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Qu GP, Jiang B, Lin C. The dual-action mechanism of Arabidopsis cryptochromes. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024; 66:883-896. [PMID: 37902426 DOI: 10.1111/jipb.13578] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 10/23/2023] [Accepted: 10/24/2023] [Indexed: 10/31/2023]
Abstract
Photoreceptor cryptochromes (CRYs) mediate blue-light regulation of plant growth and development. It has been reported that Arabidopsis CRY1and CRY2 function by physically interacting with at least 84 proteins, including transcription factors or co-factors, chromatin regulators, splicing factors, messenger RNA methyltransferases, DNA repair proteins, E3 ubiquitin ligases, protein kinases and so on. Of these 84 proteins, 47 have been reported to exhibit altered binding affinity to CRYs in response to blue light, and 41 have been shown to exhibit condensation to CRY photobodies. The blue light-regulated composition or condensation of CRY complexes results in changes of gene expression and developmental programs. In this mini-review, we analyzed recent studies of the photoregulatory mechanisms of Arabidopsis CRY complexes and proposed the dual mechanisms of action, including the "Lock-and-Key" and the "Liquid-Liquid Phase Separation (LLPS)" mechanisms. The dual CRY action mechanisms explain, at least partially, the structural diversity of CRY-interacting proteins and the functional diversity of the CRY photoreceptors.
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Affiliation(s)
- Gao-Ping Qu
- Basic Forestry and Plant Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Bochen Jiang
- Basic Forestry and Plant Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Department of Chemistry, Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, 60637, USA
| | - Chentao Lin
- Basic Forestry and Plant Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
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2
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Lee J, Yang JH, Weber APM, Bhattacharya D, Kim WY, Yoon HS. Diurnal Rhythms in the Red Seaweed Gracilariopsis chorda are Characterized by Unique Regulatory Networks of Carbon Metabolism. Mol Biol Evol 2024; 41:msae012. [PMID: 38267085 PMCID: PMC10853006 DOI: 10.1093/molbev/msae012] [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: 09/09/2023] [Revised: 01/01/2024] [Accepted: 01/08/2024] [Indexed: 01/26/2024] Open
Abstract
Cellular and physiological cycles are driven by endogenous pacemakers, the diurnal and circadian rhythms. Key functions such as cell cycle progression and cellular metabolism are under rhythmic regulation, thereby maintaining physiological homeostasis. The photoreceptors phytochrome and cryptochrome, in response to light cues, are central input pathways for physiological cycles in most photosynthetic organisms. However, among Archaeplastida, red algae are the only taxa that lack phytochromes. Current knowledge about oscillatory rhythms is primarily derived from model species such as Arabidopsis thaliana and Chlamydomonas reinhardtii in the Viridiplantae, whereas little is known about these processes in other clades of the Archaeplastida, such as the red algae (Rhodophyta). We used genome-wide expression profiling of the red seaweed Gracilariopsis chorda and identified 3,098 rhythmic genes. Here, we characterized possible cryptochrome-based regulation and photosynthetic/cytosolic carbon metabolism in this species. We found a large family of cryptochrome genes in G. chorda that display rhythmic expression over the diurnal cycle and may compensate for the lack of phytochromes in this species. The input pathway gates regulatory networks of carbon metabolism which results in a compact and efficient energy metabolism during daylight hours. The system in G. chorda is distinct from energy metabolism in most plants, which activates in the dark. The green lineage, in particular, land plants, balance water loss and CO2 capture in terrestrial environments. In contrast, red seaweeds maintain a reduced set of photoreceptors and a compact cytosolic carbon metabolism to thrive in the harsh abiotic conditions typical of intertidal zones.
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Affiliation(s)
- JunMo Lee
- Department of Oceanography, Kyungpook National University, Daegu 41566, Korea
- Kyungpook Institute of Oceanography, Kyungpook National University, Daegu 41566, Korea
| | - Ji Hyun Yang
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Korea
| | - Andreas P M Weber
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Science (CEPLAS), Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Debashish Bhattacharya
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ 08901, USA
| | - Woe-Yeon Kim
- Division of Applied Life Science (BK21 four), Research Institute of Life Science, Gyeongsang National University, Jinju 52828, Korea
| | - Hwan Su Yoon
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Korea
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3
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Kong Y, Zheng Y. Magic Blue Light: A Versatile Mediator of Plant Elongation. PLANTS (BASEL, SWITZERLAND) 2023; 13:115. [PMID: 38202422 PMCID: PMC10780743 DOI: 10.3390/plants13010115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 12/17/2023] [Accepted: 12/28/2023] [Indexed: 01/12/2024]
Abstract
Blue light plays an important role in regulating plant elongation. However, due to the limitations of older lighting technologies, the responses of plants to pure blue light have not been fully studied, and some of our understandings of the functions of blue light in the literature need to be revisited. This review consolidates and analyzes the diverse findings from previous studies on blue-light-mediated plant elongation. By synthesizing the contrasting results, we uncover the underlying mechanisms and explanations proposed in recent research. Moreover, we delve into the exploration of blue light-emitting diodes (LEDs) as a tool for manipulating plant elongation in controlled-environment plant production, highlighting the latest advancements in this area. Finally, we acknowledge the challenges faced and outline future directions for research in this promising field. This review provides valuable insights into the pivotal role of blue light in plant growth and offers a foundation for further investigations to optimize plant elongation using blue light technology.
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Affiliation(s)
| | - Youbin Zheng
- School of Environmental Sciences, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1, Canada;
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PIF7 is a master regulator of thermomorphogenesis in shade. Nat Commun 2022; 13:4942. [PMID: 36038577 PMCID: PMC9424238 DOI: 10.1038/s41467-022-32585-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 08/06/2022] [Indexed: 11/26/2022] Open
Abstract
The size of plant organs is highly responsive to environmental conditions. The plant’s embryonic stem, or hypocotyl, displays phenotypic plasticity, in response to light and temperature. The hypocotyl of shade avoiding species elongates to outcompete neighboring plants and secure access to sunlight. Similar elongation occurs in high temperature. However, it is poorly understood how environmental light and temperature cues interact to effect plant growth. We found that shade combined with warm temperature produces a synergistic hypocotyl growth response that dependent on PHYTOCHROME-INTERACTING FACTOR 7 (PIF7) and auxin. This unique but agriculturally relevant scenario was almost totally independent on PIF4 activity. We show that warm temperature is sufficient to promote PIF7 DNA binding but not transcriptional activation and we demonstrate that additional, unknown factor/s must be working downstream of the phyB-PIF-auxin module. Our findings will improve the predictions of how plants will respond to increased ambient temperatures when grown at high density. Plant hypocotyl elongation response to light and temperature. Here the authors show that shade combined with warm temperature synergistically enhances the hypocotyl growth response via the PIF7 transcription factor, auxin, and as yet unknown factor.
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5
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Emerging molecular technologies for light-mediated modulation of pancreatic beta-cell function. Mol Metab 2022; 64:101552. [PMID: 35863638 PMCID: PMC9352964 DOI: 10.1016/j.molmet.2022.101552] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Revised: 07/13/2022] [Accepted: 07/13/2022] [Indexed: 11/22/2022] Open
Abstract
Background Optogenetic modalities as well as optochemical and photopharmacological strategies, collectively termed optical methods, have revolutionized the control of cellular functions via light with great spatiotemporal precision. In comparison to the major advances in the photomodulation of signaling activities noted in neuroscience, similar applications to endocrine cells of the pancreas, particularly insulin-producing β-cells, have been limited. The availability of tools allowing light-mediated changes in the trafficking of ions such as K+ and Ca2+ and signaling intermediates such as cyclic adenosine monophosphate (cAMP), renders β-cells and their glucose-stimulated insulin secretion (GSIS) amenable to optoengineering for drug-free control of blood sugar. Scope of review The molecular circuit of the GSIS in β-cells is described with emphasis on intermediates which are targetable for optical intervention. Various pharmacological agents modifying the release of insulin are reviewed along with their documented side effects. These are contrasted with optical approaches, which have already been employed for engineering β-cell function or are considered for future such applications. Principal obstacles are also discussed as the implementation of optogenetics is pondered for tissue engineering and biology applications of the pancreas. Major Conclusions Notable advances in optogenetic, optochemical and photopharmacological tools are rendering feasible the smart engineering of pancreatic cells and tissues with light-regulated function paving the way for novel solutions for addressing pancreatic pathologies including diabetes.
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Marie TRJG, Leonardos ED, Lanoue J, Hao X, Micallef BJ, Grodzinski B. A Perspective Emphasizing Circadian Rhythm Entrainment to Ensure Sustainable Crop Production in Controlled Environment Agriculture: Dynamic Use of LED Cues. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2022. [DOI: 10.3389/fsufs.2022.856162] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
World-wide, sustainable crop production is increasingly dependent on the protection of crops from adverse local climate conditions by using controlled environment agriculture (CEA) facilities. Today's greenhouses and plant factories are becoming very technologically advanced. Important breakthroughs in our understanding of the deployment of affordable artificial lighting systems that can supplement and even replace solar radiation is the subject of this perspective article. The key to improving sustainable CEA is to synchronize those environmental cues that best entrain the natural circadian rhythm of the crop. Patterns of circadian rhythms reflect the balance of daily metabolic cycles and phenological stages of development that integrate and anticipate environmental changes for all complex organisms. Within the last decade, our understanding of the use of light-emitting diodes (LEDs) as spectrally tunable tools for stimulating plant responses has expanded rapidly. This perspective proposes that extending the photoperiod in CEA is an economically sustainable goal to for year-round productivity of tomato, using dynamic LED shifts that entrain the circadian rhythm. When the photoperiod is extended too far, tomato experiences injury. To avoid yield reduction, we look to nature for clues, and how circadian rhythms evolved in general to long-photoperiods during the summer in high-latitudes. It follows that circadian rhythm traits are good targets for breeders to select new tomato cultivars suitable for CEA. Circadian rhythm entrainment, using dynamic LED cues, can be tailored to any latitude-of-origin crop, and thus expands the strategies ensuring sustainable food security including healthy diets locally in any region of the world.
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Yao D, Arguez MA, He P, Bent AF, Song J. Coordinated regulation of plant immunity by poly(ADP-ribosyl)ation and K63-linked ubiquitination. MOLECULAR PLANT 2021; 14:2088-2103. [PMID: 34418551 PMCID: PMC9070964 DOI: 10.1016/j.molp.2021.08.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 05/24/2021] [Accepted: 08/15/2021] [Indexed: 05/02/2023]
Abstract
Poly(ADP-ribosyl)ation (PARylation) is a posttranslational modification reversibly catalyzed by poly(ADP-ribose) polymerases (PARPs) and poly(ADP-ribose) glycohydrolases (PARGs) and plays a key role in multiple cellular processes. The molecular mechanisms by which PARylation regulates innate immunity remain largely unknown in eukaryotes. Here we show that Arabidopsis UBC13A and UBC13B, the major drivers of lysine 63 (K63)-linked polyubiquitination, directly interact with PARPs/PARGs. Activation of pathogen-associated molecular pattern (PAMP)-triggered immunity promotes these interactions and enhances PARylation of UBC13. Both parp1 parp2 and ubc13a ubc13b mutants are compromised in immune responses with increased accumulation of total pathogenesis-related (PR) proteins but decreased accumulation of secreted PR proteins. Protein disulfide-isomerases (PDIs), essential components of endoplasmic reticulum quality control (ERQC) that ensure proper folding and maturation of proteins destined for secretion, complex with PARPs/PARGs and are PARylated upon PAMP perception. Significantly, PARylation of UBC13 regulates K63-linked ubiquitination of PDIs, which may further promote their disulfide isomerase activities for correct protein folding and subsequent secretion. Taken together, these results indicate that plant immunity is coordinately regulated by PARylation and K63-linked ubiquitination.
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Affiliation(s)
- Dongsheng Yao
- Texas A&M AgriLife Research Center at Dallas, Texas A&M University System, Dallas, TX 75252, USA
| | - Marcus A Arguez
- Texas A&M AgriLife Research Center at Dallas, Texas A&M University System, Dallas, TX 75252, USA
| | - Ping He
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Andrew F Bent
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Junqi Song
- Texas A&M AgriLife Research Center at Dallas, Texas A&M University System, Dallas, TX 75252, USA; Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX 77843, USA.
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A LexA-based yeast two-hybrid system for studying light-switchable interactions of phytochromes with their interacting partners. ABIOTECH 2021; 2:105-116. [PMID: 36304755 PMCID: PMC9590525 DOI: 10.1007/s42994-021-00034-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Accepted: 02/01/2021] [Indexed: 12/26/2022]
Abstract
Phytochromes are a family of photoreceptors in plants that perceive the red (R) and far-red (FR) components of their light environment. Phytochromes exist in vivo in two forms, the inactive Pr form and the active Pfr form, that are interconvertible by treatments with R or FR light. It is believed that phytochromes transduce light signals by interacting with their signaling partners. A GAL4-based light-switchable yeast two-hybrid (Y2H) system was developed two decades ago and has been successfully employed in many studies to determine phytochrome interactions with their signaling components. However, several pairs of interactions between phytochromes and their interactors, such as the phyA-COP1 and phyA-TZP interactions, were demonstrated by other assay systems but were not detected by this GAL4 Y2H system. Here, we report a modified LexA Y2H system, in which the LexA DNA-binding domain is fused to the C-terminus of a phytochrome protein. The conformational changes of phytochromes in response to R and FR light are achieved in yeast cells by exogenously supplying phycocyanobilin (PCB) extracted from Spirulina. The well-defined interaction pairs, including phyA-FHY1 and phyB-PIFs, are well reproducible in this system. Moreover, we show that our system is successful in detecting the phyA-COP1 and phyA-TZP interactions. Together, our study provides an alternative Y2H system that is highly sensitive and reproducible for detecting light-switchable interactions of phytochromes with their interacting partners. Supplementary Information The online version contains supplementary material available at 10.1007/s42994-021-00034-5.
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9
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Seong J, Lin MZ. Optobiochemistry: Genetically Encoded Control of Protein Activity by Light. Annu Rev Biochem 2021; 90:475-501. [PMID: 33781076 DOI: 10.1146/annurev-biochem-072420-112431] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Optobiochemical control of protein activities allows the investigation of protein functions in living cells with high spatiotemporal resolution. Over the last two decades, numerous natural photosensory domains have been characterized and synthetic domains engineered and assembled into photoregulatory systems to control protein function with light. Here, we review the field of optobiochemistry, categorizing photosensory domains by chromophore, describing photoregulatory systems by mechanism of action, and discussing protein classes frequently investigated using optical methods. We also present examples of how spatial or temporal control of proteins in living cells has provided new insights not possible with traditional biochemical or cell biological techniques.
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Affiliation(s)
- Jihye Seong
- Brain Science Institute, Korea Institute of Science and Technology (KIST), Seoul 02792, South Korea;
| | - Michael Z Lin
- Department of Neurobiology, Stanford University, Stanford, California 94305, USA; .,Department of Bioengineering, Stanford University, Stanford, California 94305, USA.,Department of Chemical and Systems Biology, Stanford University, Stanford, California 94305, USA
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10
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Yamada M, Nagasaki SC, Suzuki Y, Hirano Y, Imayoshi I. Optimization of Light-Inducible Gal4/UAS Gene Expression System in Mammalian Cells. iScience 2020; 23:101506. [PMID: 32919371 PMCID: PMC7491154 DOI: 10.1016/j.isci.2020.101506] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Revised: 01/06/2020] [Accepted: 08/24/2020] [Indexed: 12/23/2022] Open
Abstract
Light-inducible gene expression systems represent powerful methods for studying the functional roles of dynamic gene expression. Here, we developed an optimized light-inducible Gal4/UAS gene expression system for mammalian cells. We designed photoactivatable (PA)-Gal4 transcriptional activators based on the concept of split transcription factors, in which light-dependent interactions between Cry2-CIB1 PA-protein interaction modules can reconstitute a split Gal4 DNA-binding domain and p65 transcription activation domain. We developed a set of PA-Gal4 transcriptional activators (PA-Gal4cc), which differ in terms of induced gene expression levels following pulsed or prolonged light exposure, and which have different activation/deactivation kinetics. These systems offer optogenetic tools for the precise manipulation of gene expression at fine spatiotemporal resolution in mammalian cells.
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Affiliation(s)
- Mayumi Yamada
- Research Center for Dynamic Living Systems, Graduate School of Biostudies, Kyoto University, Kyoto 606-8501, Japan
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto 606-8507, Japan
- World Premier International Research Initiative–Institute for Integrated Cell-Material Sciences, Kyoto University, Kyoto 606-8501, Japan
- Medical Innovation Center/SK Project, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
| | - Shinji C. Nagasaki
- Research Center for Dynamic Living Systems, Graduate School of Biostudies, Kyoto University, Kyoto 606-8501, Japan
| | - Yusuke Suzuki
- Research Center for Dynamic Living Systems, Graduate School of Biostudies, Kyoto University, Kyoto 606-8501, Japan
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto 606-8507, Japan
- Medical Innovation Center/SK Project, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
| | - Yukinori Hirano
- Medical Innovation Center/SK Project, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
- The Hakubi Center, Kyoto University, Kyoto 606-8302, Japan
| | - Itaru Imayoshi
- Research Center for Dynamic Living Systems, Graduate School of Biostudies, Kyoto University, Kyoto 606-8501, Japan
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto 606-8507, Japan
- World Premier International Research Initiative–Institute for Integrated Cell-Material Sciences, Kyoto University, Kyoto 606-8501, Japan
- The Hakubi Center, Kyoto University, Kyoto 606-8302, Japan
- Japan Science and Technology Agency, Precursory Research for Embryonic Science and Technology, Saitama 332-0012, Japan
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Ponnu J. Molecular mechanisms suppressing COP1/SPA E3 ubiquitin ligase activity in blue light. PHYSIOLOGIA PLANTARUM 2020; 169:418-429. [PMID: 32248530 DOI: 10.1111/ppl.13103] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Revised: 03/19/2020] [Accepted: 03/27/2020] [Indexed: 05/23/2023]
Abstract
Arabidopsis CONSTITUTIVE PHOTOMORPHOGENIC1/SUPPRESSOR OF PHYA-105 (COP1/SPA) is an E3 ubiquitin ligase complex that prevents photomorphogenesis in darkness by ubiquitinating and subsequently degrading light-responsive transcription factors. Upon light perception, photoreceptors directly interact with the COP1/SPA complex to suppress its activity. In blue light (450-500 nm of visible spectrum), COP1/SPA activity is inhibited by the cryptochrome photoreceptors (CRY1 and CRY2), FKF1 from the ZEITLUPE family as well as phytochrome A. Together, these photoreceptors regulate vital aspects of plant growth and development from seedling stage to the induction of flowering. This review presents and discusses the recent advances in blue light-mediated suppression of COP1/SPA activity.
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Affiliation(s)
- Jathish Ponnu
- Botanical Institute and Cluster of Excellence on Plant Sciences (CEPLAS), Biocenter, University of Cologne, 50674 Cologne, Germany
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12
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Battle MW, Jones MA. Cryptochromes integrate green light signals into the circadian system. PLANT, CELL & ENVIRONMENT 2020; 43:16-27. [PMID: 31410859 PMCID: PMC6973147 DOI: 10.1111/pce.13643] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 08/06/2019] [Accepted: 08/07/2019] [Indexed: 05/04/2023]
Abstract
Plants are acutely sensitive of their light environment, adapting their growth habit and prioritizing developmental decisions to maximize fecundity. In addition to providing an energy source and directional information, light quality also contributes to entrainment of the circadian system, an endogenous timing mechanism that integrates endogenous and environmental signalling cues to promote growth. Whereas plants' perception of red and blue portions of the spectrum are well defined, green light sensitivity remains enigmatic. In this study, we show that low fluence rates of green light are sufficient to entrain and maintain circadian rhythms in Arabidopsis and that cryptochromes contribute to this response. Importantly, green light responses are distinguishable from low blue light-induced phenotypes. These data suggest a distinct signalling mechanism enables entrainment of the circadian system in green light-enriched environments, such as those found in undergrowth and in densely planted monoculture.
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Affiliation(s)
| | - Matthew Alan Jones
- School of Life SciencesUniversity of EssexColchesterCO4 3SQUK
- Institute of Molecular, Cell and Systems BiologyUniversity of GlasgowGlasgowG12 8QQUK
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Michmizos D, Hilioti Z. A roadmap towards a functional paradigm for learning & memory in plants. JOURNAL OF PLANT PHYSIOLOGY 2019; 232:209-215. [PMID: 30537608 DOI: 10.1016/j.jplph.2018.11.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2018] [Revised: 10/15/2018] [Accepted: 11/02/2018] [Indexed: 06/09/2023]
Abstract
In plants, the acquisition, processing and storage of empirical information can result in the modification of their behavior according to the nature of the stimulus, and yet this area of research remained relatively understudied until recently. As the body of evidence supporting the inclusion of plants among the higher organisms demonstrating the adaptations to accomplish these tasks keeps increasing, the resistance by traditional botanists and agricultural scientists, who were at first cautious in allowing the application of animal models onto plant physiology and development, subsides. However, the debate retains much of its heat, a good part of it originating from the controversial use of nervous system terms to describe plant processes. By focusing on the latest findings on the cellular and molecular mechanisms underlying the well established processes of Learning and Memory, recognizing what has been accomplished and what remains to be explored, and without seeking to bootstrap neuronal characteristics where none are to be found, a roadmap guiding towards a comprehensive paradigm for Learning and Memory in plants begins to emerge. Meanwhile the applications of the new field of Plant Gnosophysiology look as promising as ever.
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Affiliation(s)
- Dimitrios Michmizos
- Dept. of Agriculture, Crop Production & Rural Environment, University of Thessaly, Fytokos st, Volos, Magnesia, 384 46, Greece.
| | - Zoe Hilioti
- Institute of Applied Biosciences, Center for Research & Technology (CERTH), Thessaloniki, Greece
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14
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Paik I, Huq E. Rapid Examination of Phytochrome-Phytochrome Interacting Factor (PIF) Interaction by In Vitro Coimmunoprecipitation Assay. Methods Mol Biol 2019; 2026:21-28. [PMID: 31317400 DOI: 10.1007/978-1-4939-9612-4_2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Phytochromes are red/far-red light receptors that perceive and transduce light signals to regulate various physiological responses. A large number of phytochrome interacting proteins have been identified using genetic and biochemical approaches. A direct interaction between phytochrome and its interacting proteins, therefore, defines one of the critical steps to initiate light signaling cascades in plants. Thus it is important to thoroughly examine the light-dependent interaction between phytochromes and putative phytochrome-interacting proteins. In this chapter, a protocol for rapid and simple light dependent in vitro coimmunoprecipitation between phytochromes and phytochrome interacting factors is described. In principle, this protocol can be adapted for other putative phytochrome interacting proteins.
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Affiliation(s)
- Inyup Paik
- Department of Molecular Biosciences, The Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, USA
| | - Enamul Huq
- Department of Molecular Biosciences, The Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, USA. .,Biological Laboratories, University of Texas at Austin, Austin, TX, USA.
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15
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Sheerin DJ. Investigation of Light-Regulated Protein-Protein Interactions Using Yeast Two-Hybrid Assays. Methods Mol Biol 2019; 2026:1-19. [PMID: 31317399 DOI: 10.1007/978-1-4939-9612-4_1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Yeast two-hybrid allows for investigation of interactions between two proteins in vivo. Yeast media can be supplemented with phycocyanobilin, allowing the formation of photoactive phytochromes, and the investigation of their light-regulated interactions. Three reporter assays are described; the histidine growth selection assay for the HIS3 reporter, and the filter lift and quantitative ONPG assays for the LacZ reporter. Design considerations for yeast two- and three-hybrid experiments are also covered.
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Affiliation(s)
- David J Sheerin
- Faculty of Biology, Institute of Biology II, University of Freiburg, Freiburg, Germany.
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16
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Gallego AM, Rojas LF, Parra O, Rodriguez HA, Mazo Rivas JC, Urrea AI, Atehortúa L, Fister AS, Guiltinan MJ, Maximova SN, Pabón-Mora N. Transcriptomic analyses of cacao cell suspensions in light and dark provide target genes for controlled flavonoid production. Sci Rep 2018; 8:13575. [PMID: 30206304 PMCID: PMC6134037 DOI: 10.1038/s41598-018-31965-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 08/03/2018] [Indexed: 12/16/2022] Open
Abstract
Catechins, including catechin (C) and epicatechin (E), are the main type of flavonoids in cacao seeds. They play important roles in plant defense and have been associated with human health benefits. Although flavonoid biosynthesis has been extensively studied using in vitro and in vivo models, the regulatory mechanisms controlling their accumulation under light/dark conditions remain poorly understood. To identify differences in flavonoid biosynthesis (particularly catechins) under different light treatments, we used cacao cell suspensions exposed to white-blue light and darkness during 14 days. RNA-Seq was applied to evaluate differential gene expression. Our results indicate that light can effectively regulate flavonoid profiles, inducing a faster accumulation of phenolic compounds and shifting E/C ratios, in particular as a response to switching from white to blue light. The results demonstrated that HY5, MYB12, ANR and LAR were differentially regulated under light/dark conditions and could be targeted by overexpression aiming to improve catechin synthesis in cell cultures. In conclusion, our RNA-Seq analysis of cacao cells cultured under different light conditions provides a platform to dissect key aspects into the genetic regulatory network of flavonoids. These light-responsive candidate genes can be used further to modulate the flavonoid production in in vitro systems with value-added characteristics.
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Affiliation(s)
- Adriana M Gallego
- Universidad de Antioquia, Grupo de Biotecnología, Medellín, Colombia
| | - Luisa F Rojas
- Universidad de Antioquia, Grupo de Biotecnología-Escuela de Microbiología, Medellín, Colombia
| | - Oriana Parra
- Universidad de Antioquia, Grupo de Biotecnología, Medellín, Colombia
| | - Héctor A Rodriguez
- Corporación para Investigaciones Biológicas and Departamento de Ciencias Agronómicas, Facultad de Ciencias Agrarias, Universidad Nacional de Colombia, UNALMED-CIB, Medellín, Colombia
| | | | - Aura Inés Urrea
- Universidad de Antioquia, Grupo de Biotecnología, Medellín, Colombia
| | - Lucía Atehortúa
- Universidad de Antioquia, Grupo de Biotecnología, Medellín, Colombia
| | - Andrew S Fister
- Department of Plant Science and Huck Institutes of Life Sciences, The Pennsylvania State University, University Park, PA, United States
| | - Mark J Guiltinan
- Department of Plant Science and Huck Institutes of Life Sciences, The Pennsylvania State University, University Park, PA, United States
| | - Siela N Maximova
- Department of Plant Science and Huck Institutes of Life Sciences, The Pennsylvania State University, University Park, PA, United States.
| | - Natalia Pabón-Mora
- Universidad de Antioquia, Instituto de Biología, Grupo Evo-Devo en Plantas, Medellín, Colombia.
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17
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Wang Q, Liu Q, Wang X, Zuo Z, Oka Y, Lin C. New insights into the mechanisms of phytochrome-cryptochrome coaction. THE NEW PHYTOLOGIST 2018; 217:547-551. [PMID: 29139123 PMCID: PMC6677561 DOI: 10.1111/nph.14886] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 10/02/2017] [Indexed: 05/18/2023]
Abstract
Contents Summary 547 I. Introduction 547 II. Phytochromes mediate light-induced transcription of BICs to inactivate cryptochromes 548 III. PPKs phosphorylate light-signaling proteins and histones to affect plant development 548 IV. Prospect 550 Acknowledgements 550 References 550 SUMMARY: Plants perceive and respond to light signals by multiple sensory photoreceptors, including phytochromes and cryptochromes, which absorb different wavelengths of light to regulate genome expression and plant development. Photophysiological analyses have long revealed the coordinated actions of different photoreceptors, a phenomenon referred to as the photoreceptor coaction. The mechanistic explanations of photoreceptor coactions are not fully understood. The function of direct protein-protein interaction of phytochromes and cryptochromes and common signaling molecules of these photoreceptors, such as SPA1/COP1 E3 ubiquitin ligase complex and bHLH transcription factors PIFs, would partially explain phytochrome-cryptochrome coactions. In addition, newly discovered proteins that block cryptochrome photodimerization or catalyze cryptochrome phosphorylation may also participate in the phytochrome and cryptochrome coaction. This Tansley insight, which is not intended to make a comprehensive review of the studies of photoreceptor coactions, attempts to highlight those recent findings and their possible roles in the photoreceptor coaction.
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Affiliation(s)
- Qin Wang
- Basic Forestry and Proteomics Research Center, UCLA-FAFU Joint Research Center on Plant Proteomics, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Department of Molecular, Cell & Developmental Biology, University of California, Los Angeles, CA 90095, USA
| | - Qing Liu
- Basic Forestry and Proteomics Research Center, UCLA-FAFU Joint Research Center on Plant Proteomics, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xu Wang
- Basic Forestry and Proteomics Research Center, UCLA-FAFU Joint Research Center on Plant Proteomics, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Department of Molecular, Cell & Developmental Biology, University of California, Los Angeles, CA 90095, USA
| | - Zecheng Zuo
- Basic Forestry and Proteomics Research Center, UCLA-FAFU Joint Research Center on Plant Proteomics, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yoshito Oka
- Basic Forestry and Proteomics Research Center, UCLA-FAFU Joint Research Center on Plant Proteomics, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Chentao Lin
- Department of Molecular, Cell & Developmental Biology, University of California, Los Angeles, CA 90095, USA
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18
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Kroth PG, Wilhelm C, Kottke T. An update on aureochromes: Phylogeny - mechanism - function. JOURNAL OF PLANT PHYSIOLOGY 2017; 217:20-26. [PMID: 28797596 DOI: 10.1016/j.jplph.2017.06.010] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Revised: 06/21/2017] [Accepted: 06/23/2017] [Indexed: 05/20/2023]
Abstract
Light is important for algae, as it warrants metabolic independence via photosynthesis. In addition to the absorption of light by the photosystems, algae possess a variety of specific photoreceptors that allow the quantification of the light fluxes as well as the assessment of light qualities. About a decade ago, aureochromes have been described in the xanthophyte alga Vaucheria frigida. These proteins represent a new type of blue light photoreceptor as they possess both a light-oxygen-voltage (LOV) domain for light reception as well as a basic region leucine zipper (bZIP) domain for DNA binding, indicating that they represent light-driven transcription factors. Aureochromes so far have been detected only in a single group of algae, photosynthetic stramenopiles, but not in any other prokaryotic or eukaryotic organisms. Recent biophysical work on aureochromes in the absence and the presence of DNA revealed the mechanism of allosteric communication between the sensor and effector domains despite their unusual inversed arrangement. Different molecular models have been proposed to describe the effect of light on DNA binding. Functional characterization of mutants of the diatom Phaeodactylum tricornutum, in which the aureochrome genes have been silenced or deleted, indicate that different aureochromes may have different functions, being involved in central processes like light acclimation and regulation of the cell cycle.
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Affiliation(s)
- Peter G Kroth
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany.
| | - Christian Wilhelm
- Institute of Biology, University of Leipzig, Johannisallee 21-23, 04103 Leipzig, Germany
| | - Tilman Kottke
- Department of Chemistry, Physical and Biophysical Chemistry, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
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19
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Kainrath S, Stadler M, Reichhart E, Distel M, Janovjak H. Green-Light-Induced Inactivation of Receptor Signaling Using Cobalamin-Binding Domains. Angew Chem Int Ed Engl 2017; 56:4608-4611. [PMID: 28319307 PMCID: PMC5396336 DOI: 10.1002/anie.201611998] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Indexed: 11/10/2022]
Abstract
Optogenetics and photopharmacology provide spatiotemporally precise control over protein interactions and protein function in cells and animals. Optogenetic methods that are sensitive to green light and can be used to break protein complexes are not broadly available but would enable multichromatic experiments with previously inaccessible biological targets. Herein, we repurposed cobalamin (vitamin B12) binding domains of bacterial CarH transcription factors for green-light-induced receptor dissociation. In cultured cells, we observed oligomerization-induced cell signaling for the fibroblast growth factor receptor 1 fused to cobalamin-binding domains in the dark that was rapidly eliminated upon illumination. In zebrafish embryos expressing fusion receptors, green light endowed control over aberrant fibroblast growth factor signaling during development. Green-light-induced domain dissociation and light-inactivated receptors will critically expand the optogenetic toolbox for control of biological processes.
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Affiliation(s)
- Stephanie Kainrath
- Synthetic Physiology, Institute of Science and Technology Austria (IST Austria), Am Campus 1, 3400, Klosterneuburg, Austria
| | - Manuela Stadler
- Innovative Cancer Models, Children's Cancer Research Institute (CCRI), Zimmermannplatz 10, 1090, Vienna, Austria
| | - Eva Reichhart
- Synthetic Physiology, Institute of Science and Technology Austria (IST Austria), Am Campus 1, 3400, Klosterneuburg, Austria
| | - Martin Distel
- Innovative Cancer Models, Children's Cancer Research Institute (CCRI), Zimmermannplatz 10, 1090, Vienna, Austria
| | - Harald Janovjak
- Synthetic Physiology, Institute of Science and Technology Austria (IST Austria), Am Campus 1, 3400, Klosterneuburg, Austria
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20
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Kainrath S, Stadler M, Reichhart E, Distel M, Janovjak H. Grünlicht-induzierte Rezeptorinaktivierung durch Cobalamin-bindende Domänen. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201611998] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Stephanie Kainrath
- Synthetic Physiology; Institute of Science and Technology Austria (IST Austria); Am Campus 1 3400 Klosterneuburg Österreich
| | - Manuela Stadler
- Innovative Cancer Models; Children's Cancer Research Institute (CCRI); Zimmermannplatz 10 1090 Wien Österreich
| | - Eva Reichhart
- Synthetic Physiology; Institute of Science and Technology Austria (IST Austria); Am Campus 1 3400 Klosterneuburg Österreich
| | - Martin Distel
- Innovative Cancer Models; Children's Cancer Research Institute (CCRI); Zimmermannplatz 10 1090 Wien Österreich
| | - Harald Janovjak
- Synthetic Physiology; Institute of Science and Technology Austria (IST Austria); Am Campus 1 3400 Klosterneuburg Österreich
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21
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Kaiserli E, Páldi K, O'Donnell L, Batalov O, Pedmale UV, Nusinow DA, Kay SA, Chory J. Integration of Light and Photoperiodic Signaling in Transcriptional Nuclear Foci. Dev Cell 2015; 35:311-21. [PMID: 26555051 PMCID: PMC4654455 DOI: 10.1016/j.devcel.2015.10.008] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Revised: 08/08/2015] [Accepted: 10/09/2015] [Indexed: 10/22/2022]
Abstract
Light regulates major plant developmental transitions by orchestrating a series of nuclear events. This study uncovers the molecular function of the natural variant, TZP (Tandem Zinc-finger-Plus3), as a signal integrator of light and photoperiodic pathways in transcriptional nuclear foci. We report that TZP acts as a positive regulator of photoperiodic flowering via physical interactions with the red-light receptor phytochrome B (phyB). We demonstrate that TZP localizes in dynamic nuclear domains regulated by light quality and photoperiod. This study shows that phyB is indispensable not only for localizing TZP to transcriptionally active nuclear photobodies, but also for recruiting TZP on the promoter of the floral inducer FLOWERING LOCUS T (FT). Our findings signify a unique transcriptional regulatory role to the highly enigmatic plant nuclear photobodies, where TZP directly activates FT gene expression and promotes flowering.
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Affiliation(s)
- Eirini Kaiserli
- Howard Hughes Medical Institute and Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA; Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK.
| | - Katalin Páldi
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Liz O'Donnell
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Olga Batalov
- Howard Hughes Medical Institute and Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Ullas V Pedmale
- Howard Hughes Medical Institute and Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Dmitri A Nusinow
- Center for Chronobiology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Steve A Kay
- Center for Chronobiology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Joanne Chory
- Howard Hughes Medical Institute and Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
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22
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Lindner R, Heintz U, Winkler A. Applications of hydrogen deuterium exchange (HDX) for the characterization of conformational dynamics in light-activated photoreceptors. Front Mol Biosci 2015; 2:33. [PMID: 26157802 PMCID: PMC4477167 DOI: 10.3389/fmolb.2015.00033] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 05/26/2015] [Indexed: 11/13/2022] Open
Abstract
Rational design of optogenetic tools is inherently linked to the understanding of photoreceptor function. Structural analysis of elements involved in signal integration in individual sensor domains provides an initial idea of their mode of operation, but understanding how local structural rearrangements eventually affect signal transmission to output domains requires inclusion of the effector regions in the characterization. However, the dynamic nature of these assemblies renders their structural analysis challenging and therefore a combination of high- and low-resolution techniques is required to appreciate functional aspects of photoreceptors. This review focuses on the potential of hydrogen-deuterium exchange coupled to mass spectrometry (HDX-MS) for complementing the structural characterization of photoreceptors. In this respect, the ability of HDX-MS to provide information on conformational dynamics and the possibility to address multiple functionally relevant states in solution render this methodology ideally suitable. We highlight recent examples demonstrating the potential of HDX-MS and discuss how these results can help to improve existing optogenetic systems or guide the design of novel optogenetic tools.
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Affiliation(s)
- Robert Lindner
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research Heidelberg, Germany
| | - Udo Heintz
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research Heidelberg, Germany
| | - Andreas Winkler
- Institute of Biochemistry, Graz University of Technology Graz, Austria
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23
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Nozue K, Tat AV, Kumar Devisetty U, Robinson M, Mumbach MR, Ichihashi Y, Lekkala S, Maloof JN. Shade avoidance components and pathways in adult plants revealed by phenotypic profiling. PLoS Genet 2015; 11:e1004953. [PMID: 25874869 PMCID: PMC4398415 DOI: 10.1371/journal.pgen.1004953] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Accepted: 12/11/2014] [Indexed: 01/01/2023] Open
Abstract
Shade from neighboring plants limits light for photosynthesis; as a consequence, plants have a variety of strategies to avoid canopy shade and compete with their neighbors for light. Collectively the response to foliar shade is called the shade avoidance syndrome (SAS). The SAS includes elongation of a variety of organs, acceleration of flowering time, and additional physiological responses, which are seen throughout the plant life cycle. However, current mechanistic knowledge is mainly limited to shade-induced elongation of seedlings. Here we use phenotypic profiling of seedling, leaf, and flowering time traits to untangle complex SAS networks. We used over-representation analysis (ORA) of shade-responsive genes, combined with previous annotation, to logically select 59 known and candidate novel mutants for phenotyping. Our analysis reveals shared and separate pathways for each shade avoidance response. In particular, auxin pathway components were required for shade avoidance responses in hypocotyl, petiole, and flowering time, whereas jasmonic acid pathway components were only required for petiole and flowering time responses. Our phenotypic profiling allowed discovery of seventeen novel shade avoidance mutants. Our results demonstrate that logical selection of mutants increased success of phenotypic profiling to dissect complex traits and discover novel components.
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Affiliation(s)
- Kazunari Nozue
- Department of Plant Biology, University of California, Davis, Davis, California, United States of America
| | - An V. Tat
- Department of Plant Biology, University of California, Davis, Davis, California, United States of America
| | - Upendra Kumar Devisetty
- Department of Plant Biology, University of California, Davis, Davis, California, United States of America
| | - Matthew Robinson
- Department of Plant Biology, University of California, Davis, Davis, California, United States of America
| | - Maxwell R. Mumbach
- Department of Plant Biology, University of California, Davis, Davis, California, United States of America
| | - Yasunori Ichihashi
- Department of Plant Biology, University of California, Davis, Davis, California, United States of America
| | - Saradadevi Lekkala
- Department of Plant Biology, University of California, Davis, Davis, California, United States of America
| | - Julin N. Maloof
- Department of Plant Biology, University of California, Davis, Davis, California, United States of America
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24
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Hense A, Herman E, Oldemeyer S, Kottke T. Proton transfer to flavin stabilizes the signaling state of the blue light receptor plant cryptochrome. J Biol Chem 2014; 290:1743-51. [PMID: 25471375 DOI: 10.1074/jbc.m114.606327] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Plant cryptochromes regulate the circadian rhythm, flowering time, and photomorphogenesis in higher plants as responses to blue light. In the dark, these photoreceptors bind oxidized FAD in the photolyase homology region (PHR). Upon blue light absorption, FAD is converted to the neutral radical state, the likely signaling state, by electron transfer via a conserved tryptophan triad and proton transfer from a nearby aspartic acid. Here we demonstrate, by infrared and time-resolved UV-visible spectroscopy on the PHR domain, that replacement of the aspartic acid Asp-396 with cysteine prevents proton transfer. The lifetime of the radical is decreased by 6 orders of magnitude. This short lifetime does not permit to drive conformational changes in the C-terminal extension that have been associated with signal transduction. Only in the presence of ATP do both the wild type and mutant form a long-lived radical state. However, in the mutant, an anion radical is formed instead of the neutral radical, as found previously in animal type I cryptochromes. Infrared spectroscopic experiments demonstrate that the light-induced conformational changes of the PHR domain are conserved in the mutant despite the lack of proton transfer. These changes are not detected in the photoreduction of the non-photosensory d-amino acid oxidase to the anion radical. In conclusion, formation of the anion radical is sufficient to generate a protein response in plant cryptochromes. Moreover, the intrinsic proton transfer is required for stabilization of the signaling state in the absence of ATP.
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Affiliation(s)
- Anika Hense
- From the Physical and Biophysical Chemistry, Department of Chemistry, Bielefeld University, Universitätsstrasse 25, 33615 Bielefeld, Germany
| | - Elena Herman
- From the Physical and Biophysical Chemistry, Department of Chemistry, Bielefeld University, Universitätsstrasse 25, 33615 Bielefeld, Germany
| | - Sabine Oldemeyer
- From the Physical and Biophysical Chemistry, Department of Chemistry, Bielefeld University, Universitätsstrasse 25, 33615 Bielefeld, Germany
| | - Tilman Kottke
- From the Physical and Biophysical Chemistry, Department of Chemistry, Bielefeld University, Universitätsstrasse 25, 33615 Bielefeld, Germany
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25
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Baker AS, Deiters A. Optical control of protein function through unnatural amino acid mutagenesis and other optogenetic approaches. ACS Chem Biol 2014; 9:1398-407. [PMID: 24819585 DOI: 10.1021/cb500176x] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Biological processes are naturally regulated with high spatial and temporal resolution at the molecular, cellular, and systems level. To control and study processes with the same resolution, light-sensitive groups and domains have been employed to optically activate and deactivate protein function. Optical control is a noninvasive technique in which the amplitude, wavelength, spatial location, and timing of the light illumination can be easily controlled. This review focuses on applications of genetically encoded unnatural amino acids containing light-removable protecting groups to optically trigger protein function, while also discussing select optogenetic approaches using natural light-sensitive domains to engineer optical control of biological processes.
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Affiliation(s)
- Austin S. Baker
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Alexander Deiters
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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26
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Abstract
The light-based control of ion channels has been transformative for the neurosciences, but the optogenetic toolkit does not stop there. An expanding number of proteins and cellular functions have been shown to be controlled by light, and the practical considerations in deciding between reversible optogenetic systems (such as systems that use light-oxygen-voltage domains, phytochrome proteins, cryptochrome proteins and the fluorescent protein Dronpa) are well defined. The field is moving beyond proof of concept to answering real biological questions, such as how cell signalling is regulated in space and time, that were difficult or impossible to address with previous tools.
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27
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Pathak GP, Vrana JD, Tucker CL. Optogenetic control of cell function using engineered photoreceptors. Biol Cell 2012; 105:59-72. [PMID: 23157573 DOI: 10.1111/boc.201200056] [Citation(s) in RCA: 90] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2012] [Accepted: 11/12/2012] [Indexed: 11/29/2022]
Abstract
Over the past decades, there has been growing recognition that light can provide a powerful stimulus for biological interrogation. Light-actuated tools allow manipulation of molecular events with ultra-fine spatial and fast temporal resolution, as light can be rapidly delivered and focused with sub-micrometre precision within cells. While light-actuated chemicals such as photolabile 'caged' compounds have been in existence for decades, the use of genetically encoded natural photoreceptors for optical control of biological processes has recently emerged as a powerful new approach with several advantages over traditional methods. Here, we review recent advances using light to control basic cellular functions and discuss the engineering challenges that lie ahead for improving and expanding the ever-growing optogenetic toolkit.
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Affiliation(s)
- Gopal P Pathak
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 90045, USA
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