1
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Hughes J, Winkler A. New Insight Into Phytochromes: Connecting Structure to Function. ANNUAL REVIEW OF PLANT BIOLOGY 2024; 75:153-183. [PMID: 39038250 DOI: 10.1146/annurev-arplant-070623-110636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/24/2024]
Abstract
Red and far-red light-sensing phytochromes are widespread in nature, occurring in plants, algae, fungi, and prokaryotes. Despite at least a billion years of evolution, their photosensory modules remain structurally and functionally similar. Conversely, nature has found remarkably different ways of transmitting light signals from the photosensor to diverse physiological responses. We summarize key features of phytochrome structure and function and discuss how these are correlated, from how the bilin environment affects the chromophore to how light induces cellular signals. Recent advances in the structural characterization of bacterial and plant phytochromes have resulted in paradigm changes in phytochrome research that we discuss in the context of present-day knowledge. Finally, we highlight questions that remain to be answered and suggest some of the benefits of understanding phytochrome structure and function.
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Affiliation(s)
- Jon Hughes
- Department of Plant Physiology, Justus Liebig University, Giessen, Germany;
- Department of Physics, Free University of Berlin, Berlin, Germany
| | - Andreas Winkler
- Institute of Biochemistry, Graz University of Technology, Graz, Austria;
- BioTechMed-Graz, Graz, Austria
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2
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Balke J, Díaz Gutiérrez P, Rafaluk-Mohr T, Proksch J, Koksch B, Alexiev U. Osmolytes Modulate Photoactivation of Phytochrome: Probing Protein Hydration. Molecules 2023; 28:6121. [PMID: 37630372 PMCID: PMC10457786 DOI: 10.3390/molecules28166121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 07/23/2023] [Accepted: 07/26/2023] [Indexed: 08/27/2023] Open
Abstract
Phytochromes are bistable red/far-red light-responsive photoreceptor proteins found in plants, fungi, and bacteria. Light-activation of the prototypical phytochrome Cph1 from the cyanobacterium Synechocystis sp. PCC 6803 allows photoisomerization of the bilin chromophore in the photosensory module and a subsequent series of intermediate states leading from the red absorbing Pr to the far-red-absorbing Pfr state. We show here via osmotic and hydrostatic pressure-based measurements that hydration of the photoreceptor modulates the photoconversion kinetics in a controlled manner. While small osmolytes like sucrose accelerate Pfr formation, large polymer osmolytes like PEG 4000 delay the formation of Pfr. Thus, we hypothesize that an influx of mobile water into the photosensory domain is necessary for proceeding to the Pfr state. We suggest that protein hydration changes are a molecular event that occurs during photoconversion to Pfr, in addition to light activation, ultrafast electric field changes, photoisomerization, proton release and uptake, and the major conformational change leading to signal transmission, or simultaneously with one of these events. Moreover, we discuss this finding in light of the use of Cph1-PGP as a hydration sensor, e.g., for the characterization of novel hydrogel biomaterials.
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Affiliation(s)
- Jens Balke
- Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Paula Díaz Gutiérrez
- Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Timm Rafaluk-Mohr
- Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Jonas Proksch
- Department of Biology, Chemistry, Pharmacy, Institute of Chemistry and Biochemistry–Organic Chemistry, Freie Universität Berlin, Takustr. 3, 14195 Berlin, Germany; (J.P.); (B.K.)
| | - Beate Koksch
- Department of Biology, Chemistry, Pharmacy, Institute of Chemistry and Biochemistry–Organic Chemistry, Freie Universität Berlin, Takustr. 3, 14195 Berlin, Germany; (J.P.); (B.K.)
| | - Ulrike Alexiev
- Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
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3
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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: 10] [Impact Index Per Article: 10.0] [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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4
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Russ M, Ehret AK, Hörner M, Peschkov D, Bohnert R, Idstein V, Minguet S, Weber W, Lillemeier BF, Yousefi OS, Schamel WW. Opto-APC: Engineering of cells that display phytochrome B on their surface for optogenetic studies of cell-cell interactions. Front Mol Biosci 2023; 10:1143274. [PMID: 36936981 PMCID: PMC10016228 DOI: 10.3389/fmolb.2023.1143274] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 02/08/2023] [Indexed: 02/22/2023] Open
Abstract
The kinetics of a ligand-receptor interaction determine the responses of the receptor-expressing cell. One approach to experimentally and reversibly change this kinetics on demand is optogenetics. We have previously developed a system in which the interaction of a modified receptor with an engineered ligand can be controlled by light. In this system the ligand is a soluble Phytochrome B (PhyB) tetramer and the receptor is fused to a mutated PhyB-interacting factor (PIFS). However, often the natural ligand is not soluble, but expressed as a membrane protein on another cell. This allows ligand-receptor interactions in two dimensions. Here, we developed a strategy to generate cells that display PhyB as a membrane-bound protein by expressing the SpyCatcher fused to a transmembrane domain in HEK-293T cells and covalently coupling purified PhyB-SpyTag to these cells. As proof-of-principle, we use Jurkat T cells that express a GFP-PIFS-T cell receptor and show that these cells can be stimulated by the PhyB-coupled HEK-293T cells in a light dependent manner. Thus, we call the PhyB-coupled cells opto-antigen presenting cells (opto-APCs). Our work expands the toolbox of optogenetic technologies, allowing two-dimensional ligand-receptor interactions to be controlled by light.
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Affiliation(s)
- Marissa Russ
- Signalling Research Centres BIOSS and CIBSS, Faculty of Biology, University of Freiburg, Freiburg, Germany
- Centre for Chronic Immunodeficiency (CCI), Medical Centre Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Anna K. Ehret
- Signalling Research Centres BIOSS and CIBSS, Faculty of Biology, University of Freiburg, Freiburg, Germany
- Centre for Chronic Immunodeficiency (CCI), Medical Centre Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Freiburg, Germany
| | - Maximilian Hörner
- Signalling Research Centres BIOSS and CIBSS, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Daniel Peschkov
- Signalling Research Centres BIOSS and CIBSS, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Rebecca Bohnert
- Signalling Research Centres BIOSS and CIBSS, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Vincent Idstein
- Signalling Research Centres BIOSS and CIBSS, Faculty of Biology, University of Freiburg, Freiburg, Germany
- Centre for Chronic Immunodeficiency (CCI), Medical Centre Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Freiburg, Germany
| | - Susana Minguet
- Signalling Research Centres BIOSS and CIBSS, Faculty of Biology, University of Freiburg, Freiburg, Germany
- Centre for Chronic Immunodeficiency (CCI), Medical Centre Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Wilfried Weber
- Signalling Research Centres BIOSS and CIBSS, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Björn F. Lillemeier
- Signalling Research Centres BIOSS and CIBSS, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - O. Sascha Yousefi
- Signalling Research Centres BIOSS and CIBSS, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Wolfgang W. Schamel
- Signalling Research Centres BIOSS and CIBSS, Faculty of Biology, University of Freiburg, Freiburg, Germany
- Centre for Chronic Immunodeficiency (CCI), Medical Centre Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- *Correspondence: Wolfgang W. Schamel,
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5
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Eprintsev AT, Fedorin DN, Igamberdiev AU. Light Dependent Changes in Adenylate Methylation of the Promoter of the Mitochondrial Citrate Synthase Gene in Maize ( Zea mays L.) Leaves. Int J Mol Sci 2022; 23:13495. [PMID: 36362281 PMCID: PMC9653993 DOI: 10.3390/ijms232113495] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 10/31/2022] [Accepted: 11/03/2022] [Indexed: 09/29/2023] Open
Abstract
Limited methyl-specific restriction of genomic DNA by endonuclease MAL1 revealed the changes in its methyl status caused by adenine modification in maize (Zea mays L.) leaves under different light conditions (dark, light, irradiation by red and far-red light). Incubation in the light and irradiation by red light exhibited an activating effect on DNA adenine methylase activity, which was reflected in an increase in the number of methylated adenines in GATC sites. Far-red light and darkness exhibited an opposite effect. The use of nitrite conversion of DNA followed by methyladenine-dependent restriction by MboI nuclease revealed a phytochrome B-dependent mechanism of regulation of the methyl status of adenine in the GATC sites in the promoter of the gene encoding the mitochondrial isoform of citrate synthase. Irradiation of plants with red light caused changes in the adenine methyl status of the analyzed amplicon, as evidenced by the presence of restriction products of 290, 254, and 121 nucleotides. Adenine methylation occurred at all three GATC sites in the analyzed DNA sequence. It is concluded that adenylate methylation is controlled by phytochrome B via the transcription factor PIF4 and represents an important mechanism for the tricarboxylic acid cycle regulation by light.
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Affiliation(s)
- Alexander T. Eprintsev
- Department of Biochemistry and Cell Physiology, Voronezh State University, 394018 Voronezh, Russia
| | - Dmitry N. Fedorin
- Department of Biochemistry and Cell Physiology, Voronezh State University, 394018 Voronezh, Russia
| | - Abir U. Igamberdiev
- Department of Biology, Memorial University of Newfoundland, St. John’s, NL A1C 5S7, Canada
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6
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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: 69] [Impact Index Per Article: 34.5] [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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7
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von Horsten S, Essen LO. Conformational Change of Tetratricopeptide Repeats Region Triggers Activation of Phytochrome-Associated Protein Phosphatase 5. FRONTIERS IN PLANT SCIENCE 2021; 12:733069. [PMID: 34721460 PMCID: PMC8551457 DOI: 10.3389/fpls.2021.733069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 09/21/2021] [Indexed: 06/13/2023]
Abstract
Phytochrome activity is not only controlled by light but also by post-translational modifications, e. g. phosphorylation. One of the phosphatases responsible for plant phytochrome dephosphorylation and thereby increased activity is the phytochrome-associated protein phosphatase 5 (PAPP5). We show that PAPP5 recognizes phospho-site mimicking mutants of phytochrome B, when being activated by arachidonic acid (AA). Addition of AA to PAPP5 decreases the α-helical content as tracked by CD-spectroscopy. These changes correspond to conformational changes of the regulatory tetratricopeptide repeats (TPR) region as shown by mapping data from hydrogen deuterium exchange mass spectrometry onto a 3.0 Å crystal structure of PAPP5. Surprisingly, parts of the linker between the TPR and PP2A domains and of the so-called C-terminal inhibitory motif exhibit reduced deuterium uptake upon AA-binding. Molecular dynamics analyses of PAPP5 complexed to a phyB phosphopeptide show that this C-terminal motif remains associated with the TPR region in the substrate bound state, suggesting that this motif merely serves for restricting the orientations of the TPR region relative to the catalytic PP2A domain. Given the high similarity to mammalian PP5 these data from a plant ortholog show that the activation mode of these PPP-type protein phosphatases is highly conserved.
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Affiliation(s)
- Silke von Horsten
- Department of Biochemistry, Faculty of Chemistry, Philipps-University, Marburg, Germany
| | - Lars-Oliver Essen
- Department of Biochemistry, Faculty of Chemistry, Philipps-University, Marburg, Germany
- Center for Synthetic Microbiology, Philipps-University, Marburg, Germany
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8
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James EI, Murphree TA, Vorauer C, Engen JR, Guttman M. Advances in Hydrogen/Deuterium Exchange Mass Spectrometry and the Pursuit of Challenging Biological Systems. Chem Rev 2021; 122:7562-7623. [PMID: 34493042 PMCID: PMC9053315 DOI: 10.1021/acs.chemrev.1c00279] [Citation(s) in RCA: 102] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
![]()
Solution-phase hydrogen/deuterium
exchange (HDX) coupled to mass
spectrometry (MS) is a widespread tool for structural analysis across
academia and the biopharmaceutical industry. By monitoring the exchangeability
of backbone amide protons, HDX-MS can reveal information about higher-order
structure and dynamics throughout a protein, can track protein folding
pathways, map interaction sites, and assess conformational states
of protein samples. The combination of the versatility of the hydrogen/deuterium
exchange reaction with the sensitivity of mass spectrometry has enabled
the study of extremely challenging protein systems, some of which
cannot be suitably studied using other techniques. Improvements over
the past three decades have continually increased throughput, robustness,
and expanded the limits of what is feasible for HDX-MS investigations.
To provide an overview for researchers seeking to utilize and derive
the most from HDX-MS for protein structural analysis, we summarize
the fundamental principles, basic methodology, strengths and weaknesses,
and the established applications of HDX-MS while highlighting new
developments and applications.
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Affiliation(s)
- Ellie I James
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Taylor A Murphree
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Clint Vorauer
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - John R Engen
- Department of Chemistry & Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Miklos Guttman
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, United States
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9
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Burgie ES, Gannam ZTK, McLoughlin KE, Sherman CD, Holehouse AS, Stankey RJ, Vierstra RD. Differing biophysical properties underpin the unique signaling potentials within the plant phytochrome photoreceptor families. Proc Natl Acad Sci U S A 2021; 118:e2105649118. [PMID: 34039713 PMCID: PMC8179155 DOI: 10.1073/pnas.2105649118] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Many aspects of photoperception by plants and microorganisms are initiated by the phytochrome (Phy) family of photoreceptors that detect light through interconversion between red light- (Pr) and far-red light-absorbing (Pfr) states. Plants synthesize a small family of Phy isoforms (PhyA to PhyE) that collectively regulate photomorphogenesis and temperature perception through redundant and unique actions. While the selective roles of these isoforms have been partially attributed to their differing abundances, expression patterns, affinities for downstream partners, and turnover rates, we show here from analysis of recombinant Arabidopsis chromoproteins that the Phy isoforms also display distinct biophysical properties. Included are a hypsochromic shift in the Pr absorption for PhyC and varying rates of Pfr to Pr thermal reversion, part of which can be attributed to the core photosensory module in each. Most strikingly, PhyB combines strong temperature dependence of thermal reversion with an order-of-magnitude faster rate to likely serve as the main physiological thermosensor, whereby thermal reversion competes with photoconversion. In addition, comparisons of Pfr occupancies for PhyA and PhyB under a range of red- and white-light fluence rates imply that low-light environments are effectively sensed by PhyA, while high-light environments, such as full sun, are effectively sensed by PhyB. Parallel analyses of the Phy isoforms from potato and maize showed that the unique features within the Arabidopsis family are conserved, thus indicating that the distinct biophysical properties among plant Phy isoforms emerged early in Phy evolution, likely to enable full interrogation of their light and temperature environments.
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Affiliation(s)
- E Sethe Burgie
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
- Department of Genetics, University of Wisconsin, Madison, WI 53706
| | - Zira T K Gannam
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | | | | | - Alex S Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine in St. Louis, St. Louis, MO 63110
- Center for Science and Engineering of Living Systems, Washington University in St. Louis, St. Louis, MO 63110
| | - Robert J Stankey
- Department of Genetics, University of Wisconsin, Madison, WI 53706
| | - Richard D Vierstra
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130;
- Department of Genetics, University of Wisconsin, Madison, WI 53706
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10
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Takala H, Edlund P, Ihalainen JA, Westenhoff S. Tips and turns of bacteriophytochrome photoactivation. Photochem Photobiol Sci 2021; 19:1488-1510. [PMID: 33107538 DOI: 10.1039/d0pp00117a] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Phytochromes are ubiquitous photosensor proteins, which control the growth, reproduction and movement in plants, fungi and bacteria. Phytochromes switch between two photophysical states depending on the light conditions. In analogy to molecular machines, light absorption induces a series of structural changes that are transduced from the bilin chromophore, through the protein, and to the output domains. Recent progress towards understanding this structural mechanism of signal transduction has been manifold. We describe this progress with a focus on bacteriophytochromes. We describe the mechanism along three structural tiers, which are the chromophore-binding pocket, the photosensory module, and the output domains. We discuss possible interconnections between the tiers and conclude by presenting future directions and open questions. We hope that this review may serve as a compendium to guide future structural and spectroscopic studies designed to understand structural signaling in phytochromes.
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Affiliation(s)
- Heikki Takala
- Department of Biological and Environmental Science, Nanoscience Center, University of Jyvaskyla, Box 35, 40014 Jyvaskyla, Finland. and Department of Anatomy, Faculty of Medicine, University of Helsinki, Box 63, 00014 Helsinki, Finland
| | - Petra Edlund
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden.
| | - Janne A Ihalainen
- Department of Biological and Environmental Science, Nanoscience Center, University of Jyvaskyla, Box 35, 40014 Jyvaskyla, Finland.
| | - Sebastian Westenhoff
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden.
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11
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Wahlgren WY, Golonka D, Westenhoff S, Möglich A. Cryo-Electron Microscopy of Arabidopsis thaliana Phytochrome A in Its Pr State Reveals Head-to-Head Homodimeric Architecture. FRONTIERS IN PLANT SCIENCE 2021; 12:663751. [PMID: 34108981 PMCID: PMC8182759 DOI: 10.3389/fpls.2021.663751] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 03/29/2021] [Indexed: 06/12/2023]
Abstract
Phytochrome photoreceptors regulate vital adaptations of plant development, growth, and physiology depending on the ratio of red and far-red light. The light-triggered Z/E isomerization of a covalently bound bilin chromophore underlies phytochrome photoconversion between the red-absorbing Pr and far-red-absorbing Pfr states. Compared to bacterial phytochromes, the molecular mechanisms of signal propagation to the C-terminal module and its regulation are little understood in plant phytochromes, not least owing to a dearth of structural information. To address this deficit, we studied the Arabidopsis thaliana phytochrome A (AtphyA) at full length by cryo-electron microscopy (cryo-EM). Following heterologous expression in Escherichia coli, we optimized the solvent conditions to overcome protein aggregation and thus obtained photochemically active, near-homogenous AtphyA. We prepared grids for cryo-EM analysis of AtphyA in its Pr state and conducted single-particle analysis. The resulting two-dimensional class averages and the three-dimensional electron density map at 17 Å showed a homodimeric head-to-head assembly of AtphyA. Docking of domain structures into the electron density revealed a separation of the AtphyA homodimer at the junction of its photosensor and effector modules, as reflected in a large void in the middle of map. The overall architecture of AtphyA resembled that of bacterial phytochromes, thus hinting at commonalities in signal transduction and mechanism between these receptors. Our work paves the way toward future studies of the structure, light response, and interactions of full-length phytochromes by cryo-EM.
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Affiliation(s)
- Weixiao Yuan Wahlgren
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - David Golonka
- Lehrstuhl fur Biochemie, Universität Bayreuth, Bayreuth, Germany
| | - Sebastian Westenhoff
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Andreas Möglich
- Lehrstuhl fur Biochemie, Universität Bayreuth, Bayreuth, Germany
- Bayreuth Center for Biochemistry and Molecular Biology, Universität Bayreuth, Bayreuth, Germany
- North-Bavarian NMR Center, Universität Bayreuth, Bayreuth, Germany
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12
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Fonin AV, Antifeeva IA, Shpironok OG, Stepanenko OV, Silonov SA, Stepanenko OV, Antifeev IE, Romanovich AE, Kuznetsova IM, Kim JI, Uversky VN, Turoverov KK. Photo-dependent membrane-less organelles formed from plant phyB and PIF6 proteins in mammalian cells. Int J Biol Macromol 2021; 176:325-331. [PMID: 33582218 DOI: 10.1016/j.ijbiomac.2021.02.075] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 02/08/2021] [Accepted: 02/09/2021] [Indexed: 12/29/2022]
Abstract
Plant photobodies are the membrane-less organelles (MLOs) that can be generated by protein-protein interactions between active form of phytochrome B (phyB) and phytochrome-interacting factors (PIFs). These organelles regulate plant photomorphogenesis. In this study, we developed two chimeric proteins with fluorescent proteins, phyB fused to EGFP and PIF6 fused to mCherry, and investigated their exogenous expression in mammalian cells by confocal fluorescence microscopy. Results showed that irradiation with diffused 630-nm light induced formation and subsequent increase in sizes of the MLOs. The assembly and disassembly of the photo-inducible MLOs in the mammalian cell cytoplasm obeyed the laws inherent in the concentration-dependent phase separation of biopolymers. The sizes of MLOs formed from phyB and PIF6 in mammalian cells corresponded to the sizes of the so-called "early" photobodies in plant cells. These results suggested that the first step for the formation of plant photobodies might be based on the light-dependent liquid-liquid phase separation of PIFs and other proteins that can specifically interact with the active form of phyB. The developed chimeric proteins in principle can be used to control the assembly and disassembly of photo-inducible MLOs, and thereby to regulate various intracellular processes in mammalian cells.
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Affiliation(s)
- Alexander V Fonin
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky Ave., St. Petersburg 194064, Russian Federation; Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russian Federation.
| | - Iuliia A Antifeeva
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky Ave., St. Petersburg 194064, Russian Federation
| | - Olesya G Shpironok
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky Ave., St. Petersburg 194064, Russian Federation; Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russian Federation
| | - Olesya V Stepanenko
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky Ave., St. Petersburg 194064, Russian Federation.
| | - Sergey A Silonov
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky Ave., St. Petersburg 194064, Russian Federation
| | - Olga V Stepanenko
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky Ave., St. Petersburg 194064, Russian Federation.
| | - Ivan E Antifeev
- Institute for Analytical Instrumentation of the Russian Academy of Sciences, Rizhsky av., 26, St. Petersburg 190103, Russian Federation
| | - Anna E Romanovich
- St-Petersburg State University Science Park, Resource Center of Molecular and Cell Technologies, Universitetskaya nab. 7-9, St. Petersburg 199034, Russian Federation.
| | - Irina M Kuznetsova
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky Ave., St. Petersburg 194064, Russian Federation.
| | - Jeong-Il Kim
- Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju 61186, Republic of Korea.
| | - Vladimir N Uversky
- University of South Florida, Morsani College of Medicine, Department of Molecular Medicine and Byrd Alzheimer's Research Institute, Tampa, FL 33612, USA.
| | - Konstantin K Turoverov
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky Ave., St. Petersburg 194064, Russian Federation; Peter the Great St.-Petersburg Polytechnic University, Polytechnicheskaya 29, St. Petersburg 195251, Russian Federation.
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13
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Shah A, Tyagi S, Saratale GD, Guzik U, Hu A, Sreevathsa R, Reddy VD, Rai V, Mulla SI. A comprehensive review on the influence of light on signaling cross-talk and molecular communication against phyto-microbiome interactions. Crit Rev Biotechnol 2021; 41:370-393. [PMID: 33550862 DOI: 10.1080/07388551.2020.1869686] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Generally, plant growth, development, and their productivity are mainly affected by their growth rate and also depend on environmental factors such as temperature, pH, humidity, and light. The interaction between plants and pathogens are highly specific. Such specificity is well characterized by plants and pathogenic microbes in the form of a molecular signature such as pattern-recognition receptors (PRRs) and microbes-associated molecular patterns (MAMPs), which in turn trigger systemic acquired immunity in plants. A number of Arabidopsis mutant collections are available to investigate molecular and physiological changes in plants under the presence of different light conditions. Over the past decade(s), several studies have been performed by selecting Arabidopsis thaliana under the influence of red, green, blue, far/far-red, and white light. However, only few phenotypic and molecular based studies represent the modulatory effects in plants under the influence of green and blue lights. Apart from this, red light (RL) actively participates in defense mechanisms against several pathogenic infections. This evolutionary pattern of light sensitizes the pathologist to analyze a series of events in plants during various stress conditions of the natural and/or the artificial environment. This review scrutinizes the literature where red, blue, white, and green light (GL) act as sensory systems that affects physiological parameters in plants. Generally, white and RL are responsible for regulating various defense mechanisms, but, GL also participates in this process with a robust impact! In addition to this, we also focus on the activation of signaling pathways (salicylic acid and jasmonic acid) and their influence on plant immune systems against phytopathogen(s).
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Affiliation(s)
- Anshuman Shah
- CP College of Agriculture, Sardarkrushinagar Dantiwada Agriculture University, Dantiwada, India
| | - Shaily Tyagi
- ICAR-National Institute for Plant Biotechnology, New Delhi, India
| | | | - Urszula Guzik
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Science, University of Silesia in Katowice, Katowice, Poland
| | - Anyi Hu
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment Chinese Academy of Sciences, Xiamen, China
| | | | - Vaddi Damodara Reddy
- Department of Biochemistry, School of Applied Sciences, REVA University, Bangalore, India
| | - Vandna Rai
- ICAR-National Institute for Plant Biotechnology, New Delhi, India
| | - Sikandar I Mulla
- Department of Biochemistry, School of Applied Sciences, REVA University, Bangalore, India
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14
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Hu W, Figueroa‐Balderas R, Chi‐Ham C, Lagarias JC. Regulation of monocot and dicot plant development with constitutively active alleles of phytochrome B. PLANT DIRECT 2020; 4:e00210. [PMID: 32346668 PMCID: PMC7184922 DOI: 10.1002/pld3.210] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 02/03/2020] [Accepted: 02/25/2020] [Indexed: 05/31/2023]
Abstract
The constitutively active missense allele of Arabidopsis phytochrome B, AtPHYBY276H or AtYHB, encodes a polypeptide that adopts a light-insensitive, physiologically active conformation capable of sustaining photomorphogenesis in darkness. Here, we show that the orthologous OsYHB allele of rice phytochrome B (OsPHYBY283H ) also encodes a dominant "constitutively active" photoreceptor through comparative phenotypic analyses of AtYHB and OsYHB transgenic lines of four eudicot species, Arabidopsis thaliana, Nicotiana tabacum (tobacco), Nicotiana sylvestris and Solanum lycopersicum cv. MicroTom (tomato), and of two monocot species, Oryza sativa ssp. japonica and Brachypodium distachyon. Reciprocal transformation experiments show that the gain-of-function constitutive photomorphogenic (cop) phenotypes by YHB expression are stronger in host plants within the same class than across classes. Our studies also reveal additional YHB-dependent traits in adult plants, which include extreme shade tolerance, both early and late flowering behaviors, delayed leaf senescence, reduced tillering, and even viviparous seed germination. However, the strength of these gain-of-function phenotypes depends on the specific combination of YHB allele and species/cultivar transformed. Flowering and tillering of OsYHB- and OsPHYB-expressing lines of rice Nipponbare and Kitaake cultivars were compared, also revealing differences in YHB/PHYB allele versus genotype interaction on the phenotypic behavior of the two rice cultivars. In view of recent evidence that the regulatory activity of AtYHB is not only light insensitive but also temperature insensitive, selective YHB expression is expected to yield improved agronomic performance of both dicot and monocot crop plant species not possible with wild-type PHYB alleles.
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Affiliation(s)
- Wei Hu
- Department of Molecular and Cellular BiologyUniversity of CaliforniaDavisCAUSA
| | - Rosa Figueroa‐Balderas
- Public Intellectual Property Resource for Agriculture (PIPRA)University of CaliforniaDavisCAUSA
- Department of Viticulture and EnologyUniversity of CaliforniaDavisCAUSA
| | - Cecilia Chi‐Ham
- Public Intellectual Property Resource for Agriculture (PIPRA)University of CaliforniaDavisCAUSA
| | - J. Clark Lagarias
- Department of Molecular and Cellular BiologyUniversity of CaliforniaDavisCAUSA
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15
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Klose C, Nagy F, Schäfer E. Thermal Reversion of Plant Phytochromes. MOLECULAR PLANT 2020; 13:386-397. [PMID: 31812690 DOI: 10.1016/j.molp.2019.12.004] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 10/21/2019] [Accepted: 12/03/2019] [Indexed: 05/18/2023]
Abstract
Phytochromes are red/far-red reversible photoreceptors essential for plant growth and development. Phytochrome signaling is mediated by the physiologically active far-red-absorbing Pfr form that can be inactivated to the red-absorbing Pr ground state by light-dependent photoconversion or by light-independent thermal reversion, also termed dark reversion. Although the term "dark reversion" is justified by historical reasons and frequently used in the literature, "thermal reversion" more appropriately describes the process of light-independent but temperature-regulated Pfr relaxation that not only occurs in darkness but also in light and is used throughout the review. Thermal reversion is a critical parameter for the light sensitivity of phytochrome-mediated responses and has been studied for decades, often resulting in contradictory findings. Thermal reversion is an intrinsic property of the phytochrome molecules but can be modulated by intra- and intermolecular interactions, as well as biochemical modifications, such as phosphorylation. In this review, we outline the research history of phytochrome thermal reversion, highlighting important predictions that have been made before knowing the molecular basis. We further summarize and discuss recent findings about the molecular mechanisms regulating phytochrome thermal reversion and its functional roles in light and temperature sensing in plants.
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Affiliation(s)
- Cornelia Klose
- Institute of Biology II, University of Freiburg, 79104 Freiburg, Germany.
| | - Ferenc Nagy
- Institute of Plant Biology, Biological Research Centre, Temesvári krt. 62, 6726 Szeged, Hungary
| | - Eberhard Schäfer
- Institute of Biology II, University of Freiburg, 79104 Freiburg, Germany
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16
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Viczián A, Ádám É, Staudt AM, Lambert D, Klement E, Romero Montepaone S, Hiltbrunner A, Casal J, Schäfer E, Nagy F, Klose C. Differential phosphorylation of the N-terminal extension regulates phytochrome B signaling. THE NEW PHYTOLOGIST 2020; 225:1635-1650. [PMID: 31596952 DOI: 10.1111/nph.16243] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 09/24/2019] [Indexed: 05/04/2023]
Abstract
Phytochrome B (phyB) is an excellent light quality and quantity sensor that can detect subtle changes in the light environment. The relative amounts of the biologically active photoreceptor (phyB Pfr) are determined by the light conditions and light independent thermal relaxation of Pfr into the inactive phyB Pr, termed thermal reversion. Little is known about the regulation of thermal reversion and how it affects plants' light sensitivity. In this study we identified several serine/threonine residues on the N-terminal extension (NTE) of Arabidopsis thaliana phyB that are differentially phosphorylated in response to light and temperature, and examined transgenic plants expressing nonphosphorylatable and phosphomimic phyB mutants. The NTE of phyB is essential for thermal stability of the Pfr form, and phosphorylation of S86 particularly enhances the thermal reversion rate of the phyB Pfr-Pr heterodimer in vivo. We demonstrate that S86 phosphorylation is especially critical for phyB signaling compared with phosphorylation of the more N-terminal residues. Interestingly, S86 phosphorylation is reduced in light, paralleled by a progressive Pfr stabilization under prolonged irradiation. By investigating other phytochromes (phyD and phyE) we provide evidence that acceleration of thermal reversion by phosphorylation represents a general mechanism for attenuating phytochrome signaling.
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Affiliation(s)
- András Viczián
- Institute of Plant Biology, Biological Research Centre, Temesvári krt. 62, H-6726, Szeged, Hungary
| | - Éva Ádám
- Institute of Plant Biology, Biological Research Centre, Temesvári krt. 62, H-6726, Szeged, Hungary
- Research Institute of Translational Biomedicine, Department of Dermatology and Allergology, University of Szeged, H-6726, Szeged, Hungary
| | - Anne-Marie Staudt
- Institute of Biology II, University of Freiburg, 79104, Freiburg, Germany
| | - Dorothee Lambert
- Institute of Biology II, University of Freiburg, 79104, Freiburg, Germany
| | - Eva Klement
- Laboratory of Proteomics Research, Biological Research Centre, Temesvári krt. 62, H-6726, Szeged, Hungary
| | - Sofia Romero Montepaone
- Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura (IFEVA), Facultad de Agronomía, Universidad de Buenos Aires and Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), C1417DSE, Buenos Aires, Argentina
| | - Andreas Hiltbrunner
- Institute of Biology II, University of Freiburg, 79104, Freiburg, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, 79104, Freiburg, Germany
| | - Jorge Casal
- Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura (IFEVA), Facultad de Agronomía, Universidad de Buenos Aires and Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), C1417DSE, Buenos Aires, Argentina
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires, CONICET, C1405BWE, Buenos Aires, Argentina
| | - Eberhard Schäfer
- Institute of Biology II, University of Freiburg, 79104, Freiburg, Germany
| | - Ferenc Nagy
- Institute of Plant Biology, Biological Research Centre, Temesvári krt. 62, H-6726, Szeged, Hungary
| | - Cornelia Klose
- Institute of Biology II, University of Freiburg, 79104, Freiburg, Germany
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17
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Deconstructing and repurposing the light-regulated interplay between Arabidopsis phytochromes and interacting factors. Commun Biol 2019; 2:448. [PMID: 31815202 PMCID: PMC6888877 DOI: 10.1038/s42003-019-0687-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2019] [Accepted: 11/07/2019] [Indexed: 01/30/2023] Open
Abstract
Phytochrome photoreceptors mediate adaptive responses of plants to red and far-red light. These responses generally entail light-regulated association between phytochromes and other proteins, among them the phytochrome-interacting factors (PIF). The interaction with Arabidopsis thaliana phytochrome B (AtPhyB) localizes to the bipartite APB motif of the A. thaliana PIFs (AtPIF). To address a dearth of quantitative interaction data, we construct and analyze numerous AtPIF3/6 variants. Red-light-activated binding is predominantly mediated by the APB N-terminus, whereas the C-terminus modulates binding and underlies the differential affinity of AtPIF3 and AtPIF6. We identify AtPIF variants of reduced size, monomeric or homodimeric state, and with AtPhyB affinities between 10 and 700 nM. Optogenetically deployed in mammalian cells, the AtPIF variants drive light-regulated gene expression and membrane recruitment, in certain cases reducing basal activity and enhancing regulatory response. Moreover, our results provide hitherto unavailable quantitative insight into the AtPhyB:AtPIF interaction underpinning vital light-dependent responses in plants. David Golonka et al. report the epitopes in Arabidopsis phytochrome-interacting factors (PIF) that underlie light-dependent interactions with phytochrome B. They identify compact PIF variants that enable light-activated gene expression and membrane recruitment with reduced basal activity and enhanced regulatory response.
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18
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Oide M, Hikima T, Oroguchi T, Kato T, Yamaguchi Y, Yoshihara S, Yamamoto M, Nakasako M, Okajima K. Molecular shape under far-red light and red light-induced association of Arabidopsis phytochrome B. FEBS J 2019; 287:1612-1625. [PMID: 31621187 DOI: 10.1111/febs.15095] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Revised: 09/17/2019] [Accepted: 10/14/2019] [Indexed: 11/29/2022]
Abstract
Phytochrome B (phyB) is a plant photoreceptor protein that regulates various photomorphogenic responses to optimize plant growth and development. PhyB exists in two photoconvertible forms: a red light-absorbing (Pr) and a far-red light-absorbing (Pfr) form. Therefore, to understand the mechanism of phototransformation, the structural characterization of full-length phyB in these two forms is necessary. Here, we report the molecular structure of Arabidopsis thaliana phyB in Pr form and the molecular properties of the Pfr form determined by small-angle X-ray scattering coupled with size-exclusion chromatography. In solution, the Pr form associated as a dimer with a radius of gyration of 50 Å. The molecular shape was a crossed shape, in which the orientation of the photosensory modules differed from that in the crystal structure of dimeric photosensory module. PhyB exhibited structural reversibility in the Pfr-to-Pr phototransformation and thermal reversion from Pfr to Pr in the dark. In addition, Pfr only exhibited nonspecific association, which distinguished molecular properties of Pfr form from those of the inactive Pr form.
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Affiliation(s)
- Mao Oide
- Department of Physics, Faculty of Science and Technology, Keio University, Yokohama, Japan.,RIKEN SPring-8 Center, Sayo-gun, Japan
| | | | - Tomotaka Oroguchi
- Department of Physics, Faculty of Science and Technology, Keio University, Yokohama, Japan.,RIKEN SPring-8 Center, Sayo-gun, Japan
| | - Takayuki Kato
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
| | - Yuhki Yamaguchi
- Department of Physics, Faculty of Science and Technology, Keio University, Yokohama, Japan.,RIKEN SPring-8 Center, Sayo-gun, Japan
| | - Shizue Yoshihara
- Department of Biological Science, Osaka Prefecture University, Sakai, Japan
| | | | - Masayoshi Nakasako
- Department of Physics, Faculty of Science and Technology, Keio University, Yokohama, Japan.,RIKEN SPring-8 Center, Sayo-gun, Japan
| | - Koji Okajima
- Department of Physics, Faculty of Science and Technology, Keio University, Yokohama, Japan.,RIKEN SPring-8 Center, Sayo-gun, Japan
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19
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Hoang QTN, Han YJ, Kim JI. Plant Phytochromes and their Phosphorylation. Int J Mol Sci 2019; 20:ijms20143450. [PMID: 31337079 PMCID: PMC6678601 DOI: 10.3390/ijms20143450] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 07/10/2019] [Accepted: 07/12/2019] [Indexed: 12/12/2022] Open
Abstract
Extensive research over several decades in plant light signaling mediated by photoreceptors has identified the molecular mechanisms for how phytochromes regulate photomorphogenic development, which includes degradation of phytochrome-interacting factors (PIFs) and inactivation of COP1-SPA complexes with the accumulation of master transcription factors for photomorphogenesis, such as HY5. However, the initial biochemical mechanism for the function of phytochromes has not been fully elucidated. Plant phytochromes have long been known as phosphoproteins, and a few protein phosphatases that directly interact with and dephosphorylate phytochromes have been identified. However, there is no report thus far of a protein kinase that acts on phytochromes. On the other hand, plant phytochromes have been suggested as autophosphorylating serine/threonine protein kinases, proposing that the kinase activity might be important for their functions. Indeed, the autophosphorylation of phytochromes has been reported to play an important role in the regulation of plant light signaling. More recently, evidence that phytochromes function as protein kinases in plant light signaling has been provided using phytochrome mutants displaying reduced kinase activities. In this review, we highlight recent advances in the reversible phosphorylation of phytochromes and their functions as protein kinases in plant light signaling.
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Affiliation(s)
- Quyen T N Hoang
- Department of Biotechnology and Kumho Life Science Laboratory, Chonnam National University, Gwangju 61186, Korea
| | - Yun-Jeong Han
- Department of Biotechnology and Kumho Life Science Laboratory, Chonnam National University, Gwangju 61186, Korea
| | - Jeong-Il Kim
- Department of Biotechnology and Kumho Life Science Laboratory, Chonnam National University, Gwangju 61186, Korea.
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20
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Assafa TE, Anders K, Linne U, Essen LO, Bordignon E. Light-Driven Domain Mechanics of a Minimal Phytochrome Photosensory Module Studied by EPR. Structure 2018; 26:1534-1545.e4. [DOI: 10.1016/j.str.2018.08.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 05/30/2018] [Accepted: 08/07/2018] [Indexed: 12/15/2022]
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21
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Losi A, Bonomi HR, Michael N, Tang K, Zhao KH. Time-Resolved Energetics of Photoprocesses in Prokaryotic Phytochrome-Related Photoreceptors. Photochem Photobiol 2018; 93:733-740. [PMID: 28500712 DOI: 10.1111/php.12728] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2016] [Accepted: 12/07/2016] [Indexed: 11/28/2022]
Abstract
Time-resolved photoacoustics (PA) is uniquely able to explore the energy landscape of photoactive proteins and concomitantly detects light-induced volumetric changes (ΔV) accompanying the formation and decay of transient species in a time window between ca. 20 ns and 5 μs. Here, we report PA measurements on diverse photochromic bilin-binding photoreceptors of prokaryotic origin: (1) the chromophore-binding GAF3 domain of the red (R)/green (G) switching cyanobacteriochrome 1393 (Slr1393g3) from Synechocystis; (2) the red/far red (R/FR) Synechocystis Cph1 phytochrome; (3) full-length and truncated constructs of Xanthomonas campestris bacteriophytochrome (XccBphP), absorbing up to the NIR spectral region. In almost all cases, photoisomerization results in a large fraction of energy dissipated as heat (up to 90%) on the sub-ns scale, reflecting the low photoisomerization quantum yield (<0.2). This "prompt" step is accompanied by a positive ΔV1 = 5-12.5 mL mol-1 . Formation of the first intermediate is the sole process accessible to PA, with the notable exception of Slr1393g3-G for which ΔV1 = +4.5 mL mol-1 is followed by a time-resolved, energy-conserving contraction ΔV2 = -11.4 mL mol-1 , τ2 = 180 ns at 2.4°C. This peculiarity is possibly due to a larger solvent occupancy of the chromophore cavity for Slr1393g3-G.
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Affiliation(s)
- Aba Losi
- Department of Physics and Earth Science, University of Parma, Parma, Italy
| | - Hernán R Bonomi
- Immunology and Molecular Microbiology Laboratory, Fundación Instituto Leloir, Buenos Aires, Argentina
| | - Norbert Michael
- Institut für Chemie, Technische Universität Berlin, Berlin, Germany
| | - Kun Tang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,Max Planck Institute for Chemical Energy Conversion, Mülheim an der Ruhr, Germany
| | - Kai-Hong Zhao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
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22
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Song C, Mroginski MA, Lang C, Kopycki J, Gärtner W, Matysik J, Hughes J. 3D Structures of Plant Phytochrome A as Pr and Pfr From Solid-State NMR: Implications for Molecular Function. FRONTIERS IN PLANT SCIENCE 2018; 9:498. [PMID: 29740459 PMCID: PMC5928327 DOI: 10.3389/fpls.2018.00498] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 04/03/2018] [Indexed: 05/25/2023]
Abstract
We present structural information for oat phyA3 in the far-red-light-absorbing (Pfr) signaling state, to our knowledge the first three-dimensional (3D) information for a plant phytochrome as Pfr. Solid-state magic-angle spinning (MAS) NMR was used to detect interatomic contacts in the complete photosensory module [residues 1-595, including the NTE (N-terminal extension), PAS (Per/Arnt/Sim), GAF (cGMP phosphodiesterase/adenylyl cyclase/FhlA) and PHY (phytochrome-specific) domains but with the C-terminal PAS repeat and transmitter-like module deleted] auto-assembled in vitro with 13C- and 15N-labeled phycocyanobilin (PCB) chromophore. Thereafter, quantum mechanics/molecular mechanics (QM/MM) enabled us to refine 3D structural models constrained by the NMR data. We provide definitive atomic assignments for all carbon and nitrogen atoms of the chromophore, showing the Pfr chromophore geometry to be periplanar ZZEssa with the D -ring in a β-facial disposition incompatible with many earlier notions regarding photoconversion yet supporting circular dichroism (CD) data. The Y268 side chain is shifted radically relative to published Pfr crystal structures in order to accommodate the β-facial ring D . Our findings support a photoconversion sequence beginning with Pr photoactivation via an anticlockwise D -ring Za→Ea photoflip followed by significant shifts at the coupling of ring A to the protein, a B -ring propionate partner swap from R317 to R287, changes in the C -ring propionate hydrogen-bonding network, breakage of the D272-R552 salt bridge accompanied by sheet-to-helix refolding of the tongue region stabilized by Y326-D272-S554 hydrogen bonding, and binding of the NTE to the hydrophobic side of ring A . We discuss phyA photoconversion, including the possible roles of mesoscopic phase transitions and protonation dynamics in the chromophore pocket. We also discuss possible associations between structural changes and translocation and signaling processes within the cell.
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Affiliation(s)
- Chen Song
- Institut für Analytische Chemie, Universität Leipzig, Leipzig, Germany
- Leids Instituut voor Chemisch Onderzoek, Universiteit Leiden, Leiden, Netherlands
| | | | - Christina Lang
- Institut für Pflanzenphysiologie, Justus-Liebig-Universität, Giessen, Germany
| | - Jakub Kopycki
- Institut für Pflanzenphysiologie, Justus-Liebig-Universität, Giessen, Germany
| | - Wolfgang Gärtner
- Institut für Analytische Chemie, Universität Leipzig, Leipzig, Germany
| | - Jörg Matysik
- Institut für Analytische Chemie, Universität Leipzig, Leipzig, Germany
| | - Jon Hughes
- Institut für Pflanzenphysiologie, Justus-Liebig-Universität, Giessen, Germany
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23
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Lenngren N, Edlund P, Takala H, Stucki-Buchli B, Rumfeldt J, Peshev I, Häkkänen H, Westenhoff S, Ihalainen JA. Coordination of the biliverdin D-ring in bacteriophytochromes. Phys Chem Chem Phys 2018; 20:18216-18225. [DOI: 10.1039/c8cp01696h] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Vibrational spectroscopy and crystallography experiments provide a basis for understanding the isomerization reaction in phytochrome proteins.
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Affiliation(s)
- Nils Lenngren
- Department of Biological and Environmental Sciences
- Nanoscience Center
- University of Jyväskylä
- Finland
| | - Petra Edlund
- Department of Chemistry and Molecular Biology
- Biochemistry and Biophysics
- University of Gothenburg
- SE-40530 Gothenburg
- Sweden
| | - Heikki Takala
- Department of Biological and Environmental Sciences
- Nanoscience Center
- University of Jyväskylä
- Finland
- University of Helsinki
| | - Brigitte Stucki-Buchli
- Department of Biological and Environmental Sciences
- Nanoscience Center
- University of Jyväskylä
- Finland
| | - Jessica Rumfeldt
- Department of Biological and Environmental Sciences
- Nanoscience Center
- University of Jyväskylä
- Finland
| | - Ivan Peshev
- Department of Biological and Environmental Sciences
- Nanoscience Center
- University of Jyväskylä
- Finland
| | - Heikki Häkkänen
- Department of Biological and Environmental Sciences
- Nanoscience Center
- University of Jyväskylä
- Finland
| | - Sebastian Westenhoff
- Department of Chemistry and Molecular Biology
- Biochemistry and Biophysics
- University of Gothenburg
- SE-40530 Gothenburg
- Sweden
| | - Janne A. Ihalainen
- Department of Biological and Environmental Sciences
- Nanoscience Center
- University of Jyväskylä
- Finland
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24
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Burgie ES, Bussell AN, Lye SH, Wang T, Hu W, McLoughlin KE, Weber EL, Li H, Vierstra RD. Photosensing and Thermosensing by Phytochrome B Require Both Proximal and Distal Allosteric Features within the Dimeric Photoreceptor. Sci Rep 2017; 7:13648. [PMID: 29057954 PMCID: PMC5651913 DOI: 10.1038/s41598-017-14037-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 09/21/2017] [Indexed: 11/12/2022] Open
Abstract
Phytochromes (Phys) encompass a diverse collection of bilin-containing photoreceptors that help plants and microorganisms perceive light through photointerconversion between red light (Pr) and far-red light (Pfr)-absorbing states. In addition, Pfr reverts thermally back to Pr via a highly enthalpic process that enables temperature sensation in plants and possibly other organisms. Through domain analysis of the Arabidopsis PhyB isoform assembled recombinantly, coupled with measurements of solution size, photoconversion, and thermal reversion, we identified both proximal and distal features that influence all three metrics. Included are the downstream C-terminal histidine kinase-related domain known to promote dimerization and a conserved patch just upstream of an N-terminal Period/Arnt/Sim (PAS) domain, which upon removal dramatically accelerates thermal reversion. We also discovered that the nature of the bilin strongly influences Pfr stability. Whereas incorporation of the native bilin phytochromobilin into PhyB confers robust Pfr → Pr thermal reversion, that assembled with the cyanobacterial version phycocyanobilin, often used for optogenetics, has a dramatically stabilized Pfr state. Taken together, we conclude that Pfr acquisition and stability are impacted by a collection of opposing allosteric features that inhibit or promote photoconversion and reversion of Pfr back to Pr, thus allowing Phys to dynamically measure light, temperature, and possibly time.
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Affiliation(s)
- E Sethe Burgie
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, 63130, USA.,Department of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | - Adam N Bussell
- Department of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | - Shu-Hui Lye
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, 63130, USA.,Department of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | - Tong Wang
- Department of Biology, Brookhaven National Laboratory, Upton, New York, 11973, USA.,CUNY Advanced Science Research Center, The City University of New York, New York, New York, 10031, USA
| | - Weiming Hu
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, 63130, USA
| | - Katrice E McLoughlin
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, 63130, USA
| | - Erin L Weber
- Department of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | - Huilin Li
- Department of Biology, Brookhaven National Laboratory, Upton, New York, 11973, USA.,Van Andel Research Institute, Grand Rapids, Michigan, 49503, USA
| | - Richard D Vierstra
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, 63130, USA. .,Department of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA.
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25
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Velázquez Escobar F, Buhrke D, Fernandez Lopez M, Shenkutie SM, von Horsten S, Essen LO, Hughes J, Hildebrandt P. Structural communication between the chromophore-binding pocket and the N-terminal extension in plant phytochrome phyB. FEBS Lett 2017; 591:1258-1265. [DOI: 10.1002/1873-3468.12642] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2017] [Revised: 03/25/2017] [Accepted: 03/28/2017] [Indexed: 12/19/2022]
Affiliation(s)
| | - David Buhrke
- Institut für Chemie; Technische Universität Berlin; Germany
| | | | | | - Silke von Horsten
- Fachbereich Chemie, Strukturbiochemie; Philipps-Universität Marburg; Marburg Germany
| | - Lars-Oliver Essen
- Fachbereich Chemie, Strukturbiochemie; Philipps-Universität Marburg; Marburg Germany
- LOEWE Center for Synthetic Microbiology; Philipps-Universität; Marburg Germany
| | - Jon Hughes
- Plant Physiology; Justus-Liebig University Gießen; Giessen Germany
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