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Willige BC, Yoo CY, Saldierna Guzmán JP. What is going on inside of phytochrome B photobodies? THE PLANT CELL 2024; 36:2065-2085. [PMID: 38511271 PMCID: PMC11132900 DOI: 10.1093/plcell/koae084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 12/20/2023] [Accepted: 01/08/2024] [Indexed: 03/22/2024]
Abstract
Plants exhibit an enormous phenotypic plasticity to adjust to changing environmental conditions. For this purpose, they have evolved mechanisms to detect and measure biotic and abiotic factors in their surroundings. Phytochrome B exhibits a dual function, since it serves as a photoreceptor for red and far-red light as well as a thermosensor. In 1999, it was first reported that phytochromes not only translocate into the nucleus but also form subnuclear foci upon irradiation by red light. It took more than 10 years until these phytochrome speckles received their name; these foci were coined photobodies to describe unique phytochrome-containing subnuclear domains that are regulated by light. Since their initial discovery, there has been much speculation about the significance and function of photobodies. Their presumed roles range from pure experimental artifacts to waste deposits or signaling hubs. In this review, we summarize the newest findings about the meaning of phyB photobodies for light and temperature signaling. Recent studies have established that phyB photobodies are formed by liquid-liquid phase separation via multivalent interactions and that they provide diverse functions as biochemical hotspots to regulate gene expression on multiple levels.
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Affiliation(s)
- Björn Christopher Willige
- Department of Soil and Crop Sciences, College of Agricultural Sciences, Colorado State University, Fort Collins, CO 80521, USA
| | - Chan Yul Yoo
- School of Biological Sciences, University of Utah, UT 84112, USA
| | - Jessica Paola Saldierna Guzmán
- Department of Soil and Crop Sciences, College of Agricultural Sciences, Colorado State University, Fort Collins, CO 80521, USA
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2
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Jafari F, Wang B, Wang H, Zou J. Breeding maize of ideal plant architecture for high-density planting tolerance through modulating shade avoidance response and beyond. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024; 66:849-864. [PMID: 38131117 DOI: 10.1111/jipb.13603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 11/27/2023] [Accepted: 12/14/2023] [Indexed: 12/23/2023]
Abstract
Maize is a major staple crop widely used as food, animal feed, and raw materials in industrial production. High-density planting is a major factor contributing to the continuous increase of maize yield. However, high planting density usually triggers a shade avoidance response and causes increased plant height and ear height, resulting in lodging and yield loss. Reduced plant height and ear height, more erect leaf angle, reduced tassel branch number, earlier flowering, and strong root system architecture are five key morphological traits required for maize adaption to high-density planting. In this review, we summarize recent advances in deciphering the genetic and molecular mechanisms of maize involved in response to high-density planting. We also discuss some strategies for breeding advanced maize cultivars with superior performance under high-density planting conditions.
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Affiliation(s)
- Fereshteh Jafari
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Graduate School of Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Baobao Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- National Nanfan Research Institute, CAAS, Sanya, 572025, China
| | - Haiyang Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Junjie Zou
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- National Nanfan Research Institute, CAAS, Sanya, 572025, China
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3
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Li J, Song Y. Plant thermosensors. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 342:112025. [PMID: 38354752 DOI: 10.1016/j.plantsci.2024.112025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 01/02/2024] [Accepted: 02/06/2024] [Indexed: 02/16/2024]
Abstract
Plants dynamically regulate their genes expression and physiological outputs to adapt to changing temperatures. The underlying molecular mechanisms have been extensively studied in diverse plants and in multiple dimensions. However, the question of exactly how temperature is detected at molecular level to transform the physical information into recognizable intracellular signals remains continues to be one of the undetermined occurrences in plant science. Recent studies have provided the physical and biochemical mechanistic breakthrough of how temperature changes can influence molecular thermodynamically stability, thus changing molecular structures, activities, interaction and signaling transduction. In this review, we focus on the thermosensing mechanisms of recognized and potential plant thermosensors, to describe the multi-level thermal input system in plants. We also consider the attributes of a thermosensor on the basis of thermal-triggered changes in function, structure, and physical parameters. This study thus provides a reference for discovering more plant thermosensors and elucidating plant thermal adaptive mechanisms.
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Affiliation(s)
- Jihong Li
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Yuan Song
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, School of Life Sciences, Lanzhou University, Lanzhou, China; Gansu Province Key Laboratory of Gene Editing for Breeding, Lanzhou, China.
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4
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Huq E, Lin C, Quail PH. Light signaling in plants-a selective history. PLANT PHYSIOLOGY 2024; 195:213-231. [PMID: 38431282 PMCID: PMC11060691 DOI: 10.1093/plphys/kiae110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 12/15/2023] [Accepted: 02/16/2024] [Indexed: 03/05/2024]
Abstract
In addition to providing the radiant energy that drives photosynthesis, sunlight carries signals that enable plants to grow, develop and adapt optimally to the prevailing environment. Here we trace the path of research that has led to our current understanding of the cellular and molecular mechanisms underlying the plant's capacity to perceive and transduce these signals into appropriate growth and developmental responses. Because a fully comprehensive review was not possible, we have restricted our coverage to the phytochrome and cryptochrome classes of photosensory receptors, while recognizing that the phototropin and UV classes also contribute importantly to the full scope of light-signal monitoring by the plant.
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Affiliation(s)
- Enamul Huq
- Department of Molecular Biosciences and The Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Chentao Lin
- Basic Forestry and Plant Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Peter H Quail
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA
- Plant Gene Expression Center, Agricultural Research Service, US Department of Agriculture, Albany, CA 94710, USA
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5
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Du J, Kim K, Chen M. Distinguishing individual photobodies using Oligopaints reveals thermo-sensitive and -insensitive phytochrome B condensation at distinct subnuclear locations. Nat Commun 2024; 15:3620. [PMID: 38684657 PMCID: PMC11058242 DOI: 10.1038/s41467-024-47789-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 04/10/2024] [Indexed: 05/02/2024] Open
Abstract
Photobodies (PBs) are membraneless subnuclear organelles that self-assemble via concentration-dependent liquid-liquid phase separation (LLPS) of the plant photoreceptor and thermosensor phytochrome B (PHYB). The current PHYB LLPS model posits that PHYB phase separates randomly in the nucleoplasm regardless of the cellular or nuclear context. Here, we established a robust Oligopaints method in Arabidopsis to determine the positioning of individual PBs. We show surprisingly that even in PHYB overexpression lines - where PHYB condensation would be more likely to occur randomly - PBs positioned at twelve distinct subnuclear locations distinguishable by chromocenter and nucleolus landmarks, suggesting that PHYB condensation occurs nonrandomly at preferred seeding sites. Intriguingly, warm temperatures reduce PB number by inducing the disappearance of specific thermo-sensitive PBs, demonstrating that individual PBs possess different thermosensitivities. These results reveal a nonrandom PB nucleation model, which provides the framework for the biogenesis of spatially distinct individual PBs with diverse environmental sensitivities within a single plant nucleus.
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Affiliation(s)
- Juan Du
- Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, CA, 92521, USA
| | - Keunhwa Kim
- Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, CA, 92521, USA
- Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, 52828, Republic of Korea
| | - Meng Chen
- Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, CA, 92521, USA.
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6
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Kim RJA, Fan D, He J, Kim K, Du J, Chen M. Photobody formation spatially segregates two opposing phytochrome B signaling actions of PIF5 degradation and stabilization. Nat Commun 2024; 15:3519. [PMID: 38664420 PMCID: PMC11045832 DOI: 10.1038/s41467-024-47790-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 04/10/2024] [Indexed: 04/28/2024] Open
Abstract
Photoactivation of the plant photoreceptor and thermosensor phytochrome B (PHYB) triggers its condensation into subnuclear membraneless organelles named photobodies (PBs). However, the function of PBs in PHYB signaling remains frustratingly elusive. Here, we found that PHYB recruits PHYTOCHROME-INTERACTING FACTOR 5 (PIF5) to PBs. Surprisingly, PHYB exerts opposing roles in degrading and stabilizing PIF5. Perturbing PB size by overproducing PHYB provoked a biphasic PIF5 response: while a moderate increase in PHYB enhanced PIF5 degradation, further elevating the PHYB level stabilized PIF5 by retaining more of it in enlarged PBs. Conversely, reducing PB size by dim light, which enhanced PB dynamics and nucleoplasmic PHYB and PIF5, switched the balance towards PIF5 degradation. Together, these results reveal that PB formation spatially segregates two antagonistic PHYB signaling actions - PIF5 stabilization in PBs and PIF5 degradation in the surrounding nucleoplasm - which could enable an environmentally sensitive, counterbalancing mechanism to titrate nucleoplasmic PIF5 and environmental responses.
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Affiliation(s)
- Ruth Jean Ae Kim
- Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, CA, 92521, USA
| | - De Fan
- Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, CA, 92521, USA
| | - Jiangman He
- Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, CA, 92521, USA
| | - Keunhwa Kim
- Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, CA, 92521, USA
- Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, 52828, Republic of Korea
| | - Juan Du
- Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, CA, 92521, USA
| | - Meng Chen
- Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, CA, 92521, USA.
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7
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Chawla S, O’Neill J, Knight MI, He Y, Wang L, Maronde E, Rodríguez SG, van Ooijen G, Garbarino-Pico E, Wolf E, Dkhissi-Benyahya O, Nikhat A, Chakrabarti S, Youngstedt SD, Zi-Ching Mak N, Provencio I, Oster H, Goel N, Caba M, Oosthuizen M, Duffield GE, Chabot C, Davis SJ. Timely Questions Emerging in Chronobiology: The Circadian Clock Keeps on Ticking. J Circadian Rhythms 2024; 22:2. [PMID: 38617710 PMCID: PMC11011957 DOI: 10.5334/jcr.237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 01/17/2024] [Indexed: 04/16/2024] Open
Abstract
Chronobiology investigations have revealed much about cellular and physiological clockworks but we are far from having a complete mechanistic understanding of the physiological and ecological implications. Here we present some unresolved questions in circadian biology research as posed by the editorial staff and guest contributors to the Journal of Circadian Rhythms. This collection of ideas is not meant to be comprehensive but does reveal the breadth of our observations on emerging trends in chronobiology and circadian biology. It is amazing what could be achieved with various expected innovations in technologies, techniques, and mathematical tools that are being developed. We fully expect strengthening mechanistic work will be linked to health care and environmental understandings of circadian function. Now that most clock genes are known, linking these to physiological, metabolic, and developmental traits requires investigations from the single molecule to the terrestrial ecological scales. Real answers are expected for these questions over the next decade. Where are the circadian clocks at a cellular level? How are clocks coupled cellularly to generate organism level outcomes? How do communities of circadian organisms rhythmically interact with each other? In what way does the natural genetic variation in populations sculpt community behaviors? How will methods development for circadian research be used in disparate academic and commercial endeavors? These and other questions make it a very exciting time to be working as a chronobiologist.
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Affiliation(s)
| | - John O’Neill
- MRC Laboratory of Molecular Biology Cambridge, UK
| | | | - Yuqing He
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, China National Botanical Garden, Beijing 100093, CN
| | - Lei Wang
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, China National Botanical Garden, Beijing 100093, CN
| | - Erik Maronde
- Institut für Anatomie II, Dr. Senckenbergische Anatomie, Goethe-Universität Frankfurt, Theodor-Stern-Kai-7, 60590 Frankfurt, DE
| | - Sergio Gil Rodríguez
- School of Biological Sciences, University of Edinburgh, Max Born Crescent, Edinburgh EH9 3BF, UK
| | - Gerben van Ooijen
- School of Biological Sciences, University of Edinburgh, Max Born Crescent, Edinburgh EH9 3BF, UK
| | - Eduardo Garbarino-Pico
- Universidad Nacional de Córdoba (UNC), Facultad de Ciencias Químicas, Departamento de Química Biológica Ranwel Caputto, Córdoba, AR
- CONICET-UNC, Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC), Córdoba, AR
| | - Eva Wolf
- Institute of Molecular Physiology (IMP), Johannes Gutenberg-University Mainz, Hanns-Dieter-Hüsch- Weg 17, 55128 Mainz, DE
| | - Ouria Dkhissi-Benyahya
- Inserm, Stem Cell and Brain Research Institute U1208, Univ Lyon, UniversitéClaude Bernard Lyon 1, 18 Avenue du Doyen Lépine, 69500, Bron, FR
| | - Anjoom Nikhat
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Bangalore, Karnataka 560065, IN
| | - Shaon Chakrabarti
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Bangalore, Karnataka 560065, IN
| | - Shawn D. Youngstedt
- Edson College of Nursing and Health Innovation, Arizona State University, Phoenix, AZ, US
- Department of Medicine, University of Arizona, Tucson, AZ, US
| | | | - Ignacio Provencio
- Department of Biology and Department of Ophthalmology, University of Virginia, Charlottesville, VA, US
| | - Henrik Oster
- Institute of Neurobiology, Center for Brain, Behavior & Metabolism (CBBM), University of Luebeck, 23562 Luebeck, DE
| | - Namni Goel
- Biological Rhythms Research Laboratory, Department of Psychiatry and Behavioral Sciences, Rush University Medical Center, Chicago, IL, US
| | - Mario Caba
- Centro de Investigaciones Biomédicas, Universidad Veracruzana, Xalapa, Ver., MX
| | - Maria Oosthuizen
- Department of Zoology and Entomology, University of Pretoria, Pretoria, ZA
- Mammal Research Institute, University of Pretoria, Hatfield, ZA
| | - Giles E. Duffield
- Department of Biological Sciences, Galvin Life Science Center, University of Notre Dame, Notre Dame, US
| | - Christopher Chabot
- Department of Biological Sciences, Plymouth State University, Plymouth, NH 03264, US
| | - Seth J. Davis
- Department of Biology, University of York, York YO105DD, UK
- State Key Laboratory of Crop Stress Biology, School of Life Sciences, Henan University, Kaifeng 475004, CN
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8
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Shenkutie SM, Nagano S, Hughes J. Expression, purification and crystallization of the photosensory module of phytochrome B (phyB) from Sorghum bicolor. Acta Crystallogr F Struct Biol Commun 2024; 80:59-66. [PMID: 38376821 PMCID: PMC10910535 DOI: 10.1107/s2053230x24000827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Accepted: 01/22/2024] [Indexed: 02/21/2024] Open
Abstract
Sorghum, a short-day tropical plant, has been adapted for temperate grain production, in particular through the selection of variants at the MATURITY loci (Ma1-Ma6) that reduce photoperiod sensitivity. Ma3 encodes phytochrome B (phyB), a red/far-red photochromic biliprotein photoreceptor. The multi-domain gene product, comprising 1178 amino acids, autocatalytically binds the phytochromobilin chromophore to form the photoactive holophytochrome (Sb.phyB). This study describes the development of an efficient heterologous overproduction system which allows the production of large quantities of various holoprotein constructs, along with purification and crystallization procedures. Crystals of the Pr (red-light-absorbing) forms of NPGP, PGP and PG (residues 1-655, 114-655 and 114-458, respectively), each C-terminally tagged with His6, were successfully produced. While NPGP crystals did not diffract, those of PGP and PG diffracted to 6 and 2.1 Å resolution, respectively. Moving the tag to the N-terminus and replacing phytochromobilin with phycocyanobilin as the ligand produced PG crystals that diffracted to 1.8 Å resolution. These results demonstrate that the diffraction quality of challenging protein crystals can be improved by removing flexible regions, shifting fusion tags and altering small-molecule ligands.
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Affiliation(s)
- Sintayehu Manaye Shenkutie
- Department of Plant Physiology, Justus Liebig University Giessen, Senckenbergstrasse 3, 35390 Giessen, Germany
- Department of Chemistry, Hawassa University, PO Box 05, Hawassa, Ethiopia
| | - Soshichiro Nagano
- Department of Plant Physiology, Justus Liebig University Giessen, Senckenbergstrasse 3, 35390 Giessen, Germany
| | - Jon Hughes
- Department of Plant Physiology, Justus Liebig University Giessen, Senckenbergstrasse 3, 35390 Giessen, Germany
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9
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Xu Q, Vogt A, Frechen F, Yi C, Küçükerden M, Ngum N, Sitjà-Roqueta L, Greiner A, Parri R, Masana M, Wenger N, Wachten D, Möglich A. Engineering Bacteriophytochrome-coupled Photoactivated Adenylyl Cyclases for Enhanced Optogenetic cAMP Modulation. J Mol Biol 2024; 436:168257. [PMID: 37657609 DOI: 10.1016/j.jmb.2023.168257] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 08/27/2023] [Accepted: 08/28/2023] [Indexed: 09/03/2023]
Abstract
Sensory photoreceptors abound in nature and enable organisms to adapt behavior, development, and physiology to environmental light. In optogenetics, photoreceptors allow spatiotemporally precise, reversible, and non-invasive control by light of cellular processes. Notwithstanding the development of numerous optogenetic circuits, an unmet demand exists for efficient systems sensitive to red light, given its superior penetration of biological tissue. Bacteriophytochrome photoreceptors sense the ratio of red and far-red light to regulate the activity of enzymatic effector modules. The recombination of bacteriophytochrome photosensor modules with cyclase effectors underlies photoactivated adenylyl cyclases (PAC) that catalyze the synthesis of the ubiquitous second messenger 3', 5'-cyclic adenosine monophosphate (cAMP). Via homologous exchanges of the photosensor unit, we devised novel PACs, with the variant DmPAC exhibiting 40-fold activation of cyclase activity under red light, thus surpassing previous red-light-responsive PACs. Modifications of the PHY tongue modulated the responses to red and far-red light. Exchanges of the cyclase effector offer an avenue to further enhancing PACs but require optimization of the linker to the photosensor. DmPAC and a derivative for 3', 5'-cyclic guanosine monophosphate allow the manipulation of cyclic-nucleotide-dependent processes in mammalian cells by red light. Taken together, we advance the optogenetic control of second-messenger signaling and provide insight into the signaling and design of bacteriophytochrome receptors.
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Affiliation(s)
- Qianzhao Xu
- Department of Biochemistry, University of Bayreuth, 95447 Bayreuth, Germany
| | - Arend Vogt
- Charité - University Medicine Berlin, Department of Neurology with Experimental Neurology, 10117 Berlin, Germany. https://twitter.com/ArendVogt
| | - Fabian Frechen
- Institute of Innate Immunity, University of Bonn, 53127 Bonn, Germany
| | - Chengwei Yi
- Department of Biochemistry, University of Bayreuth, 95447 Bayreuth, Germany
| | - Melike Küçükerden
- Department of Biomedical Sciences, Institute of Neurosciences, University of Barcelona, 08036 Barcelona, Spain; Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain; Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Spain
| | - Neville Ngum
- College of Health and Life Sciences, Aston University, Birmingham B4 7ET, United Kingdom
| | - Laia Sitjà-Roqueta
- Department of Biomedical Sciences, Institute of Neurosciences, University of Barcelona, 08036 Barcelona, Spain; Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain; Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Spain
| | - Andreas Greiner
- Macromolecular Chemistry and Bavarian Polymer Institute, University of Bayreuth, Bayreuth 95440, Germany
| | - Rhein Parri
- College of Health and Life Sciences, Aston University, Birmingham B4 7ET, United Kingdom
| | - Mercè Masana
- Department of Biomedical Sciences, Institute of Neurosciences, University of Barcelona, 08036 Barcelona, Spain; Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain; Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Spain. https://twitter.com/mercemasana
| | - Nikolaus Wenger
- Charité - University Medicine Berlin, Department of Neurology with Experimental Neurology, 10117 Berlin, Germany
| | - Dagmar Wachten
- Institute of Innate Immunity, University of Bonn, 53127 Bonn, Germany. https://twitter.com/DagmarWachten
| | - Andreas Möglich
- Department of Biochemistry, University of Bayreuth, 95447 Bayreuth, Germany; Bayreuth Center for Biochemistry & Molecular Biology, Universität Bayreuth, 95447 Bayreuth, Germany; North-Bavarian NMR Center, Universität Bayreuth, 95447 Bayreuth, Germany.
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10
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Zhou N, Li C, Xie W, Liang N, Wang J, Wang B, Wu J, Shen WH, Liu B, Dong A. Histone methylation readers MRG1/2 interact with PIF4 to promote thermomorphogenesis in Arabidopsis. Cell Rep 2024; 43:113726. [PMID: 38308844 DOI: 10.1016/j.celrep.2024.113726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 10/14/2023] [Accepted: 01/15/2024] [Indexed: 02/05/2024] Open
Abstract
Warm ambient conditions induce thermomorphogenesis and affect plant growth and development. However, the chromatin regulatory mechanisms involved in thermomorphogenesis remain largely obscure. In this study, we show that the histone methylation readers MORF-related gene 1 and 2 (MRG1/2) are required to promote hypocotyl elongation in response to warm ambient conditions. A transcriptome sequencing analysis indicates that MRG1/2 and phytochrome interacting factor 4 (PIF4) coactivate a number of thermoresponsive genes, including YUCCA8, which encodes a rate-limiting enzyme in the auxin biosynthesis pathway. Additionally, MRG2 physically interacts with PIF4 to bind to thermoresponsive genes and enhances the H4K5 acetylation of the chromatin of target genes in a PIF4-dependent manner. Furthermore, MRG2 competes with phyB for binding to PIF4 and stabilizes PIF4 in planta. Our study indicates that MRG1/2 activate thermoresponsive genes by inducing histone acetylation and stabilizing PIF4 in Arabidopsis.
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Affiliation(s)
- Nana Zhou
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, Department of Biochemistry and Biophysics, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, P.R. China
| | - Chengzhang Li
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, Department of Biochemistry and Biophysics, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, P.R. China
| | - Wenhao Xie
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, Department of Biochemistry and Biophysics, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, P.R. China
| | - Ning Liang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, Department of Biochemistry and Biophysics, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, P.R. China
| | - Jiachen Wang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, Department of Biochemistry and Biophysics, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, P.R. China
| | - Baihui Wang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, Department of Biochemistry and Biophysics, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, P.R. China
| | - Jiabing Wu
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, Department of Biochemistry and Biophysics, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, P.R. China
| | - Wen-Hui Shen
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, 12 rue du Général Zimmer, 67084 Strasbourg Cédex, France
| | - Bing Liu
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, Department of Biochemistry and Biophysics, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, P.R. China; Department of Energy, Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706, USA.
| | - Aiwu Dong
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, Department of Biochemistry and Biophysics, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, P.R. China.
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11
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Kong CH, Li Z, Li FL, Xia XX, Wang P. Chemically Mediated Plant-Plant Interactions: Allelopathy and Allelobiosis. PLANTS (BASEL, SWITZERLAND) 2024; 13:626. [PMID: 38475470 DOI: 10.3390/plants13050626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 02/20/2024] [Accepted: 02/22/2024] [Indexed: 03/14/2024]
Abstract
Plant-plant interactions are a central driver for plant coexistence and community assembly. Chemically mediated plant-plant interactions are represented by allelopathy and allelobiosis. Both allelopathy and allelobiosis are achieved through specialized metabolites (allelochemicals or signaling chemicals) produced and released from neighboring plants. Allelopathy exerts mostly negative effects on the establishment and growth of neighboring plants by allelochemicals, while allelobiosis provides plant neighbor detection and identity recognition mediated by signaling chemicals. Therefore, plants can chemically affect the performance of neighboring plants through the allelopathy and allelobiosis that frequently occur in plant-plant intra-specific and inter-specific interactions. Allelopathy and allelobiosis are two probably inseparable processes that occur together in plant-plant chemical interactions. Here, we comprehensively review allelopathy and allelobiosis in plant-plant interactions, including allelopathy and allelochemicals and their application for sustainable agriculture and forestry, allelobiosis and plant identity recognition, chemically mediated root-soil interactions and plant-soil feedback, and biosynthesis and the molecular mechanisms of allelochemicals and signaling chemicals. Altogether, these efforts provide the recent advancements in the wide field of allelopathy and allelobiosis, and new insights into the chemically mediated plant-plant interactions.
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Affiliation(s)
- Chui-Hua Kong
- College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Zheng Li
- College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Feng-Li Li
- College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Xin-Xin Xia
- College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Peng Wang
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China
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12
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Li ZY, Ma N, Zhang FJ, Li LZ, Li HJ, Wang XF, Zhang Z, You CX. Functions of Phytochrome Interacting Factors (PIFs) in Adapting Plants to Biotic and Abiotic Stresses. Int J Mol Sci 2024; 25:2198. [PMID: 38396875 PMCID: PMC10888771 DOI: 10.3390/ijms25042198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Revised: 02/03/2024] [Accepted: 02/04/2024] [Indexed: 02/25/2024] Open
Abstract
Plants possess the remarkable ability to sense detrimental environmental stimuli and launch sophisticated signal cascades that culminate in tailored responses to facilitate their survival, and transcription factors (TFs) are closely involved in these processes. Phytochrome interacting factors (PIFs) are among these TFs and belong to the basic helix-loop-helix family. PIFs are initially identified and have now been well established as core regulators of phytochrome-associated pathways in response to the light signal in plants. However, a growing body of evidence has unraveled that PIFs also play a crucial role in adapting plants to various biological and environmental pressures. In this review, we summarize and highlight that PIFs function as a signal hub that integrates multiple environmental cues, including abiotic (i.e., drought, temperature, and salinity) and biotic stresses to optimize plant growth and development. PIFs not only function as transcription factors to reprogram the expression of related genes, but also interact with various factors to adapt plants to harsh environments. This review will contribute to understanding the multifaceted functions of PIFs in response to different stress conditions, which will shed light on efforts to further dissect the novel functions of PIFs, especially in adaption to detrimental environments for a better survival of plants.
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Affiliation(s)
- Zhao-Yang Li
- College of Horticulture Science and Engineering, State Key Laboratory of Wheat Improvement, Shandong Agricultural University, Tai’an 271000, China; (Z.-Y.L.); (N.M.); (F.-J.Z.); (L.-Z.L.); (H.-J.L.); (X.-F.W.)
| | - Ning Ma
- College of Horticulture Science and Engineering, State Key Laboratory of Wheat Improvement, Shandong Agricultural University, Tai’an 271000, China; (Z.-Y.L.); (N.M.); (F.-J.Z.); (L.-Z.L.); (H.-J.L.); (X.-F.W.)
| | - Fu-Jun Zhang
- College of Horticulture Science and Engineering, State Key Laboratory of Wheat Improvement, Shandong Agricultural University, Tai’an 271000, China; (Z.-Y.L.); (N.M.); (F.-J.Z.); (L.-Z.L.); (H.-J.L.); (X.-F.W.)
- Department of Horticulture, College of Agriculture, Shihezi University, Shihezi 832003, China
| | - Lian-Zhen Li
- College of Horticulture Science and Engineering, State Key Laboratory of Wheat Improvement, Shandong Agricultural University, Tai’an 271000, China; (Z.-Y.L.); (N.M.); (F.-J.Z.); (L.-Z.L.); (H.-J.L.); (X.-F.W.)
| | - Hao-Jian Li
- College of Horticulture Science and Engineering, State Key Laboratory of Wheat Improvement, Shandong Agricultural University, Tai’an 271000, China; (Z.-Y.L.); (N.M.); (F.-J.Z.); (L.-Z.L.); (H.-J.L.); (X.-F.W.)
| | - Xiao-Fei Wang
- College of Horticulture Science and Engineering, State Key Laboratory of Wheat Improvement, Shandong Agricultural University, Tai’an 271000, China; (Z.-Y.L.); (N.M.); (F.-J.Z.); (L.-Z.L.); (H.-J.L.); (X.-F.W.)
| | - Zhenlu Zhang
- College of Horticulture Science and Engineering, State Key Laboratory of Wheat Improvement, Shandong Agricultural University, Tai’an 271000, China; (Z.-Y.L.); (N.M.); (F.-J.Z.); (L.-Z.L.); (H.-J.L.); (X.-F.W.)
| | - Chun-Xiang You
- College of Horticulture Science and Engineering, State Key Laboratory of Wheat Improvement, Shandong Agricultural University, Tai’an 271000, China; (Z.-Y.L.); (N.M.); (F.-J.Z.); (L.-Z.L.); (H.-J.L.); (X.-F.W.)
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13
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Viczián A, Nagy F. Phytochrome B phosphorylation expanded: site-specific kinases are identified. THE NEW PHYTOLOGIST 2024; 241:65-72. [PMID: 37814506 DOI: 10.1111/nph.19314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 09/18/2023] [Indexed: 10/11/2023]
Abstract
The phytochrome B (phyB) photoreceptor is a key participant in red and far-red light sensing, playing a dominant role in many developmental and growth responses throughout the whole life of plants. Accordingly, phyB governs diverse signaling pathways, and although our knowledge about these pathways is constantly expanding, our view about their fine-tuning is still rudimentary. Phosphorylation of phyB is one of the relevant regulatory mechanisms, and - despite the expansion of the available methodology - it is still not easy to examine. Phosphorylated phytochromes have been detected using various techniques for decades, but the first phosphorylated phyB residues were only identified in 2013. Since then, concentrated attention has been turned toward the functional role of post-translational modifications in phyB signaling. Very recently in 2023, the first kinases that phosphorylate phyB were identified. These discoveries opened up new research avenues, especially by connecting diverse environmental impacts to light signaling and helping to explain some long-term unsolved problems such as the co-action of Ca2+ and phyB signaling. This review summarizes our recent views about the roles of the identified phosphorylated phyB residues, what we know about the enzymes that modulate the phospho-state of phyB, and how these recent discoveries impact future investigations.
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Affiliation(s)
- András Viczián
- Laboratory of Photo- and Chronobiology, Institute of Plant Biology, Biological Research Centre, Hungarian Research Network (HUN-REN), Szeged, H-6726, Hungary
| | - Ferenc Nagy
- Laboratory of Photo- and Chronobiology, Institute of Plant Biology, Biological Research Centre, Hungarian Research Network (HUN-REN), Szeged, H-6726, Hungary
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14
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Kaeser G, Krauß N, Roughan C, Sauthof L, Scheerer P, Lamparter T. Phytochrome-Interacting Proteins. Biomolecules 2023; 14:9. [PMID: 38275750 PMCID: PMC10813442 DOI: 10.3390/biom14010009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 12/15/2023] [Accepted: 12/19/2023] [Indexed: 01/27/2024] Open
Abstract
Phytochromes are photoreceptors of plants, fungi, slime molds bacteria and heterokonts. These biliproteins sense red and far-red light and undergo light-induced changes between the two spectral forms, Pr and Pfr. Photoconversion triggered by light induces conformational changes in the bilin chromophore around the ring C-D-connecting methine bridge and is followed by conformational changes in the protein. For plant phytochromes, multiple phytochrome interacting proteins that mediate signal transduction, nuclear translocation or protein degradation have been identified. Few interacting proteins are known as bacterial or fungal phytochromes. Here, we describe how the interacting partners were identified, what is known about the different interactions and in which context of signal transduction these interactions are to be seen. The three-dimensional arrangement of these interacting partners is not known. Using an artificial intelligence system-based modeling software, a few predicted and modulated examples of interactions of bacterial phytochromes with their interaction partners are interpreted.
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Affiliation(s)
- Gero Kaeser
- Karlsruhe Institute of Technology (KIT), Joseph Gottlieb Kölreuter Institut für Pflanzenwissenschaften (JKIP), Fritz-Haber-Weg 4, D-76131 Karlsruhe, Germany; (G.K.); (N.K.); (C.R.)
| | - Norbert Krauß
- Karlsruhe Institute of Technology (KIT), Joseph Gottlieb Kölreuter Institut für Pflanzenwissenschaften (JKIP), Fritz-Haber-Weg 4, D-76131 Karlsruhe, Germany; (G.K.); (N.K.); (C.R.)
| | - Clare Roughan
- Karlsruhe Institute of Technology (KIT), Joseph Gottlieb Kölreuter Institut für Pflanzenwissenschaften (JKIP), Fritz-Haber-Weg 4, D-76131 Karlsruhe, Germany; (G.K.); (N.K.); (C.R.)
| | - Luisa Sauthof
- Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Physics and Biophysics, Group Structural Biology of Cellular Signaling, Charitéplatz 1, D-10117 Berlin, Germany; (L.S.); (P.S.)
| | - Patrick Scheerer
- Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Physics and Biophysics, Group Structural Biology of Cellular Signaling, Charitéplatz 1, D-10117 Berlin, Germany; (L.S.); (P.S.)
| | - Tilman Lamparter
- Karlsruhe Institute of Technology (KIT), Joseph Gottlieb Kölreuter Institut für Pflanzenwissenschaften (JKIP), Fritz-Haber-Weg 4, D-76131 Karlsruhe, Germany; (G.K.); (N.K.); (C.R.)
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15
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Malla TN, Hernandez C, Menendez D, Bizhga D, Mendez JH, Muniyappan S, Schwander P, Stojković EA, Schmidt M. Signal Transduction in an Enzymatic Photoreceptor Revealed by Cryo-Electron Microscopy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.08.566274. [PMID: 37986774 PMCID: PMC10659365 DOI: 10.1101/2023.11.08.566274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Phytochromes are essential photoreceptor proteins in plants with homologs in bacteria and fungi that regulate a variety of important environmental responses. They display a reversible photocycle between two distinct states, the red-light absorbing Pr and the far-red light absorbing Pfr, each with its own structure. The reversible Pr to Pfr photoconversion requires covalently bound bilin chromophore and regulates the activity of a C-terminal enzymatic domain, which is usually a histidine kinase (HK). In plants, phytochromes translocate to nucleus where the C-terminal effector domain interacts with protein interaction factors (PIFs) to induce gene expression. In bacteria, the HK phosphorylates a response-regulator (RR) protein triggering downstream gene expression through a two-component signaling pathway. Although plant and bacterial phytochromes share similar structural composition, they have contrasting activity in the presence of light with most BphPs being active in the dark. The molecular mechanism that explains bacterial and plant phytochrome signaling has not been well understood due to limited structures of full-length phytochromes with enzymatic domain resolved at or near atomic resolution in both Pr and Pfr states. Here, we report the first Cryo-EM structures of a wild-type bacterial phytochrome with a HK enzymatic domain, determined in both Pr and Pfr states, between 3.75 and 4.13 Å resolution, respectively. Furthermore, we capture a distinct Pr/Pfr heterodimer of the same protein as potential signal transduction intermediate at 3.75 Å resolution. Our three Cryo-EM structures of the distinct signaling states of BphPs are further reinforced by Cryo-EM structures of the truncated PCM of the same protein determined for the Pr/Pfr heterodimer as well as Pfr state. These structures provide insight into the different light-signaling mechanisms that could explain how bacteria and plants see the light.
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16
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Jeon J, Rahman MM, Yang HW, Kim J, Gam HJ, Song JY, Jeong SW, Kim JI, Choi MG, Shin DH, Choi G, Shim D, Jung JH, Lee IJ, Jeon JS, Park YI. Modulation of warm temperature-sensitive growth using a phytochrome B dark reversion variant, phyB[G515E], in Arabidopsis and rice. J Adv Res 2023:S2090-1232(23)00324-7. [PMID: 37926145 DOI: 10.1016/j.jare.2023.11.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 09/19/2023] [Accepted: 11/02/2023] [Indexed: 11/07/2023] Open
Abstract
INTRODUCTION Ambient temperature-induced hypocotyl elongation in Arabidopsis seedlings is sensed by the epidermis-localized phytochrome B (phyB) and transduced into auxin biosynthesis via a basic helix-loop-helix transcription factor, phytochrome-interacting factor 4 (PIF4). Once synthesized, auxin travels down from the cotyledons to the hypocotyl, triggering hypocotyl cell elongation. Thus, the phyB-PIF4 module involved in thermosensing and signal transduction is a potential genetic target for engineering warm temperature-insensitive plants. OBJECTIVES This study aims to manipulate warm temperature-induced elongation of plants at the post-translational level using phyB variants with dark reversion, the expression of which is subjected to heat stress. METHODS The thermosensitive growth response of Arabidopsis was manipulated by expressing the single amino acid substitution variant of phyB (phyB[G515E]), which exhibited a lower dark reversion rate than wild-type phyB. Other variants with slow (phyB[G564E]) or rapid (phyB[S584F]) dark reversion or light insensitivity (phyB[G767R]) were also included in this study for comparison. Warming-induced transient expression of phyB variants was achieved using heat shock-inducible promoters. Arabidopsis PHYB[G515E] and PHYB[G564E] were also constitutively expressed in rice in an attempt to manipulate the heat sensitivity of a monocotyledonous plant species. RESULTS At an elevated temperature, Arabidopsis seedlings transiently expressing PHYB[G515E] under the control of a heat shock-inducible promoter exhibited shorter hypocotyls than those expressing PHYB and other PHYB variant genes. This warm temperature-insensitive growth was related to the lowered PIF4 and auxin responses. In addition, transgenic rice seedlings expressing Arabidopsis PHYB[G515E] and PHYB[G564E] showed warm temperature-insensitive shoot growth. CONCLUSION Transient expression of phyB variants with altered dark reversion rates could serve as an effective optogenetic technique for manipulating PIF4-auxin-mediated thermomorphogenic responses in plants.
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Affiliation(s)
- Jin Jeon
- Department of Biological Sciences, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Md Mizanor Rahman
- Graduate School of Green-Bio Science and Crop Biotech Institute, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Hee Wook Yang
- Department of Biological Sciences, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Jaewook Kim
- Department of Biological Sciences, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Ho-Jun Gam
- Department of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Ji Young Song
- Department of Biological Sciences, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Seok Won Jeong
- Department of Biological Sciences, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Jeong-Il Kim
- Department of Molecular Biotechnology and Kumho Life Science Laboratory, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Myoung-Goo Choi
- National Institute of Crop Science, Rural Development Administration, Wanju 55365, Republic of Korea
| | - Dong-Ho Shin
- Department of Biological Sciences, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Giltsu Choi
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Donghwan Shim
- Department of Biological Sciences, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Jae-Hoon Jung
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - In-Jung Lee
- Department of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Jong-Seong Jeon
- Graduate School of Green-Bio Science and Crop Biotech Institute, Kyung Hee University, Yongin 17104, Republic of Korea.
| | - Youn-Il Park
- Department of Biological Sciences, Chungnam National University, Daejeon 34134, Republic of Korea.
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17
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Pi K, Luo J, Lu A, Chen G, Long B, Zhang J, Mo Z, Duan L, Liu R. Negative regulation of tobacco cold stress tolerance by NtPhyA. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 204:108153. [PMID: 37931558 DOI: 10.1016/j.plaphy.2023.108153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 10/12/2023] [Accepted: 10/30/2023] [Indexed: 11/08/2023]
Abstract
Cold stress is a non-biological stressor that adversely affects tobacco yield and leaf quality. Plant photoreceptor proteins, which function as dual light-temperature sensors, play a vital role in temperature changes, making them crucial for responses to non-biological stressors. However, the regulatory mechanisms of PhyA in tobacco remain poorly understood. Therefore, in this study, we aimed to clone the NtPhyA gene from tobacco and generate overexpression (OE-NtPhyA) and mutant (KO-NtPhyA) constructs of NtPhyA. By assessing the physiological and biochemical responses of the mutants under cold stress and performing transcriptome sequencing, we determined the signalling mechanism of NtPhyA under cold stress. Comparative analysis with wild-type (WT) NtPhyA revealed that KO-NtPhyA exhibited increased seed germination rates and reduced wilting under cold stress. In additional, the degree of damage to leaf cells, cell membranes, and stomatal structures was mitigated, and the levels of reactive oxygen species (ROS) were significantly decreased. Antioxidant enzyme activity, net photosynthetic rate, and Fv/Fm were significantly enhanced in KO-NtPhyA, whereas the opposite effects were observed in OE-NtPhyA. These findings indicate that KO-NtPhyA augments tobacco tolerance to cold stress, implying a negative regulatory role of NtPhyA in tobacco during cold stress. Transcriptome analysis revealed that NtPhyA governs the expression of a cascade of genes involved in the response to oxygen-containing compounds, hydrogen peroxide (H2O2), ROS, temperature stimuli, photosystem II oxygen-evolving complex assembly, water channel activity, calcium channel activity, and carbohydrate transport. Collectively, our findings indicate that NtPhyA activates downstream gene expression to enhance the resilience of tobacco to cold stress.
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Affiliation(s)
- Kai Pi
- College of Tobacco, Guizhou University, Guiyang, 550025, PR China; Key Laboratory for Tobacco Quality Research Guizhou Province, Guizhou University, Guiyang, 550025, PR China
| | - Jiajun Luo
- College of Tobacco, Guizhou University, Guiyang, 550025, PR China; Key Laboratory for Tobacco Quality Research Guizhou Province, Guizhou University, Guiyang, 550025, PR China
| | - Anbin Lu
- College of Tobacco, Guizhou University, Guiyang, 550025, PR China; Key Laboratory for Tobacco Quality Research Guizhou Province, Guizhou University, Guiyang, 550025, PR China
| | - Gang Chen
- College of Agriculture, Guizhou University, Guiyang, 550025, PR China
| | - Benshan Long
- College of Tobacco, Guizhou University, Guiyang, 550025, PR China; Key Laboratory for Tobacco Quality Research Guizhou Province, Guizhou University, Guiyang, 550025, PR China
| | - Jingyao Zhang
- College of Tobacco, Guizhou University, Guiyang, 550025, PR China; Key Laboratory for Tobacco Quality Research Guizhou Province, Guizhou University, Guiyang, 550025, PR China
| | - Zejun Mo
- College of Tobacco, Guizhou University, Guiyang, 550025, PR China; Key Laboratory for Tobacco Quality Research Guizhou Province, Guizhou University, Guiyang, 550025, PR China; College of Agriculture, Guizhou University, Guiyang, 550025, PR China
| | - Lili Duan
- College of Tobacco, Guizhou University, Guiyang, 550025, PR China; Key Laboratory for Tobacco Quality Research Guizhou Province, Guizhou University, Guiyang, 550025, PR China; College of Agriculture, Guizhou University, Guiyang, 550025, PR China
| | - Renxiang Liu
- College of Tobacco, Guizhou University, Guiyang, 550025, PR China; Key Laboratory for Tobacco Quality Research Guizhou Province, Guizhou University, Guiyang, 550025, PR China.
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18
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Siqueira JA, Zsögön A, Fernie AR, Nunes-Nesi A, Araújo WL. Does day length matter for nutrient responsiveness? TRENDS IN PLANT SCIENCE 2023; 28:1113-1123. [PMID: 37268488 DOI: 10.1016/j.tplants.2023.04.012] [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: 11/23/2022] [Revised: 04/11/2023] [Accepted: 04/24/2023] [Indexed: 06/04/2023]
Abstract
For over 2500 years, considerable agronomic interest has been paid to soil fertility. Both crop domestication and the Green Revolution shifted photoperiodism and the circadian clock in cultivated species, although this contributed to an increase in the demand for chemical fertilisers. Thus, the uptake of nutrients depends on light signalling, whereas diel growth and circadian rhythms are affected by nutrient levels. Here, we argue that day length and circadian rhythms may be central regulators of the uptake and usage of nutrients, also modulating responses to toxic elements (e.g., aluminium and cadmium). Thus, we suggest that knowledge in this area might assist in developing next-generation crops with improved uptake and use efficiency of nutrients.
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Affiliation(s)
- João Antonio Siqueira
- National Institute of Science and Technology on Plant Physiology under Stress Conditions, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900 Viçosa, MG, Brazil.
| | - Agustin Zsögön
- National Institute of Science and Technology on Plant Physiology under Stress Conditions, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900 Viçosa, MG, Brazil
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
| | - Adriano Nunes-Nesi
- National Institute of Science and Technology on Plant Physiology under Stress Conditions, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900 Viçosa, MG, Brazil
| | - Wagner L Araújo
- National Institute of Science and Technology on Plant Physiology under Stress Conditions, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900 Viçosa, MG, Brazil.
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19
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Wang J, Zhou C, Guan Z, Wang Q, Zhao J, Wang L, Zhang L, Zhang D, Deng XW, Ma L, Yin P. Plant phytochrome A in the Pr state assembles as an asymmetric dimer. Cell Res 2023; 33:802-805. [PMID: 37402899 PMCID: PMC10542778 DOI: 10.1038/s41422-023-00847-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Accepted: 06/24/2023] [Indexed: 07/06/2023] Open
Affiliation(s)
- Jiao Wang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Chen Zhou
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Zeyuan Guan
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Qiang Wang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Jun Zhao
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang, Shandong, China
| | - Lixia Wang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Liuqing Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Delin Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Xing Wang Deng
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang, Shandong, China
| | - Ling Ma
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei, China.
| | - Ping Yin
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei, China.
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20
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Zhang Y, Lin X, Ma C, Zhao J, Shang X, Wang Z, Xu B, Gao N, Deng XW, Wang J. Structural insights into plant phytochrome A as a highly sensitized photoreceptor. Cell Res 2023; 33:806-809. [PMID: 37491602 PMCID: PMC10542756 DOI: 10.1038/s41422-023-00858-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 07/16/2023] [Indexed: 07/27/2023] Open
Affiliation(s)
- Yuxuan Zhang
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences at Weifang, Weifang, Shandong, China
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing, China
| | - Xiaoli Lin
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences at Weifang, Weifang, Shandong, China
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing, China
| | - Chengying Ma
- Peking-Tsinghua Joint Center for Life Sciences, Peking University, Beijing, China
- State Key Laboratory of Membrane Biology, School of Life Sciences, Peking University, Beijing, China
| | - Jun Zhao
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences at Weifang, Weifang, Shandong, China
| | - Xiaojin Shang
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences at Weifang, Weifang, Shandong, China
| | - Zhengdong Wang
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences at Weifang, Weifang, Shandong, China
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing, China
- Peking-Tsinghua Joint Center for Life Sciences, Peking University, Beijing, China
| | - Bin Xu
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences at Weifang, Weifang, Shandong, China
| | - Ning Gao
- Peking-Tsinghua Joint Center for Life Sciences, Peking University, Beijing, China
- State Key Laboratory of Membrane Biology, School of Life Sciences, Peking University, Beijing, China
| | - Xing Wang Deng
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences at Weifang, Weifang, Shandong, China.
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing, China.
- Peking-Tsinghua Joint Center for Life Sciences, Peking University, Beijing, China.
| | - Jizong Wang
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences at Weifang, Weifang, Shandong, China.
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing, China.
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21
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Yue X, Xu L, Lin H, Xu C, Li S. Construction of Pt/Pt-Au doped chiral nanostructures using arginine and porphyrin assemblies as templates for enantioselective photocatalysis. Sci Bull (Beijing) 2023; 68:1764-1771. [PMID: 37487791 DOI: 10.1016/j.scib.2023.07.021] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 06/08/2023] [Accepted: 07/03/2023] [Indexed: 07/26/2023]
Abstract
Chiral nanomaterials with different functions have been widely developed, but the deep understanding of the structural effects of nanocatalysts on enantioselective photocatalytic efficiency is still highly demanded. Herein, Pt and Pt-Au-bimetal-doped chiral nanostructures with various morphologies and compositions are facilely constructed using L-/D-arginine (L-/D-Arg) and mono-sulfonate tetraphenyl porphyrin (H2TPPS) assemblies as chiral templates. Interestingly, these Pt and Pt-Au-doped chiral nanostructures, including nanorods (NR) and nanospheres (NS), can be well regulated by controlling pH, ionic strength, and reaction time of the assembling system of Arg and H2TPPS. More impressively, specific Au growth direction along the Pt-doped chiral NR (L-/D-Pt-NR) is observed (from tip to middle) during the preparation of Pt-Au-bimetal-doped chiral NR (L-/D-Pt-Au-NR) and their compositions can be finely controlled by simply adjusting the concentrations of HAuCl4. As expected, the chiral nanostructures exhibit superior enantioselective photocatalytic ability toward chiral organics under visible light: the oxidation rate of L-dihydroxy-phenylalanine (L-DOPA) catalyzed by L-Pt-NR (or D-DOPA catalyzed by D-Pt-NR) is about 60% higher than that of L-DOPA catalyzed by D-Pt-NR (or L-DOPA catalyzed by D-Pt-NR). This study provides a facile strategy to construct chiral nanostructures for the photocatalytic conversion of chiral organics.
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Affiliation(s)
- Xiaoyong Yue
- International Joint Research Center for Photo-responsive Molecules and Materials, School of Chemical and Material Engineering, Jiangnan University, Wuxi 214122, China
| | - Liguang Xu
- State Key Laboratory of Food Science and Technology, International Joint Research Laboratory for Biointerface and Biodetection, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Hengwei Lin
- International Joint Research Center for Photo-responsive Molecules and Materials, School of Chemical and Material Engineering, Jiangnan University, Wuxi 214122, China
| | - Chuanlai Xu
- State Key Laboratory of Food Science and Technology, International Joint Research Laboratory for Biointerface and Biodetection, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Si Li
- International Joint Research Center for Photo-responsive Molecules and Materials, School of Chemical and Material Engineering, Jiangnan University, Wuxi 214122, China; State Key Laboratory of Food Science and Technology, International Joint Research Laboratory for Biointerface and Biodetection, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China.
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22
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Burgie ES, Li H, Gannam ZTK, McLoughlin KE, Vierstra RD, Li H. The structure of Arabidopsis phytochrome A reveals topological and functional diversification among the plant photoreceptor isoforms. NATURE PLANTS 2023; 9:1116-1129. [PMID: 37291396 PMCID: PMC10546791 DOI: 10.1038/s41477-023-01435-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 05/10/2023] [Indexed: 06/10/2023]
Abstract
Plants employ a divergent cohort of phytochrome (Phy) photoreceptors to govern many aspects of morphogenesis through reversible photointerconversion between inactive Pr and active Pfr conformers. The two most influential are PhyA whose retention of Pfr enables sensation of dim light, while the relative instability of Pfr for PhyB makes it better suited for detecting full sun and temperature. To better understand these contrasts, we solved, by cryo-electron microscopy, the three-dimensional structure of full-length PhyA as Pr. Like PhyB, PhyA dimerizes through head-to-head assembly of its C-terminal histidine kinase-related domains (HKRDs), while the remainder assembles as a head-to-tail light-responsive platform. Whereas the platform and HKRDs associate asymmetrically in PhyB dimers, these lopsided connections are absent in PhyA. Analysis of truncation and site-directed mutants revealed that this decoupling and altered platform assembly have functional consequences for Pfr stability of PhyA and highlights how plant Phy structural diversification has extended light and temperature perception.
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Affiliation(s)
- E Sethe Burgie
- Department of Biology, Washington University in St. Louis, St. Louis, MO, USA
| | - Hua Li
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, USA
| | - Zira T K Gannam
- Department of Biology, Washington University in St. Louis, St. Louis, MO, USA
| | - Katrice E McLoughlin
- Department of Biology, Washington University in St. Louis, St. Louis, MO, USA
- Burning Rock Dx, Irvine, CA, USA
| | - Richard D Vierstra
- Department of Biology, Washington University in St. Louis, St. Louis, MO, USA.
| | - Huilin Li
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, USA.
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23
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Takagi H, Hempton AK, Imaizumi T. Photoperiodic flowering in Arabidopsis: Multilayered regulatory mechanisms of CONSTANS and the florigen FLOWERING LOCUS T. PLANT COMMUNICATIONS 2023; 4:100552. [PMID: 36681863 PMCID: PMC10203454 DOI: 10.1016/j.xplc.2023.100552] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 12/20/2022] [Accepted: 01/18/2023] [Indexed: 05/11/2023]
Abstract
The timing of flowering affects the success of sexual reproduction. This developmental event also determines crop yield, biomass, and longevity. Therefore, this mechanism has been targeted for improvement along with crop domestication. The underlying mechanisms of flowering are highly conserved in angiosperms. Central to these mechanisms is how environmental and endogenous conditions control transcriptional regulation of the FLOWERING LOCUS T (FT) gene, which initiates floral development under long-day conditions in Arabidopsis. Since the identification of FT as florigen, efforts have been made to understand the regulatory mechanisms of FT expression. Although many transcriptional regulators have been shown to directly influence FT, the question of how they coordinately control the spatiotemporal expression patterns of FT still requires further investigation. Among FT regulators, CONSTANS (CO) is the primary one whose protein stability is tightly controlled by phosphorylation and ubiquitination/proteasome-mediated mechanisms. In addition, various CO interaction partners, some of them previously identified as FT transcriptional regulators, positively or negatively modulate CO protein activity. The FT promoter possesses several transcriptional regulatory "blocks," highly conserved regions among Brassicaceae plants. Different transcription factors bind to specific blocks and affect FT expression, often causing topological changes in FT chromatin structure, such as the formation of DNA loops. We discuss the current understanding of the regulation of FT expression mainly in Arabidopsis and propose future directions related to this topic.
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Affiliation(s)
- Hiroshi Takagi
- Department of Biology, University of Washington, Seattle, WA 98195-1800, USA; Center for Gene Research, Nagoya University, Nagoya 464-8602, Japan
| | - Andrew K Hempton
- Department of Biology, University of Washington, Seattle, WA 98195-1800, USA
| | - Takato Imaizumi
- Department of Biology, University of Washington, Seattle, WA 98195-1800, USA; Center for Gene Research, Nagoya University, Nagoya 464-8602, Japan.
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24
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Zhao Y, Shi H, Pan Y, Lyu M, Yang Z, Kou X, Deng XW, Zhong S. Sensory circuitry controls cytosolic calcium-mediated phytochrome B phototransduction. Cell 2023; 186:1230-1243.e14. [PMID: 36931246 DOI: 10.1016/j.cell.2023.02.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 08/23/2022] [Accepted: 02/03/2023] [Indexed: 03/18/2023]
Abstract
Although Ca2+ has long been recognized as an obligatory intermediate in visual transduction, its role in plant phototransduction remains elusive. Here, we report a Ca2+ signaling that controls photoreceptor phyB nuclear translocation in etiolated seedlings during dark-to-light transition. Red light stimulates acute cytosolic Ca2+ increases via phyB, which are sensed by Ca2+-binding protein kinases, CPK6 and CPK12 (CPK6/12). Upon Ca2+ activation, CPK6/12 in turn directly interact with and phosphorylate photo-activated phyB at Ser80/Ser106 to initiate phyB nuclear import. Non-phosphorylatable mutation, phyBS80A/S106A, abolishes nuclear translocation and fails to complement phyB mutant, which is fully restored by combining phyBS80A/S106A with a nuclear localization signal. We further show that CPK6/12 function specifically in the early phyB-mediated cotyledon expansion, while Ser80/Ser106 phosphorylation generally governs phyB nuclear translocation. Our results uncover a biochemical regulatory loop centered in phyB phototransduction and provide a paradigm for linking ubiquitous Ca2+ increases to specific responses in sensory stimulus processing.
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Affiliation(s)
- Yan Zhao
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Hui Shi
- College of Life Sciences, Capital Normal University, and Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, Beijing 100048, China
| | - Ying Pan
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Mohan Lyu
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Zhixuan Yang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Xiaoxia Kou
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Xing Wang Deng
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China; Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang 261325, China
| | - Shangwei Zhong
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China; Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang 261325, China.
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25
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Fichman Y, Xiong H, Sengupta S, Morrow J, Loog H, Azad RK, Hibberd JM, Liscum E, Mittler R. Phytochrome B regulates reactive oxygen signaling during abiotic and biotic stress in plants. THE NEW PHYTOLOGIST 2023; 237:1711-1727. [PMID: 36401805 DOI: 10.1111/nph.18626] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 11/11/2022] [Indexed: 06/16/2023]
Abstract
Reactive oxygen species (ROS) and the photoreceptor protein phytochrome B (phyB) play a key role in plant acclimation to stress. However, how phyB that primarily functions in the nuclei impacts ROS signaling mediated by respiratory burst oxidase homolog (RBOH) proteins that reside on the plasma membrane, during stress, is unknown. Arabidopsis thaliana and Oryza sativa mutants, RNA-Seq, bioinformatics, biochemistry, molecular biology, and whole-plant ROS imaging were used to address this question. Here, we reveal that phyB and RBOHs function as part of a key regulatory module that controls apoplastic ROS production, stress-response transcript expression, and plant acclimation in response to excess light stress. We further show that phyB can regulate ROS production during stress even if it is restricted to the cytosol and that phyB, respiratory burst oxidase protein D (RBOHD), and respiratory burst oxidase protein F (RBOHF) coregulate thousands of transcripts in response to light stress. Surprisingly, we found that phyB is also required for ROS accumulation in response to heat, wounding, cold, and bacterial infection. Our findings reveal that phyB plays a canonical role in plant responses to biotic and abiotic stresses, regulating apoplastic ROS production, possibly while at the cytosol, and that phyB and RBOHD/RBOHF function in the same regulatory pathway.
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Affiliation(s)
- Yosef Fichman
- Division of Plant Sciences & Technology, College of Agricultural, Food and Natural Resources, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211-7310, USA
- Interdisciplinary Plant Group, University of Missouri, Columbia, MO, 65211-7310, USA
| | - Haiyan Xiong
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK
| | - Soham Sengupta
- Department of Biological Sciences, College of Science, University of North Texas, Denton, TX, 76203-5017, USA
| | - Johanna Morrow
- Division of Biological Sciences, College of Arts & Sciences, University of Missouri, Columbia, MO, 65211-7400, USA
- Department of Biology and Environmental Sciences, Westminster College, 501 Westminster Ave, Fulton, MO, 65251, USA
| | - Hailey Loog
- Division of Plant Sciences & Technology, College of Agricultural, Food and Natural Resources, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211-7310, USA
- Interdisciplinary Plant Group, University of Missouri, Columbia, MO, 65211-7310, USA
| | - Rajeev K Azad
- Department of Biological Sciences, College of Science, University of North Texas, Denton, TX, 76203-5017, USA
- Department of Mathematics, College of Science, University of North Texas, Denton, TX, 76203-5017, USA
| | - Julian M Hibberd
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK
| | - Emmanuel Liscum
- Interdisciplinary Plant Group, University of Missouri, Columbia, MO, 65211-7310, USA
- Division of Biological Sciences, College of Arts & Sciences, University of Missouri, Columbia, MO, 65211-7400, USA
| | - Ron Mittler
- Division of Plant Sciences & Technology, College of Agricultural, Food and Natural Resources, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211-7310, USA
- Interdisciplinary Plant Group, University of Missouri, Columbia, MO, 65211-7310, USA
- Department of Surgery, Christopher S. Bond Life Sciences Center, University of Missouri School of Medicine, University of Missouri, Columbia, MO, 65211-7310, USA
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26
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Choi DM, Kim SH, Han YJ, Kim JI. Regulation of Plant Photoresponses by Protein Kinase Activity of Phytochrome A. Int J Mol Sci 2023; 24:ijms24032110. [PMID: 36768431 PMCID: PMC9916439 DOI: 10.3390/ijms24032110] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 01/17/2023] [Accepted: 01/18/2023] [Indexed: 01/25/2023] Open
Abstract
Extensive research has been conducted for decades to elucidate the molecular and regulatory mechanisms for phytochrome-mediated light signaling in plants. As a result, tens of downstream signaling components that physically interact with phytochromes are identified, among which negative transcription factors for photomorphogenesis, PHYTOCHROME-INTERACTING FACTORs (PIFs), are well known to be regulated by phytochromes. In addition, phytochromes are also shown to inactivate an important E3 ligase complex consisting of CONSTITUTIVELY PHOTOMORPHOGENIC 1 (COP1) and SUPPRESSORs OF phyA-105 (SPAs). This inactivation induces the accumulation of positive transcription factors for plant photomorphogenesis, such as ELONGATED HYPOCOTYL 5 (HY5). Although many downstream components of phytochrome signaling have been studied thus far, it is not fully elucidated which intrinsic activity of phytochromes is necessary for the regulation of these components. It should be noted that phytochromes are autophosphorylating protein kinases. Recently, the protein kinase activity of phytochrome A (phyA) has shown to be important for its function in plant light signaling using Avena sativa phyA mutants with reduced or increased kinase activity. In this review, we highlight the function of phyA as a protein kinase to explain the regulation of plant photoresponses by phyA.
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Affiliation(s)
- Da-Min Choi
- Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Seong-Hyeon Kim
- Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Yun-Jeong Han
- Kumho Life Science Laboratory, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Jeong-Il Kim
- Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju 61186, Republic of Korea
- Kumho Life Science Laboratory, Chonnam National University, Gwangju 61186, Republic of Korea
- Correspondence:
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27
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Busche M, Hake S, Brunkard JO. Terminal ear 1 and phytochromes B1/B2 regulate maize leaf initiation independently. Genetics 2022; 223:6887217. [PMID: 36495288 PMCID: PMC9910401 DOI: 10.1093/genetics/iyac182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 11/29/2022] [Accepted: 12/01/2022] [Indexed: 12/14/2022] Open
Abstract
Higher plants generate new leaves from shoot meristems throughout their vegetative lifespan. The tempo of leaf initiation is dynamically regulated by physiological cues, but little is known about the underlying genetic signaling pathways that coordinate this rate. Two maize (Zea mays) mutants, terminal ear1 (te1) and phytochrome B1;phytochrome B2 (phyB1;phyB2), oppositely affect leaf initiation rates and total leaf number at the flowering time: te1 mutants make leaves faster whereas phyB1;phyB2 mutants make leaves slower than wild-type plants. To test whether PhyB1, PhyB2, and TE1 act in overlapping or distinct pathways to regulate leaf initiation, we crossed te1 and phyB1;phyB2 created an F2 population segregating for these three mutations and quantified various phenotypes among the resulting genotypes, including leaf number, leaf initiation rate, plant height, leaf length, leaf width, number of juvenile leaves, stalk diameter, and dry shoot biomass. Leaf number and initiation rate in phyB1;phyB2;te1 plants fell between the extremes of the two parents, suggesting an additive genetic interaction between te1 and phyB1;phyB2 rather than epistasis. Therefore, we conclude that PhyB1, PhyB2, and TE1 likely control leaf initiation through distinct signaling pathways.
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Affiliation(s)
- Michael Busche
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53715, USA
| | - Sarah Hake
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA,Plant Gene Expression Center, USDA Agricultural Research Service, Albany, CA 94710, USA
| | - Jacob O Brunkard
- Corresponding author: Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53715, USA.
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28
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Westenhoff S, Meszaros P, Schmidt M. Protein motions visualized by femtosecond time-resolved crystallography: The case of photosensory vs photosynthetic proteins. Curr Opin Struct Biol 2022; 77:102481. [PMID: 36252455 DOI: 10.1016/j.sbi.2022.102481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 08/28/2022] [Accepted: 09/01/2022] [Indexed: 12/14/2022]
Abstract
Proteins are dynamic objects and undergo conformational changes when functioning. These changes range from interconversion between states in equilibrium to ultrafast and coherent structural motions within one perturbed state. Time-resolved serial femtosecond crystallography at free-electron X-ray lasers can unravel structural changes with atomic resolution and down to femtosecond time scales. In this review, we summarize recent advances on detecting structural changes for phytochrome photosensor proteins and a bacterial photosynthetic reaction center. In the phytochrome structural changes are extensive and involve major rearrangements of many amino acids and water molecules, accompanying the regulation of its biochemical activity, whereas in the photosynthetic reaction center protein the structural changes are smaller, more localized, and are optimized to facilitate electron transfer along the chromophores. The detected structural motions underpin the proteins' function, providing a showcase for the importance of detecting ultrafast protein structural dynamics.
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Affiliation(s)
- Sebastian Westenhoff
- Department of Chemistry and Molecular Biology, University of Gothenburg, 40530 Gothenburg, Sweden; Department of Chemistry - BMC, Biochemistry, Uppsala University, 75123 Uppsala, Sweden.
| | - Petra Meszaros
- Department of Chemistry - BMC, Biochemistry, Uppsala University, 75123 Uppsala, Sweden
| | - Marius Schmidt
- Physics Department, Physic, University of Wisconsin-Milwaukee, 3134 N. Maryland Ave., Milwaukee, WI 53211, United States
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29
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Zhang YX, Niu YQ, Wang XF, Wang ZH, Wang ML, Yang J, Wang YG, Zhang WJ, Song ZP, Li LF. Phenotypic and transcriptomic responses of the shade-grown species Panax ginseng to variable light conditions. ANNALS OF BOTANY 2022; 130:749-762. [PMID: 35961674 PMCID: PMC9670753 DOI: 10.1093/aob/mcac105] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 08/10/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND AND AIMS Elucidating how plant species respond to variable light conditions is important to understand the ecological adaptation to heterogeneous natural habitats. Plant performance and its underlying gene regulatory network have been well documented in sun-grown plants. However, the phenotypic and molecular responses of shade-grown plants under variable light conditions have remained largely unclear. METHODS We assessed the differences in phenotypic performance between Panax ginseng (shade-grown) and Arabidopsis thaliana (sun-grown) under sunlight, shade and deep-shade conditions. To further address the molecular bases underpinning the phenotypic responses, we compared time-course transcriptomic expression profiling and candidate gene structures between the two species. KEY RESULTS Our results show that, compared with arabidopsis, ginseng plants not only possess a lower degree of phenotypic plasticity among the three light conditions, but also exhibit higher photosynthetic efficiency under shade and deep-shade conditions. Further comparisons of the gene expression and structure reveal that differential transcriptional regulation together with increased copy number of photosynthesis-related genes (e.g. electron transfer and carbon fixation) may improve the photosynthetic efficiency of ginseng plants under the two shade conditions. In contrast, the inactivation of phytochrome-interacting factors (i.e. absent and no upregulation of the PIF genes) are potentially associated with the observed low degree of phenotypic plasticity of ginseng plants under variable light conditions. CONCLUSIONS Our study provides new insights into how shade-grown plants respond to variable light conditions. Candidate genes related to shade adaptation in ginseng provide valuable genetic resources for future molecular breeding of high-density planting crops.
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Affiliation(s)
- Yu-Xin Zhang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Yu-Qian Niu
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Xin-Feng Wang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Zhen-Hui Wang
- Department of Agronomy, Jilin Agricultural University, Changchun 130118, China
| | - Meng-Li Wang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Ji Yang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Yu-Guo Wang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Wen-Ju Zhang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Zhi-Ping Song
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Lin-Feng Li
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
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30
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Chen D, Lyu M, Kou X, Li J, Yang Z, Gao L, Li Y, Fan LM, Shi H, Zhong S. Integration of light and temperature sensing by liquid-liquid phase separation of phytochrome B. Mol Cell 2022; 82:3015-3029.e6. [PMID: 35728588 DOI: 10.1016/j.molcel.2022.05.026] [Citation(s) in RCA: 58] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 04/02/2022] [Accepted: 05/23/2022] [Indexed: 01/03/2023]
Abstract
Light and temperature in plants are perceived by a common receptor, phytochrome B (phyB). How phyB distinguishes these signals remains elusive. Here, we report that phyB spontaneously undergoes phase separation to assemble liquid-like droplets. This capacity is driven by its C terminus through self-association, whereas the intrinsically disordered N-terminal extension (NTE) functions as a biophysical modulator of phase separation. Light exposure triggers a conformational change to subsequently alter phyB condensate assembly, while temperature sensation is directly mediated by the NTE to modulate the phase behavior of phyB droplets. Multiple signaling components are selectively incorporated into phyB droplets to form concentrated microreactors, allowing switch-like control of phyB signaling activity through phase transitions. Therefore, light and temperature cues are separately read out by phyB via allosteric changes and spontaneous phase separation, respectively. We provide a conceptual framework showing how the distinct but highly correlated physical signals are interpreted and sorted by one receptor.
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Affiliation(s)
- Di Chen
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Mohan Lyu
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Xiaoxia Kou
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Jing Li
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Zhixuan Yang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Lulu Gao
- College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Yue Li
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Liu-Min Fan
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Hui Shi
- College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Shangwei Zhong
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China; Peking University Institute of Advanced Agricultural Sciences, Weifang 261325, China.
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