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Tadesse D, Yee EF, Wolabu TW, Wang H, Yun J, Grosjean N, Kumaran D, Santiago K, Kong W, Sharma A, Chen J, Paterson AH, Xie M, Tadege M. Sorghum SbGhd7 is a major regulator of floral transition and directly represses genes crucial for flowering activation. THE NEW PHYTOLOGIST 2024; 242:786-796. [PMID: 38451101 DOI: 10.1111/nph.19591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 01/29/2024] [Indexed: 03/08/2024]
Abstract
Molecular genetic understanding of flowering time regulation is crucial for sorghum development. GRAIN NUMBER, PLANT HEIGHT AND HEADING DATE 7 (SbGhd7) is one of the six classical loci conferring photoperiod sensitivity of sorghum flowering. However, its functions remain poorly studied. The molecular functions of SbGhd7 were characterized. The gene regulatory network controlled by SbGhd7 was constructed and validated. The biological roles of SbGhd7 and its major targets were studied. SbGhd7 overexpression (OE) completely prevented sorghum flowering. Additionally, we show that SbGhd7 is a major negative regulator of flowering, binding to the promoter motif TGAATG(A/T)(A/T/C) and repressing transcription of the major florigen FLOWERING LOCUS T 10 (SbFT10) and floral activators EARLY HEADING DATE (SbEhd1), FLAVIN-BINDING, KELCH REPEAT, F-BOX1 (SbFKF1) and EARLY FLOWERING 3 (SbELF3). Reinforcing the direct effect of SbGhd7, SbEhd1 OE activated the promoters of three functional florigens (SbFT1, SbFT8 and SbFT10), dramatically accelerating flowering. Our studies demonstrate that SbGhd7 is a major repressor of sorghum flowering by directly and indirectly targeting genes for flowering activation. The mechanism appears ancient. Our study extends the current model of floral transition regulation in sorghum and provides a framework for a comprehensive understanding of sorghum photoperiod response.
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Affiliation(s)
- Dimiru Tadesse
- Biology Department, Brookhaven National Laboratory, Upton, NY, 11973, USA
- Department of Plant and Soil Sciences, Institute for Agricultural Biosciences, Oklahoma State University, Ardmore, OK, 73401, USA
| | - Estella F Yee
- Biology Department, Brookhaven National Laboratory, Upton, NY, 11973, USA
- National Synchrotron Light Source, Brookhaven National Laboratory, Upton, NY, 11973, USA
| | - Tezera W Wolabu
- Department of Plant and Soil Sciences, Institute for Agricultural Biosciences, Oklahoma State University, Ardmore, OK, 73401, USA
| | - Hui Wang
- Department of Plant and Soil Sciences, Institute for Agricultural Biosciences, Oklahoma State University, Ardmore, OK, 73401, USA
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Jianfei Yun
- Department of Plant and Soil Sciences, Institute for Agricultural Biosciences, Oklahoma State University, Ardmore, OK, 73401, USA
| | - Nicolas Grosjean
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Desigan Kumaran
- Biology Department, Brookhaven National Laboratory, Upton, NY, 11973, USA
| | - Kassandra Santiago
- Biology Department, Brookhaven National Laboratory, Upton, NY, 11973, USA
| | - Wenqian Kong
- Department of Soil and Crop Science, University of Georgia, Athens, GA, 30602, USA
| | - Ankush Sharma
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, 30602, USA
| | - Jianghua Chen
- Key Laboratory of Tropical Plant Resources and Sustainable Use, Center for Excellence in Molecular Plant Sciences, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Andrew H Paterson
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, 30602, USA
| | - Meng Xie
- Biology Department, Brookhaven National Laboratory, Upton, NY, 11973, USA
| | - Million Tadege
- Department of Plant and Soil Sciences, Institute for Agricultural Biosciences, Oklahoma State University, Ardmore, OK, 73401, USA
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Arinkin V, Granzin J, Jaeger KE, Willbold D, Krauss U, Batra-Safferling R. Conserved Signal Transduction Mechanisms and Dark Recovery Kinetic Tuning in the Pseudomonadaceae Short Light, Oxygen, Voltage (LOV) Protein Family. J Mol Biol 2024; 436:168458. [PMID: 38280482 DOI: 10.1016/j.jmb.2024.168458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 01/21/2024] [Accepted: 01/23/2024] [Indexed: 01/29/2024]
Abstract
Light-Oxygen-Voltage (LOV) flavoproteins transduce a light signal into variable signaling outputs via a structural rearrangement in the sensory core domain, which is then relayed to fused effector domains via α-helical linker elements. Short LOV proteins from Pseudomonadaceae consist of a LOV sensory core and N- and C-terminal α-helices of variable length, providing a simple model system to study the molecular mechanism of allosteric activation. Here we report the crystal structures of two LOV proteins from Pseudomonas fluorescens - SBW25-LOV in the fully light-adapted state and Pf5-LOV in the dark-state. In a comparative analysis of the Pseudomonadaceae short LOVs, the structures demonstrate light-induced rotation of the core domains and splaying of the proximal A'α and Jα helices in the N and C-termini, highlighting evidence for a conserved signal transduction mechanism. Another distinguishing feature of the Pseudomonadaceae short LOV protein family is their highly variable dark recovery, ranging from seconds to days. Understanding this variability is crucial for tuning the signaling behavior of LOV-based optogenetic tools. At 37 °C, SBW25-LOV and Pf5-LOV exhibit adduct state lifetimes of 1470 min and 3.6 min, respectively. To investigate this remarkable difference in dark recovery rates, we targeted three residues lining the solvent channel entrance to the chromophore pocket where we introduced mutations by exchanging the non-conserved amino acids from SBW25-LOV into Pf5-LOV and vice versa. Dark recovery kinetics of the resulting mutants, as well as MD simulations and solvent cavity calculations on the crystal structures suggest a correlation between solvent accessibility and adduct lifetime.
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Affiliation(s)
- Vladimir Arinkin
- Institut für Biologische Informationsprozesse (IBI): Strukturbiochemie (IBI-7), Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Joachim Granzin
- Institut für Biologische Informationsprozesse (IBI): Strukturbiochemie (IBI-7), Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Karl-Erich Jaeger
- Institut für Molekulare Enzymtechnologie, Heinrich-Heine-Universität Düsseldorf, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany; Institut für Bio- und Geowissenschaften (IBG): Biotechnologie (IBG-1), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Dieter Willbold
- Institut für Biologische Informationsprozesse (IBI): Strukturbiochemie (IBI-7), Forschungszentrum Jülich, 52425 Jülich, Germany; Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
| | - Ulrich Krauss
- Institut für Molekulare Enzymtechnologie, Heinrich-Heine-Universität Düsseldorf, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany; Institut für Bio- und Geowissenschaften (IBG): Biotechnologie (IBG-1), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany; Department of Biochemistry, University of Bayreuth, 95447 Bayreuth, Germany
| | - Renu Batra-Safferling
- Institut für Biologische Informationsprozesse (IBI): Strukturbiochemie (IBI-7), Forschungszentrum Jülich, 52425 Jülich, Germany.
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3
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Xu Q, Vogt A, Frechen F, Yi C, Küçükerden M, Ngum N, Sitjà-Roqueta L, Greiner A, Parri R, Masana M, Wenger N, Wachten D, Möglich A. Engineering Bacteriophytochrome-coupled Photoactivated Adenylyl Cyclases for Enhanced Optogenetic cAMP Modulation. J Mol Biol 2024; 436:168257. [PMID: 37657609 DOI: 10.1016/j.jmb.2023.168257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 08/27/2023] [Accepted: 08/28/2023] [Indexed: 09/03/2023]
Abstract
Sensory photoreceptors abound in nature and enable organisms to adapt behavior, development, and physiology to environmental light. In optogenetics, photoreceptors allow spatiotemporally precise, reversible, and non-invasive control by light of cellular processes. Notwithstanding the development of numerous optogenetic circuits, an unmet demand exists for efficient systems sensitive to red light, given its superior penetration of biological tissue. Bacteriophytochrome photoreceptors sense the ratio of red and far-red light to regulate the activity of enzymatic effector modules. The recombination of bacteriophytochrome photosensor modules with cyclase effectors underlies photoactivated adenylyl cyclases (PAC) that catalyze the synthesis of the ubiquitous second messenger 3', 5'-cyclic adenosine monophosphate (cAMP). Via homologous exchanges of the photosensor unit, we devised novel PACs, with the variant DmPAC exhibiting 40-fold activation of cyclase activity under red light, thus surpassing previous red-light-responsive PACs. Modifications of the PHY tongue modulated the responses to red and far-red light. Exchanges of the cyclase effector offer an avenue to further enhancing PACs but require optimization of the linker to the photosensor. DmPAC and a derivative for 3', 5'-cyclic guanosine monophosphate allow the manipulation of cyclic-nucleotide-dependent processes in mammalian cells by red light. Taken together, we advance the optogenetic control of second-messenger signaling and provide insight into the signaling and design of bacteriophytochrome receptors.
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Affiliation(s)
- Qianzhao Xu
- Department of Biochemistry, University of Bayreuth, 95447 Bayreuth, Germany
| | - Arend Vogt
- Charité - University Medicine Berlin, Department of Neurology with Experimental Neurology, 10117 Berlin, Germany. https://twitter.com/ArendVogt
| | - Fabian Frechen
- Institute of Innate Immunity, University of Bonn, 53127 Bonn, Germany
| | - Chengwei Yi
- Department of Biochemistry, University of Bayreuth, 95447 Bayreuth, Germany
| | - Melike Küçükerden
- Department of Biomedical Sciences, Institute of Neurosciences, University of Barcelona, 08036 Barcelona, Spain; Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain; Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Spain
| | - Neville Ngum
- College of Health and Life Sciences, Aston University, Birmingham B4 7ET, United Kingdom
| | - Laia Sitjà-Roqueta
- Department of Biomedical Sciences, Institute of Neurosciences, University of Barcelona, 08036 Barcelona, Spain; Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain; Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Spain
| | - Andreas Greiner
- Macromolecular Chemistry and Bavarian Polymer Institute, University of Bayreuth, Bayreuth 95440, Germany
| | - Rhein Parri
- College of Health and Life Sciences, Aston University, Birmingham B4 7ET, United Kingdom
| | - Mercè Masana
- Department of Biomedical Sciences, Institute of Neurosciences, University of Barcelona, 08036 Barcelona, Spain; Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain; Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Spain. https://twitter.com/mercemasana
| | - Nikolaus Wenger
- Charité - University Medicine Berlin, Department of Neurology with Experimental Neurology, 10117 Berlin, Germany
| | - Dagmar Wachten
- Institute of Innate Immunity, University of Bonn, 53127 Bonn, Germany. https://twitter.com/DagmarWachten
| | - Andreas Möglich
- Department of Biochemistry, University of Bayreuth, 95447 Bayreuth, Germany; Bayreuth Center for Biochemistry & Molecular Biology, Universität Bayreuth, 95447 Bayreuth, Germany; North-Bavarian NMR Center, Universität Bayreuth, 95447 Bayreuth, Germany.
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4
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Chen B, Shi Y, Sun Y, Lu L, Wang L, Liu Z, Cheng S. Innovations in functional genomics and molecular breeding of pea: exploring advances and opportunities. ABIOTECH 2024; 5:71-93. [PMID: 38576433 PMCID: PMC10987475 DOI: 10.1007/s42994-023-00129-1] [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: 10/19/2023] [Accepted: 12/05/2023] [Indexed: 04/06/2024]
Abstract
The garden pea (Pisum sativum L.) is a significant cool-season legume, serving as crucial food sources, animal feed, and industrial raw materials. The advancement of functional genomics over the past two decades has provided substantial theoretical foundations and progress to pea breeding. Notably, the release of the pea reference genome has enhanced our understanding of plant architecture, symbiotic nitrogen fixation (SNF), flowering time, floral organ development, seed development, and stress resistance. However, a considerable gap remains between pea functional genomics and molecular breeding. This review summarizes the current advancements in pea functional genomics and breeding while highlighting the future challenges in pea molecular breeding.
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Affiliation(s)
- Baizhi Chen
- Agricultural Genomics Institute at Shenzhen (AGIS), Chinese Academy of Agricultural Sciences (CAAS), Shenzhen, China
| | - Yan Shi
- Agricultural Genomics Institute at Shenzhen (AGIS), Chinese Academy of Agricultural Sciences (CAAS), Shenzhen, China
| | - Yuchen Sun
- Agricultural Genomics Institute at Shenzhen (AGIS), Chinese Academy of Agricultural Sciences (CAAS), Shenzhen, China
| | - Lu Lu
- Agricultural Genomics Institute at Shenzhen (AGIS), Chinese Academy of Agricultural Sciences (CAAS), Shenzhen, China
| | - Luyao Wang
- Agricultural Genomics Institute at Shenzhen (AGIS), Chinese Academy of Agricultural Sciences (CAAS), Shenzhen, China
| | - Zijian Liu
- Agricultural Genomics Institute at Shenzhen (AGIS), Chinese Academy of Agricultural Sciences (CAAS), Shenzhen, China
| | - Shifeng Cheng
- Agricultural Genomics Institute at Shenzhen (AGIS), Chinese Academy of Agricultural Sciences (CAAS), Shenzhen, China
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5
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Salvadori G, Mazzeo P, Accomasso D, Cupellini L, Mennucci B. Deciphering Photoreceptors Through Atomistic Modeling from Light Absorption to Conformational Response. J Mol Biol 2024; 436:168358. [PMID: 37944793 DOI: 10.1016/j.jmb.2023.168358] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 10/28/2023] [Accepted: 11/02/2023] [Indexed: 11/12/2023]
Abstract
In this review, we discuss the successes and challenges of the atomistic modeling of photoreceptors. Throughout our presentation, we integrate explanations of the primary methodological approaches, ranging from quantum mechanical descriptions to classical enhanced sampling methods, all while providing illustrative examples of their practical application to specific systems. To enhance the effectiveness of our analysis, our primary focus has been directed towards the examination of applications across three distinct photoreceptors. These include an example of Blue Light-Using Flavin (BLUF) domains, a bacteriophytochrome, and the orange carotenoid protein (OCP) employed by cyanobacteria for photoprotection. Particular emphasis will be placed on the pivotal role played by the protein matrix in fine-tuning the initial photochemical event within the embedded chromophore. Furthermore, we will investigate how this localized perturbation initiates a cascade of events propagating from the binding pocket throughout the entire protein structure, thanks to the intricate network of interactions between the chromophore and the protein.
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Affiliation(s)
- Giacomo Salvadori
- Department of Chemistry and Industrial Chemistry, University of Pisa, 56124 Pisa, Italy
| | - Patrizia Mazzeo
- Department of Chemistry and Industrial Chemistry, University of Pisa, 56124 Pisa, Italy
| | - Davide Accomasso
- Department of Chemistry and Industrial Chemistry, University of Pisa, 56124 Pisa, Italy
| | - Lorenzo Cupellini
- Department of Chemistry and Industrial Chemistry, University of Pisa, 56124 Pisa, Italy
| | - Benedetta Mennucci
- Department of Chemistry and Industrial Chemistry, University of Pisa, 56124 Pisa, Italy
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Pietruschka G, Ranzani AT, Weber A, Patwari T, Pilsl S, Renzl C, Otte DM, Pyka D, Möglich A, Mayer G. An RNA Motif That Enables Optozyme Control and Light-Dependent Gene Expression in Bacteria and Mammalian Cells. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2304519. [PMID: 38227373 DOI: 10.1002/advs.202304519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 12/19/2023] [Indexed: 01/17/2024]
Abstract
The regulation of gene expression by light enables the versatile, spatiotemporal manipulation of biological function in bacterial and mammalian cells. Optoribogenetics extends this principle by molecular RNA devices acting on the RNA level whose functions are controlled by the photoinduced interaction of a light-oxygen-voltage photoreceptor with cognate RNA aptamers. Here light-responsive ribozymes, denoted optozymes, which undergo light-dependent self-cleavage and thereby control gene expression are described. This approach transcends existing aptamer-ribozyme chimera strategies that predominantly rely on aptamers binding to small molecules. The optozyme method thus stands to enable the graded, non-invasive, and spatiotemporally resolved control of gene expression. Optozymes are found efficient in bacteria and mammalian cells and usher in hitherto inaccessible optoribogenetic modalities with broad applicability in synthetic and systems biology.
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Affiliation(s)
- Georg Pietruschka
- Life and Medical Sciences (LIMES), University of Bonn, Gerhard-Domagk-Str.1, 53121, Bonn, Germany
| | - Américo T Ranzani
- Lehrstuhl für Biochemie, Photobiochemie, University of Bayreuth, Universitätsstraße 30, 95440, Bayreuth, Germany
| | - Anna Weber
- Life and Medical Sciences (LIMES), University of Bonn, Gerhard-Domagk-Str.1, 53121, Bonn, Germany
- Center of Aptamer Research & Development, University of Bonn, Gerhard-Domagk-Str. 1, 53121, Bonn, Germany
| | - Tejal Patwari
- Life and Medical Sciences (LIMES), University of Bonn, Gerhard-Domagk-Str.1, 53121, Bonn, Germany
| | - Sebastian Pilsl
- Life and Medical Sciences (LIMES), University of Bonn, Gerhard-Domagk-Str.1, 53121, Bonn, Germany
| | - Christian Renzl
- Life and Medical Sciences (LIMES), University of Bonn, Gerhard-Domagk-Str.1, 53121, Bonn, Germany
- Center of Aptamer Research & Development, University of Bonn, Gerhard-Domagk-Str. 1, 53121, Bonn, Germany
| | - David M Otte
- Life and Medical Sciences (LIMES), University of Bonn, Gerhard-Domagk-Str.1, 53121, Bonn, Germany
| | - Daniel Pyka
- Life and Medical Sciences (LIMES), University of Bonn, Gerhard-Domagk-Str.1, 53121, Bonn, Germany
| | - Andreas Möglich
- Lehrstuhl für Biochemie, Photobiochemie, University of Bayreuth, Universitätsstraße 30, 95440, Bayreuth, Germany
| | - Günter Mayer
- Life and Medical Sciences (LIMES), University of Bonn, Gerhard-Domagk-Str.1, 53121, Bonn, Germany
- Center of Aptamer Research & Development, University of Bonn, Gerhard-Domagk-Str. 1, 53121, Bonn, Germany
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7
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Tseng TS, Chen CA, Lo MH. PHOTOTROPIN1 lysine 526 functions to enhance phototropism in Arabidopsis. PLANTA 2024; 259:56. [PMID: 38305934 DOI: 10.1007/s00425-024-04332-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 01/04/2024] [Indexed: 02/03/2024]
Abstract
MAIN CONCLUSION After blue-light exposure, ubiquitination of PHOTOTROPIN1 lysine 526 enhances phototropic responses. Arabidopsis blue-light photoreceptor, PHOTOTROPIN1 (PHOT1) mediates a series of blue-light responses that function to optimize photosynthesis efficiency. Blue-light sensing through the N-terminal sensory domain activates the C-terminal kinase activity of PHOT1, resulting in autophosphorylation. In addition to phosphorylation, PHOT1 lysine residue 526 (Lys526), after blue-light exposure, was found to carry a double glycine attachment, indicative of a possible ubiquitination modification. The functionality of PHOT1 Lys526 was investigated by reverse genetic approaches. Arginine replacements of PHOT1 Lys526, together with Lys527, complemented phot1-5 phot2-1 double mutant with attenuated phototropic bending, while blue-light responses: leaf expansion and stomatal opening, were restored to wild type levels. Transgenic seedlings were not different in protein levels of phot1 Lys526 527Arg than the wild type control, suggesting the reduced phototropic responses was not caused by reduction in protein levels. Treating the transformants with proteosome inhibitor, MG132, did not restore phototropic sensitivity. Both transgenic protein and wild type PHOT1 also had similar dark recovery of kinase activity, suggesting that phot1 Lys526 527Arg replacement did not affect the protein stability to cause the phenotype. Together, our results indicate that blocking Lys526 ubiquitination by arginine substitution may have caused the reduced phototropic phenotype. Therefore, the putative ubiquitination on Lys526 functions to enhance PHOT1-mediated phototropism, rather than targeting PHOT1 for proteolysis.
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Affiliation(s)
- Tong-Seung Tseng
- Department of Agricultural Biotechnology, National Chiayi University, 300 Syuefu Road, Chiayi, 600, Taiwan.
| | - Chih-An Chen
- Department of Agricultural Biotechnology, National Chiayi University, 300 Syuefu Road, Chiayi, 600, Taiwan
| | - Ming-Hung Lo
- Department of Agricultural Biotechnology, National Chiayi University, 300 Syuefu Road, Chiayi, 600, Taiwan
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Seyedi FS, Nafchi MG, Reezi S. Effects of light spectra on morphological characteristics, primary and specialized metabolites of Thymus vulgaris L. Heliyon 2024; 10:e23032. [PMID: 38148820 PMCID: PMC10750077 DOI: 10.1016/j.heliyon.2023.e23032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 11/17/2023] [Accepted: 11/24/2023] [Indexed: 12/28/2023] Open
Abstract
Light is a crucial environmental factor that profoundly influences the growth and development of plants. However, the precise mechanisms by which light affects biochemical processes and growth and development factors in Thymus vulgaris remain unknown, necessitating further investigation. Hence, this study aimed to investigate the impact of different light spectra, including red, blue, red-blue, and white lights, on the morphological characteristics, primary, and specialized metabolites of T. vulgaris. Compared to white light, red light significantly increased leaf area (by 64 %), the number of branches (by 132 %), and dry weight (by 6.2 %), although a 40 % reduction in fresh weight was observed under red light conditions. Red-blue light notably enhanced canopy width, fresh weight, and dry weight. Gas chromatography/mass spectrometry (GC/MS) analysis of the plant's essential oil (EO) revealed that p-Cymene and γ-Terpinene were present at the highest levels. Notably, p-Cymene exhibited the highest concentrations under white light and blue light treatments, reaching 60.92 % and 59.53 %, respectively. Moreover, under the same light conditions, phenol and antioxidant levels were significantly elevated. Overall, these findings indicate that red and red-blue light spectra are the most favorable for thyme production.
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Affiliation(s)
- Forouh Sadat Seyedi
- Department of Horticulture Science, College of Agriculture, Shahrekord University, Iran
| | - Mehdi Ghasemi Nafchi
- Department of Horticulture Science, College of Agriculture, Shahrekord University, Iran
| | - Saeed Reezi
- Department of Horticulture Science, College of Agriculture, Shahrekord University, Iran
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Liu L, Xie Y, Yahaya BS, Wu F. GIGANTEA Unveiled: Exploring Its Diverse Roles and Mechanisms. Genes (Basel) 2024; 15:94. [PMID: 38254983 PMCID: PMC10815842 DOI: 10.3390/genes15010094] [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: 11/19/2023] [Revised: 01/09/2024] [Accepted: 01/10/2024] [Indexed: 01/24/2024] Open
Abstract
GIGANTEA (GI) is a conserved nuclear protein crucial for orchestrating the clock-associated feedback loop in the circadian system by integrating light input, modulating gating mechanisms, and regulating circadian clock resetting. It serves as a core component which transmits blue light signals for circadian rhythm resetting and overseeing floral initiation. Beyond circadian functions, GI influences various aspects of plant development (chlorophyll accumulation, hypocotyl elongation, stomatal opening, and anthocyanin metabolism). GI has also been implicated to play a pivotal role in response to stresses such as freezing, thermomorphogenic stresses, salinity, drought, and osmotic stresses. Positioned at the hub of complex genetic networks, GI interacts with hormonal signaling pathways like abscisic acid (ABA), gibberellin (GA), salicylic acid (SA), and brassinosteroids (BRs) at multiple regulatory levels. This intricate interplay enables GI to balance stress responses, promoting growth and flowering, and optimize plant productivity. This review delves into the multifaceted roles of GI, supported by genetic and molecular evidence, and recent insights into the dynamic interplay between flowering and stress responses, which enhance plants' adaptability to environmental challenges.
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Affiliation(s)
- Ling Liu
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin 644000, China;
| | - Yuxin Xie
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (Y.X.); (B.S.Y.)
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu 611130, China
| | - Baba Salifu Yahaya
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (Y.X.); (B.S.Y.)
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu 611130, China
| | - Fengkai Wu
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (Y.X.); (B.S.Y.)
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu 611130, China
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10
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Meier SSM, Multamäki E, Ranzani AT, Takala H, Möglich A. Multimodal Control of Bacterial Gene Expression by Red and Blue Light. Methods Mol Biol 2024; 2760:463-477. [PMID: 38468104 DOI: 10.1007/978-1-0716-3658-9_26] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/13/2024]
Abstract
By applying sensory photoreceptors, optogenetics realizes the light-dependent control of cellular events and state. Given reversibility, noninvasiveness, and exquisite spatiotemporal precision, optogenetic approaches enable innovative use cases in cell biology, synthetic biology, and biotechnology. In this chapter, we detail the implementation of the pREDusk, pREDawn, pCrepusculo, and pAurora optogenetic circuits for controlling bacterial gene expression by red and blue light, respectively. The protocols provided here guide the practical use and multiplexing of these circuits, thereby enabling graded protein production in bacteria at analytical and semi-preparative scales.
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Affiliation(s)
| | - Elina Multamäki
- Department of Anatomy, University of Helsinki, Helsinki, Finland
| | - Américo T Ranzani
- Department of Biochemistry, University of Bayreuth, Bayreuth, Germany
| | - Heikki Takala
- Department of Anatomy, University of Helsinki, Helsinki, Finland
- Department of Biological and Environmental Science, Nanoscience Center, University of Jyvaskyla, Jyvaskyla, Finland
| | - Andreas Möglich
- Department of Biochemistry, University of Bayreuth, Bayreuth, Germany.
- Bayreuth Center for Biochemistry & Molecular Biology, Universität Bayreuth, Bayreuth, Germany.
- North-Bavarian NMR Center, Universität Bayreuth, Bayreuth, Germany.
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Mat A, Vu HH, Wolf E, Tessmar-Raible K. All Light, Everywhere? Photoreceptors at Nonconventional Sites. Physiology (Bethesda) 2024; 39:0. [PMID: 37905983 DOI: 10.1152/physiol.00017.2023] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 10/29/2023] [Accepted: 10/29/2023] [Indexed: 11/02/2023] Open
Abstract
One of the biggest environmental alterations we have made to our species is the change in the exposure to light. During the day, we typically sit behind glass windows illuminated by artificial light that is >400 times dimmer and has a very different spectrum than natural daylight. On the opposite end are the nights that are now lit up by several orders of magnitude. This review aims to provide food for thought as to why this matters for humans and other animals. Evidence from behavioral neuroscience, physiology, chronobiology, and molecular biology is increasingly converging on the conclusions that the biological nonvisual functions of light and photosensory molecules are highly complex. The initial work of von Frisch on extraocular photoreceptors in fish, the identification of rhodopsins as the molecular light receptors in animal eyes and eye-like structures and cryptochromes as light sensors in nonmammalian chronobiology, still allowed for the impression that light reception would be a relatively restricted, localized sense in most animals. However, light-sensitive processes and/or sensory proteins have now been localized to many different cell types and tissues. It might be necessary to consider nonlight-responding cells as the exception, rather than the rule.
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Affiliation(s)
- Audrey Mat
- Max Perutz Labs, University of Vienna, Vienna BioCenter, Vienna, Austria
- VIPS2, Vienna BioCenter, Vienna, Austria
| | - Hong Ha Vu
- Institute of Molecular Physiology, Johannes Gutenberg-University, Mainz, Germany
| | - Eva Wolf
- Institute of Molecular Physiology, Johannes Gutenberg-University, Mainz, Germany
- Institute of Molecular Biology, Mainz, Germany
| | - Kristin Tessmar-Raible
- Max Perutz Labs, University of Vienna, Vienna BioCenter, Vienna, Austria
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
- Carl-von-Ossietzky University, Oldenburg, Germany
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12
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Hemmer S, Siedhoff NE, Werner S, Ölçücü G, Schwaneberg U, Jaeger KE, Davari MD, Krauss U. Machine Learning-Assisted Engineering of Light, Oxygen, Voltage Photoreceptor Adduct Lifetime. JACS AU 2023; 3:3311-3323. [PMID: 38155650 PMCID: PMC10751770 DOI: 10.1021/jacsau.3c00440] [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: 08/04/2023] [Revised: 11/07/2023] [Accepted: 11/07/2023] [Indexed: 12/30/2023]
Abstract
Naturally occurring and engineered flavin-binding, blue-light-sensing, light, oxygen, voltage (LOV) photoreceptor domains have been used widely to design fluorescent reporters, optogenetic tools, and photosensitizers for the visualization and control of biological processes. In addition, natural LOV photoreceptors with engineered properties were recently employed for optimizing plant biomass production in the framework of a plant-based bioeconomy. Here, the understanding and fine-tuning of LOV photoreceptor (kinetic) properties is instrumental for application. In response to blue-light illumination, LOV domains undergo a cascade of photophysical and photochemical events that yield a transient covalent FMN-cysteine adduct, allowing for signaling. The rate-limiting step of the LOV photocycle is the dark-recovery process, which involves adduct scission and can take between seconds and days. Rational engineering of LOV domains with fine-tuned dark recovery has been challenging due to the lack of a mechanistic model, the long time scale of the process, which hampers atomistic simulations, and a gigantic protein sequence space covering known mutations (combinatorial challenge). To address these issues, we used machine learning (ML) trained on scarce literature data and iteratively generated and implemented experimental data to design LOV variants with faster and slower dark recovery. Over the three prediction-validation cycles, LOV domain variants were successfully predicted, whose adduct-state lifetimes spanned 7 orders of magnitude, yielding optimized tools for synthetic (opto)biology. In summary, our results demonstrate ML as a viable method to guide the design of proteins even with limited experimental data and when no mechanistic model of the underlying physical principles is available.
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Affiliation(s)
- Stefanie Hemmer
- Institute
of Molecular Enzyme Technology, Heinrich
Heine University Düsseldorf, Wilhelm Johnen Strasse, Jülich 52426, Germany
| | - Niklas Erik Siedhoff
- Institute
of Biotechnology, RWTH Aachen University, Worringer Weg 3, 52074 Aachen, Germany
- DWI-Leibniz
Institute for Interactive Materials, Forckenbeckstraße 50, 52074 Aachen, Germany
| | - Sophia Werner
- Institute
of Molecular Enzyme Technology, Heinrich
Heine University Düsseldorf, Wilhelm Johnen Strasse, Jülich 52426, Germany
| | - Gizem Ölçücü
- Institute
of Molecular Enzyme Technology, Heinrich
Heine University Düsseldorf, Wilhelm Johnen Strasse, Jülich 52426, Germany
| | - Ulrich Schwaneberg
- Institute
of Biotechnology, RWTH Aachen University, Worringer Weg 3, 52074 Aachen, Germany
- DWI-Leibniz
Institute for Interactive Materials, Forckenbeckstraße 50, 52074 Aachen, Germany
| | - Karl-Erich Jaeger
- Institute
of Molecular Enzyme Technology, Heinrich
Heine University Düsseldorf, Wilhelm Johnen Strasse, Jülich 52426, Germany
- Institute
of Bio-and Geosciences IBG 1: Biotechnology, Forschungszentrum Jülich GmbH, Wilhelm Johnen Strasse, Jülich 52426, Germany
| | - Mehdi D. Davari
- Department
of Bioorganic Chemistry, Leibniz Institute
of Plant Biochemistry, Weinberg 3, 06120 Halle, Germany
| | - Ulrich Krauss
- Institute
of Molecular Enzyme Technology, Heinrich
Heine University Düsseldorf, Wilhelm Johnen Strasse, Jülich 52426, Germany
- Institute
of Bio-and Geosciences IBG 1: Biotechnology, Forschungszentrum Jülich GmbH, Wilhelm Johnen Strasse, Jülich 52426, Germany
- Department
of Biochemistry, University of Bayreuth, 95447 Bayreuth, Germany
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13
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Chen S, Li X, Ma X, Qing R, Chen Y, Zhou H, Yu Y, Li J, Tan Z. Lighting the way to sustainable development: Physiological response and light control strategy in microalgae-based wastewater treatment under illumination. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 903:166298. [PMID: 37591393 DOI: 10.1016/j.scitotenv.2023.166298] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 07/29/2023] [Accepted: 08/12/2023] [Indexed: 08/19/2023]
Abstract
The Sustainable Development Goals link pollutant control with carbon dioxide reduction. Toward the goal of pollutant and carbon reduction, microalgae-based wastewater treatment (MBWT), which can simultaneously remove pollutants and convert carbon dioxide into biomass with value-added metabolites, has attracted considerable attention. The photosynthetic organism microalgae and the photobioreactor are the functional body and the operational carrier of the MBWT system, respectively; thus, light conditions profoundly influence its performance. Therefore, this review takes the general rules of how light influences the performance of MBWT systems as a starting point to elaborate the light-influenced mechanisms in microalgae and the light control strategies for photobioreactors from the inside out. Wavelength, light intensity and photoperiod solely or interactively affect biomass accumulation, pollutant removal, and value-added metabolite production in MBWT. Physiological processes, including photosynthesis, photooxidative damage, light-regulated gene expression, and nutrient uptake, essentially explain the performance influence of MBWT and are instructive for specific microalgal strain improvement strategies. In addition, light causes unique reactions in MBWT systems as it interacts with components such as photooxidative damage enhancers present in types of wastewater. In order to provide guidance for photobioreactor design and light control in a large-scale MBWT system, wavelength transformation, light transmission, light source distribution, and light-dark cycle should be considered in addition to adjusting the light source characteristics. Finally, based on current research vacancies and challenges, future research orientation should focus on the improvement of microalgae and photobioreactor, as well as the integration of both.
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Affiliation(s)
- Shangxian Chen
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China; University of Chinese Academy of Sciences, Beijing 100049, China; Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China.
| | - Xin Li
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China.
| | - Xinlei Ma
- School of Energy and Environment, Southeast University, Nanjing 210096, China.
| | - Renwei Qing
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China.
| | - Yangwu Chen
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China.
| | - Houzhen Zhou
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China.
| | - Yadan Yu
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Junjie Li
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China.
| | - Zhouliang Tan
- CAS Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China.
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14
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Zeng H, Zheng T, Peng X, Tang Q, Xu H, Chen M. Transcriptomic and Targeted Metabolomics Analysis of Detached Lycium ruthenicum Leaves Reveals Mechanisms of Anthocyanin Biosynthesis Induction through Light Quality and Sucrose Treatments. Metabolites 2023; 13:1004. [PMID: 37755284 PMCID: PMC10535117 DOI: 10.3390/metabo13091004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 09/07/2023] [Accepted: 09/08/2023] [Indexed: 09/28/2023] Open
Abstract
Light quality and sucrose-induced osmotic stress are known to cause anthocyanin synthesis in detached Lycium ruthenicum leaves. To identify the mechanisms by which the kind of light quality and sucrose concentration are induced, here, we conducted transcriptome sequencing in detached L. ruthenicum leaves treated with different qualities of light and sucrose concentrations. Leaves treated with blue light or sucrose showed a significantly increased total anthocyanins content compared to those treated with white light. Delphinidin-3-O-rutinoside and delphinidin-3-O-glucoside production were differentially regulated by the BL(-S), BL(+S), and WL(+S) treatments. The structural genes CHS, CHI, F3'H, F3'5'H, ANS, and UFGT were significantly up-regulated in leaves treated with blue light or sucrose. Leaves treated with blue light additionally showed up-regulation of the light photoreceptors CRY1, PIF3, COP1, and HY5. The anthocyanin-related genes NCED1, PYR/PYL, PP2C, SnRK2, and ABI5 were significantly up-regulated in leaves treated with sucrose, promoting adaptability to sucrose osmotic stress. Co-expression and cis-regulatory analyses suggested that HY5 and ABI5 could regulate LrMYB44 and LrMYB48 through binding to the G-box element and ABRE element, respectively, inducing anthocyanin synthesis in response to blue light or sucrose treatment. Candidate genes responsive to blue light or sucrose osmotic stress in the anthocyanin biosynthesis pathway were validated through quantitative reverse transcription PCR. These findings deepen our understanding of the mechanisms by which blue light and sucrose-induced osmotic stress regulate anthocyanin synthesis, providing valuable target genes for the future improvement in anthocyanin production in L. ruthenicum.
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Affiliation(s)
- Haitao Zeng
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong 723001, China; (H.Z.); (X.P.); (Q.T.); (H.X.); (M.C.)
- Shaanxi Province Key Laboratory of Bio-Resources, Hanzhong 723001, China
- Qinba Mountain Area Collaborative Innovation Center of Bioresources Comprehensive Development, Hanzhong 723001, China
- Qinba State Key Laboratory of Biological Resources and Ecological Environment (Incubation), Hanzhong 723001, China
| | - Tao Zheng
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong 723001, China; (H.Z.); (X.P.); (Q.T.); (H.X.); (M.C.)
- Shaanxi Province Key Laboratory of Bio-Resources, Hanzhong 723001, China
- Qinba Mountain Area Collaborative Innovation Center of Bioresources Comprehensive Development, Hanzhong 723001, China
- Qinba State Key Laboratory of Biological Resources and Ecological Environment (Incubation), Hanzhong 723001, China
| | - Xue Peng
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong 723001, China; (H.Z.); (X.P.); (Q.T.); (H.X.); (M.C.)
- Shaanxi Province Key Laboratory of Bio-Resources, Hanzhong 723001, China
- Qinba Mountain Area Collaborative Innovation Center of Bioresources Comprehensive Development, Hanzhong 723001, China
- Qinba State Key Laboratory of Biological Resources and Ecological Environment (Incubation), Hanzhong 723001, China
| | - Qi Tang
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong 723001, China; (H.Z.); (X.P.); (Q.T.); (H.X.); (M.C.)
- Shaanxi Province Key Laboratory of Bio-Resources, Hanzhong 723001, China
- Qinba Mountain Area Collaborative Innovation Center of Bioresources Comprehensive Development, Hanzhong 723001, China
- Qinba State Key Laboratory of Biological Resources and Ecological Environment (Incubation), Hanzhong 723001, China
| | - Hao Xu
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong 723001, China; (H.Z.); (X.P.); (Q.T.); (H.X.); (M.C.)
- Shaanxi Province Key Laboratory of Bio-Resources, Hanzhong 723001, China
- Qinba Mountain Area Collaborative Innovation Center of Bioresources Comprehensive Development, Hanzhong 723001, China
- Qinba State Key Laboratory of Biological Resources and Ecological Environment (Incubation), Hanzhong 723001, China
| | - Mengjiao Chen
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong 723001, China; (H.Z.); (X.P.); (Q.T.); (H.X.); (M.C.)
- Shaanxi Province Key Laboratory of Bio-Resources, Hanzhong 723001, China
- Qinba Mountain Area Collaborative Innovation Center of Bioresources Comprehensive Development, Hanzhong 723001, China
- Qinba State Key Laboratory of Biological Resources and Ecological Environment (Incubation), Hanzhong 723001, China
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15
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Frascogna F, Ledermann B, Hartmann J, Pérez Patallo E, Zeqiri F, Hofmann E, Frankenberg-Dinkel N. On the evolution of the plant phytochrome chromophore biosynthesis. PLANT PHYSIOLOGY 2023; 193:246-258. [PMID: 37311159 DOI: 10.1093/plphys/kiad327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 05/25/2023] [Accepted: 05/29/2023] [Indexed: 06/15/2023]
Abstract
Phytochromes are biliprotein photoreceptors present in plants, algae, certain bacteria, and fungi. Land plant phytochromes use phytochromobilin (PΦB) as the bilin chromophore. Phytochromes of streptophyte algae, the clade within which land plants evolved, employ phycocyanobilin (PCB), leading to a more blue-shifted absorption spectrum. Both chromophores are synthesized by ferredoxin-dependent bilin reductases (FDBRs) starting from biliverdin IXα (BV). In cyanobacteria and chlorophyta, BV is reduced to PCB by the FDBR phycocyanobilin:ferredoxin oxidoreductase (PcyA), whereas, in land plants, BV is reduced to PФB by phytochromobilin synthase (HY2). However, phylogenetic studies suggested the absence of any ortholog of PcyA in streptophyte algae and the presence of only PФB biosynthesis-related genes (HY2). The HY2 of the streptophyte alga Klebsormidium nitens (formerly Klebsormidium flaccidum) has already indirectly been indicated to participate in PCB biosynthesis. Here, we overexpressed and purified a His6-tagged variant of K. nitens HY2 (KflaHY2) in Escherichia coli. Employing anaerobic bilin reductase activity assays and coupled phytochrome assembly assays, we confirmed the product and identified intermediates of the reaction. Site-directed mutagenesis revealed 2 aspartate residues critical for catalysis. While it was not possible to convert KflaHY2 into a PΦB-producing enzyme by simply exchanging the catalytic pair, the biochemical investigation of 2 additional members of the HY2 lineage enabled us to define 2 distinct clades, the PCB-HY2 and the PΦB-HY2 clade. Overall, our study gives insight into the evolution of the HY2 lineage of FDBRs.
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Affiliation(s)
- Federica Frascogna
- Department of Microbiology, University of Kaiserslautern-Landau, Kaiserslautern 67663, Germany
| | - Benjamin Ledermann
- Department of Microbiology, University of Kaiserslautern-Landau, Kaiserslautern 67663, Germany
| | - Jana Hartmann
- Department of Microbiology, University of Kaiserslautern-Landau, Kaiserslautern 67663, Germany
| | - Eugenio Pérez Patallo
- Department of Microbiology, University of Kaiserslautern-Landau, Kaiserslautern 67663, Germany
| | - Fjoralba Zeqiri
- Protein Crystallography, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum 44780, Germany
| | - Eckhard Hofmann
- Protein Crystallography, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum 44780, Germany
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16
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Bhatnagar A, Burman N, Sharma E, Tyagi A, Khurana P, Khurana JP. Two splice forms of OsbZIP1, a homolog of AtHY5, function to regulate skotomorphogenesis and photomorphogenesis in rice. PLANT PHYSIOLOGY 2023; 193:426-447. [PMID: 37300540 DOI: 10.1093/plphys/kiad334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 04/24/2023] [Accepted: 05/05/2023] [Indexed: 06/12/2023]
Abstract
Plants possess well-developed light sensing mechanisms and signal transduction systems for regulating photomorphogenesis. ELONGATED HYPOCOTYL5 (HY5), a basic leucine zipper (bZIP) transcription factor, has been extensively characterized in dicots. In this study, we show that OsbZIP1 is a functional homolog of Arabidopsis (Arabidopsis thaliana) HY5 (AtHY5) and is important for light-mediated regulation of seedling and mature plant development in rice (Oryza sativa). Ectopic expression of OsbZIP1 in rice reduced plant height and leaf length without affecting plant fertility, which contrasts with OsbZIP48, a previously characterized HY5 homolog. OsbZIP1 is alternatively spliced, and the OsbZIP1.2 isoform lacking the CONSTITUTIVELY PHOTOMORPHOGENIC1 (COP1)-binding domain regulated seedling development in the dark. Rice seedlings overexpressing OsbZIP1 were shorter than the vector control under white and monochromatic light conditions, whereas RNAi knockdown seedlings displayed the opposite phenotype. While OsbZIP1.1 was light-regulated, OsbZIP1.2 showed a similar expression profile in both light and dark conditions. Due to its interaction with OsCOP1, OsbZIP1.1 undergoes 26S proteasome-mediated degradation under dark conditions. Also, OsbZIP1.1 interacted with and was phosphorylated by CASEIN KINASE2 (OsCK2α3). In contrast, OsbZIP1.2 did not show any interaction with OsCOP1 or OsCK2α3. We propose that OsbZIP1.1 likely regulates seedling development in the light, while OsbZIP1.2 is the dominant player under dark conditions. The data presented in this study reveal that AtHY5 homologs in rice have undergone neofunctionalization, and alternative splicing of OsbZIP1 has increased the repertoire of its functions.
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Affiliation(s)
- Akanksha Bhatnagar
- Interdisciplinary Centre for Plant Genomics & Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110021, India
| | - Naini Burman
- Interdisciplinary Centre for Plant Genomics & Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110021, India
- Regional Centre for Biotechnology, Faridabad, Haryana 121001, India
| | - Eshan Sharma
- Interdisciplinary Centre for Plant Genomics & Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110021, India
| | - Akhilesh Tyagi
- Interdisciplinary Centre for Plant Genomics & Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110021, India
| | - Paramjit Khurana
- Interdisciplinary Centre for Plant Genomics & Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110021, India
| | - Jitendra P Khurana
- Interdisciplinary Centre for Plant Genomics & Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110021, India
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17
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Nishikawa K, Kuroiwa R, Tamogami J, Unno M, Fujisawa T. Raman Optical Activity of Retinal Chromophore in Sensory Rhodopsin II. J Phys Chem B 2023; 127:7244-7250. [PMID: 37556781 DOI: 10.1021/acs.jpcb.3c02391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/11/2023]
Abstract
Raman optical activity (ROA) spectroscopy was used to study the conformation of the retinal chromophore in sensory rhodopsin II (SRII), which is a blue-green light sensor of microbes. The ROA spectrum consisted of the negative vibrational bands of the chromophore, whose relative intensities are similar to those of the parent Raman spectrum. This spectral feature was explained by the left-handed helical twist of the retinal chromophore on the basis of quantum chemical calculations. On the other hand, we found that the chromophore conformation based on the crystal structures of SRII has a right-handed helical twist, which does not agree with the observation. This specific result suggests that the consistency with chiro-optical properties can be a key criterion for the accurate prediction and/or evaluation of chromophore conformation in retinal-binding proteins.
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Affiliation(s)
- Kouhei Nishikawa
- Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering, Saga University, Saga 840-8502, Japan
| | - Ryosuke Kuroiwa
- Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering, Saga University, Saga 840-8502, Japan
| | - Jun Tamogami
- College of Pharmaceutical Sciences, Matsuyama University, Matsuyama, Ehime 790-8578, Japan
| | - Masashi Unno
- Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering, Saga University, Saga 840-8502, Japan
| | - Tomotsumi Fujisawa
- Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering, Saga University, Saga 840-8502, Japan
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18
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Wei Y, Wang S, Yu D. The Role of Light Quality in Regulating Early Seedling Development. PLANTS (BASEL, SWITZERLAND) 2023; 12:2746. [PMID: 37514360 PMCID: PMC10383958 DOI: 10.3390/plants12142746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 07/09/2023] [Accepted: 07/20/2023] [Indexed: 07/30/2023]
Abstract
It is well-established that plants are sessile and photoautotrophic organisms that rely on light throughout their entire life cycle. Light quality (spectral composition) is especially important as it provides energy for photosynthesis and influences signaling pathways that regulate plant development in the complex process of photomorphogenesis. During previous years, significant progress has been made in light quality's physiological and biochemical effects on crops. However, understanding how light quality modulates plant growth and development remains a complex challenge. In this review, we provide an overview of the role of light quality in regulating the early development of plants, encompassing processes such as seed germination, seedling de-etiolation, and seedling establishment. These insights can be harnessed to improve production planning and crop quality by producing high-quality seedlings in plant factories and improving the theoretical framework for modern agriculture.
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Affiliation(s)
- Yunmin Wei
- College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
- College of Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China
| | - Shuwei Wang
- College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Dashi Yu
- College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
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19
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Bournonville C, Mori K, Deslous P, Decros G, Blomeier T, Mauxion JP, Jorly J, Gadin S, Cassan C, Maucourt M, Just D, Brès C, Rothan C, Ferrand C, Fernandez-Lochu L, Bataille L, Miura K, Beven L, Zurbriggen MD, Pétriacq P, Gibon Y, Baldet P. Blue light promotes ascorbate synthesis by deactivating the PAS/LOV photoreceptor that inhibits GDP-L-galactose phosphorylase. THE PLANT CELL 2023; 35:2615-2634. [PMID: 37052931 PMCID: PMC10291033 DOI: 10.1093/plcell/koad108] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 02/14/2023] [Accepted: 03/15/2023] [Indexed: 06/19/2023]
Abstract
Ascorbate (vitamin C) is an essential antioxidant in fresh fruits and vegetables. To gain insight into the regulation of ascorbate metabolism in plants, we studied mutant tomato plants (Solanum lycopersicum) that produce ascorbate-enriched fruits. The causal mutation, identified by a mapping-by-sequencing strategy, corresponded to a knock-out recessive mutation in a class of photoreceptor named PAS/LOV protein (PLP), which acts as a negative regulator of ascorbate biosynthesis. This trait was confirmed by CRISPR/Cas9 gene editing and further found in all plant organs, including fruit that accumulated 2 to 3 times more ascorbate than in the WT. The functional characterization revealed that PLP interacted with the 2 isoforms of GDP-L-galactose phosphorylase (GGP), known as the controlling step of the L-galactose pathway of ascorbate synthesis. The interaction with GGP occurred in the cytoplasm and the nucleus, but was abolished when PLP was truncated. These results were confirmed by a synthetic approach using an animal cell system, which additionally demonstrated that blue light modulated the PLP-GGP interaction. Assays performed in vitro with heterologously expressed GGP and PLP showed that PLP is a noncompetitive inhibitor of GGP that is inactivated after blue light exposure. This discovery provides a greater understanding of the light-dependent regulation of ascorbate metabolism in plants.
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Affiliation(s)
- Céline Bournonville
- UMR 1332 Biologie du Fruit et Pathologie, Univ. Bordeaux, INRAE,33883 Villenave d'Ornon, France
| | - Kentaro Mori
- UMR 1332 Biologie du Fruit et Pathologie, Univ. Bordeaux, INRAE,33883 Villenave d'Ornon, France
| | - Paul Deslous
- UMR 1332 Biologie du Fruit et Pathologie, Univ. Bordeaux, INRAE,33883 Villenave d'Ornon, France
| | - Guillaume Decros
- UMR 1332 Biologie du Fruit et Pathologie, Univ. Bordeaux, INRAE,33883 Villenave d'Ornon, France
| | - Tim Blomeier
- Institute of Synthetic Biology—CEPLAS—Faculty of Mathematics and Natural Sciences, Heinrich-Heine-Universität Düsseldorf, Dusseldorf 40225, Germany
| | - Jean-Philippe Mauxion
- UMR 1332 Biologie du Fruit et Pathologie, Univ. Bordeaux, INRAE,33883 Villenave d'Ornon, France
| | - Joana Jorly
- UMR 1332 Biologie du Fruit et Pathologie, Univ. Bordeaux, INRAE,33883 Villenave d'Ornon, France
| | - Stéphanie Gadin
- UMR 1332 Biologie du Fruit et Pathologie, Univ. Bordeaux, INRAE,33883 Villenave d'Ornon, France
| | - Cédric Cassan
- UMR 1332 Biologie du Fruit et Pathologie, Univ. Bordeaux, INRAE,33883 Villenave d'Ornon, France
| | - Mickael Maucourt
- UMR 1332 Biologie du Fruit et Pathologie, Univ. Bordeaux, INRAE,33883 Villenave d'Ornon, France
| | - Daniel Just
- UMR 1332 Biologie du Fruit et Pathologie, Univ. Bordeaux, INRAE,33883 Villenave d'Ornon, France
| | - Cécile Brès
- UMR 1332 Biologie du Fruit et Pathologie, Univ. Bordeaux, INRAE,33883 Villenave d'Ornon, France
| | - Christophe Rothan
- UMR 1332 Biologie du Fruit et Pathologie, Univ. Bordeaux, INRAE,33883 Villenave d'Ornon, France
| | - Carine Ferrand
- UMR 1332 Biologie du Fruit et Pathologie, Univ. Bordeaux, INRAE,33883 Villenave d'Ornon, France
| | - Lucie Fernandez-Lochu
- UMR 1332 Biologie du Fruit et Pathologie, Univ. Bordeaux, INRAE,33883 Villenave d'Ornon, France
| | - Laure Bataille
- UMR 1332 Biologie du Fruit et Pathologie, Univ. Bordeaux, INRAE,33883 Villenave d'Ornon, France
| | - Kenji Miura
- Tsukuba Innovation Plant Research Center, University of Tsukuba, 1-1-1 Tennodai, 305-8577 Ibaraki, Tsukuba, Japan
| | - Laure Beven
- UMR 1332 Biologie du Fruit et Pathologie, Univ. Bordeaux, INRAE,33883 Villenave d'Ornon, France
| | - Matias D Zurbriggen
- Institute of Synthetic Biology—CEPLAS—Faculty of Mathematics and Natural Sciences, Heinrich-Heine-Universität Düsseldorf, Dusseldorf 40225, Germany
| | - Pierre Pétriacq
- UMR 1332 Biologie du Fruit et Pathologie, Univ. Bordeaux, INRAE,33883 Villenave d'Ornon, France
| | - Yves Gibon
- UMR 1332 Biologie du Fruit et Pathologie, Univ. Bordeaux, INRAE,33883 Villenave d'Ornon, France
| | - Pierre Baldet
- UMR 1332 Biologie du Fruit et Pathologie, Univ. Bordeaux, INRAE,33883 Villenave d'Ornon, France
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20
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Cerón-Bustamante M, Tini F, Beccari G, Benincasa P, Covarelli L. Effect of Different Light Wavelengths on Zymoseptoria tritici Development and Leaf Colonization in Bread Wheat. J Fungi (Basel) 2023; 9:670. [PMID: 37367606 DOI: 10.3390/jof9060670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 06/07/2023] [Accepted: 06/12/2023] [Indexed: 06/28/2023] Open
Abstract
The wheat pathogen Zymoseptoria tritici can respond to light by modulating its gene expression. Because several virulence-related genes are differentially expressed in response to light, different wavelengths could have a crucial role in the Z. tritici-wheat interaction. To explore this opportunity, the aim of this study was to analyze the effect of blue (470 nm), red (627 nm), blue-red, and white light on the in vitro and in planta development of Z. tritici. The morphology (mycelium appearance, color) and phenotypic (mycelium growth) characteristics of a Z. tritici strain were evaluated after 14 days under the different light conditions in two independent experiments. In addition, bread wheat plants were artificially inoculated with Z. tritici and grown for 35 days under the same light treatments. The disease incidence, severity, and fungal DNA were analyzed in a single experiment. Statistical differences were determined by using an ANOVA. The obtained results showed that the different light wavelengths induced specific morphological changes in mycelial growth. The blue light significantly reduced colony growth, while the dark and red light favored fungal development (p < 0.05). The light quality also influenced host colonization, whereby the white and red light had stimulating and repressing effects, respectively (p < 0.05). This precursory study demonstrated the influence of light on Z. tritici colonization in bread wheat.
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Affiliation(s)
- Minely Cerón-Bustamante
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Borgo XX Giugno 74, 06121 Perugia, Italy
| | - Francesco Tini
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Borgo XX Giugno 74, 06121 Perugia, Italy
| | - Giovanni Beccari
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Borgo XX Giugno 74, 06121 Perugia, Italy
| | - Paolo Benincasa
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Borgo XX Giugno 74, 06121 Perugia, Italy
| | - Lorenzo Covarelli
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Borgo XX Giugno 74, 06121 Perugia, Italy
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21
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Zhang Y, Liu Y, Ling L, Huo W, Li Y, Xu L, Xiang L, Yang Y, Xiong X, Zhang D, Yu X, Li Y. Phenotypic, Physiological, and Molecular Response of Loropetalum chinense var. rubrum under Different Light Quality Treatments Based on Leaf Color Changes. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12112169. [PMID: 37299148 DOI: 10.3390/plants12112169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Revised: 05/23/2023] [Accepted: 05/25/2023] [Indexed: 06/12/2023]
Abstract
Light quality is a vital environmental signal used to trigger growth and to develop structural differentiation in plants, and it influences morphological, physiological, and biochemical metabolites. In previous studies, different light qualities were found to regulate the synthesis of anthocyanin. However, the mechanism of the synthesis and accumulation of anthocyanins in leaves in response to light quality remains unclear. In this study, the Loropetalum chinense var. rubrum "Xiangnong Fendai" plant was treated with white light (WL), blue light (BL), ultraviolet-A light (UL), and blue light plus ultraviolet-A light (BL + UL), respectively. Under BL, the leaves were described as increasing in redness from "olive green" to "reddish-brown". The chlorophyll, carotenoid, anthocyanin, and total flavonoid content were significantly higher at 7 d than at 0 d. In addition, BL treatment also significantly increased the accumulation of soluble sugar and soluble protein. In contrast to BL, ultraviolet-A light increased the malondialdehyde (MDA) content and the activities of three antioxidant enzymes in the leaves, including catalase (CAT), peroxidase (POD), and superoxide dismutase (SOD), in varying degrees over time. Moreover, we also found that the CRY-like gene, HY5-like gene, BBX-like gene, MYB-like gene, CHS-like gene, DFR-like gene, ANS-like gene, and UFGT-like gene were significantly upregulated. Furthermore, the SOD-like, POD-like, and CAT-like gene expressions related to antioxidase synthesis were found under ultraviolet-A light conditions. In summary, BL is more conducive to reddening the leaves of "Xiangnong Fendai" and will not lead to excessive photooxidation. This provides an effective ecological strategy for light-induced leaf-color changes, thereby promoting the ornamental and economic value of L. chinense var. rubrum.
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Affiliation(s)
- Yifan Zhang
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China
- Engineering Research Center for Horticultural Crop Germplasm Creation and New Variety Breeding, Ministry of Education, Changsha 410128, China
| | - Yang Liu
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China
- Engineering Research Center for Horticultural Crop Germplasm Creation and New Variety Breeding, Ministry of Education, Changsha 410128, China
| | - Lin Ling
- School of Economics, Hunan Agricultural University, Changsha 410128, China
| | - Wenwen Huo
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China
- Engineering Research Center for Horticultural Crop Germplasm Creation and New Variety Breeding, Ministry of Education, Changsha 410128, China
| | - Yang Li
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China
- Engineering Research Center for Horticultural Crop Germplasm Creation and New Variety Breeding, Ministry of Education, Changsha 410128, China
| | - Lu Xu
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China
- Engineering Research Center for Horticultural Crop Germplasm Creation and New Variety Breeding, Ministry of Education, Changsha 410128, China
| | - Lili Xiang
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China
- Engineering Research Center for Horticultural Crop Germplasm Creation and New Variety Breeding, Ministry of Education, Changsha 410128, China
| | - Yujie Yang
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China
- Engineering Research Center for Horticultural Crop Germplasm Creation and New Variety Breeding, Ministry of Education, Changsha 410128, China
| | - Xingyao Xiong
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China
- Kunpeng Institute of Modern Agriculture, Foshan 528225, China
- Agricultural Genomics Institute at Shenzheng, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Donglin Zhang
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China
- Engineering Research Center for Horticultural Crop Germplasm Creation and New Variety Breeding, Ministry of Education, Changsha 410128, China
- Department of Horticulture, University of Georgia, Athens, GA 30602, USA
| | - Xiaoying Yu
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China
- Engineering Research Center for Horticultural Crop Germplasm Creation and New Variety Breeding, Ministry of Education, Changsha 410128, China
- Hunan Mid-Subtropical Quality Plant Breeding and Utilization Engineering Technology Research Center, Changsha 410128, China
| | - Yanlin Li
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China
- Engineering Research Center for Horticultural Crop Germplasm Creation and New Variety Breeding, Ministry of Education, Changsha 410128, China
- Kunpeng Institute of Modern Agriculture, Foshan 528225, China
- Hunan Mid-Subtropical Quality Plant Breeding and Utilization Engineering Technology Research Center, Changsha 410128, China
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
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22
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Konrad KR, Gao S, Zurbriggen MD, Nagel G. Optogenetic Methods in Plant Biology. ANNUAL REVIEW OF PLANT BIOLOGY 2023; 74:313-339. [PMID: 37216203 DOI: 10.1146/annurev-arplant-071122-094840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Optogenetics is a technique employing natural or genetically engineered photoreceptors in transgene organisms to manipulate biological activities with light. Light can be turned on or off, and adjusting its intensity and duration allows optogenetic fine-tuning of cellular processes in a noninvasive and spatiotemporally resolved manner. Since the introduction of Channelrhodopsin-2 and phytochrome-based switches nearly 20 years ago, optogenetic tools have been applied in a variety of model organisms with enormous success, but rarely in plants. For a long time, the dependence of plant growth on light and the absence of retinal, the rhodopsin chromophore, prevented the establishment of plant optogenetics until recent progress overcame these difficulties. We summarize the recent results of work in the field to control plant growth and cellular motion via green light-gated ion channels and present successful applications to light-control gene expression with single or combined photoswitches in plants. Furthermore, we highlight the technical requirements and options for future plant optogenetic research.
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Affiliation(s)
- Kai R Konrad
- Molecular Plant Physiology and Biophysics, Julius-von-Sachs Institute for Biosciences, Biocenter, University of Würzburg, Würzburg, Germany;
| | - Shiqiang Gao
- Department of Neurophysiology, Institute of Physiology, Biocenter, University of Würzburg, Würzburg, Germany; ,
| | - Matias D Zurbriggen
- Institute of Synthetic Biology and CEPLAS, University of Düsseldorf, Düsseldorf, Germany;
| | - Georg Nagel
- Department of Neurophysiology, Institute of Physiology, Biocenter, University of Würzburg, Würzburg, Germany; ,
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23
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Kircher S, Schopfer P. Photosynthetic sucrose drives the lateral root clock in Arabidopsis seedlings. Curr Biol 2023:S0960-9822(23)00543-2. [PMID: 37207646 DOI: 10.1016/j.cub.2023.04.061] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 12/20/2022] [Accepted: 04/25/2023] [Indexed: 05/21/2023]
Abstract
The development of plant roots is subject to control by light. Here, we show that, similar to monotonous root elongation, the periodic induction of lateral roots (LRs) depends on the activation by light of photomorphogenic and photosynthetic photoreceptors in the shoot in a hierarchical order. The prevailing belief is that the plant hormone auxin serves as a mobile signal transmitter, responsible for interorgan communication, including light-controlled shoot-to-root connections. Alternatively, it has been proposed that the transcription factor HY5 assumes the role as a mobile shoot-to-root signal transmitter. Here, we provide evidence that photosynthetic sucrose produced in the shoot acts as the long-distance signal carrier regulating the local, tryptophan-based biosynthesis of auxin in the LR generation zone of the primary root tip, where the LR clock controls the pace of LR initiation in an auxin-tunable manner. Synchronization of LR formation with primary root elongation allows the adjustment of overall root growth to the photosynthetic performance of the shoot and the maintenance of a constant LR density during light-dark changes in a variable light environment.
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Affiliation(s)
- Stefan Kircher
- Department of Molecular Plant Physiology, Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany.
| | - Peter Schopfer
- Department of Molecular Plant Physiology, Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany.
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24
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Woods DP, Li W, Sibout R, Shao M, Laudencia-Chingcuanco D, Vogel JP, Dubcovsky J, Amasino RM. PHYTOCHROME C regulation of photoperiodic flowering via PHOTOPERIOD1 is mediated by EARLY FLOWERING 3 in Brachypodium distachyon. PLoS Genet 2023; 19:e1010706. [PMID: 37163541 PMCID: PMC10171608 DOI: 10.1371/journal.pgen.1010706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 03/17/2023] [Indexed: 05/12/2023] Open
Abstract
Daylength sensing in many plants is critical for coordinating the timing of flowering with the appropriate season. Temperate climate-adapted grasses such as Brachypodium distachyon flower during the spring when days are becoming longer. The photoreceptor PHYTOCHROME C is essential for long-day (LD) flowering in B. distachyon. PHYC is required for the LD activation of a suite of genes in the photoperiod pathway including PHOTOPERIOD1 (PPD1) that, in turn, result in the activation of FLOWERING LOCUS T (FT1)/FLORIGEN, which causes flowering. Thus, B. distachyon phyC mutants are extremely delayed in flowering. Here we show that PHYC-mediated activation of PPD1 occurs via EARLY FLOWERING 3 (ELF3), a component of the evening complex in the circadian clock. The extreme delay of flowering of the phyC mutant disappears when combined with an elf3 loss-of-function mutation. Moreover, the dampened PPD1 expression in phyC mutant plants is elevated in phyC/elf3 mutant plants consistent with the rapid flowering of the double mutant. We show that loss of PPD1 function also results in reduced FT1 expression and extremely delayed flowering consistent with results from wheat and barley. Additionally, elf3 mutant plants have elevated expression levels of PPD1, and we show that overexpression of ELF3 results in delayed flowering associated with a reduction of PPD1 and FT1 expression, indicating that ELF3 represses PPD1 transcription consistent with previous studies showing that ELF3 binds to the PPD1 promoter. Indeed, PPD1 is the main target of ELF3-mediated flowering as elf3/ppd1 double mutant plants are delayed flowering. Our results indicate that ELF3 operates downstream from PHYC and acts as a repressor of PPD1 in the photoperiod flowering pathway of B. distachyon.
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Affiliation(s)
- Daniel P. Woods
- Dept. Plant Sciences, University of California, Davis, California, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
| | - Weiya Li
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Richard Sibout
- Institut Jean-Pierre Bourgin, UMR1318 INRAE-AgroParisTech, Versailles Cedex, France
- UR1268 BIA, INRAE, Nantes, France
| | - Mingqin Shao
- DOE Joint Genome Institute, Berkeley, California, United States of America
| | - Debbie Laudencia-Chingcuanco
- USDA-Agricultural Research Service, Western Regional Research Center, Albany, California, United States of America
| | - John P. Vogel
- DOE Joint Genome Institute, Berkeley, California, United States of America
| | - Jorge Dubcovsky
- Dept. Plant Sciences, University of California, Davis, California, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
| | - Richard M. Amasino
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin, United States of America
- United States Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, Wisconsin, United States of America
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25
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Wei Z, Yang H, Shi J, Duan Y, Wu W, Lyu L, Li W. Effects of Different Light Wavelengths on Fruit Quality and Gene Expression of Anthocyanin Biosynthesis in Blueberry ( Vaccinium corymbosm). Cells 2023; 12:cells12091225. [PMID: 37174623 PMCID: PMC10177116 DOI: 10.3390/cells12091225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 04/15/2023] [Accepted: 04/21/2023] [Indexed: 05/15/2023] Open
Abstract
Different light wavelengths display diverse effects on fruit quality formation and anthocyanin biosynthesis. Blueberry is a kind of fruit rich in anthocyanin with important economic and nutritional values. This study explored the effects of different light wavelengths (white (W), red (R), blue (B) and yellow (Y)) on fruit quality and gene expression of anthocyanin biosynthesis in blueberry. We found that the B and W treatments attained the maximum values of fruit width, fruit height and fruit weight in blueberry fruits. The R treatment attained the maximum activities of superoxide dismutase (SOD) and peroxidase (POD), and the Y treatment displayed the maximum contents of ascorbic acid (AsA), glutathione (GSH) and total phenol in fruits, thus improving blueberry-fruit antioxidant capacity. Interestingly, there were differences in the solidity-acid ratio of fruit under different light-wavelength treatments. Moreover, blue light could significantly improve the expression levels of anthocyanin biosynthesis genes and anthocyanin content in fruits. Correlation and principal component analysis showed that total acid content and antioxidant enzymes were significantly negatively correlated with anthocyanin content in blueberry fruits. These results provide new insights for the application of light wavelength to improve blueberry fruit quality and anthocyanin content.
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Affiliation(s)
- Zhiwen Wei
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing 210037, China
| | - Haiyan Yang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Nanjing 210014, China
| | - Jie Shi
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing 210037, China
| | - Yongkang Duan
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing 210037, China
| | - Wenlong Wu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Nanjing 210014, China
| | - Lianfei Lyu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Nanjing 210014, China
| | - Weilin Li
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing 210037, China
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26
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Ruf J, Bindschedler F, Buhrke D. The molecular mechanism of light-induced bond formation and breakage in the cyanobacteriochrome TePixJ. Phys Chem Chem Phys 2023; 25:6016-6024. [PMID: 36752541 PMCID: PMC9945933 DOI: 10.1039/d2cp05856a] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
Cyanobacteriochromes (CBCRs) are small and versatile photoreceptor proteins with high potential for biotechnological applications. Among them, the so-called DXCF-CBCRs exhibit an intricate secondary photochemistry: miliseconds after activation with light, a covalent linkage between a conserved cysteine residue and the light-absorbing tetrapyrrole chromophore is reversibly formed or broken. We employed time-resolved IR spectroscopy over ten orders of magnitude in time in conjunction with 2D-IR spectroscopy to investigate the molecular mechanism of this intriguing reaction in the DXCF-CBCR model system TePixJ from T. elongatus. The crosspeak pattern in the 2D-IR spectrum facilitated the assignment of the dominant signals to vibrational modes of the chromophore, which in turn enabled us to construct a mechanistic model for the photocycle reactions from the time-resolved IR spectra. Here, we assigned the time-resolved signals to several proton transfer steps and distinct geometric changes of the chromophore. We propose a model that describes how these events lead to the rearrangement of charges in the chromophore binding pocket, which serves as the trigger for the light-induced bond formation and breakage with the nearby cysteine.
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Affiliation(s)
- Jeannette Ruf
- Department of Chemistry, University of Zurich, Zurich, Switzerland.
| | | | - David Buhrke
- Department of Chemistry, University of Zurich, Zurich, Switzerland. .,Institute of Biology, Humboldt University Berlin, Germany
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27
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Priyadarshini N, Steube N, Wiens D, Narikawa R, Wilde A, Hochberg GKA, Enomoto G. Evidence for an early green/red photocycle that precedes the diversification of GAF domain photoreceptor cyanobacteriochromes. PHOTOCHEMICAL & PHOTOBIOLOGICAL SCIENCES : OFFICIAL JOURNAL OF THE EUROPEAN PHOTOCHEMISTRY ASSOCIATION AND THE EUROPEAN SOCIETY FOR PHOTOBIOLOGY 2023:10.1007/s43630-023-00387-4. [PMID: 36781703 DOI: 10.1007/s43630-023-00387-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 02/01/2023] [Indexed: 02/15/2023]
Abstract
Phytochromes are linear tetrapyrrole-binding photoreceptors in eukaryotes and bacteria, primarily responding to red and far-red light signals reversibly. Among the GAF domain-based phytochrome superfamily, cyanobacteria-specific cyanobacteriochromes show various optical properties covering the entire visible region. It is unknown what physiological demands drove the evolution of cyanobacteriochromes in cyanobacteria. Here, we utilize ancestral sequence reconstruction and biochemical verification to show that the resurrected ancestral cyanobacteriochrome proteins reversibly respond to green and red light signals. pH titration analyses indicate that the deprotonation of the bound phycocyanobilin chromophore is crucial to perceive green light. The ancestral cyanobacteriochromes show only modest thermal reversion to the green light-absorbing form, suggesting that they evolved to sense the incident green/red light ratio. Many cyanobacteria can utilize green light for photosynthesis using phycobilisome light-harvesting complexes. The green/red sensing cyanobacteriochromes may have allowed better acclimation to changing light environments by rearranging the absorption capacity of the phycobilisome through chromatic acclimation.
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Affiliation(s)
- Nibedita Priyadarshini
- Faculty of Biology, Institute of Biology III, University of Freiburg, Schänzlestr. 1, 79104, Freiburg, Germany.,Spemann Graduate School of Biology and Medicine, Albertstr. 19, 79104, Freiburg, Germany
| | - Niklas Steube
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043, Marburg, Germany
| | - Dennis Wiens
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043, Marburg, Germany
| | - Rei Narikawa
- Graduate School of Biological Sciences, Faculty of Science, Tokyo Metropolitan University, 1-1 Minami-Ohsawa, Hachioji, Tokyo, 192-0397, Japan
| | - Annegret Wilde
- Faculty of Biology, Institute of Biology III, University of Freiburg, Schänzlestr. 1, 79104, Freiburg, Germany
| | - Georg K A Hochberg
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043, Marburg, Germany. .,Faculty of Chemistry, University of Marburg, Hans-Meerwein-Str. 4, 35032, Marburg, Germany. .,Center for Synthetic Microbiology (SYNMIKRO), Karl-von-Frisch-Str. 14, 35032, Marburg, Germany.
| | - Gen Enomoto
- Faculty of Biology, Institute of Biology III, University of Freiburg, Schänzlestr. 1, 79104, Freiburg, Germany. .,Department of Engineering Science, Graduate School of Informatics and Engineering, The University of Electro-Communications, 1-5-1 Chofugaoka, Chofu, Tokyo, 182-8585, Japan.
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28
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Wang E, Zhou T, Jing S, Dong L, Sun X, Fan Y, Shen Y, Liu T, Song B. Leaves and stolons transcriptomic analysis provide insight into the role of phytochrome F in potato flowering and tuberization. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 113:402-415. [PMID: 36562774 DOI: 10.1111/tpj.16056] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Revised: 11/28/2022] [Accepted: 12/06/2022] [Indexed: 06/17/2023]
Abstract
Photoperiod plays a critical role in controlling the formation of sexual or vegetative reproductive organs in potato. Although StPHYF-silenced plants overcome day-length limitations to tuberize through a systemic effect on tuberigen StSP6A expression in the stolon, the comprehensive regulatory network of StPHYF remains obscure. Therefore, the present study investigated the transcriptomes of StPHYF-silenced plants and observed that, in addition to known components of the photoperiodic tuberization pathway, florigen StSP3D and other flowering-related genes were activated in StPHYF-silenced plants, exhibiting an early flowering response. Additionally, grafting experiments uncovered the long-distance effect of StPHYF silencing on gene expression in the stolon, including the circadian clock components, flowering-associated MADSs, and tuberization-related regulatory genes. Similar to the AtFT-AtAP1 regulatory module in Arabidopsis, the present study established that the AP1-like StMADS1 functions downstream of the tuberigen activation complex (TAC) and that suppressing StMADS1 inhibits tuberization in vitro and delays tuberization in vivo. Moreover, the expression of StSP6A was downregulated in StMADS1-silenced plants, implying the expression of StSP6A may be feedback-regulated by StMADS1. Overall, these results reveal that the regulatory network of StPHYF controls flowering and tuberization and targets the crucial tuberization factor StMADS1 through TAC, thereby providing a better understanding of StPHYF-mediated day-length perception during potato reproduction.
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Affiliation(s)
- Enshuang Wang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education (HZAU), Wuhan, 430070, China
- Key Laboratory of Potato Biology and Biotechnology (HZAU), Ministry of Agriculture and Rural Affairs, Wuhan, 430070, China
- Potato Engineering and Technology Research Center of Hubei Province, Huazhong Agricultural University, Wuhan, 430070, China
- College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Tingting Zhou
- Key Laboratory of Horticultural Plant Biology, Ministry of Education (HZAU), Wuhan, 430070, China
- Key Laboratory of Potato Biology and Biotechnology (HZAU), Ministry of Agriculture and Rural Affairs, Wuhan, 430070, China
- Potato Engineering and Technology Research Center of Hubei Province, Huazhong Agricultural University, Wuhan, 430070, China
| | - Shenglin Jing
- Key Laboratory of Horticultural Plant Biology, Ministry of Education (HZAU), Wuhan, 430070, China
- Key Laboratory of Potato Biology and Biotechnology (HZAU), Ministry of Agriculture and Rural Affairs, Wuhan, 430070, China
- Potato Engineering and Technology Research Center of Hubei Province, Huazhong Agricultural University, Wuhan, 430070, China
- College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Liepeng Dong
- Key Laboratory of Horticultural Plant Biology, Ministry of Education (HZAU), Wuhan, 430070, China
- Key Laboratory of Potato Biology and Biotechnology (HZAU), Ministry of Agriculture and Rural Affairs, Wuhan, 430070, China
- Potato Engineering and Technology Research Center of Hubei Province, Huazhong Agricultural University, Wuhan, 430070, China
- College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Xiaomeng Sun
- Key Laboratory of Horticultural Plant Biology, Ministry of Education (HZAU), Wuhan, 430070, China
- Key Laboratory of Potato Biology and Biotechnology (HZAU), Ministry of Agriculture and Rural Affairs, Wuhan, 430070, China
- Potato Engineering and Technology Research Center of Hubei Province, Huazhong Agricultural University, Wuhan, 430070, China
- College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Yujie Fan
- Key Laboratory of Horticultural Plant Biology, Ministry of Education (HZAU), Wuhan, 430070, China
- Key Laboratory of Potato Biology and Biotechnology (HZAU), Ministry of Agriculture and Rural Affairs, Wuhan, 430070, China
- Potato Engineering and Technology Research Center of Hubei Province, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yunlong Shen
- Key Laboratory of Horticultural Plant Biology, Ministry of Education (HZAU), Wuhan, 430070, China
- Key Laboratory of Potato Biology and Biotechnology (HZAU), Ministry of Agriculture and Rural Affairs, Wuhan, 430070, China
- Potato Engineering and Technology Research Center of Hubei Province, Huazhong Agricultural University, Wuhan, 430070, China
| | - Tengfei Liu
- Key Laboratory of Horticultural Plant Biology, Ministry of Education (HZAU), Wuhan, 430070, China
- Key Laboratory of Potato Biology and Biotechnology (HZAU), Ministry of Agriculture and Rural Affairs, Wuhan, 430070, China
- Potato Engineering and Technology Research Center of Hubei Province, Huazhong Agricultural University, Wuhan, 430070, China
- College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Botao Song
- Key Laboratory of Horticultural Plant Biology, Ministry of Education (HZAU), Wuhan, 430070, China
- Key Laboratory of Potato Biology and Biotechnology (HZAU), Ministry of Agriculture and Rural Affairs, Wuhan, 430070, China
- Potato Engineering and Technology Research Center of Hubei Province, Huazhong Agricultural University, Wuhan, 430070, China
- College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
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Imsande KG, Batzli JM. Additional green light induces shade response symptoms in Brassica rapa as evidenced by increased lateral root spread. MICROPUBLICATION BIOLOGY 2022; 2022:10.17912/micropub.biology.000723. [PMID: 36618026 PMCID: PMC9813772 DOI: 10.17912/micropub.biology.000723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 11/29/2022] [Accepted: 12/16/2022] [Indexed: 01/10/2023]
Abstract
In some plant species, green light (500 to 570 nm) has been shown to act as a shade signal, which stimulates non-photosynthetic photoreceptors to initiate a response that promotes shading symptoms, including lateral root formation. No studies to date have examined whether green light induces shading symptoms in Brassica rapa specifically. Here, we report increased hypocotyl length, root width, and increased width:depth ratio of root architecture in plants grown under additional green light compared to red and blue light, and white light alone. Results indicate that green light acts as a shade signal in B. rapa to induce shading symptoms, including wider roots.
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Affiliation(s)
- Kaylynn G Imsande
- Department of Biology Core Curriculum (Biocore), University of Wisconsin – Madison, WI, USA
,
Correspondence to: Kaylynn G Imsande (
)
| | - Janet M Batzli
- Department of Biology Core Curriculum (Biocore), University of Wisconsin – Madison, WI, USA
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30
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Stafen CF, Kleine-Vehn J, Maraschin FDS. Signaling events for photomorphogenic root development. TRENDS IN PLANT SCIENCE 2022; 27:1266-1282. [PMID: 36057533 DOI: 10.1016/j.tplants.2022.08.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 07/26/2022] [Accepted: 08/02/2022] [Indexed: 06/15/2023]
Abstract
A germinating seedling incorporates environmental signals such as light into developmental outputs. Light is not only a source of energy, but also a central coordinative signal in plants. Traditionally, most research focuses on aboveground organs' response to light; therefore, our understanding of photomorphogenesis in roots is relatively scarce. However, root development underground is highly responsive to light signals from the shoot and understanding these signaling mechanisms will give a better insight into early seedling development. Here, we review the central light signaling hubs and their role in root growth promotion of Arabidopsis thaliana seedlings.
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Affiliation(s)
- Cássia Fernanda Stafen
- PPGBM - Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, RS, Brazil
| | - Jürgen Kleine-Vehn
- Institute of Biology II, Chair of Molecular Plant Physiology (MoPP), University of Freiburg, Freiburg, Germany; Center for Integrative Biological Signalling Studies (CIBSS), University of Freiburg, 79104 Freiburg, Germany
| | - Felipe Dos Santos Maraschin
- PPGBM - Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, RS, Brazil; Departamento de Botânica, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, RS, Brazil.
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31
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Weik M, Domratcheva T. Insight into the structural dynamics of light sensitive proteins from time-resolved crystallography and quantum chemical calculations. Curr Opin Struct Biol 2022; 77:102496. [PMID: 36462226 DOI: 10.1016/j.sbi.2022.102496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 10/14/2022] [Accepted: 10/14/2022] [Indexed: 12/03/2022]
Abstract
The structural dynamics underlying molecular mechanisms of light-sensitive proteins can be studied by a variety of experimental and computational biophysical techniques. Here we review recent progress in combining time-resolved crystallography at X-ray free electron lasers and quantum chemical calculations to study structural changes in photoenzymes, photosynthetic proteins, photoreceptors, and photoswitchable fluorescent proteins following photoexcitation.
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Affiliation(s)
- Martin Weik
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, F-38044 Grenoble, France.
| | - Tatiana Domratcheva
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia; Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120 Heidelberg, Germany.
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32
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Protein control of photochemistry and transient intermediates in phytochromes. Nat Commun 2022; 13:6838. [PMID: 36369284 PMCID: PMC9652276 DOI: 10.1038/s41467-022-34640-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 11/01/2022] [Indexed: 11/13/2022] Open
Abstract
Phytochromes are ubiquitous photoreceptors responsible for sensing light in plants, fungi and bacteria. Their photoactivation is initiated by the photoisomerization of the embedded chromophore, triggering large conformational changes in the protein. Despite numerous experimental and computational studies, the role of chromophore-protein interactions in controlling the mechanism and timescale of the process remains elusive. Here, we combine nonadiabatic surface hopping trajectories and adiabatic molecular dynamics simulations to reveal the molecular details of such control for the Deinococcus radiodurans bacteriophytochrome. Our simulations reveal that chromophore photoisomerization proceeds through a hula-twist mechanism whose kinetics is mainly determined by the hydrogen bond of the chromophore with a close-by histidine. The resulting photoproduct relaxes to an early intermediate stabilized by a tyrosine, and finally evolves into a late intermediate, featuring a more disordered binding pocket and a weakening of the aspartate-to-arginine salt-bridge interaction, whose cleavage is essential to interconvert the phytochrome to the active state.
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33
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Ranzani AT, Wehrmann M, Kaiser J, Juraschitz M, Weber AM, Pietruschka G, Gerken U, Mayer G, Möglich A. Light-Dependent Control of Bacterial Expression at the mRNA Level. ACS Synth Biol 2022; 11:3482-3492. [PMID: 36129831 DOI: 10.1021/acssynbio.2c00365] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Sensory photoreceptors mediate numerous light-dependent adaptations across organisms. In optogenetics, photoreceptors achieve the reversible, non-invasive, and spatiotemporally precise control by light of gene expression and other cellular processes. The light-oxygen-voltage receptor PAL binds to small RNA aptamers with sequence specificity upon blue-light illumination. By embedding the responsive aptamer in the ribosome-binding sequence of genes of interest, their expression can be downregulated by light. We developed the pCrepusculo and pAurora optogenetic systems that are based on PAL and allow to down- and upregulate, respectively, bacterial gene expression using blue light. Both systems are realized as compact, single plasmids that exhibit stringent blue-light responses with low basal activity and up to several 10-fold dynamic range. As PAL exerts light-dependent control at the RNA level, it can be combined with other optogenetic circuits that control transcription initiation. By integrating regulatory mechanisms operating at the DNA and mRNA levels, optogenetic circuits with emergent properties can thus be devised. As a case in point, the pEnumbra setup permits to upregulate gene expression under moderate blue light whereas strong blue light shuts off expression again. Beyond providing novel signal-responsive expression systems for diverse applications in biotechnology and synthetic biology, our work also illustrates how the light-dependent PAL-aptamer interaction can be harnessed for the control and interrogation of RNA-based processes.
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Affiliation(s)
- Américo T Ranzani
- Department of Biochemistry, University of Bayreuth, 95447 Bayreuth, Germany
| | - Markus Wehrmann
- Department of Biochemistry, University of Bayreuth, 95447 Bayreuth, Germany
| | - Jennifer Kaiser
- Department of Biochemistry, University of Bayreuth, 95447 Bayreuth, Germany
| | - Marc Juraschitz
- Department of Biochemistry, University of Bayreuth, 95447 Bayreuth, Germany
| | - Anna M Weber
- Life and Medical Sciences (LIMES), University of Bonn, 53121 Bonn, Germany
| | - Georg Pietruschka
- Life and Medical Sciences (LIMES), University of Bonn, 53121 Bonn, Germany
| | - Uwe Gerken
- Lehrstuhl für Spektroskopie weicher Materie, University of Bayreuth, 95447 Bayreuth, Germany
| | - Günter Mayer
- Life and Medical Sciences (LIMES), University of Bonn, 53121 Bonn, Germany.,Center of Aptamer Research & Development, University of Bonn, 53121 Bonn, Germany
| | - Andreas Möglich
- Department of Biochemistry, University of Bayreuth, 95447 Bayreuth, Germany.,Bayreuth Center for Biochemistry & Molecular Biology, Universität Bayreuth, 95447 Bayreuth, Germany.,North-Bavarian NMR Center, Universität Bayreuth, 95447 Bayreuth, Germany
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34
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Feng Z, Ducos B, Scerbo P, Aujard I, Jullien L, Bensimon D. The Development and Application of Opto-Chemical Tools in the Zebrafish. Molecules 2022; 27:molecules27196231. [PMID: 36234767 PMCID: PMC9572478 DOI: 10.3390/molecules27196231] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 09/19/2022] [Accepted: 09/20/2022] [Indexed: 11/18/2022] Open
Abstract
The zebrafish is one of the most widely adopted animal models in both basic and translational research. This popularity of the zebrafish results from several advantages such as a high degree of similarity to the human genome, the ease of genetic and chemical perturbations, external fertilization with high fecundity, transparent and fast-developing embryos, and relatively low cost-effective maintenance. In particular, body translucency is a unique feature of zebrafish that is not adequately obtained with other vertebrate organisms. The animal’s distinctive optical clarity and small size therefore make it a successful model for optical modulation and observation. Furthermore, the convenience of microinjection and high embryonic permeability readily allow for efficient delivery of large and small molecules into live animals. Finally, the numerous number of siblings obtained from a single pair of animals offers large replicates and improved statistical analysis of the results. In this review, we describe the development of opto-chemical tools based on various strategies that control biological activities with unprecedented spatiotemporal resolution. We also discuss the reported applications of these tools in zebrafish and highlight the current challenges and future possibilities of opto-chemical approaches, particularly at the single cell level.
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Affiliation(s)
- Zhiping Feng
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA
- Correspondence: (Z.F.); (D.B.)
| | - Bertrand Ducos
- Laboratoire de Physique de l’Ecole Normale Supérieure, Paris Sciences Letters University, Sorbonne Université, Université de Paris, Centre National de la Recherche Scientifique, 24 Rue Lhomond, 75005 Paris, France
- High Throughput qPCR Core Facility, Ecole Normale Supérieure, Paris Sciences Letters University, 46 Rue d’Ulm, 75005 Paris, France
| | - Pierluigi Scerbo
- Laboratoire de Physique de l’Ecole Normale Supérieure, Paris Sciences Letters University, Sorbonne Université, Université de Paris, Centre National de la Recherche Scientifique, 24 Rue Lhomond, 75005 Paris, France
- Inovarion, 75005 Paris, France
| | - Isabelle Aujard
- Laboratoire PASTEUR, Département de Chimie, Ecole Normale Supérieure, Paris Sciences Letters University, Sorbonne Université, Centre National de la Recherche Scientifique, 24 Rue Lhomond, 75005 Paris, France
| | - Ludovic Jullien
- Laboratoire PASTEUR, Département de Chimie, Ecole Normale Supérieure, Paris Sciences Letters University, Sorbonne Université, Centre National de la Recherche Scientifique, 24 Rue Lhomond, 75005 Paris, France
| | - David Bensimon
- Laboratoire de Physique de l’Ecole Normale Supérieure, Paris Sciences Letters University, Sorbonne Université, Université de Paris, Centre National de la Recherche Scientifique, 24 Rue Lhomond, 75005 Paris, France
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
- Correspondence: (Z.F.); (D.B.)
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35
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Gao Y, Li G, Cai B, Zhang Z, Li N, Liu Y, Li Q. Effects of rare-earth light conversion film on the growth and fruit quality of sweet pepper in a solar greenhouse. FRONTIERS IN PLANT SCIENCE 2022; 13:989271. [PMID: 36147241 PMCID: PMC9485565 DOI: 10.3389/fpls.2022.989271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 08/19/2022] [Indexed: 06/16/2023]
Abstract
Light is an important environmental factor influencing plant growth and development. However, artificial light supplement is difficult to spread for its high energy consumption. In recent years, rare-earth light conversion film (RPO) covering is being focused on to be a new technology to study the mechanism of light affecting plant growth and development. Compared with the polyolefin film (PO), the RPO film advanced the temperature and light environment inside the greenhouse. Ultimately, improved growth and higher yield were detected because of a higher photosynthesis, Rubisco activity and Rubisco small subunit transcription. Compared with that in the greenhouse with polyolefin film, the plant height, stem diameter and internode length of sweet pepper treated with RPO increased by 11.05, 16.96 and 25.27%, respectively. In addition, Gibberellic acid 3 (GA3), Indole-3-acetic acid (IAA), Zeatin Riboside contents were increased by 11.95, 2.84 and 16.19%, respectively, compared with that with PO film. The fruit quality was improved, and the contents of ascorbic acid (Vc), soluble protein and soluble sugar were significantly higher than those of PO film, respectively, increased by 14.29, 47.10 and 67.69%. On the basis of improved fruit quality, the yield of RPO treatment increased by 20.34% compared with PO film. This study introduces an effective and low-energy method to study the mechanism and advancing plant growth in fruit vegetables production.
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36
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Kurttila M, Etzl S, Rumfeldt J, Takala H, Galler N, Winkler A, Ihalainen JA. The structural effect between the output module and chromophore-binding domain is a two-way street via the hairpin extension. PHOTOCHEMICAL & PHOTOBIOLOGICAL SCIENCES : OFFICIAL JOURNAL OF THE EUROPEAN PHOTOCHEMISTRY ASSOCIATION AND THE EUROPEAN SOCIETY FOR PHOTOBIOLOGY 2022; 21:1881-1894. [PMID: 35984631 PMCID: PMC9630206 DOI: 10.1007/s43630-022-00265-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 06/30/2022] [Indexed: 11/23/2022]
Abstract
Signal transduction typically starts with either ligand binding or cofactor activation, eventually affecting biological activities in the cell. In red light-sensing phytochromes, isomerization of the bilin chromophore results in regulation of the activity of diverse output modules. During this process, several structural elements and chemical events influence signal propagation. In our study, we have studied the full-length bacteriophytochrome from Deinococcus radiodurans as well as a previously generated optogenetic tool where the native histidine kinase output module has been replaced with an adenylate cyclase. We show that the composition of the output module influences the stability of the hairpin extension. The hairpin, often referred as the PHY tongue, is one of the central structural elements for signal transduction. It extends from a distinct domain establishing close contacts with the chromophore binding site. If the coupling between these interactions is disrupted, the dynamic range of the enzymatic regulation is reduced. Our study highlights the complex conformational properties of the hairpin extension as a bidirectional link between the chromophore-binding site and the output module, as well as functional properties of diverse output modules.
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Affiliation(s)
- Moona Kurttila
- Nanoscience Center, Department of Biological and Environmental Science, University of Jyväskylä, 40014, Jyväskylä, Finland
| | - Stefan Etzl
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/II, 8010, Graz, Austria
| | - Jessica Rumfeldt
- Nanoscience Center, Department of Biological and Environmental Science, University of Jyväskylä, 40014, Jyväskylä, Finland
| | - Heikki Takala
- Nanoscience Center, Department of Biological and Environmental Science, University of Jyväskylä, 40014, Jyväskylä, Finland
| | - Nadine Galler
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/II, 8010, Graz, Austria
| | - Andreas Winkler
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/II, 8010, Graz, Austria.
| | - Janne A Ihalainen
- Nanoscience Center, Department of Biological and Environmental Science, University of Jyväskylä, 40014, Jyväskylä, Finland.
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37
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Genomewide Identification and Characterization of the Genes Involved in the Flowering of Cotton. Int J Mol Sci 2022; 23:ijms23147940. [PMID: 35887288 PMCID: PMC9323069 DOI: 10.3390/ijms23147940] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 07/12/2022] [Accepted: 07/16/2022] [Indexed: 01/27/2023] Open
Abstract
Flowering is a prerequisite for flowering plants to complete reproduction, and flowering time has an important effect on the high and stable yields of crops. However, there are limited reports on flowering-related genes at the genomic level in cotton. In this study, genomewide analysis of the evolutionary relationship of flowering-related genes in different cotton species shows that the numbers of flowering-related genes in the genomes of tetraploid cotton species Gossypium hirsutum and Gossypium barbadense were similar, and that these numbers were approximately twice as much as the number in diploid cotton species Gossypium arboretum. The classification of flowering-related genes shows that most of them belong to the photoperiod and circadian clock flowering pathway. The distribution of flowering-related genes on the chromosomes of the At and Dt subgenomes was similar, with no subgenomic preference detected. In addition, most of the flowering-related core genes in Arabidopsis thaliana had homologs in the cotton genome, but the copy numbers and expression patterns were disparate; moreover, flowering-related genes underwent purifying selection throughout the evolutionary and selection processes. Although the differentiation and reorganization of many key genes of the cotton flowering regulatory network occurred throughout the evolutionary and selection processes, most of them, especially those involved in the important flowering regulatory networks, have been relatively conserved and preferentially selected.
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38
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Toda MJ, Lodowski P, Mamun AA, Kozlowski PM. Photoproduct formation in coenzyme B 12-dependent CarH via a singlet pathway. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY. B, BIOLOGY 2022; 232:112471. [PMID: 35644067 DOI: 10.1016/j.jphotobiol.2022.112471] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 03/26/2022] [Accepted: 05/10/2022] [Indexed: 06/15/2023]
Abstract
The CarH photoreceptor exploits of the light-sensing ability of coenzyme B12 ( adenosylcobalamin = AdoCbl) to perform its catalytic function, which includes large-scale structural changes to regulate transcription. In daylight, transcription is activated in CarH via the photo-cleavage of the Co-C5' bond of coenzyme B12. Subsequently, the photoproduct, 4',5'-anhydroadenosine (anhAdo) is formed inducing dissociation of the CarH tetramer from DNA. Several experimental studies have proposed that hydridocoblamin (HCbl) may be formed in process with anhAdo. The photolytic cleavage of the Co-C5' bond of AdoCbl was previously investigated using photochemical techniques and the involvement of both singlet and triplet excited states were explored. Herein, QM/MM calculations were employed to probe (1) the photolytic processes which may involve singlet excited states, (2) the mechanism of anhAdo formation, and (3) whether HCbl is a viable intermediate in CarH. Time-dependent density functional theory (TD-DFT) calculations indicate that the mechanism of photodissociation of the Ado ligand involves the ligand field (LF) portion of the lowest singlet excited state (S1) potential energy surface (PES). This is followed by deactivation to a point on the S0 PES where the Co-C5' bond remains broken. This species corresponds to a singlet diradical intermediate. From this point, the PES for anhAdo formation was explored, using the Co-C5' and Co-C4' bond distances as active coordinates, and a local minimum representing anhAdo and HCbl formation was found. The transition state (TS) for the formation of the Co-H bond of HCbl was located and its identity was confirmed by a single imaginary frequency of i1592 cm-1. Comparisons to experimental studies and the potential role of rotation around the N-glycosidic bond of the Ado ligand were discussed.
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Affiliation(s)
- Megan J Toda
- Department of Chemistry, University of Louisville, Louisville, KY 40292, United States
| | - Piotr Lodowski
- Institute of Chemistry, Faculty of Science and Technology, University of Silesia in Katowice, Szkolna 9, PL-40 006 Katowice, Poland
| | - Abdullah Al Mamun
- Department of Chemistry, University of Louisville, Louisville, KY 40292, United States
| | - Pawel M Kozlowski
- Department of Chemistry, University of Louisville, Louisville, KY 40292, United States.
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Influence of the PHY domain on the ms-photoconversion dynamics of a knotless phytochrome. Photochem Photobiol Sci 2022; 21:1627-1636. [PMID: 35687310 DOI: 10.1007/s43630-022-00245-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 05/11/2022] [Indexed: 10/18/2022]
Abstract
The ability of some knotless phytochromes to photoconvert without the PHY domain allows evaluation of the distinct effect of the PHY domain on their photodynamics. Here, we compare the ms dynamics of the single GAF domain (g1) and the GAF-PHY (g1g2) construct of the knotless phytochrome All2699 from cyanobacterium Nostoc punctiforme. While the spectral signatures and occurrence of the intermediates are mostly unchanged by the domain composition, the presence of the PHY domain slows down the early forward and reverse dynamics involving chromophore and protein binding pocket relaxation. We assign this effect to a more restricted binding pocket imprinted by the PHY domain. The photoproduct formation is also slowed down by the presence of the PHY domain but to a lesser extent than the early dynamics. This indicates a rate limiting step within the GAF and not the PHY domain. We further identify a pH dependence of the biphasic photoproduct formation hinting towards a pKa dependent tuning mechanism. Our findings add to the understanding of the role of the individual domains in the photocycle dynamics and provide a basis for engineering of phytochromes towards biotechnological applications.
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40
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Piccinini L, Iacopino S, Cazzaniga S, Ballottari M, Giuntoli B, Licausi F. A synthetic switch based on orange carotenoid protein to control blue-green light responses in chloroplasts. PLANT PHYSIOLOGY 2022. [PMID: 35289909 DOI: 10.1101/2021.01.27.428448] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Synthetic biology approaches to engineer light-responsive systems are widely used, but their applications in plants are still limited due to the interference with endogenous photoreceptors and the intrinsic requirement of light for photosynthesis. Cyanobacteria possess a family of soluble carotenoid-associated proteins named orange carotenoid proteins (OCPs) that, when activated by blue-green light, undergo a reversible conformational change that enables the photoprotection mechanism that occurs on the phycobilisome. Exploiting this system, we developed a chloroplast-localized synthetic photoswitch based on a protein complementation assay where two nanoluciferase fragments were fused to separate polypeptides corresponding to the OCP2 domains. Since Arabidopsis (Arabidopsis thaliana) does not possess the prosthetic group needed for the assembly of the OCP2 complex, we first implemented the carotenoid biosynthetic pathway with a bacterial β-carotene ketolase enzyme (crtW) to generate keto-carotenoid-producing plants. The photoswitch was tested and characterized in Arabidopsis protoplasts and stably transformed plants with experiments aimed to uncover its regulation by a range of light intensities, wavelengths, and its conversion dynamics. Finally, we applied the OCP-based photoswitch to control transcriptional responses in chloroplasts in response to green light illumination by fusing the two OCP fragments with the plastidial SIGMA FACTOR 2 and bacteriophage T4 anti-sigma factor AsiA. This pioneering study establishes the basis for future implementation of plastid optogenetics to regulate organelle responses upon exposure to specific light spectra.
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Affiliation(s)
- Luca Piccinini
- Plantlab, Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa 56127, Italy
| | - Sergio Iacopino
- Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, UK
| | - Stefano Cazzaniga
- Department of Biotechnology, University of Verona, Verona 37134, Italy
| | - Matteo Ballottari
- Department of Biotechnology, University of Verona, Verona 37134, Italy
| | - Beatrice Giuntoli
- Plantlab, Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa 56127, Italy
- Department of Biology, University of Pisa, Pisa 56126, Italy
| | - Francesco Licausi
- Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, UK
- Department of Biology, University of Pisa, Pisa 56126, Italy
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41
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Piccinini L, Iacopino S, Cazzaniga S, Ballottari M, Giuntoli B, Licausi F. A synthetic switch based on orange carotenoid protein to control blue-green light responses in chloroplasts. PLANT PHYSIOLOGY 2022; 189:1153-1168. [PMID: 35289909 PMCID: PMC9157063 DOI: 10.1093/plphys/kiac122] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 02/20/2022] [Indexed: 05/11/2023]
Abstract
Synthetic biology approaches to engineer light-responsive systems are widely used, but their applications in plants are still limited due to the interference with endogenous photoreceptors and the intrinsic requirement of light for photosynthesis. Cyanobacteria possess a family of soluble carotenoid-associated proteins named orange carotenoid proteins (OCPs) that, when activated by blue-green light, undergo a reversible conformational change that enables the photoprotection mechanism that occurs on the phycobilisome. Exploiting this system, we developed a chloroplast-localized synthetic photoswitch based on a protein complementation assay where two nanoluciferase fragments were fused to separate polypeptides corresponding to the OCP2 domains. Since Arabidopsis (Arabidopsis thaliana) does not possess the prosthetic group needed for the assembly of the OCP2 complex, we first implemented the carotenoid biosynthetic pathway with a bacterial β-carotene ketolase enzyme (crtW) to generate keto-carotenoid-producing plants. The photoswitch was tested and characterized in Arabidopsis protoplasts and stably transformed plants with experiments aimed to uncover its regulation by a range of light intensities, wavelengths, and its conversion dynamics. Finally, we applied the OCP-based photoswitch to control transcriptional responses in chloroplasts in response to green light illumination by fusing the two OCP fragments with the plastidial SIGMA FACTOR 2 and bacteriophage T4 anti-sigma factor AsiA. This pioneering study establishes the basis for future implementation of plastid optogenetics to regulate organelle responses upon exposure to specific light spectra.
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Affiliation(s)
- Luca Piccinini
- Plantlab, Institute of Life Sciences, Scuola Superiore Sant’Anna, Pisa 56127, Italy
| | - Sergio Iacopino
- Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, UK
| | - Stefano Cazzaniga
- Department of Biotechnology, University of Verona, Verona 37134, Italy
| | - Matteo Ballottari
- Department of Biotechnology, University of Verona, Verona 37134, Italy
| | - Beatrice Giuntoli
- Plantlab, Institute of Life Sciences, Scuola Superiore Sant’Anna, Pisa 56127, Italy
- Department of Biology, University of Pisa, Pisa 56126, Italy
| | - Francesco Licausi
- Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, UK
- Department of Biology, University of Pisa, Pisa 56126, Italy
- Author for correspondence:
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Morozov D, Modi V, Mironov V, Groenhof G. The Photocycle of Bacteriophytochrome Is Initiated by Counterclockwise Chromophore Isomerization. J Phys Chem Lett 2022; 13:4538-4542. [PMID: 35576453 PMCID: PMC9150100 DOI: 10.1021/acs.jpclett.2c00899] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Photoactivation of bacteriophytochrome involves a cis-trans photoisomerization of a biliverdin chromophore, but neither the precise sequence of events nor the direction of the isomerization is known. Here, we used nonadiabatic molecular dynamics simulations on the photosensory protein dimer to resolve the isomerization mechanism in atomic detail. In our simulations the photoisomerization of the D ring occurs in the counterclockwise direction. On a subpicosecond time scale, the photoexcited chromophore adopts a short-lived intermediate with a highly twisted configuration stabilized by an extended hydrogen-bonding network. Within tens of picoseconds, these hydrogen bonds break, allowing the chromophore to adopt a more planar configuration, which we assign to the early Lumi-R state. The isomerization process is completed via helix inversion of the biliverdin chromophore to form the late Lumi-R state. The mechanistic insights into the photoisomerization process are essential to understand how bacteriophytochrome has evolved to mediate photoactivation and to engineer this protein for new applications.
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Affiliation(s)
- Dmitry Morozov
- Nanoscience
Center and Department of Chemistry, University
of Jyväskylä, P.O. Box 35, 40014 Jyväskylä, Finland
| | - Vaibhav Modi
- Nanoscience
Center and Department of Chemistry, University
of Jyväskylä, P.O. Box 35, 40014 Jyväskylä, Finland
| | - Vladimir Mironov
- Department
of Chemistry, Kyungpook National University, Daegu 702-701, South Korea
| | - Gerrit Groenhof
- Nanoscience
Center and Department of Chemistry, University
of Jyväskylä, P.O. Box 35, 40014 Jyväskylä, Finland
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Dietler J, Gelfert R, Kaiser J, Borin V, Renzl C, Pilsl S, Ranzani AT, García de Fuentes A, Gleichmann T, Diensthuber RP, Weyand M, Mayer G, Schapiro I, Möglich A. Signal transduction in light-oxygen-voltage receptors lacking the active-site glutamine. Nat Commun 2022; 13:2618. [PMID: 35552382 PMCID: PMC9098866 DOI: 10.1038/s41467-022-30252-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 04/22/2022] [Indexed: 11/12/2022] Open
Abstract
In nature as in biotechnology, light-oxygen-voltage photoreceptors perceive blue light to elicit spatiotemporally defined cellular responses. Photon absorption drives thioadduct formation between a conserved cysteine and the flavin chromophore. An equally conserved, proximal glutamine processes the resultant flavin protonation into downstream hydrogen-bond rearrangements. Here, we report that this glutamine, long deemed essential, is generally dispensable. In its absence, several light-oxygen-voltage receptors invariably retained productive, if often attenuated, signaling responses. Structures of a light-oxygen-voltage paradigm at around 1 Å resolution revealed highly similar light-induced conformational changes, irrespective of whether the glutamine is present. Naturally occurring, glutamine-deficient light-oxygen-voltage receptors likely serve as bona fide photoreceptors, as we showcase for a diguanylate cyclase. We propose that without the glutamine, water molecules transiently approach the chromophore and thus propagate flavin protonation downstream. Signaling without glutamine appears intrinsic to light-oxygen-voltage receptors, which pertains to biotechnological applications and suggests evolutionary descendance from redox-active flavoproteins. Light-oxygen-voltage (LOV) photoreceptors perceive blue light to elicit spatio-temporally defined cellular responses, and their signalling process has been extensively characterized. Here the authors report that the light signal is still transduced in the absence of a conserved Gln residue, thought to be key.
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Affiliation(s)
- Julia Dietler
- Department of Biochemistry, University of Bayreuth, 95447, Bayreuth, Germany
| | - Renate Gelfert
- Department of Biochemistry, University of Bayreuth, 95447, Bayreuth, Germany
| | - Jennifer Kaiser
- Department of Biochemistry, University of Bayreuth, 95447, Bayreuth, Germany
| | - Veniamin Borin
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Christian Renzl
- Life and Medical Sciences (LIMES), University of Bonn, 53121, Bonn, Germany
| | - Sebastian Pilsl
- Life and Medical Sciences (LIMES), University of Bonn, 53121, Bonn, Germany
| | | | | | - Tobias Gleichmann
- Biophysical Chemistry, Humboldt-University Berlin, 10115, Berlin, Germany
| | | | - Michael Weyand
- Department of Biochemistry, University of Bayreuth, 95447, Bayreuth, Germany
| | - Günter Mayer
- Life and Medical Sciences (LIMES), University of Bonn, 53121, Bonn, Germany.,Center of Aptamer Research & Development, University of Bonn, 53121, Bonn, Germany
| | - Igor Schapiro
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Andreas Möglich
- Department of Biochemistry, University of Bayreuth, 95447, Bayreuth, Germany. .,Biophysical Chemistry, Humboldt-University Berlin, 10115, Berlin, Germany. .,Bayreuth Center for Biochemistry & Molecular Biology, Universität Bayreuth, 95447, Bayreuth, Germany. .,North-Bavarian NMR Center, Universität Bayreuth, 95447, Bayreuth, Germany.
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Optogenetic tools for microbial synthetic biology. Biotechnol Adv 2022; 59:107953. [DOI: 10.1016/j.biotechadv.2022.107953] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 03/09/2022] [Accepted: 04/04/2022] [Indexed: 12/22/2022]
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45
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Kneuttinger AC. A guide to designing photocontrol in proteins: methods, strategies and applications. Biol Chem 2022; 403:573-613. [PMID: 35355495 DOI: 10.1515/hsz-2021-0417] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 03/08/2022] [Indexed: 12/20/2022]
Abstract
Light is essential for various biochemical processes in all domains of life. In its presence certain proteins inside a cell are excited, which either stimulates or inhibits subsequent cellular processes. The artificial photocontrol of specifically proteins is of growing interest for the investigation of scientific questions on the organismal, cellular and molecular level as well as for the development of medicinal drugs or biocatalytic tools. For the targeted design of photocontrol in proteins, three major methods have been developed over the last decades, which employ either chemical engineering of small-molecule photosensitive effectors (photopharmacology), incorporation of photoactive non-canonical amino acids by genetic code expansion (photoxenoprotein engineering), or fusion with photoreactive biological modules (hybrid protein optogenetics). This review compares the different methods as well as their strategies and current applications for the light-regulation of proteins and provides background information useful for the implementation of each technique.
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Affiliation(s)
- Andrea C Kneuttinger
- Institute of Biophysics and Physical Biochemistry and Regensburg Center for Biochemistry, University of Regensburg, D-93040 Regensburg, Germany
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46
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Lata K, Singh M, Chatterjee S, Chattopadhyay K. Membrane Dynamics and Remodelling in Response to the Action of the Membrane-Damaging Pore-Forming Toxins. J Membr Biol 2022; 255:161-173. [PMID: 35305136 DOI: 10.1007/s00232-022-00227-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 03/02/2022] [Indexed: 12/11/2022]
Abstract
Pore-forming protein toxins (PFTs) represent a diverse class of membrane-damaging proteins that are produced by a wide variety of organisms. PFT-mediated membrane perforation is largely governed by the chemical composition and the physical properties of the plasma membranes. The interaction between the PFTs with the target membranes is critical for the initiation of the pore-formation process, and can lead to discrete membrane reorganization events that further aids in the process of pore-formation. Punching holes on the plasma membranes by the PFTs interferes with the cellular homeostasis by disrupting the ion-balance inside the cells that in turn can turn on multiple signalling cascades required to restore membrane integrity and cellular homeostasis. In this review, we discuss the physicochemical attributes of the plasma membranes associated with the pore-formation processes by the PFTs, and the subsequent membrane remodelling events that may start off the membrane-repair mechanisms.
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Affiliation(s)
- Kusum Lata
- Department of Biological Sciences, Indian Institute of Science Education and Research Mohali, Sector 81, SAS Nagar, Manauli, Mohali, Punjab, 140306, India
| | - Mahendra Singh
- Department of Biological Sciences, Indian Institute of Science Education and Research Mohali, Sector 81, SAS Nagar, Manauli, Mohali, Punjab, 140306, India
| | - Shamaita Chatterjee
- Department of Biological Sciences, Indian Institute of Science Education and Research Mohali, Sector 81, SAS Nagar, Manauli, Mohali, Punjab, 140306, India
| | - Kausik Chattopadhyay
- Department of Biological Sciences, Indian Institute of Science Education and Research Mohali, Sector 81, SAS Nagar, Manauli, Mohali, Punjab, 140306, India.
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47
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Boral A, Khamaru M, Mitra D. Designing synthetic transcription factors: A structural perspective. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2022; 130:245-287. [PMID: 35534109 DOI: 10.1016/bs.apcsb.2021.12.003] [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: 06/14/2023]
Abstract
In this chapter, we discuss different design strategies of synthetic proteins, especially synthetic transcription factors. Design and engineering of synthetic transcription factors is particularly relevant for the need-based manipulation of gene expression. With recent advances in structural biology techniques and with the emergence of other precision biochemical/physical tools, accurate knowledge on structure-function relations is increasingly becoming available. Besides discussing the underlying principles of design, we go through individual cases, especially those involving four major groups of transcription factors-basic leucine zippers, zinc fingers, helix-turn-helix and homeodomains. We further discuss how synthetic biology can come together with structural biology to alter the genetic blueprint of life.
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Affiliation(s)
- Aparna Boral
- Department of Life Sciences, Presidency University, Kolkata, West Bengal, India
| | - Madhurima Khamaru
- Department of Life Sciences, Presidency University, Kolkata, West Bengal, India
| | - Devrani Mitra
- Department of Life Sciences, Presidency University, Kolkata, West Bengal, India.
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Bouché F, Woods DP, Linden J, Li W, Mayer KS, Amasino RM, Périlleux C. EARLY FLOWERING 3 and Photoperiod Sensing in Brachypodium distachyon. FRONTIERS IN PLANT SCIENCE 2022; 12:769194. [PMID: 35069625 PMCID: PMC8770904 DOI: 10.3389/fpls.2021.769194] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 12/13/2021] [Indexed: 05/26/2023]
Abstract
The proper timing of flowering, which is key to maximize reproductive success and yield, relies in many plant species on the coordination between environmental cues and endogenous developmental programs. The perception of changes in day length is one of the most reliable cues of seasonal change, and this involves the interplay between the sensing of light signals and the circadian clock. Here, we describe a Brachypodium distachyon mutant allele of the evening complex protein EARLY FLOWERING 3 (ELF3). We show that the elf3 mutant flowers more rapidly than wild type plants in short days as well as under longer photoperiods but, in very long (20 h) days, flowering is equally rapid in elf3 and wild type. Furthermore, flowering in the elf3 mutant is still sensitive to vernalization, but not to ambient temperature changes. Molecular analyses revealed that the expression of a short-day marker gene is suppressed in elf3 grown in short days, and the expression patterns of clock genes and flowering time regulators are altered. We also explored the mechanisms of photoperiodic perception in temperate grasses by exposing B. distachyon plants grown under a 12 h photoperiod to a daily night break consisting of a mixture of red and far-red light. We showed that 2 h breaks are sufficient to accelerate flowering in B. distachyon under non-inductive photoperiods and that this acceleration of flowering is mediated by red light. Finally, we discuss advances and perspectives for research on the perception of photoperiod in temperate grasses.
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Affiliation(s)
- Frédéric Bouché
- Laboratory of Plant Physiology, InBioS-PhytoSYSTEMS, Department of Life Sciences, University of Liège, Liège, Belgium
| | - Daniel P. Woods
- Plant Sciences Department, University of California, Davis, Davis, CA, United States
- Laboratory of Genetics, University of Wisconsin, Madison, WI, United States
- Department of Biochemistry, University of Wisconsin, Madison, WI, United States
- United States Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, WI, United States
- Howard Hughes Medical Institute, Chevy Chase, MD, United States
| | - Julie Linden
- Laboratory of Plant Physiology, InBioS-PhytoSYSTEMS, Department of Life Sciences, University of Liège, Liège, Belgium
| | - Weiya Li
- Department of Biochemistry, University of Wisconsin, Madison, WI, United States
| | - Kevin S. Mayer
- Laboratory of Genetics, University of Wisconsin, Madison, WI, United States
| | - Richard M. Amasino
- Laboratory of Genetics, University of Wisconsin, Madison, WI, United States
- Department of Biochemistry, University of Wisconsin, Madison, WI, United States
- United States Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, WI, United States
| | - Claire Périlleux
- Laboratory of Plant Physiology, InBioS-PhytoSYSTEMS, Department of Life Sciences, University of Liège, Liège, Belgium
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Otero LH, Foscaldi S, Antelo GT, Rosano GL, Sirigu S, Klinke S, Defelipe LA, Sánchez-Lamas M, Battocchio G, Conforte V, Vojnov AA, Chavas LMG, Goldbaum FA, Mroginski MA, Rinaldi J, Bonomi HR. Structural basis for the Pr-Pfr long-range signaling mechanism of a full-length bacterial phytochrome at the atomic level. SCIENCE ADVANCES 2021; 7:eabh1097. [PMID: 34818032 PMCID: PMC8612531 DOI: 10.1126/sciadv.abh1097] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 09/22/2021] [Indexed: 06/13/2023]
Abstract
Phytochromes constitute a widespread photoreceptor family that typically interconverts between two photostates called Pr (red light–absorbing) and Pfr (far-red light–absorbing). The lack of full-length structures solved at the (near-)atomic level in both pure Pr and Pfr states leaves gaps in the structural mechanisms involved in the signal transmission pathways during the photoconversion. Here, we present the crystallographic structures of three versions from the plant pathogen Xanthomonas campestris virulence regulator XccBphP bacteriophytochrome, including two full-length proteins, in the Pr and Pfr states. The structures show a reorganization of the interaction networks within and around the chromophore-binding pocket, an α-helix/β-sheet tongue transition, and specific domain reorientations, along with interchanging kinks and breaks at the helical spine as a result of the photoswitching, which subsequently affect the quaternary assembly. These structural findings, combined with multidisciplinary studies, allow us to describe the signaling mechanism of a full-length bacterial phytochrome at the atomic level.
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Affiliation(s)
- Lisandro H. Otero
- Fundación Instituto Leloir, IIBBA-CONICET, Av. Patricias Argentinas 435 (C1405BWE), Buenos Aires, Argentina
- Plataforma Argentina de Biología Estructural y Metabolómica PLABEM, Av. Patricias Argentinas 435 (C1405BWE), Buenos Aires, Argentina
| | - Sabrina Foscaldi
- Fundación Instituto Leloir, IIBBA-CONICET, Av. Patricias Argentinas 435 (C1405BWE), Buenos Aires, Argentina
| | - Giuliano T. Antelo
- Fundación Instituto Leloir, IIBBA-CONICET, Av. Patricias Argentinas 435 (C1405BWE), Buenos Aires, Argentina
| | - Germán L. Rosano
- Unidad de Espectrometría de Masa, Instituto de Biología Molecular y Celular de Rosario, UEM-IBR, CONICET, Bv. 27 de Febrero (S2000EZP), Rosario, Argentina
| | - Serena Sirigu
- Proxima-1, Synchrotron SOLEIL, L’Orme des Merisiers, Saint-Aubin, BP 48 (91192), Gif-sur-Yvette Cedex, France
| | - Sebastián Klinke
- Fundación Instituto Leloir, IIBBA-CONICET, Av. Patricias Argentinas 435 (C1405BWE), Buenos Aires, Argentina
- Plataforma Argentina de Biología Estructural y Metabolómica PLABEM, Av. Patricias Argentinas 435 (C1405BWE), Buenos Aires, Argentina
| | - Lucas A. Defelipe
- European Molecular Biology Laboratory (EMBL), Hamburg Unit, Notkestrasse 85 (22607), Hamburg, Germany
| | - Maximiliano Sánchez-Lamas
- Fundación Instituto Leloir, IIBBA-CONICET, Av. Patricias Argentinas 435 (C1405BWE), Buenos Aires, Argentina
| | - Giovanni Battocchio
- Technische Universität Berlin, Institute of Chemistry, Strasse des 17. Juni 135 (D-10623), Berlin, Germany
| | - Valeria Conforte
- Instituto de Ciencia y Tecnología Dr. César Milstein, Fundación Pablo Cassará, CONICET, Saladillo 2468 (C1440FFX), Buenos Aires, Argentina
| | - Adrián A. Vojnov
- Instituto de Ciencia y Tecnología Dr. César Milstein, Fundación Pablo Cassará, CONICET, Saladillo 2468 (C1440FFX), Buenos Aires, Argentina
| | - Leonard M. G. Chavas
- Proxima-1, Synchrotron SOLEIL, L’Orme des Merisiers, Saint-Aubin, BP 48 (91192), Gif-sur-Yvette Cedex, France
- Synchrotron Radiation Research Center, Nagoya University, Nagoya 464-8603, Japan
| | - Fernando A. Goldbaum
- Fundación Instituto Leloir, IIBBA-CONICET, Av. Patricias Argentinas 435 (C1405BWE), Buenos Aires, Argentina
- Plataforma Argentina de Biología Estructural y Metabolómica PLABEM, Av. Patricias Argentinas 435 (C1405BWE), Buenos Aires, Argentina
| | - Maria-Andrea Mroginski
- Technische Universität Berlin, Institute of Chemistry, Strasse des 17. Juni 135 (D-10623), Berlin, Germany
| | - Jimena Rinaldi
- Fundación Instituto Leloir, IIBBA-CONICET, Av. Patricias Argentinas 435 (C1405BWE), Buenos Aires, Argentina
| | - Hernán R. Bonomi
- Fundación Instituto Leloir, IIBBA-CONICET, Av. Patricias Argentinas 435 (C1405BWE), Buenos Aires, Argentina
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50
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Timsit Y, Grégoire SP. Towards the Idea of Molecular Brains. Int J Mol Sci 2021; 22:ijms222111868. [PMID: 34769300 PMCID: PMC8584932 DOI: 10.3390/ijms222111868] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 10/24/2021] [Accepted: 10/28/2021] [Indexed: 02/06/2023] Open
Abstract
How can single cells without nervous systems perform complex behaviours such as habituation, associative learning and decision making, which are considered the hallmark of animals with a brain? Are there molecular systems that underlie cognitive properties equivalent to those of the brain? This review follows the development of the idea of molecular brains from Darwin’s “root brain hypothesis”, through bacterial chemotaxis, to the recent discovery of neuron-like r-protein networks in the ribosome. By combining a structural biology view with a Bayesian brain approach, this review explores the evolutionary labyrinth of information processing systems across scales. Ribosomal protein networks open a window into what were probably the earliest signalling systems to emerge before the radiation of the three kingdoms. While ribosomal networks are characterised by long-lasting interactions between their protein nodes, cell signalling networks are essentially based on transient interactions. As a corollary, while signals propagated in persistent networks may be ephemeral, networks whose interactions are transient constrain signals diffusing into the cytoplasm to be durable in time, such as post-translational modifications of proteins or second messenger synthesis. The duration and nature of the signals, in turn, implies different mechanisms for the integration of multiple signals and decision making. Evolution then reinvented networks with persistent interactions with the development of nervous systems in metazoans. Ribosomal protein networks and simple nervous systems display architectural and functional analogies whose comparison could suggest scale invariance in information processing. At the molecular level, the significant complexification of eukaryotic ribosomal protein networks is associated with a burst in the acquisition of new conserved aromatic amino acids. Knowing that aromatic residues play a critical role in allosteric receptors and channels, this observation suggests a general role of π systems and their interactions with charged amino acids in multiple signal integration and information processing. We think that these findings may provide the molecular basis for designing future computers with organic processors.
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Affiliation(s)
- Youri Timsit
- Aix Marseille Université, Université de Toulon, CNRS, IRD, MIO UM110, 13288 Marseille, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 3 rue Michel-Ange, 75016 Paris, France
- Correspondence:
| | - Sergeant-Perthuis Grégoire
- Institut de Mathématiques de Jussieu—Paris Rive Gauche (IMJ-PRG), UMR 7586, CNRS-Université Paris Diderot, 75013 Paris, France;
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