expression of RcPIF1, RcPIF3, or RcPIF4 in the Arabidopsis (Arabidopsis thaliana) pifq quadruple mutant partially rescued the mutant's shorter hypocotyl length. Simultaneous silencing of three RcPIFs in R. chinensis accelerated flowering under both LL and HL, with a more robust effect in LL, establishing RcPIFs as flowering suppressors in response to light intensity. The RcPIFs interacted with the transcription factor CONSTANS (RcCO) to form a RcPIFs-RcCO complex, which interfered with the binding of RcCO to the promoter of FLOWERING LOCUS T (RcFT), thereby inhibiting its expression. Furthermore, this inhibition was enhanced when RcPIFs were stabilized by LL, leading to delayed flowering under LL compared with HL. Our results not only revealed another layer of PIF functioning in the flowering of woody perennial plants, but also established a mechanism of light response in DN plants.
Collapse
Affiliation(s)
- Jingjing Sun
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Jun Lu
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Mengjuan Bai
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Yeqing Chen
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Weinan Wang
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Chunguo Fan
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Jinyi Liu
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Guogui Ning
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Changquan Wang
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
- Author for communication:
| |
Collapse
|
17
|
Casal JJ, Estevez JM. Auxin-Environment Integration in Growth Responses to Forage for Resources. Cold Spring Harb Perspect Biol 2021; 13:a040030. [PMID: 33431585 PMCID: PMC8015692 DOI: 10.1101/cshperspect.a040030] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Plant fitness depends on the adequate morphological adjustment to the prevailing conditions of the environment. Therefore, plants sense environmental cues through their life cycle, including the presence of full darkness, light, or shade, the range of ambient temperatures, the direction of light and gravity vectors, and the presence of water and mineral nutrients (such as nitrate and phosphate) in the soil. The environmental information impinges on different aspects of the auxin system such as auxin synthesis, degradation, transport, perception, and downstream transcriptional regulation to modulate organ growth. Although a single environmental cue can affect several of these points, the relative impacts differ significantly among the various growth processes and cues. While stability in the generation of precise auxin gradients serves to guide the basic developmental pattern, dynamic changes in the auxin system fine-tune body shape to optimize the capture of environmental resources.
Collapse
Affiliation(s)
- Jorge J Casal
- Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura (IFEVA), Facultad de Agronomía, Buenos Aires 1417, Argentina
- Fundación Instituto Leloir and IIBBA-CONICET, Buenos Aires C1405BWE, Argentina
| | - José M Estevez
- Fundación Instituto Leloir and IIBBA-CONICET, Buenos Aires C1405BWE, Argentina
- Centro de Biotecnología Vegetal, Facultad de Ciencias de la Vida, Universidad Andres Bello and Millennium Institute for Integrative Biology (iBio), Santiago 8370146, Chile
| |
Collapse
|
18
|
Legendre R, van Iersel MW. Supplemental Far-Red Light Stimulates Lettuce Growth: Disentangling Morphological and Physiological Effects. PLANTS (BASEL, SWITZERLAND) 2021; 10:166. [PMID: 33467138 PMCID: PMC7829796 DOI: 10.3390/plants10010166] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 01/12/2021] [Accepted: 01/14/2021] [Indexed: 11/16/2022]
Abstract
Light-emitting diodes allow for the application of specific wavelengths of light to induce various morphological and physiological responses. In lettuce (Lactuca sativa), far-red light (700-800 nm) is integral to initiating shade responses which can increase plant growth. In the first of two studies, plants were grown with a similar photosynthetic photon flux density (PPFD) but different intensities of far-red light. The second study used perpendicular gradients of far-red light and PPFD, allowing for examination of interactive effects. The far-red gradient study revealed that increasing supplemental far-red light increased leaf length and width, which was associated with increased projected canopy size (PCS). The higher PCS was associated with increased cumulative incident light received by plants, which increased dry matter accumulation. In the perpendicular gradient study, far-red light was 57% and 183% more effective at increasing the amount of light received by the plant, as well as 92.5% and 162% more effective at increasing plant biomass at the early and late harvests, respectively, as compared to PPFD. Light use efficiency (LUE, biomass/mol incident light) was generally negatively correlated with specific leaf area (SLA). Far-red light provided by LEDs increases the canopy size to capture more light to drive photosynthesis and shows promise for inclusion in the growth light spectrum for lettuce under sole-source lighting.
Collapse
Affiliation(s)
| | - Marc W. van Iersel
- Department of Horticulture, University of Georgia, Athens, GA 30602, USA;
| |
Collapse
|
19
|
Paulišić S, Qin W, Arora Verasztó H, Then C, Alary B, Nogue F, Tsiantis M, Hothorn M, Martínez‐García JF. Adjustment of the PIF7-HFR1 transcriptional module activity controls plant shade adaptation. EMBO J 2021; 40:e104273. [PMID: 33264441 PMCID: PMC7780144 DOI: 10.15252/embj.2019104273] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Revised: 10/01/2020] [Accepted: 10/16/2020] [Indexed: 01/29/2023] Open
Abstract
Shade caused by the proximity of neighboring vegetation triggers a set of acclimation responses to either avoid or tolerate shade. Comparative analyses between the shade-avoider Arabidopsis thaliana and the shade-tolerant Cardamine hirsuta revealed a role for the atypical basic-helix-loop-helix LONG HYPOCOTYL IN FR 1 (HFR1) in maintaining the shade tolerance in C. hirsuta, inhibiting hypocotyl elongation in shade and constraining expression profile of shade-induced genes. We showed that C. hirsuta HFR1 protein is more stable than its A. thaliana counterpart, likely due to its lower binding affinity to CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1), contributing to enhance its biological activity. The enhanced HFR1 total activity is accompanied by an attenuated PHYTOCHROME INTERACTING FACTOR (PIF) activity in C. hirsuta. As a result, the PIF-HFR1 module is differently balanced, causing a reduced PIF activity and attenuating other PIF-mediated responses such as warm temperature-induced hypocotyl elongation (thermomorphogenesis) and dark-induced senescence. By this mechanism and that of the already-known of phytochrome A photoreceptor, plants might ensure to properly adapt and thrive in habitats with disparate light amounts.
Collapse
Affiliation(s)
- Sandi Paulišić
- Centre for Research in Agricultural Genomics (CRAG)CSIC‐IRTA‐UAB‐UB, Cerdanyola del Vallès, Campus UABBarcelonaSpain
| | - Wenting Qin
- Centre for Research in Agricultural Genomics (CRAG)CSIC‐IRTA‐UAB‐UB, Cerdanyola del Vallès, Campus UABBarcelonaSpain
| | - Harshul Arora Verasztó
- Structural Plant Biology LaboratorySection of BiologyDepartment of Botany and Plant BiologyUniversity of GenevaGenevaSwitzerland
| | - Christiane Then
- Centre for Research in Agricultural Genomics (CRAG)CSIC‐IRTA‐UAB‐UB, Cerdanyola del Vallès, Campus UABBarcelonaSpain
- Present address:
Department for Epidemiology and Pathogen DiagnosticsJulius Kühn‐InstitutFederal Research Institute for Cultivated PlantsBraunschweigGermany
| | - Benjamin Alary
- Centre for Research in Agricultural Genomics (CRAG)CSIC‐IRTA‐UAB‐UB, Cerdanyola del Vallès, Campus UABBarcelonaSpain
| | - Fabien Nogue
- Institut Jean‐Pierre BourginINRA, AgroParisTech, CNRSUniversité Paris‐SaclayVersaillesFrance
| | - Miltos Tsiantis
- Department of Comparative Development and GeneticsMax Planck Institute from Plant Breeding ResearchCologneGermany
| | - Michael Hothorn
- Structural Plant Biology LaboratorySection of BiologyDepartment of Botany and Plant BiologyUniversity of GenevaGenevaSwitzerland
| | - Jaime F Martínez‐García
- Centre for Research in Agricultural Genomics (CRAG)CSIC‐IRTA‐UAB‐UB, Cerdanyola del Vallès, Campus UABBarcelonaSpain
- Institució Catalana de Recerca i Estudis Avançats (ICREA)BarcelonaSpain
- Institute for Plant Molecular and Cellular Biology (IBMCP)CSIC‐UPVValènciaSpain
| |
Collapse
|
20
|
Perrella G, Zioutopoulou A, Hamilton A, Kaiserli E. Photobody Detection Using Immunofluorescence and Super-Resolution Imaging in Arabidopsis. Methods Mol Biol 2021; 2297:7-19. [PMID: 33656665 DOI: 10.1007/978-1-0716-1370-2_2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Light triggers changes in plant nuclear architecture to control differentiation, adaptation, and growth. A series of genetic, molecular, and imaging approaches have revealed that the nucleus forms a hub for photo-induced protein interactions and gene regulatory events. However, the mechanism and function of light-induced nuclear compartmentalization is still unclear. This chapter provides detailed experimental protocols for examining the morphology and potential functional significance of light signaling components that localize in light-induced subnuclear domains, also known as photobodies. We describe how immunolabeling of endogenous proteins and fluorescent in situ hybridization (FISH) could be combined with confocal imaging of fluorescently tagged proteins to assess co-localization in Arabidopsis nuclei. Furthermore, we employ a super-resolution imaging approach to study the morphology of photobodies at unprecedented detail.
Collapse
Affiliation(s)
- Giorgio Perrella
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, Bower Building, University of Glasgow, Glasgow, Scotland, UK.,ENEA Italian National Agency for New Technologies, Energy and Sustainable Economic Development, Trisaia Research Center, Rotondella, Italy
| | - Anna Zioutopoulou
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, Bower Building, University of Glasgow, Glasgow, Scotland, UK
| | - Andrew Hamilton
- School of Medicine, Dentistry and Nursing, College of Medical, Veterinary and Life Sciences, Bower Building, University of Glasgow, Glasgow, Scotland, UK
| | - Eirini Kaiserli
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, Bower Building, University of Glasgow, Glasgow, Scotland, UK.
| |
Collapse
|
21
|
Lyu X, Li H, Liu B. Protoplast System for Studying Blue-Light-Dependent Formation of Cryptochrome Photobody. Methods Mol Biol 2021; 2297:105-113. [PMID: 33656674 DOI: 10.1007/978-1-0716-1370-2_11] [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: 12/17/2023]
Abstract
Cryptochromes (CRYs) belong to an ancient and conserved class of blue-light receptor regulating circadian clock and development in animals and plants. Arabidopsis CRY2 form physiologically active homodimers in response to blue light treatment and further oligomerize into photobodies, which are expected to be the foci harboring protein interaction, phosphorylation, and ubiquitination. Here we describe two efficient methods developed to test the formation of blue-light-dependent photobodies of CRY-GFP fusing proteins using the mesophyll protoplasts of Arabidopsis or soybean, respectively.
Collapse
Affiliation(s)
- Xiangguang Lyu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, People's Republic of China
| | - Hongyu Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, People's Republic of China
| | - Bin Liu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, People's Republic of China.
| |
Collapse
|
22
|
Sun Z, Huang K, Han Z, Wang P, Fang Y. Genome-wide identification of Arabidopsis long noncoding RNAs in response to the blue light. Sci Rep 2020; 10:6229. [PMID: 32277122 PMCID: PMC7148362 DOI: 10.1038/s41598-020-63187-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 03/17/2020] [Indexed: 01/11/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) have been shown in animals to play roles in a wide range of biological processes. In plant, light modulates the growth and development as a key external signal. However, little is known about the role of plant lncRNA in response to light. In this study, we sequenced the messenger RNAs (mRNAs), lncRNAs and microRNAs (miRNAs) in Arabidopsis seedlings under blue light for 2 h and 8 h. Compared to dark, we identified 4197 mRNAs, 375 miRNAs and 481 lncRNAs, or 5207 mRNAs, 286 miRNAs and 545 lncRNAs of differential expressions under blue light treatments for 2 h or 8 h respectively. Subsequently, a total of 407 competing endogenous RNA (ceRNA) pairs (lncRNA-mRNA-miRNA) were constructed. We identified a blue light-induced lncRNA which plays roles in blue light-directed plant photomorphogenesis and response to mannitol stress by serving as a ceRNA to sequester miR167 in a type of target mimicry. These results revealed previously unknown roles of the lncRNA in blue light signaling and mannitol stress, and provided useful resources of lncRNAs associated with miRNAs in response to blue light.
Collapse
Affiliation(s)
- Zhenfei Sun
- Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China.,National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai, 200032, China
| | - Kai Huang
- Beijing igeneCode Biotech CO., Ltd, Beijing, 100096, China
| | - Zujing Han
- Beijing igeneCode Biotech CO., Ltd, Beijing, 100096, China
| | - Pan Wang
- Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yuda Fang
- Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China. .,National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai, 200032, China.
| |
Collapse
|
23
|
Hahm J, Kim K, Qiu Y, Chen M. Increasing ambient temperature progressively disassembles Arabidopsis phytochrome B from individual photobodies with distinct thermostabilities. Nat Commun 2020; 11:1660. [PMID: 32245953 PMCID: PMC7125078 DOI: 10.1038/s41467-020-15526-z] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2019] [Accepted: 03/10/2020] [Indexed: 12/30/2022] Open
Abstract
Warm temperature is postulated to induce plant thermomorphogenesis through a signaling mechanism similar to shade, as both destabilize the active form of the photoreceptor and thermosensor phytochrome B (phyB). At the cellular level, shade antagonizes phyB signaling by triggering phyB disassembly from photobodies. Here we report temperature-dependent photobody localization of fluorescent protein-tagged phyB (phyB-FP) in the epidermal cells of Arabidopsis hypocotyl and cotyledon. Our results demonstrate that warm temperature elicits different photobody dynamics than those by shade. Increases in temperature from 12 °C to 27 °C incrementally reduce photobody number by stimulating phyB-FP disassembly from selective thermo-unstable photobodies. The thermostability of photobodies relies on phyB's photosensory module. Surprisingly, elevated temperatures inflict opposite effects on phyB's functions in the hypocotyl and cotyledon despite inducing similar photobody dynamics, indicative of tissue/organ-specific temperature signaling circuitry either downstream of photobody dynamics or independent of phyB. Our results thus provide direct cell biology evidence supporting an early temperature signaling mechanism via dynamic assembly/disassembly of individual photobodies possessing distinct thermostabilities.
Collapse
Affiliation(s)
- Joseph Hahm
- 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
| | - Yongjian Qiu
- 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.
| |
Collapse
|
24
|
Kozuka T, Sawada Y, Imai H, Kanai M, Hirai MY, Mano S, Uemura M, Nishimura M, Kusaba M, Nagatani A. Regulation of Sugar and Storage Oil Metabolism by Phytochrome during De-etiolation. PLANT PHYSIOLOGY 2020; 182:1114-1129. [PMID: 31748417 PMCID: PMC6997681 DOI: 10.1104/pp.19.00535] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 11/02/2019] [Indexed: 05/02/2023]
Abstract
Exposure of dark-grown (etiolated) seedlings to light induces the heterotrophic-to-photoautotrophic transition (de-etiolation) processes, including the formation of photosynthetic machinery in the chloroplast and cotyledon expansion. Phytochrome is a red (R)/far-red (FR) light photoreceptor that is involved in the various aspects of de-etiolation. However, how phytochrome regulates metabolic dynamics in response to light stimulus has remained largely unknown. In this study, to elucidate the involvement of phytochrome in the metabolic response during de-etiolation, we performed widely targeted metabolomics in Arabidopsis (Arabidopsis thaliana) wild-type and phytochrome A and B double mutant seedlings de-etiolated under R or FR light. The results revealed that phytochrome had strong impacts on the primary and secondary metabolism during the first 24 h of de-etiolation. Among those metabolites, sugar levels decreased during de-etiolation in a phytochrome-dependent manner. At the same time, phytochrome upregulated processes requiring sugars. Triacylglycerols are stored in the oil bodies as a source of sugars in Arabidopsis seedlings. Sugars are provided from triacylglycerols through fatty acid β-oxidation and the glyoxylate cycle in glyoxysomes. We examined if and how phytochrome regulates sugar production from oil bodies. Irradiation of the etiolated seedlings with R and FR light dramatically accelerated oil body mobilization in a phytochrome-dependent manner. Glyoxylate cycle-deficient mutants not only failed to mobilize oil bodies but also failed to develop thylakoid membranes and expand cotyledon cells upon exposure to light. Hence, phytochrome plays a key role in the regulation of metabolism during de-etiolation.
Collapse
Affiliation(s)
- Toshiaki Kozuka
- Graduate School of Integrated Science for Life, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8526 Japan
| | - Yuji Sawada
- RIKEN Center for Sustainable Resource Science, RIKEN, Yokohama, Kanagawa 230-0045, Japan
| | - Hiroyuki Imai
- United Graduate School of Agricultural Science, Iwate University, Morioka, Iwate 020-8550, Japan
| | - Masatake Kanai
- Department of Cell Biology, National Institute for Basic Biology, Okazaki, Aichi 444-8585, Japan
| | - Masami Yokota Hirai
- RIKEN Center for Sustainable Resource Science, RIKEN, Yokohama, Kanagawa 230-0045, Japan
| | - Shoji Mano
- Department of Cell Biology, National Institute for Basic Biology, Okazaki, Aichi 444-8585, Japan
- Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi 444-8585, Japan
| | - Matsuo Uemura
- United Graduate School of Agricultural Science, Iwate University, Morioka, Iwate 020-8550, Japan
| | - Mikio Nishimura
- Department of Cell Biology, National Institute for Basic Biology, Okazaki, Aichi 444-8585, Japan
| | - Makoto Kusaba
- Graduate School of Integrated Science for Life, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8526 Japan
| | - Akira Nagatani
- Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| |
Collapse
|
25
|
Phytochrome activates the plastid-encoded RNA polymerase for chloroplast biogenesis via nucleus-to-plastid signaling. Nat Commun 2019; 10:2629. [PMID: 31201355 PMCID: PMC6570650 DOI: 10.1038/s41467-019-10518-0] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 05/17/2019] [Indexed: 11/08/2022] Open
Abstract
Light initiates chloroplast biogenesis by activating photosynthesis-associated genes encoded by not only the nuclear but also the plastidial genome, but how photoreceptors control plastidial gene expression remains enigmatic. Here we show that the photoactivation of phytochromes triggers the expression of photosynthesis-associated plastid-encoded genes (PhAPGs) by stimulating the assembly of the bacterial-type plastidial RNA polymerase (PEP) into a 1000-kDa complex. Using forward genetic approaches, we identified REGULATOR OF CHLOROPLAST BIOGENESIS (RCB) as a dual-targeted nuclear/plastidial phytochrome signaling component required for PEP assembly. Surprisingly, RCB controls PhAPG expression primarily from the nucleus by interacting with phytochromes and promoting their localization to photobodies for the degradation of the transcriptional regulators PIF1 and PIF3. RCB-dependent PIF degradation in the nucleus signals the plastids for PEP assembly and PhAPG expression. Thus, our findings reveal the framework of a nucleus-to-plastid anterograde signaling pathway by which phytochrome signaling in the nucleus controls plastidial transcription.
Collapse
|
26
|
Xue P, El Kurdi A, Kohler A, Ma H, Kaeser G, Ali A, Fischer R, Krauß N, Lamparter T. Evidence for weak interaction between phytochromes Agp1 and Agp2 from Agrobacterium fabrum. FEBS Lett 2019; 593:926-941. [PMID: 30941759 DOI: 10.1002/1873-3468.13376] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 03/25/2019] [Accepted: 03/28/2019] [Indexed: 11/09/2022]
Abstract
During bacterial conjugation, plasmid DNA is transferred from cell to cell. In Agrobacterium fabrum, conjugation is regulated by the phytochrome photoreceptors Agp1 and Agp2. Both contribute equally to this regulation. Agp1 and Agp2 are histidine kinases, but, for Agp2, we found no autophosphorylation activity. A clear autophosphorylation signal, however, was obtained with mutants in which the phosphoaccepting Asp of the C-terminal response regulator domain is replaced. Thus, the Agp2 histidine kinase differs from the classical transphosphorylation pattern. We performed size exclusion, photoconversion, dark reversion, autophosphorylation, chromophore assembly kinetics and fluorescence resonance energy transfer measurements on mixed Agp1/Agp2 samples. These assays pointed to an interaction between both proteins. This could partially explain the coaction of both phytochromes in the cell.
Collapse
Affiliation(s)
- Peng Xue
- Botanical Institute, Karlsruhe Institute of Technology, Germany
| | - Afaf El Kurdi
- Botanical Institute, Karlsruhe Institute of Technology, Germany
| | - Anja Kohler
- Botanical Institute, Karlsruhe Institute of Technology, Germany
| | - Hongju Ma
- Botanical Institute, Karlsruhe Institute of Technology, Germany
| | - Gero Kaeser
- Botanical Institute, Karlsruhe Institute of Technology, Germany
| | - Arin Ali
- Institute for Applied Biosciences, Karlsruhe Institute of Technology, Germany
| | - Reinhard Fischer
- Institute for Applied Biosciences, Karlsruhe Institute of Technology, Germany
| | - Norbert Krauß
- Botanical Institute, Karlsruhe Institute of Technology, Germany
| | | |
Collapse
|
27
|
Transcriptome Analysis of Diurnal Gene Expression in Chinese Cabbage. Genes (Basel) 2019; 10:genes10020130. [PMID: 30754711 PMCID: PMC6409912 DOI: 10.3390/genes10020130] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Revised: 01/31/2019] [Accepted: 02/04/2019] [Indexed: 12/17/2022] Open
Abstract
Plants have developed timing mechanisms that enable them to maintain synchrony with daily environmental events. These timing mechanisms, i.e., circadian clocks, include transcriptional/translational feedback loops that drive 24 h transcriptional rhythms, which underlie oscillations in protein abundance, thus mediating circadian rhythms of behavior, physiology, and metabolism. Circadian clock genes have been investigated in the diploid model plant Arabidopsis thaliana. Crop plants with polyploid genomes—such as Brassica species—have multiple copies of some clock-related genes. Over the last decade, numerous studies have been aimed at identifying and understanding the function of paralogous genes with conserved sequences, or those that diverged during evolution. Brassica rapa’s triplicate genomes retain sequence-level collinearity with Arabidopsis. In this study, we used RNA sequencing (RNAseq) to profile the diurnal transcriptome of Brassica rapa seedlings. We identified candidate paralogs of circadian clock-related genes and assessed their expression levels. These genes and their related traits that modulate the diurnal rhythm of gene expression contribute to the adaptation of crop cultivars. Our findings will contribute to the mechanistic study of circadian clock regulation inherent in polyploidy genome crops, which differ from those of model plants, and thus will be useful for future breeding studies using clock genes.
Collapse
|
28
|
Abstract
Posttranslational modifications (PTMs) happen after or during protein translation. Small Ubiquitin-like Modifier (SUMO) proteins are covalently attached to certain lysine residues of the target proteins to modify their activity, stability, or localization. This process is called SUMOylation, which is a reversible PTM: SUMO protease enzymes can cleave SUMOs off the target protein backbone. Although many ubiquitinated proteins are targeted for degradation, SUMOylation does not necessary lead to the degradation of the modified protein but lead to the regulation of various physiological responses. SUMOylation of the examined protein cannot simply be monitored by immunoblotting techniques performed on total protein extracts, due to the SUMO-specific signals derived from other modified molecules. Furthermore, the fact that only a limited fraction of the target protein pool is SUMOylated makes the detection of SUMOylated proteins challenging. This protocol shows how SUMOylated phytochrome B (phyB) molecules can be detected using homologous and heterologous experimental systems in planta.
Collapse
Affiliation(s)
- Beatriz Orosa
- School of Biological and Biomedical Sciences, University of Durham, Durham, County Durham, UK
| | - András Viczián
- Biological Research Centre, Plant Biology Institute, Szeged, Hungary.
| |
Collapse
|
29
|
Ermert AL, Stahl F, Gans T, Hughes J. Analysis of Physcomitrella Phytochrome Mutants via Phototropism and Polarotropism. Methods Mol Biol 2019; 2026:225-236. [PMID: 31317417 DOI: 10.1007/978-1-4939-9612-4_19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
In mosses such as Physcomitrella patens phytochrome photoreceptors steer directional/vectorial responses to unilateral/polarized light. In this chapter, we describe procedures to assay phototropism and polarotropism quantitatively in wild type and mutant lines. Protonemata are placed on agar-based medium in square Petri dishes in darkness for 1 week, allowing caulonemata to develop and grow negatively gravitropically. For phototropism, the dishes are placed vertically in black boxes and unilaterally irradiated with continuous red light. For polarotropism, Petri dishes are placed horizontally and irradiated with linearly polarized red light from above. After irradiation, the filaments are photographed using a macroscope with CCD camera and the bending angles measured using image processing software. The data are transfered to a spreadsheet program, placed into 10° bending angle classes and illustrated using a circular histogram.
Collapse
Affiliation(s)
- Anna Lena Ermert
- Institute for Plant Physiology, Justus Liebig University, Giessen, Germany
| | - Fabian Stahl
- Institute for Plant Physiology, Justus Liebig University, Giessen, Germany
| | - Tanja Gans
- Institute for Plant Physiology, Justus Liebig University, Giessen, Germany
| | - Jon Hughes
- Institute for Plant Physiology, Justus Liebig University, Giessen, Germany.
| |
Collapse
|
30
|
Paik I, Huq E. Rapid Examination of Phytochrome-Phytochrome Interacting Factor (PIF) Interaction by In Vitro Coimmunoprecipitation Assay. Methods Mol Biol 2019; 2026:21-28. [PMID: 31317400 DOI: 10.1007/978-1-4939-9612-4_2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Phytochromes are red/far-red light receptors that perceive and transduce light signals to regulate various physiological responses. A large number of phytochrome interacting proteins have been identified using genetic and biochemical approaches. A direct interaction between phytochrome and its interacting proteins, therefore, defines one of the critical steps to initiate light signaling cascades in plants. Thus it is important to thoroughly examine the light-dependent interaction between phytochromes and putative phytochrome-interacting proteins. In this chapter, a protocol for rapid and simple light dependent in vitro coimmunoprecipitation between phytochromes and phytochrome interacting factors is described. In principle, this protocol can be adapted for other putative phytochrome interacting proteins.
Collapse
Affiliation(s)
- Inyup Paik
- Department of Molecular Biosciences, The Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, USA
| | - Enamul Huq
- Department of Molecular Biosciences, The Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, USA. .,Biological Laboratories, University of Texas at Austin, Austin, TX, USA.
| |
Collapse
|
31
|
Abstract
Photobodies are membraneless subnuclear organelles that contain the red and far-red photoreceptors, phytochromes. Photobody biogenesis has been postulated to play important roles in early light signaling events. The size and number of photobodies are highly dynamic in response to the quality and quantity of light and correlated tightly with phytochrome-mediated seedling morphogenesis. Here, we provide a detailed protocol for characterization of the three-dimensional morphology of photobodies, including sample preparation, fluorescence microscopy, and image analysis. Although this method was developed initially for characterizing photobodies, it can be adopted to analyze other membraneless or membrane-bound subcellular organelles.
Collapse
Affiliation(s)
- Chan Yul Yoo
- Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, CA, USA
| | - Desiree Williams
- Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, CA, USA
| | - Meng Chen
- Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, CA, USA.
| |
Collapse
|
32
|
Park E, Kim Y, Choi G. Phytochrome B Requires PIF Degradation and Sequestration to Induce Light Responses across a Wide Range of Light Conditions. THE PLANT CELL 2018; 30:1277-1292. [PMID: 29764986 PMCID: PMC6048787 DOI: 10.1105/tpc.17.00913] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 03/23/2018] [Accepted: 05/10/2018] [Indexed: 05/04/2023]
Abstract
Phytochrome B (phyB) inhibits the function of phytochrome-interacting factors (PIFs) by inducing their degradation and sequestration, but the relative physiological importance of these two phyB activities is unclear. In an analysis of published Arabidopsis thaliana phyB mutations, we identified a point mutation in the N-terminal half of phyB (phyBG111D) that abolishes its PIF sequestration activity without affecting its PIF degradation activity. We also identified a point mutation in the phyB C-terminal domain, which, when combined with a deletion of the C-terminal end (phyB990G767R), does the opposite; it blocks PIF degradation without affecting PIF sequestration. The resulting phyB proteins, phyB990G767R and phyBG111D, are equally capable of inducing light responses under continuous red light. However, phyBG111D, which exhibits only the PIF degradation activity, induces stronger light responses than phyB990G767R under white light with prolonged dark periods (i.e., diurnal cycles). In contrast, phyB990G767R, which exhibits only the PIF sequestration activity, induces stronger light responses in flickering light (a condition that mimics sunflecks). Together, our results indicate that both of these separable phyB activities are required for light responses in varying light conditions.
Collapse
Affiliation(s)
- Eunae Park
- Department of Biological Sciences, KAIST, Daejeon 34141, Korea
| | - Yeojae Kim
- Department of Biological Sciences, KAIST, Daejeon 34141, Korea
| | - Giltsu Choi
- Department of Biological Sciences, KAIST, Daejeon 34141, Korea
| |
Collapse
|
33
|
Grima R, Sonntag S, Venezia F, Kircher S, Smith RW, Fleck C. Insight into nuclear body formation of phytochromes through stochastic modelling and experiment. Phys Biol 2018; 15:056003. [PMID: 29714708 DOI: 10.1088/1478-3975/aac193] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Spatial relocalization of proteins is crucial for the correct functioning of living cells. An interesting example of spatial ordering is the light-induced clustering of plant photoreceptor proteins. Upon irradiation by white or red light, the red light-active phytochrome, phytochrome B, enters the nucleus and accumulates in large nuclear bodies (NBs). The underlying physical process of nuclear body formation remains unclear, but phytochrome B is thought to coagulate via a simple protein-protein binding process. We measure, for the first time, the distribution of the number of phytochrome B-containing NBs as well as their volume distribution. We show that the experimental data cannot be explained by a stochastic model of nuclear body formation via simple protein-protein binding processes using physically meaningful parameter values. Rather modelling suggests that the data is consistent with a two step process: a fast nucleation step leading to macroparticles followed by a subsequent slow step in which the macroparticles bind to form the nuclear body. An alternative explanation for the observed nuclear body distribution is that the phytochromes bind to a so far unknown molecular structure. We believe it is likely this result holds more generally for other nuclear body-forming plant photoreceptors and proteins.
Collapse
Affiliation(s)
- Ramon Grima
- Centre for Synthetic and Systems Biology (SynthSys), University of Edinburgh, United Kingdom. School of Biological Sciences, University of Edinburgh, United Kingdom. Freiburg Institute for Advanced Studies, University of Freiburg, Germany
| | | | | | | | | | | |
Collapse
|
34
|
Qiu Y, Pasoreck EK, Reddy AK, Nagatani A, Ma W, Chory J, Chen M. Mechanism of early light signaling by the carboxy-terminal output module of Arabidopsis phytochrome B. Nat Commun 2017. [PMID: 29199270 DOI: 10.1038/s41467-107-02062-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023] Open
Abstract
Plant phytochromes are thought to transduce light signals by mediating the degradation of phytochrome-interacting transcription factors (PIFs) through the N-terminal photosensory module, while the C-terminal module, including a histidine kinase-related domain (HKRD), does not participate in signaling. Here we show that the C-terminal module of Arabidopsis phytochrome B (PHYB) is sufficient to mediate the degradation of PIF3 specifically and to activate photosynthetic genes in the dark. The HKRD is a dimerization domain for PHYB homo and heterodimerization. A D1040V mutation, which disrupts the dimerization of HKRD and the interaction between C-terminal module and PIF3, abrogates PHYB nuclear accumulation, photobody biogenesis, and PIF3 degradation. By contrast, disrupting the interaction between PIF3 and PHYB's N-terminal module has little effect on PIF3 degradation. Together, this study demonstrates that the dimeric form of the C-terminal module plays important signaling roles by targeting PHYB to subnuclear photobodies and interacting with PIF3 to trigger its degradation.
Collapse
Affiliation(s)
- Yongjian Qiu
- Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, CA, 92521, USA
| | | | - Amit K Reddy
- Department of Biology, Duke University, Durham, NC, 27708, USA
| | - Akira Nagatani
- Department of Botany, Graduate School of Science, Kyoto University, Kyoto, 606-8502, Japan
| | - Wenxiu Ma
- Department of Statistics, University of California, Riverside, CA, 92521, USA
| | - Joanne Chory
- Howard Hughes Medical Institute, Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Meng Chen
- Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, CA, 92521, USA.
| |
Collapse
|
35
|
Mechanism of early light signaling by the carboxy-terminal output module of Arabidopsis phytochrome B. Nat Commun 2017; 8:1905. [PMID: 29199270 PMCID: PMC5712524 DOI: 10.1038/s41467-017-02062-6] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 11/03/2017] [Indexed: 11/08/2022] Open
Abstract
Plant phytochromes are thought to transduce light signals by mediating the degradation of phytochrome-interacting transcription factors (PIFs) through the N-terminal photosensory module, while the C-terminal module, including a histidine kinase-related domain (HKRD), does not participate in signaling. Here we show that the C-terminal module of Arabidopsis phytochrome B (PHYB) is sufficient to mediate the degradation of PIF3 specifically and to activate photosynthetic genes in the dark. The HKRD is a dimerization domain for PHYB homo and heterodimerization. A D1040V mutation, which disrupts the dimerization of HKRD and the interaction between C-terminal module and PIF3, abrogates PHYB nuclear accumulation, photobody biogenesis, and PIF3 degradation. By contrast, disrupting the interaction between PIF3 and PHYB's N-terminal module has little effect on PIF3 degradation. Together, this study demonstrates that the dimeric form of the C-terminal module plays important signaling roles by targeting PHYB to subnuclear photobodies and interacting with PIF3 to trigger its degradation.
Collapse
|
36
|
Singh M, Gupta A, Singh D, Khurana JP, Laxmi A. Arabidopsis RSS1 Mediates Cross-Talk Between Glucose and Light Signaling During Hypocotyl Elongation Growth. Sci Rep 2017; 7:16101. [PMID: 29170398 PMCID: PMC5701026 DOI: 10.1038/s41598-017-16239-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 11/09/2017] [Indexed: 11/11/2022] Open
Abstract
Plants possess exuberant plasticity that facilitates its ability to adapt and survive under challenging environmental conditions. The developmental plasticity largely depends upon cellular elongation which is governed by a complex network of environmental and phytohormonal signals. Here, we report role of glucose (Glc) and Glc-regulated factors in controlling elongation growth and shade response in Arabidopsis. Glc controls shade induced hypocotyl elongation in a dose dependent manner. We have identified a Glc repressed factor REGULATED BY SUGAR AND SHADE1 (RSS1) encoding for an atypical basic helix-loop-helix (bHLH) protein of unknown biological function that is required for normal Glc actions. Phenotype analysis of mutant and overexpression lines suggested RSS1 to be a negative regulator of elongation growth. RSS1 affects overall auxin homeostasis. RSS1 interacts with the elongation growth-promoting proteins HOMOLOG OF BEE2 INTERACTING WITH IBH 1 (HBI1) and BR ENHANCED EXPRESSION2 (BEE2) and negatively affects the transcription of their downstream targets such as YUCs, INDOLE-3-ACETIC ACID INDUCIBLE (IAAs), LONG HYPOCOTYL IN FAR-RED1 (HFR1), HOMEOBOX PROTEIN 2 (ATHB2), XYLOGLUCAN ENDOTRANSGLUCOSYLASE/HYDROLASES (XTHs) and EXPANSINS. We propose, Glc signals might maintain optimal hypocotyl elongation under multiple signals such as light, shade and phytohormones through the central growth regulatory bHLH/HLH module.
Collapse
Affiliation(s)
- Manjul Singh
- National Institute of Plant Genome Research, New Delhi, 110067, India.,Interdisciplinary center for Plant Genomics and Department of Plant Molecular biology, University of Delhi South Campus, New Delhi, 110021, India
| | - Aditi Gupta
- National Institute of Plant Genome Research, New Delhi, 110067, India.,Interdisciplinary center for Plant Genomics and Department of Plant Molecular biology, University of Delhi South Campus, New Delhi, 110021, India
| | - Dhriti Singh
- National Institute of Plant Genome Research, New Delhi, 110067, India
| | - Jitendra P Khurana
- Interdisciplinary center for Plant Genomics and Department of Plant Molecular biology, University of Delhi South Campus, New Delhi, 110021, India
| | - Ashverya Laxmi
- National Institute of Plant Genome Research, New Delhi, 110067, India.
| |
Collapse
|
37
|
Biological activity and dimerization state of modified phytochrome A proteins. PLoS One 2017; 12:e0186468. [PMID: 29049346 PMCID: PMC5648194 DOI: 10.1371/journal.pone.0186468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 10/02/2017] [Indexed: 11/29/2022] Open
Abstract
To assess potential physical interactions of type I phyA with the type II phyB-phyE phytochromes in vivo, transgenes expressing fusion gene forms of phyA were introduced into the Arabidopsis phyA mutant background. When a single c-Myc (myc) epitope is added to either the N- or C-terminus of phyA, the constructs completely complement phyA mutant phenotypes. However, addition of larger tags, such as six consecutive myc epitopes or the yellow fluorescent protein sequence, result in fusion proteins that show reduced activity. All the tagged phyA proteins migrate as dimers on native gels and co-immunoprecipitation reveals no binding interaction of phyA to any of the type II phys in the dark or under continuous far-red light. Dimers of the phyA 1–615 amino acid N-terminal photosensory domain (NphyA), generated in vivo with a yeast GAL4 dimerization domain and attached to a constitutive nuclear localization sequence, are expressed at a low level and, although they cause a cop phenotype in darkness and mediate a very low fluence response to pulses of FR, have no activity under continuous FR. It is concluded that type I phyA in its Pr form is present in plants predominantly or exclusively as a homodimer and does not stably interact with type II phys in a dimer-to-dimer manner. In addition, its activity in mediating response to continuous FR is sensitive to modification of its N- or C-terminus.
Collapse
|
38
|
Kim JH, Lee HJ, Park CM. HOS1 acts as a key modulator of hypocotyl photomorphogenesis. PLANT SIGNALING & BEHAVIOR 2017; 12:e1315497. [PMID: 28426369 PMCID: PMC5501242 DOI: 10.1080/15592324.2017.1315497] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Plants recognize light as an environmental signal to determine the proper timing of growth and development. In Arabidopsis seedlings, hypocotyl growth is promoted in the dark but suppressed in the light. It is known that the red/far-red light-sensing receptor phytochrome B (phyB) suppresses the function of PHYTOCHROME INTERACTING FACTOR (PIF) transcription factors, which act as photomorphogenic repressors. However, molecular mechanisms underlying the phyB-mediated inhibition of PIF functioning remain unclear. We recently demonstrated that HIGH EXPRESSION OF OSMOTICALLY RESPONSIVE GENES 1 (HOS1) facilitates the phyB-mediated suppression of PIF4 during the light period to achieve hypocotyl photomorphogenesis. HOS1 inhibits the transcriptional activation activity of PIF4 by forming protein complexes. Notably, phyB-mediated light signals induce HOS1 activity, thus promoting hypocotyl photomorphogenesis. While HOS1 is known to act as an E3 ubiquitin ligase or a chromatin remodeling factor, our data illustrate a novel role of HOS1: it acts as a component of phyB-mediated light signaling in hypocotyl photomorphogenesis.
Collapse
Affiliation(s)
- Ju-Heon Kim
- Department of Chemistry, Seoul National University, Seoul, South Korea
| | - Hyo-Jun Lee
- Department of Chemistry, Seoul National University, Seoul, South Korea
| | - Chung-Mo Park
- Department of Chemistry, Seoul National University, Seoul, South Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, South Korea
- CONTACT Chung-Mo Park , Department of Chemistry, Seoul National University, 599 Kwanak-Ro, Seoul 151-742, Republic of South Korea
| |
Collapse
|
39
|
Pacurar DI, Pacurar ML, Lakehal A, Pacurar AM, Ranjan A, Bellini C. The Arabidopsis Cop9 signalosome subunit 4 (CNS4) is involved in adventitious root formation. Sci Rep 2017; 7:628. [PMID: 28377589 PMCID: PMC5429640 DOI: 10.1038/s41598-017-00744-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 03/14/2017] [Indexed: 11/09/2022] Open
Abstract
The COP9 signalosome (CSN) is an evolutionary conserved multiprotein complex that regulates many aspects of plant development by controlling the activity of CULLIN-RING E3 ubiquitin ligases (CRLs). CRLs ubiquitinate and target for proteasomal degradation a vast number of specific substrate proteins involved in many developmental and physiological processes, including light and hormone signaling and cell division. As a consequence of CSN pleiotropic function, complete loss of CSN activity results in seedling lethality. Therefore, a detailed analysis of CSN physiological functions in adult Arabidopsis plants has been hampered by the early seedling lethality of csn null mutants. Here we report the identification and characterization of a viable allele of the Arabidopsis COP9 signalosome subunit 4 (CSN4). The allele, designated csn4-2035, suppresses the adventitious root (AR) phenotype of the Arabidopsis superroot2-1 mutant, potentially by altering its auxin signaling. Furthermore, we show that although the csn4-2035 mutation affects primary and lateral root (LR) formation in the 2035 suppressor mutant, CSN4 and other subunits of the COP9 complex seem to differentially control AR and LR development.
Collapse
Affiliation(s)
- Daniel Ioan Pacurar
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, SE-90187, Umeå, Sweden. .,SweTree Technologies AB, P.O. Box 4095, SE-904 03, Umeå, Sweden.
| | - Monica Lacramioara Pacurar
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, SE-90187, Umeå, Sweden.,University of Agricultural Sciences and Veterinary Medicine, 400372, Cluj Napoca, Romania.,SweTree Technologies AB, P.O. Box 4095, SE-904 03, Umeå, Sweden
| | - Abdellah Lakehal
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, SE-90187, Umeå, Sweden
| | - Andrea Mariana Pacurar
- University of Agricultural Sciences and Veterinary Medicine, 400372, Cluj Napoca, Romania
| | - Alok Ranjan
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, SE-90187, Umeå, Sweden
| | - Catherine Bellini
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, SE-90187, Umeå, Sweden. .,Institut National de la Research Agronomic, UMR1318 INRA-AgroParisTech, Institut Jean-Pierre Bourgin, Univ. Paris-Sud, F-78000, Versailles, France.
| |
Collapse
|
40
|
Nevarez PA, Qiu Y, Inoue H, Yoo CY, Benfey PN, Schnell DJ, Chen M. Mechanism of Dual Targeting of the Phytochrome Signaling Component HEMERA/pTAC12 to Plastids and the Nucleus. PLANT PHYSIOLOGY 2017; 173:1953-1966. [PMID: 28232584 PMCID: PMC5373053 DOI: 10.1104/pp.16.00116] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 02/21/2017] [Indexed: 05/20/2023]
Abstract
HEMERA (HMR) is a nuclear and plastidial dual-targeted protein. While it functions in the nucleus as a transcriptional coactivator in phytochrome signaling to regulate a distinct set of light-responsive, growth-relevant genes, in plastids it is known as pTAC12, which associates with the plastid-encoded RNA polymerase, and is essential for inducing the plastomic photosynthetic genes and initiating chloroplast biogenesis. However, the mechanism of targeting HMR to the nucleus and plastids is still poorly understood. Here, we show that HMR can be directly imported into chloroplasts through a transit peptide residing in the N-terminal 50 amino acids. Upon cleavage of the transit peptide and additional proteolytic processing, mature HMR, which begins from Lys-58, retains its biochemical properties in phytochrome signaling. Unexpectedly, expression of mature HMR failed to rescue not only the plastidial but also the nuclear defects of the hmr mutant. This is because the predicted nuclear localization signals of HMR are nonfunctional, and therefore mature HMR is unable to accumulate in either plastids or the nucleus. Surprisingly, fusing the transit peptide of the small subunit of Rubisco with mature HMR rescues both its plastidial and nuclear localization and functions. These results, combined with the observation that the nuclear form of HMR has the same reduced molecular mass as plastidial HMR, support a retrograde protein translocation mechanism in which HMR is targeted first to plastids, processed to the mature form, and then relocated to the nucleus.
Collapse
Affiliation(s)
- P Andrew Nevarez
- Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, California 92521 (Y.Q., C.Y., M.C.)
- Department of Biology, Duke University, Durham, North Carolina 27708 (P.A.N., Y.Q., C.Y., P.N.B., M.C.); and
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824 (H.I., D.J.S.)
| | - Yongjian Qiu
- Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, California 92521 (Y.Q., C.Y., M.C.)
- Department of Biology, Duke University, Durham, North Carolina 27708 (P.A.N., Y.Q., C.Y., P.N.B., M.C.); and
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824 (H.I., D.J.S.)
| | - Hitoshi Inoue
- Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, California 92521 (Y.Q., C.Y., M.C.)
- Department of Biology, Duke University, Durham, North Carolina 27708 (P.A.N., Y.Q., C.Y., P.N.B., M.C.); and
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824 (H.I., D.J.S.)
| | - Chan Yul Yoo
- Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, California 92521 (Y.Q., C.Y., M.C.)
- Department of Biology, Duke University, Durham, North Carolina 27708 (P.A.N., Y.Q., C.Y., P.N.B., M.C.); and
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824 (H.I., D.J.S.)
| | - Philip N Benfey
- Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, California 92521 (Y.Q., C.Y., M.C.)
- Department of Biology, Duke University, Durham, North Carolina 27708 (P.A.N., Y.Q., C.Y., P.N.B., M.C.); and
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824 (H.I., D.J.S.)
| | - Danny J Schnell
- Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, California 92521 (Y.Q., C.Y., M.C.)
- Department of Biology, Duke University, Durham, North Carolina 27708 (P.A.N., Y.Q., C.Y., P.N.B., M.C.); and
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824 (H.I., D.J.S.)
| | - Meng Chen
- Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, California 92521 (Y.Q., C.Y., M.C.);
- Department of Biology, Duke University, Durham, North Carolina 27708 (P.A.N., Y.Q., C.Y., P.N.B., M.C.); and
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824 (H.I., D.J.S.)
| |
Collapse
|
41
|
Lee HJ, Ha JH, Park CM. Underground roots monitor aboveground environment by sensing stem-piped light. Commun Integr Biol 2016; 9:e1261769. [PMID: 28042383 PMCID: PMC5193042 DOI: 10.1080/19420889.2016.1261769] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 11/13/2016] [Indexed: 12/19/2022] Open
Abstract
Light is a critical environmental cue for plant growth and development. Plants actively monitor surrounding environments by sensing changes in light wavelength and intensity. Therefore, plants have evolved a series of photoreceptors to perceive a broad wavelength range of light. Phytochrome photoreceptors sense red and far-red light, which serves as a major photomorphogenic signal in shoot growth and morphogenesis. Notably, plants also express phytochromes in the roots, obscuring whether and how they perceive light in the soil. We have recently demonstrated that plants directly channel light to the roots through plant body to activate root phytochrome B (phyB). Stem light facilitates the nuclear import of phyB in the roots, and the photoactivated phyB triggers the accumulation of the photomorphogenic regulator ELONGATED HYPOCOTYL 5 in modulating root growth and gravitropism. Optical experiments revealed that red to far-red light is efficiently transduced through plant body. Our findings provide physical and molecular evidence, supporting that photoreceptors expressed in the underground roots directly sense light. We propose that the roots are not a passive organ but a central organ that actively monitors changes in the aboveground environment by perceiving light information from the shoots.
Collapse
Affiliation(s)
- Hyo-Jun Lee
- Department of Chemistry, Seoul National University , Seoul, Korea
| | - Jun-Ho Ha
- Department of Chemistry, Seoul National University , Seoul, Korea
| | - Chung-Mo Park
- Department of Chemistry, Seoul National University, Seoul, Korea; Plant Genomics and Breeding Institute, Seoul National University, Seoul, Korea
| |
Collapse
|
42
|
Kim J, Song K, Park E, Kim K, Bae G, Choi G. Epidermal Phytochrome B Inhibits Hypocotyl Negative Gravitropism Non-Cell-Autonomously. THE PLANT CELL 2016; 28:2770-2785. [PMID: 27758895 PMCID: PMC5155346 DOI: 10.1105/tpc.16.00487] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Revised: 09/27/2016] [Accepted: 10/06/2016] [Indexed: 05/20/2023]
Abstract
Seedling hypocotyls display negative gravitropism in the dark but agravitropism in the light. The Arabidopsis thaliana pif quadruple mutant (pifQ), which lacks four PHYTOCHROME-INTERACTING FACTORS (PIFs), is agravitropic in the dark. Endodermis-specific expression of PIF1 rescues gravitropism in pifQ mutant seedlings. Since phytochromes induce light responses by inhibiting PIFs and the COP1-SPA ubiquitin E3 ligase complex in the nucleus, we asked whether phyB can cell autonomously inhibit hypocotyl negative gravitropism in the endodermis. We found that while epidermis-specific expression of PHYB rescues hypocotyl negative gravitropism and all other phyB mutant phenotypes, endodermis-specific expression of PHYB does not. Epidermal phyB induces the phosphorylation and degradation of endodermal PIFs in response to red light. This induces a global gene expression pattern similar to that induced by red light treatment of seedlings expressing PHYB under the control of its own endogenous promoter. Our results imply that epidermal phyB generates an unidentified mobile signal that travels to the endodermis where it promotes PIF degradation and inhibits hypocotyl negative gravitropism.
Collapse
Affiliation(s)
- Jaewook Kim
- Department of Biological Sciences, KAIST, Daejeon 34141, Korea
| | - Kijong Song
- Department of Biological Sciences, KAIST, Daejeon 34141, Korea
| | - Eunae Park
- Department of Biological Sciences, KAIST, Daejeon 34141, Korea
| | - Keunhwa Kim
- Department of Biological Sciences, KAIST, Daejeon 34141, Korea
| | - Gabyong Bae
- Department of Biological Sciences, KAIST, Daejeon 34141, Korea
| | - Giltsu Choi
- Department of Biological Sciences, KAIST, Daejeon 34141, Korea
| |
Collapse
|
43
|
Inoue K, Nishihama R, Kataoka H, Hosaka M, Manabe R, Nomoto M, Tada Y, Ishizaki K, Kohchi T. Phytochrome Signaling Is Mediated by PHYTOCHROME INTERACTING FACTOR in the Liverwort Marchantia polymorpha. THE PLANT CELL 2016; 28:1406-21. [PMID: 27252292 PMCID: PMC4944405 DOI: 10.1105/tpc.15.01063] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Revised: 05/18/2016] [Accepted: 05/30/2016] [Indexed: 05/18/2023]
Abstract
Phytochromes are red light (R) and far-red light (FR) receptors that play important roles in many aspects of plant growth and development. Phytochromes mainly function in the nucleus and regulate sets of genes by inhibiting negatively acting basic helix-loop-helix transcription factors named PHYTOCHROME INTERACTING FACTORs (PIFs) in Arabidopsis thaliana Although R/FR photoreversible responses and phytochrome genes are well documented in diverse lineages of plants, the extent to which phytochrome signaling is mediated by gene regulation beyond angiosperms remains largely unclear. Here, we show that the liverwort Marchantia polymorpha, an emerging model basal land plant, has only one phytochrome gene, Mp-PHY, and only one PIF gene, Mp-PIF These genes mediate typical low fluence responses, which are reversibly elicited by R and FR, and regulate gene expression. Mp-phy is light-stable and translocates into the nucleus upon irradiation with either R or FR, demonstrating that the single phytochrome Mp-phy exhibits combined biochemical and cell-biological characteristics of type I and type II phytochromes. Mp-phy photoreversibly regulates gemma germination and downstream gene expression by interacting with Mp-PIF and targeting it for degradation in an R-dependent manner. Our findings suggest that the molecular mechanisms for light-dependent transcriptional regulation mediated by PIF transcription factors were established early in land plant evolution.
Collapse
Affiliation(s)
- Keisuke Inoue
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Ryuichi Nishihama
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Hideo Kataoka
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Masashi Hosaka
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Ryo Manabe
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Mika Nomoto
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa, Nagoya 464-8602, Japan
| | - Yasuomi Tada
- Center for Gene Research, Nagoya University, Chikusa, Nagoya 464-8602, Japan
| | - Kimitsune Ishizaki
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan Graduate School of Science, Kobe University, Kobe 657-8501, Japan
| | - Takayuki Kohchi
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| |
Collapse
|
44
|
Kim J, Kang H, Park J, Kim W, Yoo J, Lee N, Kim J, Yoon TY, Choi G. PIF1-Interacting Transcription Factors and Their Binding Sequence Elements Determine the in Vivo Targeting Sites of PIF1. THE PLANT CELL 2016; 28:1388-405. [PMID: 27303023 PMCID: PMC4944412 DOI: 10.1105/tpc.16.00125] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Revised: 06/06/2016] [Accepted: 06/10/2016] [Indexed: 05/18/2023]
Abstract
The bHLH transcription factor PHYTOCHROME INTERACTING FACTOR1 (PIF1) binds G-box elements in vitro and inhibits light-dependent germination in Arabidopsis thaliana A previous genome-wide analysis of PIF1 targeting indicated that PIF1 binds 748 sites in imbibed seeds, only 59% of which possess G-box elements. This suggests the G-box is not the sole determinant of PIF1 targeting. The targeting of PIF1 to specific sites could be stabilized by PIF1-interacting transcription factors (PTFs) that bind other nearby sequence elements. Here, we report PIF1 targeting sites are enriched with not only G-boxes but also with other hexameric sequence elements we named G-box coupling elements (GCEs). One of these GCEs possesses an ACGT core and serves as a binding site for group A bZIP transcription factors, including ABSCISIC ACID INSENSITIVE5 (ABI5), which inhibits seed germination in abscisic acid signaling. PIF1 interacts with ABI5 and other group A bZIP transcription factors and together they target a subset of PIF1 binding sites in vivo. In vitro single-molecule fluorescence imaging confirms that ABI5 facilitates PIF1 binding to DNA fragments possessing multiple G-boxes or the GCE alone. Thus, we show in vivo PIF1 targeting to specific binding sites is determined by its interaction with PTFs and their binding to GCEs.
Collapse
Affiliation(s)
- Junghyun Kim
- Department of Biological Sciences, KAIST, Daejeon 34141, Korea
| | - Hyojin Kang
- Department of Convergence Technology Research, KISTI, Daejeon 34141, Korea
| | - Jeongmoo Park
- Department of Biological Sciences, KAIST, Daejeon 34141, Korea
| | - Woohyun Kim
- Department of Biological Sciences, KAIST, Daejeon 34141, Korea
| | - Janghyun Yoo
- Department of Physics, KAIST, Daejeon 34141, Korea
| | - Nayoung Lee
- Department of Biological Sciences, KAIST, Daejeon 34141, Korea
| | - Jaewook Kim
- Department of Biological Sciences, KAIST, Daejeon 34141, Korea
| | | | - Giltsu Choi
- Department of Biological Sciences, KAIST, Daejeon 34141, Korea
| |
Collapse
|
45
|
Kaiserli E, Páldi K, O'Donnell L, Batalov O, Pedmale UV, Nusinow DA, Kay SA, Chory J. Integration of Light and Photoperiodic Signaling in Transcriptional Nuclear Foci. Dev Cell 2015; 35:311-21. [PMID: 26555051 PMCID: PMC4654455 DOI: 10.1016/j.devcel.2015.10.008] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Revised: 08/08/2015] [Accepted: 10/09/2015] [Indexed: 10/22/2022]
Abstract
Light regulates major plant developmental transitions by orchestrating a series of nuclear events. This study uncovers the molecular function of the natural variant, TZP (Tandem Zinc-finger-Plus3), as a signal integrator of light and photoperiodic pathways in transcriptional nuclear foci. We report that TZP acts as a positive regulator of photoperiodic flowering via physical interactions with the red-light receptor phytochrome B (phyB). We demonstrate that TZP localizes in dynamic nuclear domains regulated by light quality and photoperiod. This study shows that phyB is indispensable not only for localizing TZP to transcriptionally active nuclear photobodies, but also for recruiting TZP on the promoter of the floral inducer FLOWERING LOCUS T (FT). Our findings signify a unique transcriptional regulatory role to the highly enigmatic plant nuclear photobodies, where TZP directly activates FT gene expression and promotes flowering.
Collapse
Affiliation(s)
- Eirini Kaiserli
- Howard Hughes Medical Institute and Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA; Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK.
| | - Katalin Páldi
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Liz O'Donnell
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Olga Batalov
- Howard Hughes Medical Institute and Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Ullas V Pedmale
- Howard Hughes Medical Institute and Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Dmitri A Nusinow
- Center for Chronobiology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Steve A Kay
- Center for Chronobiology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Joanne Chory
- Howard Hughes Medical Institute and Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
| |
Collapse
|
46
|
Geilen K, Böhmer M. Dynamic subnuclear relocalisation of WRKY40 in response to Abscisic acid in Arabidopsis thaliana. Sci Rep 2015; 5:13369. [PMID: 26293691 PMCID: PMC4642543 DOI: 10.1038/srep13369] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Accepted: 07/23/2015] [Indexed: 11/20/2022] Open
Abstract
WRKY18, WRKY40 and WRKY60 are members of the WRKY transcription factor family and function as transcriptional regulators in ABA signal transduction in Arabidopsis thaliana. Here we show that WRKY18 and WRKY40, but not WRKY60, co-localise with PIF3, PIF4 and PHYB to Phytochrome B-containing nuclear bodies (PNBs). Localisation to the PNBs is phosphorylation-dependent and is inhibited by the general Ser/Thr-kinase inhibitor Staurosporine. Upon ABA treatment, WRKY40 relocalises from PNBs to the nucleoplasm in an OST1-dependent manner. This stimulus-induced relocalisation was not observed in response to other abiotic or biotic stimuli, including NaCl, MeJA or flg22 treatment. Bimolecular fluorescence complementation experiments indicate that while PIF3, PIF4 and PHYB physically interact in these bodies, PHYB, PIF3 and PIF4 do not interact with the two WRKY transcription factors, which may suggest a more general role for these bodies in regulation of transcriptional activity.
Collapse
Affiliation(s)
- Katja Geilen
- Institut für Biologie und Biotechnologie der Pflanzen, Westfälische Wilhelms-Universität, Münster, Germany
| | - Maik Böhmer
- Institut für Biologie und Biotechnologie der Pflanzen, Westfälische Wilhelms-Universität, Münster, Germany
| |
Collapse
|
47
|
SUMOylation of phytochrome-B negatively regulates light-induced signaling in Arabidopsis thaliana. Proc Natl Acad Sci U S A 2015; 112:11108-13. [PMID: 26283376 DOI: 10.1073/pnas.1415260112] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The red/far red light absorbing photoreceptor phytochrome-B (phyB) cycles between the biologically inactive (Pr, λmax, 660 nm) and active (Pfr; λmax, 730 nm) forms and functions as a light quality and quantity controlled switch to regulate photomorphogenesis in Arabidopsis. At the molecular level, phyB interacts in a conformation-dependent fashion with a battery of downstream regulatory proteins, including PHYTOCHROME INTERACTING FACTOR transcription factors, and by modulating their activity/abundance, it alters expression patterns of genes underlying photomorphogenesis. Here we report that the small ubiquitin-like modifier (SUMO) is conjugated (SUMOylation) to the C terminus of phyB; the accumulation of SUMOylated phyB is enhanced by red light and displays a diurnal pattern in plants grown under light/dark cycles. Our data demonstrate that (i) transgenic plants expressing the mutant phyB(Lys996Arg)-YFP photoreceptor are hypersensitive to red light, (ii) light-induced SUMOylation of the mutant phyB is drastically decreased compared with phyB-YFP, and (iii) SUMOylation of phyB inhibits binding of PHYTOCHROME INTERACTING FACTOR 5 to phyB Pfr. In addition, we show that OVERLY TOLERANT TO SALT 1 (OTS1) de-SUMOylates phyB in vitro, it interacts with phyB in vivo, and the ots1/ots2 mutant is hyposensitive to red light. Taken together, we conclude that SUMOylation of phyB negatively regulates light signaling and it is mediated, at least partly, by the action of OTS SUMO proteases.
Collapse
|
48
|
Lee N, Park J, Kim K, Choi G. The Transcriptional Coregulator LEUNIG_HOMOLOG Inhibits Light-Dependent Seed Germination in Arabidopsis. THE PLANT CELL 2015; 27:2301-13. [PMID: 26276832 PMCID: PMC4568510 DOI: 10.1105/tpc.15.00444] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Accepted: 07/27/2015] [Indexed: 05/11/2023]
Abstract
PHYTOCHROME-INTERACTING FACTOR1 (PIF1) is a basic helix-loop-helix transcription factor that inhibits light-dependent seed germination in Arabidopsis thaliana. However, it remains unclear whether PIF1 requires other factors to regulate its direct targets. Here, we demonstrate that LEUNIG_HOMOLOG (LUH), a Groucho family transcriptional corepressor, binds to PIF1 and coregulates its targets. Not only are the transcriptional profiles of the luh and pif1 mutants remarkably similar, more than 80% of the seeds of both genotypes germinate in the dark. We show by chromatin immunoprecipitation that LUH binds a subset of PIF1 targets in a partially PIF1-dependent manner. Unexpectedly, we found LUH binds and coregulates not only PIF1-activated targets but also PIF1-repressed targets. Together, our results indicate LUH functions with PIF1 as a transcriptional coregulator to inhibit seed germination.
Collapse
Affiliation(s)
- Nayoung Lee
- Department of Biological Sciences, KAIST, Daejeon 305-701, Korea
| | - Jeongmoo Park
- Department of Biological Sciences, KAIST, Daejeon 305-701, Korea
| | - Keunhwa Kim
- Department of Biological Sciences, KAIST, Daejeon 305-701, Korea
| | - Giltsu Choi
- Department of Biological Sciences, KAIST, Daejeon 305-701, Korea
| |
Collapse
|
49
|
Klose C, Viczián A, Kircher S, Schäfer E, Nagy F. Molecular mechanisms for mediating light-dependent nucleo/cytoplasmic partitioning of phytochrome photoreceptors. THE NEW PHYTOLOGIST 2015; 206:965-71. [PMID: 26042244 PMCID: PMC4406131 DOI: 10.1111/nph.13207] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Accepted: 11/05/2014] [Indexed: 05/19/2023]
Abstract
The photoreceptors phytochromes monitor the red/far-red part of the spectrum, exist in the biologically active Pfr (far-red absorbing) or inactive Pr (red absorbing) forms, and function as red/far-red light-regulated molecular switches to modulate plant development and growth. Phytochromes are synthesized in the cytoplasm, and light induces translocation of the Pfr conformer into the nucleus. Nuclear import of phytochromes is a highly regulated process and is fine-tuned by the quality and quantity of light. It appears that phytochrome A (phyA) and phytochrome B (phyB) do not possess active endogenous nuclear import signals (NLSs), thus light-induced translocation of these photoreceptors into the nucleus requires direct protein–protein interactions with their NLS-containing signaling partners. Sub-cellular partitioning of the various phytochrome species is mediated by different molecular machineries. Translocation of phyA into the nucleus is promoted by FAR-RED ELONGATED HYPOCOTYL 1 (FHY1) and FHY1-LIKE (FHL), but the identity of nuclear transport facilitators mediating the import of phyB-E into the nucleus remains elusive. Phytochromes localized in the nucleus are associated with specific protein complexes, termed photobodies. The size and distribution of these structures are regulated by the intensity and duration of irradiation, and circumstantial evidence indicates that they are involved in fine-tuning phytochrome signaling.
Collapse
Affiliation(s)
- Cornelia Klose
- Institute of Botany, University of FreiburgSchänzlestrasse 1, D-79104, Freiburg, Germany
| | - András Viczián
- Institute of Plant Biology, Biological Research CentreTemesvári krt. 62, H-6726, Szeged, Hungary
| | - Stefan Kircher
- Institute of Botany, University of FreiburgSchänzlestrasse 1, D-79104, Freiburg, Germany
| | - Eberhard Schäfer
- Institute of Botany, University of FreiburgSchänzlestrasse 1, D-79104, Freiburg, Germany
| | - Ferenc Nagy
- Institute of Plant Biology, Biological Research CentreTemesvári krt. 62, H-6726, Szeged, Hungary
- School of Biological Sciences, Institute of Molecular Plant Science, University of EdinburghEdinburgh, EH9 3JH, UK
- Author for correspondence: Ferenc Nagy Tel: +36 62599718
| |
Collapse
|
50
|
Phytochrome controls alternative splicing to mediate light responses in Arabidopsis. Proc Natl Acad Sci U S A 2014; 111:18781-6. [PMID: 25512548 DOI: 10.1073/pnas.1407147112] [Citation(s) in RCA: 122] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Plants monitor the ambient light conditions using several informational photoreceptors, including red/far-red light absorbing phytochrome. Phytochrome is widely believed to regulate the transcription of light-responsive genes by modulating the activity of several transcription factors. Here we provide evidence that phytochrome significantly changes alternative splicing (AS) profiles at the genomic level in Arabidopsis, to approximately the same degree as it affects steady-state transcript levels. mRNA sequencing analysis revealed that 1,505 and 1,678 genes underwent changes in their AS and steady-state transcript level profiles, respectively, within 1 h of red light exposure in a phytochrome-dependent manner. Furthermore, we show that splicing factor genes were the main early targets of AS control by phytochrome, whereas transcription factor genes were the primary direct targets of phytochrome-mediated transcriptional regulation. We experimentally validated phytochrome-induced changes in the AS of genes that are involved in RNA splicing, phytochrome signaling, the circadian clock, and photosynthesis. Moreover, we show that phytochrome-induced AS changes of SPA1-RELATED 3, the negative regulator of light signaling, physiologically contributed to promoting photomorphogenesis. Finally, photophysiological experiments demonstrated that phytochrome transduces the signal from its photosensory domain to induce light-dependent AS alterations in the nucleus. Taking these data together, we show that phytochrome directly induces AS cascades in parallel with transcriptional cascades to mediate light responses in Arabidopsis.
Collapse
|