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Kim C, Yun SR, Lee SJ, Kim SO, Lee H, Choi J, Kim JG, Kim TW, You S, Kosheleva I, Noh T, Baek J, Ihee H. Structural dynamics of protein-protein association involved in the light-induced transition of Avena sativa LOV2 protein. Nat Commun 2024; 15:6991. [PMID: 39143073 PMCID: PMC11324726 DOI: 10.1038/s41467-024-51461-z] [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: 02/05/2024] [Accepted: 08/07/2024] [Indexed: 08/16/2024] Open
Abstract
The Light-oxygen-voltage-sensing domain (LOV) superfamily, found in enzymes and signal transduction proteins, plays a crucial role in converting light signals into structural signals, mediating various biological mechanisms. While time-resolved spectroscopic studies have revealed the dynamics of the LOV-domain chromophore's electronic structures, understanding the structural changes in the protein moiety, particularly regarding light-induced dimerization, remains challenging. Here, we utilize time-resolved X-ray liquidography to capture the light-induced dimerization of Avena sativa LOV2. Our analysis unveils that dimerization occurs within milliseconds after the unfolding of the A'α and Jα helices in the microsecond time range. Notably, our findings suggest that protein-protein interactions (PPIs) among the β-scaffolds, mediated by helix unfolding, play a key role in dimerization. In this work, we offer structural insights into the dimerization of LOV2 proteins following structural changes in the A'α and Jα helices, as well as mechanistic insights into the protein-protein association process driven by PPIs.
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Affiliation(s)
- Changin Kim
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
- Center for Advanced Reaction Dynamics, Institute for Basic Science (IBS), Daejeon, 34141, Republic of Korea
| | - So Ri Yun
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
- Center for Advanced Reaction Dynamics, Institute for Basic Science (IBS), Daejeon, 34141, Republic of Korea
| | - Sang Jin Lee
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
- Center for Advanced Reaction Dynamics, Institute for Basic Science (IBS), Daejeon, 34141, Republic of Korea
| | - Seong Ok Kim
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
- Center for Advanced Reaction Dynamics, Institute for Basic Science (IBS), Daejeon, 34141, Republic of Korea
| | - Hyosub Lee
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
- Center for Advanced Reaction Dynamics, Institute for Basic Science (IBS), Daejeon, 34141, Republic of Korea
| | - Jungkweon Choi
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
- Center for Advanced Reaction Dynamics, Institute for Basic Science (IBS), Daejeon, 34141, Republic of Korea
| | - Jong Goo Kim
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
- Center for Advanced Reaction Dynamics, Institute for Basic Science (IBS), Daejeon, 34141, Republic of Korea
| | - Tae Wu Kim
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
- Center for Advanced Reaction Dynamics, Institute for Basic Science (IBS), Daejeon, 34141, Republic of Korea
| | - Seyoung You
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
- Center for Advanced Reaction Dynamics, Institute for Basic Science (IBS), Daejeon, 34141, Republic of Korea
| | - Irina Kosheleva
- Center for Advanced Radiation Sources, The University of Chicago, Chicago, IL, 60637, USA
| | - Taeyoon Noh
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
- Center for Advanced Reaction Dynamics, Institute for Basic Science (IBS), Daejeon, 34141, Republic of Korea
| | - Jonghoon Baek
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
- Center for Advanced Reaction Dynamics, Institute for Basic Science (IBS), Daejeon, 34141, Republic of Korea
| | - Hyotcherl Ihee
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea.
- Center for Advanced Reaction Dynamics, Institute for Basic Science (IBS), Daejeon, 34141, Republic of Korea.
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2
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Panda R, Panda PK, Krishnamoorthy J, Kar RK. Network analysis of chromophore binding site in LOV domain. Comput Biol Med 2023; 161:106996. [PMID: 37201443 DOI: 10.1016/j.compbiomed.2023.106996] [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: 12/08/2022] [Revised: 03/16/2023] [Accepted: 05/01/2023] [Indexed: 05/20/2023]
Abstract
Photoreceptor proteins are versatile toolbox for developing biosensors for optogenetic applications. These molecular tools get activated upon illumination of blue light, which in turn offers a non-invasive method for gaining high spatiotemporal resolution and precise control of cellular signal transduction. The Light-Oxygen-Voltage (LOV) domain family of proteins is a well-recognized system for constructing optogenetic devices. Translation of these proteins into efficient cellular sensors is possible by tuning their photochemistry lifetime. However, the bottleneck is the need for more understanding of the relationship between the protein environment and photocycle kinetics. Significantly, the effect of the local environment also modulates the electronic structure of chromophore, which perturbs the electrostatic and hydrophobic interaction within the binding site. This work highlights the critical factors hidden in the protein networks, linking with their experimental photocycle kinetics. It presents an opportunity to quantitatively examine the alternation in chromophore's equilibrium geometry and identify details which have substantial implications in designing synthetic LOV constructs with desirable photocycle efficiency.
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Affiliation(s)
- Rishab Panda
- Department of Chemical Sciences, Indian Institute of Science Education and Research Mohali, Punjab, India
| | - Pritam K Panda
- Condensed Matter Theory Group, Materials Theory Division, Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20, Uppsala, Sweden; Division of Immunology and Chronic Disease, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | | | - Rajiv K Kar
- Jyoti and Bhupat Mehta School of Health Sciences and Technology, Indian Institute of Technology Guwahati, Guwahati, Assam, 781039, India.
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3
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Aumonier S, Engilberge S, Caramello N, von Stetten D, Gotthard G, Leonard GA, Mueller-Dieckmann C, Royant A. Slow protein dynamics probed by time-resolved oscillation crystallography at room temperature. IUCRJ 2022; 9:756-767. [PMID: 36381146 PMCID: PMC9634615 DOI: 10.1107/s2052252522009150] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 09/14/2022] [Indexed: 05/23/2023]
Abstract
The development of serial crystallography over the last decade at XFELs and synchrotrons has produced a renaissance in room-temperature macromolecular crystallography (RT-MX), and fostered many technical and methodological breakthroughs designed to study phenomena occurring in proteins on the picosecond-to-second timescale. However, there are components of protein dynamics that occur in much slower regimes, of which the study could readily benefit from state-of-the-art RT-MX. Here, the room-temperature structural study of the relaxation of a reaction intermediate at a synchrotron, exploiting a handful of single crystals, is described. The intermediate in question is formed in microseconds during the photoreaction of the LOV2 domain of phototropin 2 from Arabidopsis thaliana, which then decays in minutes. This work monitored its relaxation in the dark using a fast-readout EIGER X 4M detector to record several complete oscillation X-ray diffraction datasets, each of 1.2 s total exposure time, at different time points in the relaxation process. Coupled with in crystallo UV-Vis absorption spectroscopy, this RT-MX approach allowed the authors to follow the relaxation of the photoadduct, a thio-ether covalent bond between the chromophore and a cysteine residue. Unexpectedly, the return of the chromophore to its spectroscopic ground state is followed by medium-scale protein rearrangements that trigger a crystal phase transition and hinder the full recovery of the structural ground state of the protein. In addition to suggesting a hitherto unexpected role of a conserved tryptophan residue in the regulation of the photocycle of LOV2, this work provides a basis for performing routine time-resolved protein crystallography experiments at synchrotrons for phenomena occurring on the second-to-hour timescale.
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Affiliation(s)
- Sylvain Aumonier
- Structural Biology Group, European Synchrotron Radiation Facility, 71 avenue des Martyrs CS 40220, Grenoble 38043, France
| | - Sylvain Engilberge
- Structural Biology Group, European Synchrotron Radiation Facility, 71 avenue des Martyrs CS 40220, Grenoble 38043, France
| | - Nicolas Caramello
- Structural Biology Group, European Synchrotron Radiation Facility, 71 avenue des Martyrs CS 40220, Grenoble 38043, France
- Hamburg Centre for Ultrafast Imaging, Universität Hamburg, HARBOR, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - David von Stetten
- Structural Biology Group, European Synchrotron Radiation Facility, 71 avenue des Martyrs CS 40220, Grenoble 38043, France
| | - Guillaume Gotthard
- Structural Biology Group, European Synchrotron Radiation Facility, 71 avenue des Martyrs CS 40220, Grenoble 38043, France
| | - Gordon A. Leonard
- Structural Biology Group, European Synchrotron Radiation Facility, 71 avenue des Martyrs CS 40220, Grenoble 38043, France
| | - Christoph Mueller-Dieckmann
- Structural Biology Group, European Synchrotron Radiation Facility, 71 avenue des Martyrs CS 40220, Grenoble 38043, France
| | - Antoine Royant
- Structural Biology Group, European Synchrotron Radiation Facility, 71 avenue des Martyrs CS 40220, Grenoble 38043, France
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), 71 avenue des Martyrs, Grenoble 38044, France
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4
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Łabuz J, Sztatelman O, Hermanowicz P. Molecular insights into the phototropin control of chloroplast movements. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:6034-6051. [PMID: 35781490 DOI: 10.1093/jxb/erac271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 06/22/2022] [Indexed: 06/15/2023]
Abstract
Chloroplast movements are controlled by ultraviolet/blue light through phototropins. In Arabidopsis thaliana, chloroplast accumulation at low light intensities and chloroplast avoidance at high light intensities are observed. These responses are controlled by two homologous photoreceptors, the phototropins phot1 and phot2. Whereas chloroplast accumulation is triggered by both phototropins in a partially redundant manner, sustained chloroplast avoidance is elicited only by phot2. Phot1 is able to trigger only a small, transient chloroplast avoidance, followed by the accumulation phase. The source of this functional difference is not fully understood at either the photoreceptor or the signalling pathway levels. In this article, we review current understanding of phototropin functioning and try to dissect the differences that result in signalling to elicit two distinct chloroplast responses. First, we focus on phototropin structure and photochemical and biochemical activity. Next, we analyse phototropin expression and localization patterns. We also summarize known photoreceptor systems controlling chloroplast movements. Finally, we focus on the role of environmental stimuli in controlling phototropin activity. All these aspects impact the signalling to trigger chloroplast movements and raise outstanding questions about the mechanism involved.
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Affiliation(s)
- Justyna Łabuz
- Laboratory of Photobiology, Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa, Kraków, Poland
| | - Olga Sztatelman
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego, Warszawa, Poland
| | - Paweł Hermanowicz
- Laboratory of Photobiology, Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa, Kraków, Poland
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5
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Talloji P, Nehlin L, Hüttel B, Winter N, Černý M, Dufková H, Hamali B, Hanczaryk K, Novák J, Hermanns M, Drexler N, Eifler K, Schlaich N, Brzobohatý B, Bachmair A. Transcriptome, metabolome and suppressor analysis reveal an essential role for the ubiquitin-proteasome system in seedling chloroplast development. BMC PLANT BIOLOGY 2022; 22:183. [PMID: 35395773 PMCID: PMC8991883 DOI: 10.1186/s12870-022-03536-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 03/15/2022] [Indexed: 05/25/2023]
Abstract
BACKGROUND Many regulatory circuits in plants contain steps of targeted proteolysis, with the ubiquitin proteasome system (UPS) as the mediator of these proteolytic events. In order to decrease ubiquitin-dependent proteolysis, we inducibly expressed a ubiquitin variant with Arg at position 48 instead of Lys (ubK48R). This variant acts as an inhibitor of proteolysis via the UPS, and allowed us to uncover processes that are particularly sensitive to UPS perturbation. RESULTS Expression of ubK48R during germination leads to seedling death. We analyzed the seedling transcriptome, proteome and metabolome 24 h post ubK48R induction and confirmed defects in chloroplast development. We found that mutations in single genes can suppress seedling lethality, indicating that a single process in seedlings is critically sensitive to decreased performance of the UPS. Suppressor mutations in phototropin 2 (PHOT2) suggest that a contribution of PHOT2 to chloroplast protection is compromised by proteolysis inhibition. CONCLUSIONS Overall, the results reveal protein turnover as an integral part of a signal transduction chain that protects chloroplasts during development.
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Affiliation(s)
- Prabhavathi Talloji
- Department of Biochemistry and Cell Biology, Max Perutz Labs/Center for Molecular Biology, University of Vienna, A-1030, Vienna, Austria
| | - Lilian Nehlin
- Department of Biochemistry and Cell Biology, Max Perutz Labs/Center for Molecular Biology, University of Vienna, A-1030, Vienna, Austria
| | - Bruno Hüttel
- Max Planck Genome Centre Cologne, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
| | - Nikola Winter
- Department of Biochemistry and Cell Biology, Max Perutz Labs/Center for Molecular Biology, University of Vienna, A-1030, Vienna, Austria
| | - Martin Černý
- Department of Molecular Biology and Radiobiology, Faculty of AgriSciences, Mendel University in Brno, CZ-613 00, Brno, Czech Republic
| | - Hana Dufková
- Department of Molecular Biology and Radiobiology, Faculty of AgriSciences, Mendel University in Brno, CZ-613 00, Brno, Czech Republic
| | - Bulut Hamali
- Department of Biochemistry and Cell Biology, Max Perutz Labs/Center for Molecular Biology, University of Vienna, A-1030, Vienna, Austria
- Present address: Department of Integrative Biology, Oregon State University, 3029 Cordley Hall, Corvallis, OR, 97331, USA
| | - Katarzyna Hanczaryk
- Department of Biochemistry and Cell Biology, Max Perutz Labs/Center for Molecular Biology, University of Vienna, A-1030, Vienna, Austria
| | - Jan Novák
- Department of Molecular Biology and Radiobiology, Faculty of AgriSciences, Mendel University in Brno, CZ-613 00, Brno, Czech Republic
| | - Monika Hermanns
- Institute of Plant Physiology (Bio III), RWTH-Aachen, 52056, Aachen, Germany
| | - Nicole Drexler
- Vienna Biocenter Core Facilities, Electron Microscopy, A-1030, Vienna, Austria
| | - Karolin Eifler
- Department of Biochemistry and Cell Biology, Max Perutz Labs/Center for Molecular Biology, University of Vienna, A-1030, Vienna, Austria
| | - Nikolaus Schlaich
- Institute of Plant Physiology (Bio III), RWTH-Aachen, 52056, Aachen, Germany
| | - Břetislav Brzobohatý
- Department of Molecular Biology and Radiobiology, Faculty of AgriSciences, Mendel University in Brno, CZ-613 00, Brno, Czech Republic
- CEITEC - Central European Institute of Technology, Mendel University in Brno, CZ-61300, Brno, Czech Republic
| | - Andreas Bachmair
- Department of Biochemistry and Cell Biology, Max Perutz Labs/Center for Molecular Biology, University of Vienna, A-1030, Vienna, Austria.
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6
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Red light-induced structure changes in phytochrome A from Pisum sativum. Sci Rep 2021; 11:2827. [PMID: 33531580 PMCID: PMC7854702 DOI: 10.1038/s41598-021-82544-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 01/15/2021] [Indexed: 12/17/2022] Open
Abstract
Phytochrome A (phyA) is a photoreceptor protein of plants that regulates the red/far-red light photomorphogenic responses of plants essential for growth and development. PhyA, composed of approximately 1100 amino acid residues, folds into photosensory and output signaling modules. The photosensory module covalently binds phytochromobilin as a chromophore for photoreversible interconversion between inactive red light-absorbing (Pr) and active far-red light-absorbing (Pfr) forms to act as a light-driven phosphorylation enzyme. To understand the molecular mechanism in the initial process of photomorphogenic response, we studied the molecular structures of large phyA (LphyA) from Pisum sativum, which lacks the 52 residues in the N-terminal, by small-angle X-ray scattering combined with multivariate analyses applied to molecular models predicted from the scattering profiles. According to our analyses, Pr was in a dimer and had a four-leaf shape, and the subunit was approximated as a bent rod of 175 × 50 Å. The scattering profile of Pfr was calculated from that recorded for a mixture of Pr and Pfr under red-light irradiation by using their population determined from the absorption spectrum. The Pfr dimer exhibited a butterfly shape composed of subunits with a straight rod of 175 × 50 Å. The shape differences between Pr and Pfr indicated conformational changes in the Pr/Pfr interconversion which would be essential to the interaction with protein molecules involved in transcriptional control.
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7
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Hart JE, Gardner KH. Lighting the way: Recent insights into the structure and regulation of phototropin blue light receptors. J Biol Chem 2021; 296:100594. [PMID: 33781746 PMCID: PMC8086140 DOI: 10.1016/j.jbc.2021.100594] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 03/24/2021] [Accepted: 03/25/2021] [Indexed: 02/06/2023] Open
Abstract
The phototropins (phots) are light-activated kinases that are critical for plant physiology and the many diverse optogenetic tools that they have inspired. Phototropins combine two blue-light-sensing Light-Oxygen-Voltage (LOV) domains (LOV1 and LOV2) and a C-terminal serine/threonine kinase domain, using the LOV domains to control the catalytic activity of the kinase. While much is known about the structure and photochemistry of the light-perceiving LOV domains, particularly in how activation of the LOV2 domain triggers the unfolding of alpha helices that communicate the light signal to the kinase domain, many questions about phot structure and mechanism remain. Recent studies have made progress addressing these questions by utilizing small-angle X-ray scattering (SAXS) and other biophysical approaches to study multidomain phots from Chlamydomonas and Arabidopsis, leading to models where the domains have an extended linear arrangement, with the regulatory LOV2 domain contacting the kinase domain N-lobe. We discuss this and other advances that have improved structural and mechanistic understanding of phot regulation in this review, along with the challenges that will have to be overcome to obtain high-resolution structural information on these exciting photoreceptors. Such information will be essential to advancing fundamental understanding of plant physiology while enabling engineering efforts at both the whole plant and molecular levels.
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Affiliation(s)
- Jaynee E Hart
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, New York, USA
| | - Kevin H Gardner
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, New York, USA; Department of Chemistry and Biochemistry, City College of New York, New York, USA; PhD Programs in Biochemistry, Chemistry, and Biology, Graduate Center, City University of New York, New York, USA.
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8
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Domain Organization in Plant Blue-Light Receptor Phototropin2 of Arabidopsis thaliana Studied by Small-Angle X-ray Scattering. Int J Mol Sci 2020; 21:ijms21186638. [PMID: 32927860 PMCID: PMC7555306 DOI: 10.3390/ijms21186638] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 09/06/2020] [Accepted: 09/07/2020] [Indexed: 01/10/2023] Open
Abstract
Phototropin2 (phot2) is a blue-light (BL) receptor protein that regulates the BL-dependent activities of plants for efficient photosynthesis. Phot2 is composed of two light-oxygen-voltage sensing domains (LOV1 and LOV2) to absorb BL, and a kinase domain. Photo-activated LOV domains, especially LOV2, play a major role in photo-dependent increase in the phosphorylation activity of the kinase domain. The atomic details of the overall structure of phot2 and the intramolecular mechanism to convert BL energy to a phosphorylation signal remain unknown. We performed structural studies on the LOV fragments LOV1, LOV2, LOV2-linker, and LOV2-kinase, and full-length phot2, using small-angle X-ray scattering (SAXS). The aim of the study was to understand structural changes under BL irradiation and discuss the molecular mechanism that enhance the phosphorylation activity under BL. SAXS is a suitable technique for visualizing molecular structures of proteins in solution at low resolution and is advantageous for monitoring their structural changes in the presence of external physical and/or chemical stimuli. Structural parameters and molecular models of the recombinant specimens were obtained from SAXS profiles in the dark, under BL irradiation, and after dark reversion. LOV1, LOV2, and LOV2-linker fragments displayed minimal structural changes. However, BL-induced rearrangements of functional domains were noted for LOV2-kinase and full-length phot2. Based on the molecular model together with the absorption measurements and biochemical assays, we discuss the intramolecular interactions and domain motions necessary for BL-enhanced phosphorylation activity of phot2.
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9
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Nakasone Y, Ohshima M, Okajima K, Tokutomi S, Terazima M. Photoreaction Dynamics of Full-Length Phototropin from Chlamydomonas reinhardtii. J Phys Chem B 2019; 123:10939-10950. [PMID: 31790257 DOI: 10.1021/acs.jpcb.9b09685] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Phototropin (phot) is a blue light sensor involved in the light responses of several species from green algae to higher plants. Phot consists of two photoreceptive domains (LOV1 and LOV2) and a Ser/Thr kinase domain. These domains are connected by a hinge and a linker domain. So far, studies on the photochemical reaction dynamics of phot have been limited to short fragments, and the reactions of intact phot have not been well elucidated. Here, the photoreactions of full-length phot and of several mutants from Chlamydomonas reinhardtii (Cr) were investigated by the transient grating and circular dichroism (CD) methods. Full-length Cr phot is in monomeric form in both dark and light states and shows conformational changes upon photoexcitation. When LOV1 is excited, the hinge helix unfolds with a time constant of 77 ms. Upon excitation of LOV2, the linker helix unfolds initially followed by a tertiary structural change of the kinase domain with a time constant of 91 ms. The quantum yield of conformational change after adduct formation of LOV2 is much smaller than that of LOV1, indicating that reactive and nonreactive forms exist. The conformational changes associated with the excitations of LOV1 and LOV2 occur independently and additively, even when they are excited simultaneously. Hence, the role of LOV1 is not to enhance the kinase activity in addition to LOV2 function; we suggest LOV1 has different functions such as regulation of intermolecular interactions.
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Affiliation(s)
- Yusuke Nakasone
- Department of Chemistry, Graduate School of Science , Kyoto University , Kyoto , Kyoto 606-8502 , Japan
| | - Masumi Ohshima
- Department of Chemistry, Graduate School of Science , Kyoto University , Kyoto , Kyoto 606-8502 , Japan
| | - Koji Okajima
- Graduate School of Science and Technology , Keio University , Yokohama , Kanagawa 223-8522 , Japan
| | - Satoru Tokutomi
- Department of Biological Science, Graduate School of Science , Osaka Prefecture University , Sakai , Osaka 599-8531 , Japan
| | - Masahide Terazima
- Department of Chemistry, Graduate School of Science , Kyoto University , Kyoto , Kyoto 606-8502 , Japan
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Ko S, Hwang B, Na JH, Lee J, Jung ST. Engineered Arabidopsis Blue Light Receptor LOV Domain Variants with Improved Quantum Yield, Brightness, and Thermostability. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:12037-12043. [PMID: 31581772 DOI: 10.1021/acs.jafc.9b05473] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Despite remarkable contribution of green fluorescent protein and its variants for better understanding of various biological functions, its application for anaerobic microorganisms has been limited because molecular oxygen is essential for chromophore formation. To overcome the limitation, we engineered a plant-derived light, oxygen, or voltage (LOV) domain containing flavin mononucleotide for enhanced spectral properties. The resulting LOV variants exhibited improved fluorescence intensity (20 and 70% higher for SH3 and 70% for BR1, respectively) compared to iLOV, an LOV variant isolated in a previous study, and the quantum yields of the LOV variants (0.40 for SH3 and 0.45 for BR1) were also improved relative to that of iLOV (Q = 0.37). In addition to fluorescence intensity, the identified mutations of SH3 enabled an improved thermostability of the protein. The engineered LOV variants with enhanced spectral properties could provide a valuable tool for fluorescent molecular probes under anaerobic conditions.
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Affiliation(s)
- Sanghwan Ko
- Department of Biomedical Sciences, Graduate School of Medicine , Korea University , Seoul 02841 , Republic of Korea
- Department of Applied Chemistry , Kookmin University , Seoul 02707 , Republic of Korea
| | - Bora Hwang
- Department of Applied Chemistry , Kookmin University , Seoul 02707 , Republic of Korea
| | - Jung-Hyun Na
- Department of Applied Chemistry , Kookmin University , Seoul 02707 , Republic of Korea
- Division of Discovery and Optimization, New Drug Development Center , Osong Medical Innovation Foundation , Cheongju , Chungcheongbuk-do 28160 , Republic of Korea
| | - Jisun Lee
- Department of Biomedical Sciences, Graduate School of Medicine , Korea University , Seoul 02841 , Republic of Korea
| | - Sang Taek Jung
- Department of Biomedical Sciences, Graduate School of Medicine , Korea University , Seoul 02841 , Republic of Korea
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11
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Suzuki H, Koshiba T, Fujita C, Yamauchi Y, Kimura T, Isobe T, Sakai T, Taoka M, Okamoto T. Low-fluence blue light-induced phosphorylation of Zmphot1 mediates the first positive phototropism. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:5929-5941. [PMID: 31376280 PMCID: PMC6812725 DOI: 10.1093/jxb/erz344] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 07/25/2019] [Indexed: 05/05/2023]
Abstract
Phototropin1 (phot1) perceives low- to high-fluence blue light stimuli and mediates both the first and second positive phototropisms. High-fluence blue light is known to induce autophosphorylation of phot1, leading to the second positive phototropism. However, the phosphorylation status of phot1 by low-fluence blue light that induces the first positive phototropism had not been observed. Here, we conducted a phosphoproteomic analysis of maize coleoptiles to investigate the fluence-dependent phosphorylation status of Zmphot1. High-fluence blue light induced phosphorylation of Zmphot1 at several sites. Notably, low-fluence blue light significantly increased the phosphorylation level of Ser291 in Zmphot1. Furthermore, Ser291-phosphorylated and Ser369Ser376-diphosphorylated peptides were found to be more abundant in the low-fluence blue light-irradiated sides than in the shaded sides of coleoptiles. The roles of these phosphorylation events in phototropism were explored by heterologous expression of ZmPHOT1 in the Arabidopsis thaliana phot1phot2 mutant. The first positive phototropism was restored in wild-type ZmPHOT1-expressing plants; however, plants expressing S291A-ZmPHOT1 or S369AS376A-ZmPHOT1 showed significantly reduced complementation rates. All transgenic plants tested in this study exhibited a normal second positive phototropism. These findings provide the first indication that low-fluence blue light induces phosphorylation of Zmphot1 and that this induced phosphorylation is crucial for the first positive phototropism.
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Affiliation(s)
- Hiromi Suzuki
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji-shi, Tokyo, Japan
- Japan Society for the Promotion of Science, Kojimachi Business Center Building, Chiyoda-ku, Tokyo, Japan
- Correspondence: or
| | - Tomokazu Koshiba
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji-shi, Tokyo, Japan
| | - Chiharu Fujita
- Department of Chemistry, Tokyo Metropolitan University, Hachioji-shi, Tokyo, Japan
| | - Yoshio Yamauchi
- Department of Chemistry, Tokyo Metropolitan University, Hachioji-shi, Tokyo, Japan
| | - Taro Kimura
- Japan Society for the Promotion of Science, Kojimachi Business Center Building, Chiyoda-ku, Tokyo, Japan
- Graduate School of Science and Technology, Niigata University, Niigata-shi, Niigata, Japan
| | - Toshiaki Isobe
- Department of Chemistry, Tokyo Metropolitan University, Hachioji-shi, Tokyo, Japan
| | - Tatsuya Sakai
- Graduate School of Science and Technology, Niigata University, Niigata-shi, Niigata, Japan
| | - Masato Taoka
- Department of Chemistry, Tokyo Metropolitan University, Hachioji-shi, Tokyo, Japan
| | - Takashi Okamoto
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji-shi, Tokyo, Japan
- Correspondence: or
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Measurements of Photoreaction and Kinase Activity of Phototropin, a Photoreceptor Protein for Tropic Response in Plants: Involvement of Kinase Activity in the Photosensitivity of Tropic Response. Methods Mol Biol 2019. [PMID: 30694475 DOI: 10.1007/978-1-4939-9015-3_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Phototropin is a photoreceptor protein responsible for phototropic responses in plants. A phototropin molecule has two photoreceptive domains named LOV1 and LOV2 in the N-terminal region. Blue light absorbed by a chromophore in these domains triggers conformational changes in the protein moiety. The C-terminal region of phototropin forms a Ser/Thr kinase that is activated by these conformational changes. The activated phototropin kinase transmits signals downstream leading to tropic responses. The lifetime of the activated state may concern the sensitivity of the tropic responses to light. Thus, spectrophotometric and kinase activity analyses of phototropin are important to understand the light signaling processes related to the photosensitivity. The preparation of polypeptide samples of Arabidopsis phototropin and the methods of spectroscopic measurements and kinase assay of these samples are shown in this chapter.
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Oide M, Sekiguchi Y, Fukuda A, Okajima K, Oroguchi T, Nakasako M. Classification of ab initio models of proteins restored from small-angle X-ray scattering. JOURNAL OF SYNCHROTRON RADIATION 2018; 25:1379-1388. [PMID: 30179176 DOI: 10.1107/s1600577518010342] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 07/18/2018] [Indexed: 06/08/2023]
Abstract
In structure analyses of proteins in solution by using small-angle X-ray scattering (SAXS), the molecular models are restored by using ab initio molecular modeling algorithms. There can be variation among restored models owing to the loss of phase information in the scattering profiles, averaging with regard to the orientation of proteins against the direction of the incident X-ray beam, and also conformational fluctuations. In many cases, a representative molecular model is obtained by averaging models restored in a number of ab initio calculations, which possibly provide nonrealistic models inconsistent with the biological and structural information about the target protein. Here, a protocol for classifying predicted models by multivariate analysis to select probable and realistic models is proposed. In the protocol, each structure model is represented as a point in a hyper-dimensional space describing the shape of the model. Principal component analysis followed by the clustering method is applied to visualize the distribution of the points in the hyper-dimensional space. Then, the classification provides an opportunity to exclude nonrealistic models. The feasibility of the protocol was examined through the application to the SAXS profiles of four proteins.
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Affiliation(s)
- Mao Oide
- Department of Physics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa 223-8522, Japan
| | - Yuki Sekiguchi
- Department of Physics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa 223-8522, Japan
| | - Asahi Fukuda
- Department of Physics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa 223-8522, Japan
| | - Koji Okajima
- Department of Physics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa 223-8522, Japan
| | - Tomotaka Oroguchi
- Department of Physics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa 223-8522, Japan
| | - Masayoshi Nakasako
- Department of Physics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa 223-8522, Japan
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