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Feng Z, Wang M, Liu Y, Li C, Zhang S, Duan J, Chen J, Qi L, Liu Y, Li H, Wu J, Liu Y, Terzaghi W, Tian F, Zhong B, Fang X, Qian W, Guo Y, Deng XW, Li J. Liquid-liquid phase separation of TZP promotes PPK-mediated phosphorylation of the phytochrome A photoreceptor. NATURE PLANTS 2024; 10:798-814. [PMID: 38714768 DOI: 10.1038/s41477-024-01679-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 03/28/2024] [Indexed: 05/10/2024]
Abstract
Phytochrome A (phyA) is the plant far-red (FR) light photoreceptor and plays an essential role in regulating photomorphogenic development in FR-rich conditions, such as canopy shade. It has long been observed that phyA is a phosphoprotein in vivo; however, the protein kinases that could phosphorylate phyA remain largely unknown. Here we show that a small protein kinase family, consisting of four members named PHOTOREGULATORY PROTEIN KINASES (PPKs) (also known as MUT9-LIKE KINASES), directly phosphorylate phyA in vitro and in vivo. In addition, TANDEM ZINC-FINGER/PLUS3 (TZP), a recently characterized phyA-interacting protein required for in vivo phosphorylation of phyA, is also directly phosphorylated by PPKs. We reveal that TZP contains two intrinsically disordered regions in its amino-terminal domain that undergo liquid-liquid phase separation (LLPS) upon light exposure. The LLPS of TZP promotes colocalization and interaction between PPKs and phyA, thus facilitating PPK-mediated phosphorylation of phyA in FR light. Our study identifies PPKs as a class of protein kinases mediating the phosphorylation of phyA and demonstrates that the LLPS of TZP contributes significantly to more production of the phosphorylated phyA form in FR light.
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Affiliation(s)
- Ziyi Feng
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, Frontiers Science Center for Molecular Design Breeding (MOE), China Agricultural University, Beijing, China
| | - Meijiao Wang
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, Frontiers Science Center for Molecular Design Breeding (MOE), China Agricultural University, Beijing, China
| | - Yan Liu
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, Frontiers Science Center for Molecular Design Breeding (MOE), China Agricultural University, Beijing, China
| | - Cong Li
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, Frontiers Science Center for Molecular Design Breeding (MOE), China Agricultural University, Beijing, China
| | - Shaoman Zhang
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, Frontiers Science Center for Molecular Design Breeding (MOE), China Agricultural University, Beijing, China
| | - Jie Duan
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, Frontiers Science Center for Molecular Design Breeding (MOE), China Agricultural University, Beijing, China
| | - Jiaqi Chen
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, Frontiers Science Center for Molecular Design Breeding (MOE), China Agricultural University, Beijing, China
| | - Lijuan Qi
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, Frontiers Science Center for Molecular Design Breeding (MOE), China Agricultural University, Beijing, China
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Yanru Liu
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, Frontiers Science Center for Molecular Design Breeding (MOE), China Agricultural University, Beijing, China
| | - Hong Li
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, Frontiers Science Center for Molecular Design Breeding (MOE), China Agricultural University, Beijing, China
| | - Jie Wu
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Yannan Liu
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | | | - Feng Tian
- State Key Laboratory of Plant Environmental Resilience, Frontiers Science Center for Molecular Design Breeding (MOE), China Agricultural University, Beijing, China
| | - Bojian Zhong
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Xiaofeng Fang
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Weiqiang Qian
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
- State Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, China
| | - Yan Guo
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, Frontiers Science Center for Molecular Design Breeding (MOE), China Agricultural University, Beijing, China
| | - Xing Wang Deng
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
- State Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, China
| | - Jigang Li
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, Frontiers Science Center for Molecular Design Breeding (MOE), China Agricultural University, Beijing, China.
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2
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Chan A, Stasolla C. Light induction of somatic embryogenesis in Arabidopsis is regulated by PHYTOCHROME E. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 195:163-169. [PMID: 36640683 DOI: 10.1016/j.plaphy.2023.01.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 01/01/2023] [Accepted: 01/06/2023] [Indexed: 06/17/2023]
Abstract
The requirement of light on somatic embryogenesis (SE) has been documented in many species; however, no mechanism of action has been elucidated. Using Arabidopsis SE as a model, the effect of red light (660 nm) during the induction phase corresponding to the formation of the embryogenic tissue was examined. Analyses of several phytochrome mutants revealed that red light signaling, conducive to SE, was mediated by PHYTOCHROME E (PHYE). Both phyE and darkness were sufficient to repress the formation of somatic embryos and reduced the expression of CONSTITUTIVE PHOTOMORPHIC DWARF 3 (CPD3), a rate limiting step in brassinosteroid (BR) biosynthesis, as well as AGAMOUS LIKE 15 (AGL15), a key inducer of many SE genes. We further integrated BR signaling and nitric oxide (NO) with PHYE by demonstrating that applications of both compounds to phyE explants and WT explants cultured in the dark partially restored AGL15 expression. These results demonstrate that SE induction by red light operates via PHYE through BR signaling and NO required to induce AGL15.
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Affiliation(s)
- Aaron Chan
- Department of Plant Science, University of Manitoba, Winnipeg, R3T2N2, Canada
| | - Claudio Stasolla
- Department of Plant Science, University of Manitoba, Winnipeg, R3T2N2, Canada.
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3
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Sun C, He C, Zhong C, Liu S, Liu H, Luo X, Li J, Zhang Y, Guo Y, Yang B, Wang P, Deng X. Bifunctional regulators of photoperiodic flowering in short day plant rice. FRONTIERS IN PLANT SCIENCE 2022; 13:1044790. [PMID: 36340409 PMCID: PMC9630834 DOI: 10.3389/fpls.2022.1044790] [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: 09/15/2022] [Accepted: 10/07/2022] [Indexed: 06/16/2023]
Abstract
Photoperiod is acknowledged as a crucial environmental factor for plant flowering. According to different responses to photoperiod, plants were divided into short-day plants (SDPs), long-day plants (LDPs), and day-neutral plants (DNPs). The day length measurement system of SDPs is different from LDPs. Many SDPs, such as rice, have a critical threshold for day length (CDL) and can even detect changes of 15 minutes for flowering decisions. Over the last 20 years, molecular mechanisms of flowering time in SDP rice and LDP Arabidopsis have gradually clarified, which offers a chance to elucidate the differences in day length measurement between the two types of plants. In Arabidopsis, CO is a pivotal hub in integrating numerous internal and external signals for inducing photoperiodic flowering. By contrast, Hd1 in rice, the homolog of CO, promotes and prevents flowering under SD and LD, respectively. Subsequently, numerous dual function regulators, such as phytochromes, Ghd7, DHT8, OsPRR37, OsGI, OsLHY, and OsELF3, were gradually identified. This review assesses the relationship among these regulators and a proposed regulatory framework for the reversible mechanism, which will deepen our understanding of the CDL regulation mechanism and the negative response to photoperiod between SDPs and LDPs.
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Affiliation(s)
- Changhui Sun
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Rice Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Changcai He
- Rice Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Chao Zhong
- Rice Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Shihang Liu
- Rice Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Hongying Liu
- Rice Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Xu Luo
- Rice Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Jun Li
- Rice Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yuxiu Zhang
- Rice Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yuting Guo
- Rice Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Bin Yang
- Rice Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Pingrong Wang
- Rice Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Xiaojian Deng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Rice Research Institute, Sichuan Agricultural University, Chengdu, China
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4
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Ahn G, Jung IJ, Cha JY, Jeong SY, Shin GI, Ji MG, Kim MG, Lee SY, Kim WY. Phytochrome B Positively Regulates Red Light-Mediated ER Stress Response in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2022; 13:846294. [PMID: 35283886 PMCID: PMC8905361 DOI: 10.3389/fpls.2022.846294] [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: 12/31/2021] [Accepted: 02/02/2022] [Indexed: 06/14/2023]
Abstract
Light plays a crucial role in plant growth and development, and light signaling is integrated with various stress responses to adapt to different environmental changes. During this process, excessive protein synthesis overwhelms the protein-folding ability of the endoplasmic reticulum (ER), causing ER stress. Although crosstalk between light signaling and ER stress response has been reported in plants, the molecular mechanisms underlying this crosstalk are poorly understood. Here, we demonstrate that the photoreceptor phytochrome B (phyB) induces the expression of ER luminal protein chaperones as well as that of unfolded protein response (UPR) genes. The phyB-5 mutant was less sensitive to tunicamycin (TM)-induced ER stress than were the wild-type plants, whereas phyB-overexpressing plants displayed a more sensitive phenotype under white light conditions. ER stress response genes (BiP2 and BiP3), UPR-related bZIP transcription factors (bZIP17, bZIP28, and bZIP60), and programmed cell death (PCD)-associated genes (OXI1, NRP1, and MC8) were upregulated in phyB-overexpressing plants, but not in phyB-5, under ER stress conditions. The ER stress-sensitive phenotype of phyB-5 under red light conditions was eliminated with a reduction in photo-equilibrium by far-red light and darkness. The N-terminal domain of phyB is essential for signal transduction of the ER stress response in the nucleus, which is similar to light signaling. Taken together, our results suggest that phyB integrates light signaling with the UPR to relieve ER stress and maintain proper plant growth.
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Affiliation(s)
- Gyeongik Ahn
- Division of Applied Life Science (BK21 Four), Institute of Agricultural and Life Science, Research Institute of Life Science, Gyeongsang National University, Jinju, South Korea
| | - In Jung Jung
- National Institute of Wildlife Disease Control and Prevention (NIWDC), Ministry of Environment, Gwangju, South Korea
| | - Joon-Yung Cha
- Division of Applied Life Science (BK21 Four), Institute of Agricultural and Life Science, Research Institute of Life Science, Gyeongsang National University, Jinju, South Korea
| | - Song Yi Jeong
- Division of Applied Life Science (BK21 Four), Institute of Agricultural and Life Science, Research Institute of Life Science, Gyeongsang National University, Jinju, South Korea
| | - Gyeong-Im Shin
- Division of Applied Life Science (BK21 Four), Institute of Agricultural and Life Science, Research Institute of Life Science, Gyeongsang National University, Jinju, South Korea
| | - Myung Geun Ji
- Division of Applied Life Science (BK21 Four), Institute of Agricultural and Life Science, Research Institute of Life Science, Gyeongsang National University, Jinju, South Korea
| | - Min Gab Kim
- College of Pharmacy and Research Institute of Pharmaceutical Science, Gyeongsang National University, Jinju, South Korea
| | - Sang Yeol Lee
- Division of Applied Life Science (BK21 Four), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, South Korea
| | - Woe-Yeon Kim
- Division of Applied Life Science (BK21 Four), Institute of Agricultural and Life Science, Research Institute of Life Science, Gyeongsang National University, Jinju, South Korea
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5
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Makita Y, Suzuki S, Fushimi K, Shimada S, Suehisa A, Hirata M, Kuriyama T, Kurihara Y, Hamasaki H, Okubo-Kurihara E, Yoshitake K, Watanabe T, Sakuta M, Gojobori T, Sakami T, Narikawa R, Yamaguchi H, Kawachi M, Matsui M. Identification of a dual orange/far-red and blue light photoreceptor from an oceanic green picoplankton. Nat Commun 2021; 12:3593. [PMID: 34135337 PMCID: PMC8209157 DOI: 10.1038/s41467-021-23741-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 05/11/2021] [Indexed: 11/09/2022] Open
Abstract
Photoreceptors are conserved in green algae to land plants and regulate various developmental stages. In the ocean, blue light penetrates deeper than red light, and blue-light sensing is key to adapting to marine environments. Here, a search for blue-light photoreceptors in the marine metagenome uncover a chimeric gene composed of a phytochrome and a cryptochrome (Dualchrome1, DUC1) in a prasinophyte, Pycnococcus provasolii. DUC1 detects light within the orange/far-red and blue spectra, and acts as a dual photoreceptor. Analyses of its genome reveal the possible mechanisms of light adaptation. Genes for the light-harvesting complex (LHC) are duplicated and transcriptionally regulated under monochromatic orange/blue light, suggesting P. provasolii has acquired environmental adaptability to a wide range of light spectra and intensities.
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Affiliation(s)
- Yuko Makita
- Synthetic Genomics Research Group, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Shigekatsu Suzuki
- Biodiversity Division, National Institute for Environmental Studies, Tsukuba, Japan
| | - Keiji Fushimi
- Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka, Japan
- Research Institute of Green Science and Technology, Shizuoka University, Shizuoka, Japan
- Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, Saitama, Japan
| | - Setsuko Shimada
- Synthetic Genomics Research Group, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Aya Suehisa
- Synthetic Genomics Research Group, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Manami Hirata
- Synthetic Genomics Research Group, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Tomoko Kuriyama
- Synthetic Genomics Research Group, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Yukio Kurihara
- Synthetic Genomics Research Group, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Hidefumi Hamasaki
- Synthetic Genomics Research Group, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- Yokohama City University, Kihara Institute for Biological Research, Yokohama, Japan
| | - Emiko Okubo-Kurihara
- Synthetic Genomics Research Group, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Kazutoshi Yoshitake
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Tsuyoshi Watanabe
- Fisheries Resources Institute, Japan Fisheries Research and Education Agency, Kushiro, Hokkaido, Japan
| | - Masaaki Sakuta
- Department of Biological Sciences, Ochanomizu University, Tokyo, Japan
| | - Takashi Gojobori
- Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
| | - Tomoko Sakami
- Fisheries Resources Institute, Japan Fisheries Research and Education Agency, Minami-ise, Mie, Japan
| | - Rei Narikawa
- Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka, Japan
- Research Institute of Green Science and Technology, Shizuoka University, Shizuoka, Japan
- Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, Saitama, Japan
- Department of Biological Sciences, Graduate School of Science, Tokyo Metropolitan University, Tokyo, Japan
| | - Haruyo Yamaguchi
- Biodiversity Division, National Institute for Environmental Studies, Tsukuba, Japan
| | - Masanobu Kawachi
- Biodiversity Division, National Institute for Environmental Studies, Tsukuba, Japan
| | - Minami Matsui
- Synthetic Genomics Research Group, RIKEN Center for Sustainable Resource Science, Yokohama, Japan.
- Yokohama City University, Kihara Institute for Biological Research, Yokohama, Japan.
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6
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Burgie ES, Gannam ZTK, McLoughlin KE, Sherman CD, Holehouse AS, Stankey RJ, Vierstra RD. Differing biophysical properties underpin the unique signaling potentials within the plant phytochrome photoreceptor families. Proc Natl Acad Sci U S A 2021; 118:e2105649118. [PMID: 34039713 PMCID: PMC8179155 DOI: 10.1073/pnas.2105649118] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Many aspects of photoperception by plants and microorganisms are initiated by the phytochrome (Phy) family of photoreceptors that detect light through interconversion between red light- (Pr) and far-red light-absorbing (Pfr) states. Plants synthesize a small family of Phy isoforms (PhyA to PhyE) that collectively regulate photomorphogenesis and temperature perception through redundant and unique actions. While the selective roles of these isoforms have been partially attributed to their differing abundances, expression patterns, affinities for downstream partners, and turnover rates, we show here from analysis of recombinant Arabidopsis chromoproteins that the Phy isoforms also display distinct biophysical properties. Included are a hypsochromic shift in the Pr absorption for PhyC and varying rates of Pfr to Pr thermal reversion, part of which can be attributed to the core photosensory module in each. Most strikingly, PhyB combines strong temperature dependence of thermal reversion with an order-of-magnitude faster rate to likely serve as the main physiological thermosensor, whereby thermal reversion competes with photoconversion. In addition, comparisons of Pfr occupancies for PhyA and PhyB under a range of red- and white-light fluence rates imply that low-light environments are effectively sensed by PhyA, while high-light environments, such as full sun, are effectively sensed by PhyB. Parallel analyses of the Phy isoforms from potato and maize showed that the unique features within the Arabidopsis family are conserved, thus indicating that the distinct biophysical properties among plant Phy isoforms emerged early in Phy evolution, likely to enable full interrogation of their light and temperature environments.
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Affiliation(s)
- E Sethe Burgie
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
- Department of Genetics, University of Wisconsin, Madison, WI 53706
| | - Zira T K Gannam
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | | | | | - Alex S Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine in St. Louis, St. Louis, MO 63110
- Center for Science and Engineering of Living Systems, Washington University in St. Louis, St. Louis, MO 63110
| | - Robert J Stankey
- Department of Genetics, University of Wisconsin, Madison, WI 53706
| | - Richard D Vierstra
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130;
- Department of Genetics, University of Wisconsin, Madison, WI 53706
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Kusuma P, Bugbee B. Improving the Predictive Value of Phytochrome Photoequilibrium: Consideration of Spectral Distortion Within a Leaf. FRONTIERS IN PLANT SCIENCE 2021; 12:596943. [PMID: 34108976 PMCID: PMC8181145 DOI: 10.3389/fpls.2021.596943] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 04/28/2021] [Indexed: 06/01/2023]
Abstract
The ratio of active phytochrome (Pfr) to total phytochrome (Pr + Pfr), called phytochrome photo-equilibrium (PPE; also called phytochrome photostationary state, PSS) has been used to explain shade avoidance responses in both natural and controlled environments. PPE is commonly estimated using measurements of the spectral photon distribution (SPD) above the canopy and photoconversion coefficients. This approach has effectively predicted morphological responses when only red and far-red (FR) photon fluxes have varied, but controlled environment research often utilizes unique ratios of wavelengths so a more rigorous evaluation of the predictive ability of PPE on morphology is warranted. Estimations of PPE have rarely incorporated the optical effects of spectral distortion within a leaf caused by pigment absorbance and photon scattering. We studied stem elongation rate in the model plant cucumber under diverse spectral backgrounds over a range of one to 45% FR (total photon flux density, 400-750 nm, of 400 μmol m-2 s-1) and found that PPE was not predictive when blue and green varied. Preferential absorption of red and blue photons by chlorophyll results in an SPD that is relatively enriched in green and FR at the phytochrome molecule within a cell. This can be described by spectral distortion functions for specific layers of a leaf. Multiplying the photoconversion coefficients by these distortion functions yields photoconversion weighting factors that predict phytochrome conversion at the site of photon perception within leaf tissue. Incorporating spectral distortion improved the predictive value of PPE when phytochrome was assumed to be homogeneously distributed within the whole leaf. In a supporting study, the herbicide norflurazon was used to remove chlorophyll in seedlings. Using distortion functions unique to either green or white cotyledons, we came to the same conclusions as with whole plants in the longer-term study. Leaves of most species have similar spectral absorbance so this approach for predicting PPE should be broadly applicable. We provide a table of the photoconversion weighting factors. Our analysis indicates that the simple, intuitive ratio of FR (700-750 nm) to total photon flux (far-red fraction) is also a reliable predictor of morphological responses like stem length.
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8
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Li J, Hiltbrunner A. Is the Pr form of phytochrome biologically active in the nucleus? MOLECULAR PLANT 2021; 14:535-537. [PMID: 33676024 DOI: 10.1016/j.molp.2021.03.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 02/18/2021] [Accepted: 02/28/2021] [Indexed: 06/12/2023]
Affiliation(s)
- Jigang Li
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China.
| | - Andreas Hiltbrunner
- Institute of Biology II, Faculty of Biology and Signalling Research Centres BIOSS and CIBSS, University of Freiburg, 79104 Freiburg, Germany.
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9
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Red light-induced structure changes in phytochrome A from Pisum sativum. Sci Rep 2021; 11:2827. [PMID: 33531580 PMCID: PMC7854702 DOI: 10.1038/s41598-021-82544-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 01/15/2021] [Indexed: 12/17/2022] Open
Abstract
Phytochrome A (phyA) is a photoreceptor protein of plants that regulates the red/far-red light photomorphogenic responses of plants essential for growth and development. PhyA, composed of approximately 1100 amino acid residues, folds into photosensory and output signaling modules. The photosensory module covalently binds phytochromobilin as a chromophore for photoreversible interconversion between inactive red light-absorbing (Pr) and active far-red light-absorbing (Pfr) forms to act as a light-driven phosphorylation enzyme. To understand the molecular mechanism in the initial process of photomorphogenic response, we studied the molecular structures of large phyA (LphyA) from Pisum sativum, which lacks the 52 residues in the N-terminal, by small-angle X-ray scattering combined with multivariate analyses applied to molecular models predicted from the scattering profiles. According to our analyses, Pr was in a dimer and had a four-leaf shape, and the subunit was approximated as a bent rod of 175 × 50 Å. The scattering profile of Pfr was calculated from that recorded for a mixture of Pr and Pfr under red-light irradiation by using their population determined from the absorption spectrum. The Pfr dimer exhibited a butterfly shape composed of subunits with a straight rod of 175 × 50 Å. The shape differences between Pr and Pfr indicated conformational changes in the Pr/Pfr interconversion which would be essential to the interaction with protein molecules involved in transcriptional control.
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10
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Kim C, Kim SJ, Jeong J, Park E, Oh E, Park YI, Lim PO, Choi G. High Ambient Temperature Accelerates Leaf Senescence via PHYTOCHROME-INTERACTING FACTOR 4 and 5 in Arabidopsis. Mol Cells 2020; 43:645-661. [PMID: 32732458 PMCID: PMC7398796 DOI: 10.14348/molcells.2020.0117] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 06/10/2020] [Accepted: 06/10/2020] [Indexed: 11/30/2022] Open
Abstract
Leaf senescence is a developmental process by which a plant actively remobilizes nutrients from aged and photosynthetically inefficient leaves to young growing ones by disassembling organelles and degrading macromolecules. Senescence is accelerated by age and environmental stresses such as prolonged darkness. Phytochrome B (phyB) inhibits leaf senescence by inhibiting phytochrome-interacting factor 4 (PIF4) and PIF5 in prolonged darkness. However, it remains unknown whether phyB mediates the temperature signal that regulates leaf senescence. We found the light-activated form of phyB (Pfr) remains active at least four days after a transfer to darkness at 20°C but is inactivated more rapidly at 28°C. This faster inactivation of Pfr further increases PIF4 protein levels at the higher ambient temperature. In addition, PIF4 mRNA levels rise faster after the transfer to darkness at high ambient temperature via a mechanism that depends on ELF3 but not phyB. Increased PIF4 protein then binds to the ORE1 promoter and activates its expression together with ABA and ethylene signaling, accelerating leaf senescence at high ambient temperature. Our results support a role for the phy-PIF signaling module in integrating not only light signaling but also temperature signaling in the regulation of leaf senescence.
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Affiliation(s)
- Chanhee Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 344, Korea
| | - Sun Ji Kim
- Center for Plant Aging Research, Institute for Basic Science, Daegu 4988, Korea
| | - Jinkil Jeong
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 9207, USA
| | - Eunae Park
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 344, Korea
| | - Eunkyoo Oh
- Division of Life Sciences, Korea University, Seoul 0281, Korea
| | - Youn-Il Park
- Department of Biological Sciences and Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon 34134, Korea
| | - Pyung Ok Lim
- Department of New Biology, Daegu Gyeongbuk Institute of Science & Technology (DGIST), Daegu 42988, Korea
| | - Giltsu Choi
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 344, Korea
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11
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Klose C, Nagy F, Schäfer E. Thermal Reversion of Plant Phytochromes. MOLECULAR PLANT 2020; 13:386-397. [PMID: 31812690 DOI: 10.1016/j.molp.2019.12.004] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 10/21/2019] [Accepted: 12/03/2019] [Indexed: 05/18/2023]
Abstract
Phytochromes are red/far-red reversible photoreceptors essential for plant growth and development. Phytochrome signaling is mediated by the physiologically active far-red-absorbing Pfr form that can be inactivated to the red-absorbing Pr ground state by light-dependent photoconversion or by light-independent thermal reversion, also termed dark reversion. Although the term "dark reversion" is justified by historical reasons and frequently used in the literature, "thermal reversion" more appropriately describes the process of light-independent but temperature-regulated Pfr relaxation that not only occurs in darkness but also in light and is used throughout the review. Thermal reversion is a critical parameter for the light sensitivity of phytochrome-mediated responses and has been studied for decades, often resulting in contradictory findings. Thermal reversion is an intrinsic property of the phytochrome molecules but can be modulated by intra- and intermolecular interactions, as well as biochemical modifications, such as phosphorylation. In this review, we outline the research history of phytochrome thermal reversion, highlighting important predictions that have been made before knowing the molecular basis. We further summarize and discuss recent findings about the molecular mechanisms regulating phytochrome thermal reversion and its functional roles in light and temperature sensing in plants.
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Affiliation(s)
- Cornelia Klose
- Institute of Biology II, University of Freiburg, 79104 Freiburg, Germany.
| | - Ferenc Nagy
- Institute of Plant Biology, Biological Research Centre, Temesvári krt. 62, 6726 Szeged, Hungary
| | - Eberhard Schäfer
- Institute of Biology II, University of Freiburg, 79104 Freiburg, Germany
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12
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Molecular mechanisms underlying phytochrome-controlled morphogenesis in plants. Nat Commun 2019; 10:5219. [PMID: 31745087 PMCID: PMC6864062 DOI: 10.1038/s41467-019-13045-0] [Citation(s) in RCA: 183] [Impact Index Per Article: 36.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 10/17/2019] [Indexed: 11/08/2022] Open
Abstract
Phytochromes are bilin-binding photosensory receptors which control development over a broad range of environmental conditions and throughout the whole plant life cycle. Light-induced conformational changes enable phytochromes to interact with signaling partners, in particular transcription factors or proteins that regulate them, resulting in large-scale transcriptional reprograming. Phytochromes also regulate promoter usage, mRNA splicing and translation through less defined routes. In this review we summarize our current understanding of plant phytochrome signaling, emphasizing recent work performed in Arabidopsis. We compare and contrast phytochrome responses and signaling mechanisms among land plants and highlight open questions in phytochrome research.
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Beattie GA, Hatfield BM, Dong H, McGrane RS. Seeing the Light: The Roles of Red- and Blue-Light Sensing in Plant Microbes. ANNUAL REVIEW OF PHYTOPATHOLOGY 2018; 56:41-66. [PMID: 29768135 DOI: 10.1146/annurev-phyto-080417-045931] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Plants collect, concentrate, and conduct light throughout their tissues, thus enhancing light availability to their resident microbes. This review explores the role of photosensing in the biology of plant-associated bacteria and fungi, including the molecular mechanisms of red-light sensing by phytochromes and blue-light sensing by LOV (light-oxygen-voltage) domain proteins in these microbes. Bacteriophytochromes function as major drivers of the bacterial transcriptome and mediate light-regulated suppression of virulence, motility, and conjugation in some phytopathogens and light-regulated induction of the photosynthetic apparatus in a stem-nodulating symbiont. Bacterial LOV proteins also influence light-mediated changes in both symbiotic and pathogenic phenotypes. Although red-light sensing by fungal phytopathogens is poorly understood, fungal LOV proteins contribute to blue-light regulation of traits, including asexual development and virulence. Collectively, these studies highlight that plant microbes have evolved to exploit light cues and that light sensing is often coupled with sensing other environmental signals.
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Affiliation(s)
- Gwyn A Beattie
- Department of Plant Pathology & Microbiology, Iowa State University, Ames, Iowa 50011, USA;
| | - Bridget M Hatfield
- Department of Plant Pathology & Microbiology, Iowa State University, Ames, Iowa 50011, USA;
| | - Haili Dong
- Department of Plant Pathology & Microbiology, Iowa State University, Ames, Iowa 50011, USA;
| | - Regina S McGrane
- Department of Biological Sciences, Southwestern Oklahoma State University, Weatherford, Oklahoma 73096, USA
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14
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PCH1 and PCHL promote photomorphogenesis in plants by controlling phytochrome B dark reversion. Nat Commun 2017; 8:2221. [PMID: 29263319 PMCID: PMC5738371 DOI: 10.1038/s41467-017-02311-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 11/18/2017] [Indexed: 11/08/2022] Open
Abstract
Phytochrome B (phyB) is the primary red light photoreceptor in plants, and regulates both growth and development. The relative levels of phyB in the active state are determined by the light conditions, such as direct sunlight or shade, but are also affected by light-independent dark reversion. Dark reversion is a temperature-dependent thermal relaxation process, by which phyB reverts from the active to the inactive state. Here, we show that the homologous phyB-binding proteins PCH1 and PCHL suppress phyB dark reversion, resulting in plants with dramatically enhanced light sensitivity. Moreover, far-red and blue light upregulate the expression of PCH1 and PCHL in a phyB independent manner, thereby increasing the response to red light perceived by phyB. PCH1 and PCHL therefore provide a node for the molecular integration of different light qualities by regulation of phyB dark reversion, allowing plants to adapt growth and development to the ambient environment.
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Sheerin DJ, Hiltbrunner A. Molecular mechanisms and ecological function of far-red light signalling. PLANT, CELL & ENVIRONMENT 2017; 40:2509-2529. [PMID: 28102581 DOI: 10.1111/pce.12915] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 01/11/2017] [Accepted: 01/13/2017] [Indexed: 05/18/2023]
Abstract
Land plants possess the ability to sense and respond to far-red light (700-760 nm), which serves as an important environmental cue. Due to the nature of far-red light, it is not absorbed by chlorophyll and thus is enriched in canopy shade and will also penetrate deeper into soil than other visible wavelengths. Far-red light responses include regulation of seed germination, suppression of hypocotyl growth, induction of flowering and accumulation of anthocyanins, which depend on one member of the phytochrome photoreceptor family, phytochrome A (phyA). Here, we review the current understanding of the underlying molecular mechanisms of how plants sense far-red light through phyA and the physiological responses to this light quality. Light-activated phytochromes act on two primary pathways within the nucleus; suppression of the E3 ubiquitin ligase complex CUL4/DDB1COP1/SPA and inactivation of the PHYTOCHROME INTERACTING FACTOR (PIF) family of bHLH transcription factors. These pathways integrate with other signal transduction pathways, including phytohormones, for tissue and developmental stage specific responses. Unlike other phytochromes that mediate red-light responses, phyA is transported from the cytoplasm to the nucleus in far-red light by the shuttle proteins FAR-RED ELONGATED HYPOCOTYL 1 (FHY1) and FHY1-LIKE (FHL). However, additional mechanisms must exist that shift the action of phyA to far-red light; current hypotheses are discussed.
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Affiliation(s)
- David J Sheerin
- Institute of Biology II, Faculty of Biology, University of Freiburg, 79104, Freiburg, Germany
| | - Andreas Hiltbrunner
- Institute of Biology II, Faculty of Biology, University of Freiburg, 79104, Freiburg, Germany
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104, Freiburg, Germany
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Viczián A, Klose C, Ádám É, Nagy F. New insights of red light-induced development. PLANT, CELL & ENVIRONMENT 2017; 40:2457-2468. [PMID: 27943362 DOI: 10.1111/pce.12880] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Revised: 12/04/2016] [Accepted: 12/05/2016] [Indexed: 05/14/2023]
Abstract
The red/far-red light absorbing photoreceptors phytochromes regulate development and growth and thus play an essential role in optimizing adaptation of the sessile plants to the ever-changing environment. Our understanding of how absorption of a red/far-red photon by phytochromes initiates/modifies diverse physiological responses has been steadily improving. Research performed in the last 5 years has been especially productive and led to significant conceptual changes about the mode of action of these photoreceptors. In this review, we focus on the phytochrome B photoreceptor, the major phytochrome species active in light-grown plants. We discuss how its light-independent inactivation (termed dark/thermal reversion), post-translational modification, including ubiquitination, phosphorylation and sumoylation, as well as heterodimerization with other phytochrome species modify red light-controlled physiological responses. Finally, we discuss how photobiological properties of phytochrome B enable this photoreceptor to function also as a thermosensor.
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Affiliation(s)
- András Viczián
- Institute of Plant Biology, Biological Research Centre, Hungarian Academy of Sciences, Temesvári krt. 62, H-6726, Szeged, Hungary
| | - Cornelia Klose
- Institute of Biology2/Botany, University of Freiburg, Schänzlestrasse 1, D-79104, Freiburg, Germany
| | - Éva Ádám
- Institute of Plant Biology, Biological Research Centre, Hungarian Academy of Sciences, Temesvári krt. 62, H-6726, Szeged, Hungary
| | - Ferenc Nagy
- Institute of Plant Biology, Biological Research Centre, Hungarian Academy of Sciences, Temesvári krt. 62, H-6726, Szeged, Hungary
- Institute of Molecular Plant Science, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3JH, UK
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Wang P, Hendron RW, Kelly S. Transcriptional control of photosynthetic capacity: conservation and divergence from Arabidopsis to rice. THE NEW PHYTOLOGIST 2017; 216:32-45. [PMID: 28727145 DOI: 10.1111/nph.14682] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Accepted: 05/16/2017] [Indexed: 05/12/2023]
Abstract
Contents 32 I. 32 II. 33 III. 36 IV. 41 43 References 43 SUMMARY: Photosynthesis is one of the most important biological processes on Earth. It provides the consumable energy upon which almost all organisms are dependent, and modulates the composition of the planet's atmosphere. To carry out photosynthesis, plants require a large cohort of genes. These genes encode proteins that capture light energy, store energy in sugars and build the subcellular structures required to facilitate this energy capture. Although the function of many of these genes is known, little is understood about the transcriptional networks that coordinate their expression. This review places our understanding of the transcriptional regulation of photosynthesis in Arabidopsis thaliana in an evolutionary context, to provide new insight into transcriptional regulatory networks that control photosynthesis gene expression in grasses. The similarities and differences between the rice and Arabidopsis networks are highlighted, revealing substantial disparity between the two systems. In addition, avenues are identified that may be exploited for photosynthesis engineering projects in the future.
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Affiliation(s)
- Peng Wang
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | - Ross-William Hendron
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | - Steven Kelly
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
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Klose C, Venezia F, Hussong A, Kircher S, Schäfer E, Fleck C. Systematic analysis of how phytochrome B dimerization determines its specificity. NATURE PLANTS 2015; 1:15090. [PMID: 27250256 DOI: 10.1038/nplants.2015.90] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Accepted: 06/01/2015] [Indexed: 05/12/2023]
Abstract
Phytochromes are red/far-red-light detecting photoreceptors that regulate plant growth and development. They photo-interconvert between an inactive Pr (red-light absorbing) and a physiologically active Pfr (far-red-light absorbing) form, acting as light-controlled molecular switches. Although the two major plant phytochromes A (phyA) and B (phyB) share similar absorption properties, they exhibit dramatic differences in their action spectra. Since both phytochromes antagonistically regulate seedling development under vegetative shade, it is essential for plants to clearly distinguish between phyA and phyB action. This discrimination is not comprehensible solely by the molecular properties of the phytochromes, but is evidently due to the dynamics of the phytochrome system. Using an integrated experimental and mathematical modelling approach we show that phytochrome dimerization is an essential element for phyB function. Our findings reveal that light-independent Pfr to Pr relaxation (dark reversion) and association/dissociation to nuclear bodies (NBs) severely depend on the conformational state of the phyB dimer. We conclude that only Pfr-Pfr homodimers of phyB can be responsible for triggering physiological responses, leading to a suppression of phyB function in the far-red range of the light spectrum.
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Affiliation(s)
- Cornelia Klose
- Institute of Biology II, University of Freiburg, Schänzlestrasse 1, Freiburg 79104, Germany
| | - Filippo Venezia
- Institute of Biology II, University of Freiburg, Schänzlestrasse 1, Freiburg 79104, Germany
- Centre for Biological Systems Analysis, University of Freiburg, Habsburgerstr. 49, Freiburg 79104, Germany
| | - Andrea Hussong
- Institute of Biology II, University of Freiburg, Schänzlestrasse 1, Freiburg 79104, Germany
| | - Stefan Kircher
- Institute of Biology II, University of Freiburg, Schänzlestrasse 1, Freiburg 79104, Germany
| | - Eberhard Schäfer
- Institute of Biology II, University of Freiburg, Schänzlestrasse 1, Freiburg 79104, Germany
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, Schänzlestr. 18, Freiburg 79104, Germany
| | - Christian Fleck
- Laboratory for Systems and Synthetic Biology, Wageningen UR, Dreijenplein 10, Wageningen 6703 HB, The Netherlands
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Arabidopsis DET1 degrades HFR1 but stabilizes PIF1 to precisely regulate seed germination. Proc Natl Acad Sci U S A 2015; 112:3817-22. [PMID: 25775589 DOI: 10.1073/pnas.1502405112] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Seed is an essential propagation organ and a critical strategy adopted by terrestrial flowering plants to colonize the land. The ability of seeds to accurately respond to light is vital for plant survival. However, the underlying mechanism is largely unknown. In this study, we reveal a circuit of triple feed-forward loops adopted by Arabidopsis seeds to exclusively repress germination in dark conditions and precisely initiate germination under diverse light conditions. We identify that de-etiolated 1 (DET1), an evolutionarily conserved protein, is a central repressor of light-induced seed germination. Genetic analysis demonstrates that DET1 functions upstream of long hypocotyl in far-red 1 (HFR1) and phytochrome interacting factor 1 (PIF1), the key positive and negative transcription regulators in seed germination. We further find that DET1 and constitutive photomorphogenic 10 (COP10) target HFR1 for protein degradation by assembling a COP10-DET1-damaged DNA binding protein 1-cullin4 E3 ligase complex. Moreover, DET1 and COP10 directly interact with and promote the protein stability of PIF1. Computational modeling reveals that phytochrome B (phyB)-DET1-HFR1-PIF1 and phyB-DET1-Protease-PIF1 are new signaling pathways, independent of the previously identified phyB-PIF1 pathway, respectively mediating the rapid and time-lapse responses to light irradiation. The model-simulated results are highly consistent with their experimental validations, suggesting that our mathematical model captures the essence of Arabidopsis seed germination networks. Taken together, this study provides a comprehensive molecular framework for light-regulated seed germination, improving our understanding of how plants respond to changeable environments.
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20
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Gibbs DC, Donohue K. Gene duplication and the environmental regulation of physiology and development. Ecol Evol 2014; 4:2202-16. [PMID: 25360261 PMCID: PMC4201434 DOI: 10.1002/ece3.1099] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Accepted: 04/07/2014] [Indexed: 11/08/2022] Open
Abstract
When different life stages have different environmental tolerances, development needs to be regulated so that each life stage experiences environmental conditions that are suitable for it, if fitness is to be maintained. Restricting the timing of developmental transitions to occur under specific combinations of environmental conditions is therefore adaptively important. However, impeding development can itself incur demographic and fitness costs. How do organisms regulate development and physiological processes so that they occur under the broadest range of permissive conditions? Gene duplication offers one solution: Multiple genes contribute to the same downstream process, but do so under distinct combinations of environmental conditions. We present a simple model to examine how environmental sensitivities of genes and how gene duplication influence the distribution of environmental conditions under which an end process will proceed. The model shows that the duplication of genes that retain their downstream function but diverge in environmental sensitivities can allow an end process to proceed under more than one distinct combination of environmental conditions. The outcomes depend on how upstream genes regulate downstream components, which genes in the pathway have diversified in their sensitivities, and the structure of the pathway.
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Affiliation(s)
- David C Gibbs
- Department of Biology, Duke University Box 90338, Durham, North Carolina, 27708
| | - Kathleen Donohue
- Department of Biology, Duke University Box 90338, Durham, North Carolina, 27708
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21
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Xie X, Kagawa T, Takano M. The phytochrome B/phytochrome C heterodimer is necessary for phytochrome C-mediated responses in rice seedlings. PLoS One 2014; 9:e97264. [PMID: 24853557 PMCID: PMC4031084 DOI: 10.1371/journal.pone.0097264] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2013] [Accepted: 04/16/2014] [Indexed: 01/19/2023] Open
Abstract
Background PhyC levels have been observed to be markedly lower in phyB mutants than in Arabidopsis or rice wild type etiolated seedlings, but the mechanism of this phenomenon has not been fully elucidated. Results In the present study, we investigated the mechanism by which phyB affects the protein concentration and photo-sensing abilities of phyC and demonstrated that rice phyC exists predominantly as phyB/phyC heterodimers in etiolated seedlings. PHYC-GFP protein was detected when expressed in phyA phyC mutants, but not in phyA phyB mutants, suggesting that phyC requires phyB for its photo-sensing abilities. Interestingly, when a mutant PHYB gene that has no chromophore binding site, PHYB(C364A), was introduced into phyB mutants, the phyC level was restored. Moreover, when PHYB(C364A) was introduced into phyA phyB mutants, the seedlings exhibited de-etiolation under both far-red light (FR) and red light (R) conditions, while the phyA phyB mutants were blind to both FR and R. These results are the first direct evidence that phyC is responsible for regulating seedling de-etiolation under both FR and R. These findings also suggest that phyB is indispensable for the expression and function of phyC, which depends on the formation of phyB/phyC heterodimers. Significance The present report clearly demonstrates the similarities and differences in the properties of phyC between Arabidopsis and rice and will advance our understanding of phytochrome functions in monocots and dicots.
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Affiliation(s)
- Xianzhi Xie
- Photobiology and Photosynthesis Research Unit, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, Japan
- Shandong Rice Research Institute, Shandong Academy of Agricultural Sciences, Jinan, Shandong, China
| | - Takatoshi Kagawa
- Photobiology and Photosynthesis Research Unit, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, Japan
| | - Makoto Takano
- Photobiology and Photosynthesis Research Unit, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, Japan
- * E-mail:
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22
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Possart A, Fleck C, Hiltbrunner A. Shedding (far-red) light on phytochrome mechanisms and responses in land plants. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2014; 217-218:36-46. [PMID: 24467894 DOI: 10.1016/j.plantsci.2013.11.013] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Revised: 11/20/2013] [Accepted: 11/21/2013] [Indexed: 05/20/2023]
Abstract
In order to monitor ambient light conditions, plants rely on functionally diversified photoreceptors. Among these, phytochromes perceive red (R) and far-red (FR) light. FR light does not constitute a photosynthetic energy source; it however influences adaptive and developmental processes. In seed plants, phytochrome A (phyA) acts as FR receptor and mediates FR high irradiance responses (FR-HIRs). It exerts a dual role by promoting e.g. germination and seedling de-etiolation in canopy shade and by antagonising shade avoidance growth. Even though cryptogam plants such as mosses and ferns do not have phyA, they show FR-induced responses. In the present review we discuss the mechanistic basis of phyA-dependent FR-HIRs as well as their dual role in seed plants. We compare FR responses in seed plants and cryptogam plants and conclude on different potential concepts for the detection of canopy shade. Scenarios for the evolution of FR perception and responses are discussed.
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Affiliation(s)
- Anja Possart
- Center for Plant Molecular Biology, University of Tübingen, 72076 Tübingen, Germany; Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Christian Fleck
- Laboratory for Systems and Synthetic Biology, Wageningen University, 6703 HB Wageningen, The Netherlands.
| | - Andreas Hiltbrunner
- Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany.
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Donohue K. WHY ONTOGENY MATTERS DURING ADAPTATION: DEVELOPMENTAL NICHE CONSTRUCTION AND PLEIOTORPY ACROSS THE LIFE CYCLE INARABIDOPSIS THALIANA. Evolution 2013; 68:32-47. [DOI: 10.1111/evo.12284] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2013] [Accepted: 09/25/2013] [Indexed: 12/14/2022]
Affiliation(s)
- Kathleen Donohue
- Department of Biology; Duke University; Box 90338 Durham NC 27708
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24
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Herbel V, Orth C, Wenzel R, Ahmad M, Bittl R, Batschauer A. Lifetimes of Arabidopsis cryptochrome signaling states in vivo. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2013; 74:583-92. [PMID: 23398192 DOI: 10.1111/tpj.12144] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2012] [Revised: 01/16/2013] [Accepted: 02/03/2013] [Indexed: 05/20/2023]
Abstract
One crucial component in light signaling is the quantity of photoreceptor present in the active signaling state. The lifetime of the signaling state of a photoreceptor is limited because of thermal or otherwise back reversion of the chromophore to the ground state, and/or degradation of the photoreceptor in the light-activated state. It was previously shown that the lit state of plant cryptochromes contains flavin-neutral semiquinone, and that the half-lives of the lit state were in the range of 3-4 min in vitro. However, it was unknown how long-lived the signaling states of plant cryptochromes are in situ. Based on the loss of degradation of cry2 after prolonged dark incubation and loss of reversibility of photoactivated cry1 by a pulse of green light, we estimate the in vivo half-lives of the signaling states of cry1 and cry2 to be in the range of 5 and 16 min, respectively. Based on electron paramagnetic resonance measurements, the lifetime of the Arabidopsis cry1 lit state in insect cells was found to be ~6 min, and thus very similar to the lifetime of the signaling state in planta. Thus, the signaling state lifetimes of plant cryptochromes are not, or are only moderately, stabilized in planta.
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Affiliation(s)
- Vera Herbel
- Department of Plant Physiology and Photobiology, Faculty of Biology, Philipps-University, 35032, Marburg, Germany
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25
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Possart A, Hiltbrunner A. An evolutionarily conserved signaling mechanism mediates far-red light responses in land plants. THE PLANT CELL 2013; 25:102-14. [PMID: 23303916 PMCID: PMC3584528 DOI: 10.1105/tpc.112.104331] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2012] [Revised: 11/22/2012] [Accepted: 12/18/2012] [Indexed: 05/18/2023]
Abstract
Phytochromes are plant photoreceptors important for development and adaptation to the environment. Phytochrome A (PHYA) is essential for the far-red (FR) high-irradiance responses (HIRs), which are of particular ecological relevance as they enable plants to establish under shade conditions. PHYA and HIRs have been considered unique to seed plants because the divergence of seed plants and cryptogams (e.g., ferns and mosses) preceded the evolution of PHYA. Seed plant phytochromes translocate into the nucleus and regulate gene expression. By contrast, there has been little evidence of a nuclear localization and function of cryptogam phytochromes. Here, we identified responses to FR light in cryptogams, which are highly reminiscent of PHYA signaling in seed plants. In the moss Physcomitrella patens and the fern Adiantum capillus-veneris, phytochromes accumulate in the nucleus in response to light. Although P. patens phytochromes evolved independently of PHYA, we have found that one clade of P. patens phytochromes exhibits the molecular properties of PHYA. We suggest that HIR-like responses had evolved in the last common ancestor of modern seed plants and cryptogams and that HIR signaling is more ancient than PHYA. Thus, other phytochromes in seed plants may have lost the capacity to mediate HIRs during evolution, rather than that PHYA acquired it.
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Affiliation(s)
- Anja Possart
- Centre for Plant Molecular Biology, University of Tübingen, 72076 Tuebingen, Germany
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Chen Y, Zhang J, Luo J, Tu JM, Zeng XL, Xie J, Zhou M, Zhao JQ, Scheer H, Zhao KH. Photophysical diversity of two novel cyanobacteriochromes with phycocyanobilin chromophores: photochemistry and dark reversion kinetics. FEBS J 2011; 279:40-54. [PMID: 22008418 DOI: 10.1111/j.1742-4658.2011.08397.x] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Cyanobacteriochromes are phytochrome homologues in cyanobacteria that act as sensory photoreceptors. We compare two cyanobacteriochromes, RGS (coded by slr1393) from Synechocystis sp. PCC 6803 and AphC (coded by all2699) from Nostoc sp. PCC 7120. Both contain three GAF (cGMP phosphodiesterase, adenylyl cyclase and FhlA protein) domains (GAF1, GAF2 and GAF3). The respective full-length, truncated and cysteine point-mutated genes were expressed in Escherichia coli together with genes for chromophore biosynthesis. The resulting chromoproteins were analyzed by UV-visible absorption, fluorescence and circular dichroism spectroscopy as well as by mass spectrometry. RGS shows a red-green photochromism (λ(max) = 650 and 535 nm) that is assigned to the reversible 15Z/E isomerization of a single phycocyanobilin-chromophore (PCB) binding to Cys528 of GAF3. Of the three GAF domains, only GAF3 binds a chromophore and the binding is autocatalytic. RGS autophosphorylates in vitro; this reaction is photoregulated: the 535 nm state containing E-PCB was more active than the 650 nm state containing Z-PCB. AphC from Nostoc could be chromophorylated at two GAF domains, namely GAF1 and GAF3. PCB-GAF1 is photochromic, with the proposed 15E state (λ(max) = 685 nm) reverting slowly thermally to the thermostable 15Z state (λ(max) = 635 nm). PCB-GAF3 showed a novel red-orange photochromism; the unstable state (putative 15E, λ(max) = 595 nm) reverts very rapidly (τ ~ 20 s) back to the thermostable Z state (λ(max) = 645 nm). The photochemistry of doubly chromophorylated AphC is accordingly complex, as is the autophosphorylation: E-GAF1/E-GAF3 shows the highest rate of autophosphorylation activity, while E-GAF1/Z-GAF3 has intermediate activity, and Z-GAF1/Z-GAF3 is the least active state.
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Affiliation(s)
- Yu Chen
- College of Environmental Science and Engineering, Huazhong University of Science and Technology, Wuhan, China
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Rausenberger J, Tscheuschler A, Nordmeier W, Wüst F, Timmer J, Schäfer E, Fleck C, Hiltbrunner A. Photoconversion and Nuclear Trafficking Cycles Determine Phytochrome A's Response Profile to Far-Red Light. Cell 2011; 146:813-25. [DOI: 10.1016/j.cell.2011.07.023] [Citation(s) in RCA: 123] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2011] [Revised: 06/10/2011] [Accepted: 07/13/2011] [Indexed: 12/23/2022]
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Li J, Li G, Wang H, Wang Deng X. Phytochrome signaling mechanisms. THE ARABIDOPSIS BOOK 2011; 9:e0148. [PMID: 22303272 PMCID: PMC3268501 DOI: 10.1199/tab.0148] [Citation(s) in RCA: 234] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Phytochromes are red (R)/far-red (FR) light photoreceptors that play fundamental roles in photoperception of the light environment and the subsequent adaptation of plant growth and development. There are five distinct phytochromes in Arabidopsis thaliana, designated phytochrome A (phyA) to phyE. phyA is light-labile and is the primary photoreceptor responsible for mediating photomorphogenic responses in FR light, whereas phyB-phyE are light stable, and phyB is the predominant phytochrome regulating de-etiolation responses in R light. Phytochromes are synthesized in the cytosol in their inactive Pr form. Upon light irradiation, phytochromes are converted to the biologically active Pfr form, and translocate into the nucleus. phyB can enter the nucleus by itself in response to R light, whereas phyA nuclear import depends on two small plant-specific proteins FAR-RED ELONGATED HYPOCOTYL 1 (FHY1) and FHY1-LIKE (FHL). Phytochromes may function as light-regulated serine/threonine kinases, and can phosphorylate several substrates, including themselves in vitro. Phytochromes are phosphoproteins, and can be dephosphorylated by a few protein phosphatases. Photoactivated phytochromes rapidly change the expression of light-responsive genes by repressing the activity of CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1), an E3 ubiquitin ligase targeting several photomorphogenesis-promoting transcription factors for degradation, and by inducing rapid phosphorylation and degradation of Phytochrome-Interacting Factors (PIFs), a group of bHLH transcription factors repressing photomorphogenesis. Phytochromes are targeted by COP1 for degradation via the ubiquitin/26S proteasome pathway.
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Affiliation(s)
- Jigang Li
- Peking-Yale Joint Center for Plant Molecular Genetics and Agro-biotechnology, State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing 100871, China
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, 06520-8104
| | - Gang Li
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, 06520-8104
| | - Haiyang Wang
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, 06520-8104
| | - Xing Wang Deng
- Peking-Yale Joint Center for Plant Molecular Genetics and Agro-biotechnology, State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing 100871, China
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, 06520-8104
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Mathews S. Evolutionary studies illuminate the structural-functional model of plant phytochromes. THE PLANT CELL 2010; 22:4-16. [PMID: 20118225 PMCID: PMC2828699 DOI: 10.1105/tpc.109.072280] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2009] [Revised: 01/12/2010] [Accepted: 01/13/2010] [Indexed: 05/18/2023]
Abstract
A synthesis of insights from functional and evolutionary studies reveals how the phytochrome photoreceptor system has evolved to impart both stability and flexibility. Phytochromes in seed plants diverged into three major forms, phyA, phyB, and phyC, very early in the history of seed plants. Two additional forms, phyE and phyD, are restricted to flowering plants and Brassicaceae, respectively. While phyC, D, and E are absent from at least some taxa, phyA and phyB are present in all sampled seed plants and are the principal mediators of red/far-red-induced responses. Conversely, phyC-E apparently function in concert with phyB and, where present, expand the repertoire of phyB activities. Despite major advances, aspects of the structural-functional models for these photoreceptors remain elusive. Comparative sequence analyses expand the array of locus-specific mutant alleles for analysis by revealing historic mutations that occurred during gene lineage splitting and divergence. With insights from crystallographic data, a subset of these mutants can be chosen for functional studies to test their importance and determine the molecular mechanism by which they might impact light perception and signaling. In the case of gene families, where redundancy hinders isolation of some proportion of the relevant mutants, the approach may be particularly useful.
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Affiliation(s)
- Sarah Mathews
- Arnold Arboretum of Harvard University, Cambridge, Massachusetts 02138, USA.
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Brandt S, von Stetten D, Günther M, Hildebrandt P, Frankenberg-Dinkel N. The fungal phytochrome FphA from Aspergillus nidulans. J Biol Chem 2008; 283:34605-14. [PMID: 18931394 DOI: 10.1074/jbc.m805506200] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The red light-sensing photoreceptor FphA from Aspergillus nidulans is involved in the regulation of developmental processes in response to light. Here we present extended biochemical and spectroscopic characterization of recombinant FphA using a synthetic gene with host-adapted codon usage. The recombinant photosensory domain FphAN753 was shown to display all features of a bona fide phytochrome. It covalently binds biliverdin as chromophore and undergoes red/far-red light-inducible photoconversion with both parent states being protonated. The large N-terminal variable extension of FphA exerts a stabilizing effect on the active Pfr state. Upon substitution of the highly conserved histidine 504, involved in the hydrogen-bonding network of the protein moiety and the chromophore, chromophore attachment and photoreversibility were completely impaired. FphA is a functional sensor histidine kinase with a strong red-light-dependent autophosphorylation activity. Furthermore, intermolecular trans-phosphorylation to the response regulator domain of a second monomer could be demonstrated. Interestingly, co-incubation of FphA and FphA variants led to enhanced autophosphorylation, including the "inactive" Pr form. The latter observed phenomenon might suggest that auto- and trans-phosphorylation activity is modulated by additional interaction partners leading to variable phosphorylation events that trigger a specific output response.
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Affiliation(s)
- Sonja Brandt
- Physiologie der Mikroorganismen, Ruhr-Universität Bochum, Universitätsstrasse 150, Bochum D-44780, Germany
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31
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Electronic Properties and Conformation Analysis of Phytochromobilins, Chromophore in Phytochrome. B KOREAN CHEM SOC 2008. [DOI: 10.5012/bkcs.2008.29.9.1678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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32
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Rivadossi A, Garlaschi FM, Casazza AP, Zucchelli G, Jennings RC. On phytochrome absorption and the phytochrome photoequilibrium in a green leaf: environmental sensitivity and photoequilibrium time. Photochem Photobiol Sci 2008; 7:986-90. [DOI: 10.1039/b806142d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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33
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Sineshchekov V, Hennig L, Lamparter T, Hughes J, Gärtner W, Schäfer E. Recombinant Phytochrome A in Yeast Differs by its Spectroscopic and Photochemical Properties from the Major phyA′ and is Close to the Minor phyA″: Evidence for Posttranslational Modification of the Pigment in Plants¶. Photochem Photobiol 2007. [DOI: 10.1562/0031-8655(2001)0730692rpaiyd2.0.co2] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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34
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Mathews S. Phytochrome-mediated development in land plants: red light sensing evolves to meet the challenges of changing light environments. Mol Ecol 2006; 15:3483-503. [PMID: 17032252 DOI: 10.1111/j.1365-294x.2006.03051.x] [Citation(s) in RCA: 113] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Phytochromes are photoreceptors that provide plants with circadian, seasonal, and positional information critical for the control of germination, seedling development, shade avoidance, reproduction, dormancy, and sleep movements. Phytochromes are unique among photoreceptors in their capacity to interconvert between a red-absorbing form (absorption maximum of approximately 660 nm) and a far-red absorbing form (absorption maximum of approximately 730 nm), which occur in a dynamic equilibrium within plant cells, corresponding to the proportions of red and far-red energy in ambient light. Because pigments in stems and leaves absorb wavelengths below about 700 nm, this provides plants with an elegant system for detecting their position relative to other plants, with which the plants compete for light. Certain aspects of phytochrome-mediated development outside of flowering plants are strikingly similar to those that have been characterized in Arabidopsis thaliana and other angiosperms. However, early diverging land plants have fewer distinct phytochrome gene lineages, suggesting that both diversification and subfunctionalization have been important in the evolution of the phytochrome gene family. There is evidence that subfunctionalization proceeded by the partitioning among paralogues of photosensory specificity, physiological response modes, and light-regulated gene expression and protein stability. Parallel events of duplication and functional divergence may have coincided with the evolution of canopy shade and the increasing complexity of the light environment. Within angiosperms, patterns of functional divergence are clade-specific and the roles of phytochromes in A. thaliana change across environments, attesting to the evolutionary flexibility and contemporaneous plasticity of phytochrome signalling in the control of development.
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Affiliation(s)
- Sarah Mathews
- Arnold Arboretum of Harvard University, Cambridge, MA 02138, USA.
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35
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Abstract
Plants utilize several families of photoreceptors to fine-tune growth and development over a large range of environmental conditions. The UV-A/blue light sensing phototropins mediate several light responses enabling optimization of photosynthetic yields. The initial event occurring upon photon capture is a conformational change of the photoreceptor that activates its protein kinase activity. The UV-A/blue light sensing cryptochromes and the red/far-red sensing phytochromes coordinately control seedling establishment, entrainment of the circadian clock, and the transition from vegetative to reproductive growth. In addition, the phytochromes control seed germination and shade-avoidance responses. The molecular mechanisms involved include light-regulated subcellular localization of the photoreceptors, a large reorganization of the transcriptional program, and light-regulated proteolytic degradation of several photoreceptors and signaling components.
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Affiliation(s)
- Meng Chen
- Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA.
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36
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Li WZ, Chinnappa CC. Isolation and characterization of PHYC gene from Stellaria longipes: differential expression regulated by different red/far-red light ratios and photoperiods. PLANTA 2004; 220:318-330. [PMID: 15290294 DOI: 10.1007/s00425-004-1337-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2004] [Accepted: 06/10/2004] [Indexed: 05/24/2023]
Abstract
We have cloned and characterized the phytochrome C ( PHYC) gene from Stellaria longipes. The PHYC gene is composed of a 110-bp 5'-untranslated leader sequence, a 3,342-bp coding region, and a 351-bp 3'-untranslated sequence. The Stellaria PHYC contains three long introns within the coding region at conserved locations as in most angiosperm PHY genes. DNA blot analysis indicates that the Stellaria genome contains a single copy of PHYC. Stellaria PHYC shares 60%, 58%, and 57% deduced amino acid identities with rice, Sorghum, and Arabidopsis PHYC, respectively. Phylogenetic analysis indicates that Stellaria PHYC is located in the dicot branch, but is divergent from Arabidopsis PHYC. The Stellaria PHYC is constitutively expressed in different plant organs, though the level of PHYC gene transcript in roots is slightly higher than in flowers, leaves, and stems. When 2-week old seedlings grown in the dark were exposed to constant white light, PHYC mRNA quickly accumulates within 1-12 h. When plants grown in darkness for 7 days were exposed to different red/far-red light (R/FR) ratios, the levels of PHYC mRNA at R/FR = 0.7 are much lower than under R/FR = 3.5. The levels of PHYC mRNA under short-day (SD) photoperiod are higher than under long-day (LD) photoperiod. Plants under SD conditions do not elongate, and are only about 1.7 cm tall at 19 days. In contrast, plants under LD conditions elongate with an average height of 21.2 cm at 19 days. The plants do not flower under SD conditions, but do so at 18-19 days under LD conditions. These results indicate that under SD conditions the high level of PHYC mRNA may inhibit stem elongation and flower initiation. In contrast, under LD conditions the high level of PHYC mRNA may promote stem elongation and flowering.
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Affiliation(s)
- Wen-Ze Li
- Department of Biological Sciences, University of Calgary, 2500 University Dr., N.W. Calgary, Alberta, T2N 1N4, Canada
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37
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Schepens I, Duek P, Fankhauser C. Phytochrome-mediated light signalling in Arabidopsis. CURRENT OPINION IN PLANT BIOLOGY 2004; 7:564-569. [PMID: 15337099 DOI: 10.1016/j.pbi.2004.07.004] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The phytochrome photoreceptors regulate all major transitions during the life cycle of plants. The role of each member of the phytochrome family in Arabidopsis is starting to be understood, and a molecular description of phytochrome-regulated flowering time and shade avoidance is emerging. Recent publications have challenged some areas of well-accepted models concerning phytochrome signalling. Moreover, the importance of proteolysis during phytochrome signalling is becoming very apparent.
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Affiliation(s)
- Isabelle Schepens
- Department of Molecular Biology, Sciences III, University of Geneva, 1211 Geneva 4, Switzerland.
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38
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Affiliation(s)
- Haiyang Wang
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY 14853, USA
| | - Xing Wang Deng
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520-8104, USA
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39
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Chen M, Schwab R, Chory J. Characterization of the requirements for localization of phytochrome B to nuclear bodies. Proc Natl Acad Sci U S A 2003; 100:14493-8. [PMID: 14612575 PMCID: PMC283619 DOI: 10.1073/pnas.1935989100] [Citation(s) in RCA: 125] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Phytochromes are red- and far-red-sensing photoreceptors that detect the quantity, quality, and duration of light throughout the entire life cycle of plants. Phytochromes accumulate in the cytoplasm in the dark. As one of the earliest responses after light illumination, phytochromes localize to the nucleus where they become associated with discrete nuclear bodies (NBs). Here, we describe the steady-state dynamics of Arabidopsis phytochrome B (phyB) localization in response to different light conditions and define four phyB subnuclear localization patterns: diffuse nuclear localization, small and numerous NBs only, both small and large NBs, and large NBs only. We show that phyB nuclear import is not sufficient for phyB NB formation. Rather, phyB accumulation in NBs is mainly determined by the percentage of the total amount of phyB protein that is in the active phyB conformer, with large NBs always correlating with strong phyB responses. A genetic screen to identify determinants required for subnuclear localization of phyB resulted in several phyB mutants, mutants deficient in phytochrome chromophore biosynthesis, and mutations in at least one previously uninvestigated locus. This study lays the groundwork for future investigations to identify the molecular mechanisms of light-regulated partitioning of plant photoreceptors to discrete subnuclear domains.
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Affiliation(s)
- Meng Chen
- Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
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40
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Sharrock RA, Clack T, Goosey L. Signaling activities among the Arabidopsis phyB/D/E-type phytochromes: a major role for the central region of the apoprotein. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2003; 34:317-326. [PMID: 12713538 DOI: 10.1046/j.1365-313x.2003.01722.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The Arabidopsis phyB, phyD, and phyE phytochromes regulate plant developmental and growth responses to continuous red light (R) and to the ratio of R to far-red (FR) light. The activities of these three photoreceptors in the control of seedling growth have been compared using a transgenic assay based upon induction of R-hypersensitivity of hypocotyl elongation by overexpression of the apoproteins from the 35S promoter. 35S-phyB, 35S-phyD, and 35S-phyE lines expressing similar levels of the respective phytochromes were isolated. Under pulses of R, phyB is very active in inducing a dwarf hypocotyl phenotype, whereas phyD and phyE are inactive. Under high-fluence continuous R, phyD shows a gain in activity whereas phyE does not. These results demonstrate significant differences in the inherent regulatory activities of these receptor apoproteins. To localize the sequence determinants of these functional differences, chimeric proteins were constructed by shuffling amino-terminal, central, and carboxy-terminal regions of phyB and phyD. Overexpression analysis of the phyB/D chimeras shows that it is the central region of these proteins that is most critical in determining their respective activities.
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Affiliation(s)
- Robert A Sharrock
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman 59717, USA.
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41
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Halliday KJ, Whitelam GC. Changes in photoperiod or temperature alter the functional relationships between phytochromes and reveal roles for phyD and phyE. PLANT PHYSIOLOGY 2003; 131:1913-20. [PMID: 12692350 PMCID: PMC166947 DOI: 10.1104/pp.102.018135] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2002] [Revised: 01/02/2003] [Accepted: 01/02/2003] [Indexed: 05/18/2023]
Abstract
The phytochromes are one of the means via which plants obtain information about their immediate environment and the changing seasons. Phytochromes have important roles in developmental events such as the switch to flowering, the timing of which can be crucial for the reproductive success of the plant. Analysis of phyB mutants has revealed that phyB plays a major role in this process. We have recently shown, however, that the flowering phenotype of the phyB monogenic mutant is temperature dependent. A modest reduction in temperature to 16 degrees C was sufficient to abolish the phyB mutant early-flowering phenotype present at 22 degrees C. Using mutants null for one or more phytochrome species, we have now shown that phyA, phyD, and phyE, play greater roles with respect to phyB in the control of flowering under cooler conditions. This change in the relative contributions of individual phytochromes appears to be important for maintaining control of flowering in response to modest alterations in ambient temperature. We demonstrate that changes in ambient temperature or photoperiod can alter the hierarchy and/or the functional relationships between phytochrome species. These experiments reveal new roles for phyD and phyE and provide valuable insights into how the phytochromes help to maintain development in the natural environment.
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Affiliation(s)
- Karen J Halliday
- School of Biological Sciences, University of Bristol, United Kingdom.
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42
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Kevei E, Nagy F. Phytochrome controlled signalling cascades in higher plants. PHYSIOLOGIA PLANTARUM 2003; 117:305-313. [PMID: 12654030 DOI: 10.1034/j.1399-3054.2003.00049.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Plants can sense the changes in the environmental light conditions with highly specialized photoreceptors. Phytochromes are sensitive to red and far-red light and have a dual role in the life of plants. These photoreceptors play an important role in plant growth and development from germination to seed maturation and they are also involved in synchronizing the circadian clock with light/dark cycles. Biochemical, cell biological and genetic studies have been carried out to elucidate the molecular mechanism by which phytochromes transduce light signals. A major step in this process seems to be the light-dependent nuclear import of phytochromes. In the nuclei phytochromes interact with transcription factors and regulate the expression of numerous genes, resulting in complex physiological and developmental responses to light. This review focuses on the recently obtained results leading to the identification of some factors and processes involved in phytochrome signalling.
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Affiliation(s)
- Eva Kevei
- Institute of Plant Biology, Biological Research Centre, Temesvári krt 62., H-6726 Szeged, Hungary Institute of Plant Biology, Agricultural Biotechnological Centre, Szent-Györgyi A. 4, H-2101 Gödöllõ, Hungary
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43
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Sharrock RA, Clack T. Patterns of expression and normalized levels of the five Arabidopsis phytochromes. PLANT PHYSIOLOGY 2002; 130:442-56. [PMID: 12226523 PMCID: PMC166576 DOI: 10.1104/pp.005389] [Citation(s) in RCA: 207] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2002] [Revised: 04/14/2002] [Accepted: 05/10/2002] [Indexed: 05/18/2023]
Abstract
Using monoclonal antibodies specific for each apoprotein and full-length purified apoprotein standards, the levels of the five Arabidopsis phytochromes and their patterns of expression in seedlings and mature plants and under different light conditions have been characterized. Phytochrome levels are normalized to the DNA content of the various tissue extracts to approximate normalization to the number of cells in the tissue. One phytochrome, phytochrome A, is highly light labile. The other four phytochromes are much more light stable, although among these, phytochromes B and C are reduced 4- to 5-fold in red- or white-light-grown seedlings compared with dark-grown seedlings. The total amount of extractable phytochrome is 23-fold lower in light-grown than dark-grown tissues, and the percent ratios of the five phytochromes, A:B:C:D:E, are measured as 85:10:2:1.5:1.5 in etiolated seedlings and 5:40:15:15:25 in seedlings grown in continuous white light. The four light-stable phytochromes are present at nearly unchanging levels throughout the course of development of mature rosette and reproductive-stage plants and are present in leaves, stems, roots, and flowers. Phytochrome protein expression patterns over the course of seed germination and under diurnal and circadian light cycles are also characterized. Little cycling in response to photoperiod is observed, and this very low amplitude cycling of some phytochrome proteins is out of phase with previously reported cycling of PHY mRNA levels. These studies indicate that, with the exception of phytochrome A, the family of phytochrome photoreceptors in Arabidopsis constitutes a quite stable and very broadly distributed array of sensory molecules.
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Affiliation(s)
- Robert A Sharrock
- Department of Plant Sciences and Plant Pathology, 119 ABS Building, Montana State University, Bozeman, Montana 59717-3140, USA.
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Izawa T, Oikawa T, Sugiyama N, Tanisaka T, Yano M, Shimamoto K. Phytochrome mediates the external light signal to repress FT orthologs in photoperiodic flowering of rice. Genes Dev 2002; 16:2006-20. [PMID: 12154129 PMCID: PMC186415 DOI: 10.1101/gad.999202] [Citation(s) in RCA: 289] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2002] [Accepted: 06/11/2002] [Indexed: 11/25/2022]
Abstract
Phytochromes confer the photoperiodic control of flowering in rice (Oryza sativa), a short-day plant. To better understand the molecular mechanisms of day-length recognition, we examined the interaction between phytochrome signals and circadian clocks in photoperiodic-flowering mutants of rice. Monitoring behaviors of circadian clocks revealed that phase setting of circadian clocks is not affected either under short-day (SD) or under long-day (LD) conditions in a phytochrome-deficient mutant that shows an early-flowering phenotype with no photoperiodic response. Non-24-hr-light/dark-cycle experiments revealed that a rice counterpart gene of Arabidopsis CONSTANS (CO), named PHOTOPERIOD SENSITIVITY 1 (Heading date 1) [SE1 (Hd1)], functions as an output of circadian clocks. In addition, the phytochrome deficiency does not affect the diurnal mRNA expression of SE1 upon floral transition. Downstream floral switch genes were further identified with rice orthologs of Arabidopsis FLOWERING LOCUS T (FT). Our RT-PCR data indicate that phytochrome signals repress mRNA expression of FT orthologs, whereas SE1 can function to promote and suppress mRNA expression of the FT orthologs under SD and LD, respectively. This SE1 transcriptional activity may be posttranscriptionally regulated and may depend on the coincidence with Pfr phytochromes. We propose a model to explain how a short-day plant recognizes the day length in photoperiodic flowering.
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Affiliation(s)
- Takeshi Izawa
- Laboratory of Plant Molecular Genetics, Nara Institute of Science and Technology, Ikoma, Nara 630-0101, Japan.
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45
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Hanzawa H, Shinomura T, Inomata K, Kakiuchi T, Kinoshita H, Wada K, Furuya M. Structural requirement of bilin chromophore for the photosensory specificity of phytochromes A and B. Proc Natl Acad Sci U S A 2002; 99:4725-9. [PMID: 11930018 PMCID: PMC123715 DOI: 10.1073/pnas.062713399] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Phytochromes are an important class of chromoproteins that regulate many cellular and developmental responses to light in plants. The model plant species Arabidopsis thaliana possesses five phytochromes, which mediate distinct and overlapping responses to light. Photobiological analyses have established that, under continuous irradiation, phytochrome A is primarily responsible for plant's sensitivity to far-red light, whereas the other phytochromes respond mainly to red light. The present study reports that the far-red light sensitivity of phytochrome A depends on the structure of the linear tetrapyrrole (bilin) prosthetic group. By reconstitution of holophytochrome in vivo through feeding various synthetic bilins to chromophore-deficient mutants of Arabidopsis, the requirement for a double bond on the bilin D-ring for rescuing phytochrome A function has been established. In contrast, we show that phytochrome B function can be rescued with various bilin analogs with saturated D-ring substituents.
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Affiliation(s)
- Hiroko Hanzawa
- Hitachi Advanced Research Laboratory, Hatoyama, Saitama 350-0395, Japan
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Hennig L, Stoddart WM, Dieterle M, Whitelam GC, Schäfer E. Phytochrome E controls light-induced germination of Arabidopsis. PLANT PHYSIOLOGY 2002; 128:194-200. [PMID: 11788765 DOI: 10.1104/pp.010559] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Germination of Arabidopsis seeds is light dependent and under phytochrome control. Previously, phytochromes A and B and at least one additional, unspecified phytochrome were shown to be involved in this process. Here, we used a set of photoreceptor mutants to test whether phytochrome D and/or phytochrome E can control germination of Arabidopsis. The results show that only phytochromes B and E, but not phytochrome D, participate directly in red/far-red light (FR)-reversible germination. Unlike phytochromes B and D, phytochrome E did not inhibit phytochrome A-mediated germination. Surprisingly, phytochrome E was required for germination of Arabidopsis seeds in continuous FR. However, inhibition of hypocotyl elongation by FR, induction of cotyledon unfolding, and induction of agravitropic growth were not affected by loss of phytochrome E. Therefore, phytochrome E is not required per se for phytochrome A-mediated very low fluence responses and the high irradiance response. Immunoblotting revealed that the need of phytochrome E for germination in FR was not caused by altered phytochrome A levels. These results uncover a novel role of phytochrome E in plant development and demonstrate the considerable functional diversification of the closely related phytochromes B, D, and E.
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Affiliation(s)
- Lars Hennig
- Department of Biology, Leicester University, Leicester LE1 7RH, United Kingdom
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Nagy F, Schäfer E. Phytochromes control photomorphogenesis by differentially regulated, interacting signaling pathways in higher plants. ANNUAL REVIEW OF PLANT BIOLOGY 2002; 53:329-355. [PMID: 12221979 DOI: 10.1146/annurev.arplant.53.100301.135302] [Citation(s) in RCA: 164] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
In this review the kinetic properties of both phytochrome A and B measured by in vivo spectroscopy in Arabidopsis are described. Inactivation of phyA is mediated by destruction and that of phyB by fast dark reversion. Recent observations, describing a complex interaction network of various phytochromes and cryptochromes, are also discussed. The review describes recent analysis of light-dependent nuclear translocation of phytochromes and genetic and molecular dissection of phyA- and phyB-mediated signal transduction. After nuclear transport, both phyA- and phyB-mediated signal transduction probably include the formation of light-dependent transcriptional complexes. Although this hypothesis is quite attractive and probably true for some responses, it cannot account for the complex network of phyA-mediated signaling and the interaction with the circadian clock. In addition, the biological function of phytochromes localized in the cytosol remains to be elucidated.
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Affiliation(s)
- Ferenc Nagy
- Institute of Plant Biology, Biological Research Center, H-6701 Szeged, Hungary.
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48
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Sineshchekov V, Hennig L, Lamparter T, Hughes J, Gärtner W, Schäfer E. Recombinant Phytochrome A in Yeast Differs by its Spectroscopic and Photochemical Properties from the Major phyA′ and is Close to the Minor phyA″: Evidence for Posttranslational Modification of the Pigment in Plants¶. Photochem Photobiol 2001; 73:692-696. [DOI: https:/doi.org/10.1562/0031-8655(2001)0730692rpaiyd2.0.co2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2023]
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49
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Dieterle M, Zhou YC, Schäfer E, Funk M, Kretsch T. EID1, an F-box protein involved in phytochrome A-specific light signaling. Genes Dev 2001; 15:939-44. [PMID: 11316788 PMCID: PMC312672 DOI: 10.1101/gad.197201] [Citation(s) in RCA: 151] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
To perceive red and far-red light, plants have evolved specific photoreceptors called phytochromes. Even though the spectral properties of all phytochromes are very similar, they show a distinct mode of action. Here we describe EID1, a negatively acting component of the signaling cascade that shifts the responsiveness of the phytochrome A (phyA) signaling system associated with hypocotyl elongation from red to far-red wavelengths. EID1 is a novel nuclear F-box protein that contains a leucine zipper whose integrity is necessary for its biological function. EID1 most probably acts by targeting activated components of the phyA signaling pathway to ubiquitin-dependent proteolysis.
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Affiliation(s)
- M Dieterle
- Universität Freiburg, Institut für Biologie 2/Botanik, D-79104 Freiburg, Germany
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Affiliation(s)
- C Fankhauser
- Department of Molecular Biology, University of Geneva, 1211 Geneva 4, Switzerland.
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