1
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Sharma S, Gautam AK, Singh R, Gourinath S, Kateriya S. Unusual photodynamic characteristics of the light-oxygen-voltage domain of phototropin linked to terrestrial adaptation of Klebsormidium nitens. FEBS J 2024. [PMID: 39344087 DOI: 10.1111/febs.17284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 05/17/2024] [Accepted: 09/13/2024] [Indexed: 10/01/2024]
Abstract
Phototropin (Phot), a blue light-sensing LOV domain protein, mediates blue light responses and is evolutionarily conserved across the green lineage. Klebsormidium nitens, a green terrestrial alga, presents a valuable opportunity to study adaptive responses from aquatic to land habitat transitions. We determined the crystal structure of Klebsormidium nitens Phot LOV1 domain (KnLOV1) in the dark and engineered different mutations (R60K, Q122N, and D33N) to modulate the lifetime of the photorecovery cycle. We observed unusual, slow recovery kinetics in the wild-type KnLOV1 domain (τ = 41 ± 3 min) compared to different mutants (R60K: τ = 2.0 ± 0.1 min, Q122N: τ = 1.7 ± 0.1 min, D33N: τ = 9.6 ± 0.1 min). Crystal structures of wild-type KnLOV1 and mutants revealed subtle but critical changes near the protein chromophore that is responsible for modulating protein dark recovery time. Our findings shed light on the unique structural and biochemical characteristics of the newly studied KnLOV1 and its evolutionary importance for phototropin-mediated physiology.
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Affiliation(s)
- Sunita Sharma
- Laboratory of Optobiotechnology, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
- Department of Cellular Biology, University of Georgia, Athens, Georgia, USA
| | - Avinash Kumar Gautam
- Structural Biology Lab, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Rajani Singh
- Laboratory of Optobiotechnology, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Samudrala Gourinath
- Structural Biology Lab, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Suneel Kateriya
- Laboratory of Optobiotechnology, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
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2
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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: 1] [Impact Index Per Article: 1.0] [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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Flores-Ibarra A, Maia RNA, Olasz B, Church JR, Gotthard G, Schapiro I, Heberle J, Nogly P. Light-Oxygen-Voltage (LOV)-sensing Domains: Activation Mechanism and Optogenetic Stimulation. J Mol Biol 2024; 436:168356. [PMID: 37944792 DOI: 10.1016/j.jmb.2023.168356] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 10/11/2023] [Accepted: 11/02/2023] [Indexed: 11/12/2023]
Abstract
The light-oxygen-voltage (LOV) domains of phototropins emerged as essential constituents of light-sensitive proteins, helping initiate blue light-triggered responses. Moreover, these domains have been identified across all kingdoms of life. LOV domains utilize flavin nucleotides as co-factors and undergo structural rearrangements upon exposure to blue light, which activates an effector domain that executes the final output of the photoreaction. LOV domains are versatile photoreceptors that play critical roles in cellular signaling and environmental adaptation; additionally, they can noninvasively sense and control intracellular processes with high spatiotemporal precision, making them ideal candidates for use in optogenetics, where a light signal is linked to a cellular process through a photoreceptor. The ongoing development of LOV-based optogenetic tools, driven by advances in structural biology, spectroscopy, computational methods, and synthetic biology, has the potential to revolutionize the study of biological systems and enable the development of novel therapeutic strategies.
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Affiliation(s)
- Andrea Flores-Ibarra
- Dioscuri Center for Structural Dynamics of Receptors, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Krakow, Poland
| | - Raiza N A Maia
- Department of Chemistry, The University of Texas at Austin, 78712-1224 Austin, TX, USA
| | - Bence Olasz
- Dioscuri Center for Structural Dynamics of Receptors, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Krakow, Poland
| | - Jonathan R Church
- Institute of Chemistry, The Hebrew University of Jerusalem, 91905 Jerusalem, Israel
| | | | - Igor Schapiro
- Institute of Chemistry, The Hebrew University of Jerusalem, 91905 Jerusalem, Israel
| | - Joachim Heberle
- Department of Physics, Freie Universität Berlin, 14195 Berlin, Germany
| | - Przemyslaw Nogly
- Dioscuri Center for Structural Dynamics of Receptors, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Krakow, Poland.
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4
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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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5
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Ding Y, Zhao Z, Matysik J, Gärtner W, Losi A. Mapping the role of aromatic amino acids within a blue-light sensing LOV domain. Phys Chem Chem Phys 2021; 23:16767-16775. [PMID: 34319324 DOI: 10.1039/d1cp02217b] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Photosensing LOV (Light, Oxygen, Voltage) domains detect and respond to UVA/Blue (BL) light by forming a covalent adduct between the flavin chromophore and a nearby cysteine, via the decay of the flavin triplet excited state. LOV domains where the reactive cysteine has been mutated are valuable fluorescent tools for microscopy and as genetically encoded photosensitisers for reactive oxygen species. Besides being convenient tools for applications, LOV domains without the reactive cysteine (naturally occurring or engineered) can still be functionally photoactivated via formation of a neutral flavin radical. Tryptophans and tyrosines are held as the main partners as potential electron donors to the flavin excited states. In this work, we explore the relevance of aromatic amino acids in determining the photophysical features of the LOV protein Mr4511 from Methylobacterium radiotolerans by introducing point mutations into the C71S variant that does not form the covalent adduct. By using an array of spectroscopic techniques we measured the fluorescence quantum yields and lifetimes, the triplet yields and lifetimes, and the efficiency of singlet oxygen (SO) formation for eleven Mr4511 variants. Insertion of Trp residues at distances between 0.6 and 1.5 nm from the flavin chromophore results in strong quenching of the flavin excited triplet state and, at the shorter distances even of the singlet excited state. The mutation F130W (ca. 0.6 nm) completely quenches the singlet excited state, preventing triplet formation: in this case, even if the cysteine is present, the photo-adduct is not formed. Tyrosines are also quenchers for the flavin excited states, although not as efficient as Trp residues, as demonstrated with their substitution with the inert phenylalanine. For one of these variants, C71S/Y116F, we found that the quantum yield of formation for singlet oxygen is 0.44 in aqueous aerobic solution, vs 0.17 for C71S. Based on our study with Mr4511 and on literature data for other LOV domains we suggest that Trp and Tyr residues too close to the flavin chromophore (at distances less than 0.9 nm) reduce the yield of photoproduct formation and that introduction of inert Phe residues in key positions can help in developing efficient, LOV-based photosensitisers.
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Affiliation(s)
- Yonghong Ding
- Institute for Analytical Chemistry, University of Leipzig, Linnéstrasse 3, 04103 Leipzig, Germany
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6
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Consiglieri E, Xu QZ, Zhao KH, Gärtner W, Losi A. The first molecular characterisation of blue- and red-light photoreceptors from Methylobacterium radiotolerans. Phys Chem Chem Phys 2020; 22:12434-12446. [PMID: 32458860 DOI: 10.1039/d0cp02014a] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Methylobacteria are facultative methylotrophic phytosymbionts of great industrial and agronomical interest, and they are considered as opportunistic pathogens posing a health threat to humans. So far only a few reports mention photoreceptor coding sequences in Methylobacteria genomes, but no investigation at the molecular level has been performed yet. We here present comprehensive in silico research into potential photoreceptors in this bacterial phylum and report the photophysical and photochemical characterisation of two representatives of the most widespread photoreceptor classes, a blue-light sensing LOV (light, oxygen, voltage) protein and a red/far red light sensing BphP (biliverdin-binding bacterial phytochrome) from M. radiotolerans JCM 2831. Overall, both proteins undergo the expected light-triggered reactions, but peculiar features were also identified. The LOV protein Mr4511 has an extremely long photocycle and lacks a tryptophan conserved in ca. 75% of LOV domains. Mutation I37V accelerates the photocycle by one order of magnitude, while the Q112W change underscores the ability of tryptophan in this position to perform efficient energy transfer to the flavin chromophore. Time-resolved photoacoustic experiments showed that Mr4511 has a higher triplet quantum yield than other LOV domains and that the formation of the photoproduct results in a volume expansion, in sharp contrast to other LOV proteins. Mr4511 was found to be astonishingly resistant to denaturation by urea, still showing light-triggered reactions after incubation in urea for more than 20 h. The phytochrome MrBphP1 exhibits the so far most red-shifted absorption maxima for its Pr- and Pfr forms (λmax = 707 nm and 764 nm for the Pr and Pfr forms). The light-driven conversions in both directions occur with relatively high quantum yields of 0.2. Transient ns absorption spectroscopy (μs-ms time range) identifies the decay of the instantaneously formed lumi-intermediate, followed by only one additional intermediate before the formation of the respective final photoproducts for Pr-to-Pfr or Pfr-to-Pr photoconversion, in contrast to other BphPs. The relatively simple photoconversion patterns suggest the absence of the shunt pathways reported for other bacterial phytochromes.
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Affiliation(s)
- Eleonora Consiglieri
- Department of Mathematical, Physical and Computer Sciences, University of Parma, Parco Area delle Scienze 7/A, 43124 Parma, Italy.
| | - Qian-Zhao Xu
- Institute for Analytical Chemistry, University of Leipzig, Linnéstrasse 3, 04103 Leipzig, Germany and State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Kai-Hong Zhao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Wolfgang Gärtner
- Institute for Analytical Chemistry, University of Leipzig, Linnéstrasse 3, 04103 Leipzig, Germany
| | - Aba Losi
- Department of Mathematical, Physical and Computer Sciences, University of Parma, Parco Area delle Scienze 7/A, 43124 Parma, Italy.
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7
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Polverini E, Schackert FK, Losi A. Interplay among the “flipping” glutamine, a conserved phenylalanine, water and hydrogen bonds within a blue-light sensing LOV domain. Photochem Photobiol Sci 2020; 19:892-904. [DOI: 10.1039/d0pp00082e] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
A combined photoacoustics and molecular dynamics approach highlights the crucial role of a conserved phenyalanine in photosensing LOV domains.
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Affiliation(s)
- Eugenia Polverini
- Department of Mathematical
- Physical and Computer Sciences
- University of Parma
- 43124 Parma
- Italy
| | - Florian Karl Schackert
- Department of Mathematical
- Physical and Computer Sciences
- University of Parma
- 43124 Parma
- Italy
| | - Aba Losi
- Department of Mathematical
- Physical and Computer Sciences
- University of Parma
- 43124 Parma
- Italy
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8
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Bannister S, Böhm E, Zinn T, Hellweg T, Kottke T. Arguments for an additional long-lived intermediate in the photocycle of the full-length aureochrome 1c receptor: A time-resolved small-angle X-ray scattering study. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2019; 6:034701. [PMID: 31263739 PMCID: PMC6588521 DOI: 10.1063/1.5095063] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 06/05/2019] [Indexed: 06/09/2023]
Abstract
Aureochromes (AUREO) act as blue-light photoreceptors in algae. They consist of a light-, oxygen-, voltage-sensitive (LOV) domain and a DNA-binding basic region/leucine zipper. Illumination of the flavin cofactor in LOV leads to the formation of an adduct, followed by global structural changes. Here, we first applied UV/vis spectroscopy to characterize the photocycle of full-length aureochrome 1c (PtAUREO1c) from the diatom Phaeodactylum tricornutum. With a time constant of 850 s and a quantum yield of 23%, PtAUREO1c reveals a faster recovery time and a much lower sensitivity toward light than PtAUREO1a, pointing to its role as a high light sensor in vivo. UV/vis spectroscopy offers details on the local recovery of the flavin chromophore. However, kinetic information on the global structural recovery of full-length AUREO or any other multidomain LOV protein is missing. This information is essential not least for the photoreceptors' applications as optogenetic devices. Therefore, we established a procedure to apply small-angle X-ray scattering on PtAUREO1c in a time-resolved manner employing an in-house setup. In combination with UV/vis spectroscopy under similar conditions, we revealed a discrepancy between the recovery of the global protein structure and the adduct lifetime. Accordingly, we propose to supplement the photocycle by an intermediate state (I447), which decays with a time constant of about 800 s and prolongs the lifetime of the signaling state.
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Affiliation(s)
- Saskia Bannister
- Physical and Biophysical Chemistry, Department of Chemistry, Bielefeld University, Universitaetsstr. 25, 33615 Bielefeld, Germany
| | - Elena Böhm
- Physical and Biophysical Chemistry, Department of Chemistry, Bielefeld University, Universitaetsstr. 25, 33615 Bielefeld, Germany
| | - Thomas Zinn
- ESRF–The European Synchrotron, 71, Avenue des Martyrs, 38043 Grenoble Cedex 9, France
| | - Thomas Hellweg
- Physical and Biophysical Chemistry, Department of Chemistry, Bielefeld University, Universitaetsstr. 25, 33615 Bielefeld, Germany
| | - Tilman Kottke
- Physical and Biophysical Chemistry, Department of Chemistry, Bielefeld University, Universitaetsstr. 25, 33615 Bielefeld, Germany
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9
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Schroeder L, Oldemeyer S, Kottke T. Time-Resolved Infrared Spectroscopy on Plant Cryptochrome—Relevance of Proton Transfer and ATP Binding for Signaling. J Phys Chem A 2017; 122:140-147. [DOI: 10.1021/acs.jpca.7b10249] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Lea Schroeder
- Physical and Biophysical
Chemistry, Department of Chemistry, Bielefeld University, Universitätsstraße
25, 33615 Bielefeld, Germany
| | - Sabine Oldemeyer
- Physical and Biophysical
Chemistry, Department of Chemistry, Bielefeld University, Universitätsstraße
25, 33615 Bielefeld, Germany
| | - Tilman Kottke
- Physical and Biophysical
Chemistry, Department of Chemistry, Bielefeld University, Universitätsstraße
25, 33615 Bielefeld, Germany
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10
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Ganguly A, Thiel W, Crane BR. Glutamine Amide Flip Elicits Long Distance Allosteric Responses in the LOV Protein Vivid. J Am Chem Soc 2017; 139:2972-2980. [PMID: 28145707 PMCID: PMC5902025 DOI: 10.1021/jacs.6b10701] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Light-oxygen-voltage (LOV) domains sense blue light through the photochemical formation of a cysteinyl-flavin covalent adduct. Concurrent protonation at the flavin N5 position alters the hydrogen bonding interactions of an invariant Gln residue that has been proposed to flip its amide side chain as a critical step in the propagation of conformational change. Traditional molecular dynamics (MD) and replica-exchange MD (REMD) simulations of the well-characterized LOV protein Vivid (VVD) demonstrate that the Gln182 amide indeed reorients by ∼180° in response to either adduct formation or reduction of the isoalloxazine ring to the neutral semiquinone, both of which involve N5 protonation. Free energy simulations reveal that the relative free energies of the flipped Gln conformation and the flipping barrier are significantly lower in the light-adapted state. The Gln182 flip stabilizes an important hinge-bβ region between the PAS β-sheet and the N-terminal cap helix that in turn destabilizes an N-terminal latch region against the PAS core. Release of the latch, observed both experimentally and in the simulations, is known to mediate light-induced VVD dimerization. This computational study of a LOV protein, unprecedented in its agreement with experiment, provides an atomistic view of long-range allosteric coupling in a photoreceptor.
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Affiliation(s)
- Abir Ganguly
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1. 45470 Mülheim an der Ruhr, Germany
| | - Walter Thiel
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1. 45470 Mülheim an der Ruhr, Germany
| | - Brian R. Crane
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA
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11
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Losi A, Gärtner W. Solving Blue Light Riddles: New Lessons from Flavin-binding LOV Photoreceptors. Photochem Photobiol 2017; 93:141-158. [PMID: 27861974 DOI: 10.1111/php.12674] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2016] [Accepted: 10/22/2016] [Indexed: 12/15/2022]
Abstract
Detection of blue light (BL) via flavin-binding photoreceptors (Fl-Blues) has evolved throughout all three domains of life. Although the main BL players, that is light, oxygen and voltage (LOV), blue light sensing using flavins (BLUF) and Cry (cryptochrome) proteins, have been characterized in great detail with respect to structure and function, still several unresolved issues at different levels of complexity remain and novel unexpected findings were reported. Here, we review the most prevailing riddles of LOV-based photoreceptors, for example: the relevance of water and/or small metabolites for the dynamics of the photocycle; molecular details of light-to-signal transduction events; the interplay of BL sensing by LOV domains with other environmental stimuli, such as BL plus oxygen-mediating photodamage and its impact on microbial lifestyles; the importance of the cell or chromophore redox state in determining the fate of BL-driven reactions; the evolutionary pathways of LOV-based BL sensing and associated functions through the diverse phyla. We will discuss major novelties emerged during the last few years on these intriguing aspects of LOV proteins by presenting paradigmatic examples from prokaryotic photosensors that exhibit the largest complexity and richness in associated functions.
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Affiliation(s)
- Aba Losi
- Department of Physics and Earth Sciences, University of Parma, Parma, Italy
| | - Wolfgang Gärtner
- Max-Planck-Institute for Chemical Energy Conversion, Mülheim, Germany
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12
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Domratcheva T, Fedorov R, Schlichting I. Analysis of the Primary Photocycle Reactions Occurring in the Light, Oxygen, and Voltage Blue-Light Receptor by Multiconfigurational Quantum-Chemical Methods. J Chem Theory Comput 2015; 2:1565-74. [PMID: 26627027 DOI: 10.1021/ct0600114] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The photocycle reactions occurring between the flavin mononucleotide cofactor and the reactive cysteine residue in the blue-light photoreceptor domain light, oxygen, and voltage (LOV) were modeled for a system consisting of lumiflavin and thiomethanol. The electronic structure and energies of the reactive species were estimated using the CASSCF and MCQDPT2 quantum-chemical methods. The reaction pathway for the S-C4a covalent adduct formation in the triplet state was determined. Concerted electron and proton transfer from the thiol to the flavin in the triplet electronic state results in a biradical complex that is, however, unstable because its structure corresponds to a triplet-singlet crossing. The covalent adduct dissociation in the ground electronic state is a reverse of the photoreaction proceeding via a single energy barrier for hydrogen transfer. Thus, both photo- and dark reactions were found to be single-step chemical transformations occurring without stable intermediates. The photoreaction yielding the S-C4a covalent adduct is an intrinsic property of the isoalloxazine-thiol complex in the specific geometry arranged by the protein in LOV. The S-C4a covalent adduct between lumiflavin and thiomethanol is rather stable implying that in LOV its dissociation is facilitated by the protein.
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Affiliation(s)
- Tatiana Domratcheva
- Max-Planck Institute for Medical Research, Department of Biomolecular Mechanisms, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Roman Fedorov
- Max-Planck Institute for Medical Research, Department of Biomolecular Mechanisms, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Ilme Schlichting
- Max-Planck Institute for Medical Research, Department of Biomolecular Mechanisms, Jahnstrasse 29, 69120 Heidelberg, Germany
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Torra J, Burgos-Caminal A, Endres S, Wingen M, Drepper T, Gensch T, Ruiz-González R, Nonell S. Singlet oxygen photosensitisation by the fluorescent protein Pp2FbFP L30M, a novel derivative of Pseudomonas putida flavin-binding Pp2FbFP. Photochem Photobiol Sci 2015; 14:280-7. [DOI: 10.1039/c4pp00338a] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The flavin-binding protein Pp2FbFP L30M shows a high singlet oxygen quantum yield.
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Affiliation(s)
- Joaquim Torra
- Institut Químic de Sarrià
- Universitat Ramon Llull
- Barcelona
- Spain
| | | | - Stephan Endres
- Institute of Molecular Enzyme Technology
- Heinrich-Heine-University Düsseldorf
- 52425 Jülich
- Germany
| | - Marcus Wingen
- Institute of Molecular Enzyme Technology
- Heinrich-Heine-University Düsseldorf
- 52425 Jülich
- Germany
| | - Thomas Drepper
- Institute of Molecular Enzyme Technology
- Heinrich-Heine-University Düsseldorf
- 52425 Jülich
- Germany
| | - Thomas Gensch
- Institute of Complex Systems 4 (ICS-4
- Cellular Biophysics)
- 52425 Jülich
- Germany
| | | | - Santi Nonell
- Institut Químic de Sarrià
- Universitat Ramon Llull
- Barcelona
- Spain
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14
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Pennacchietti F, Abbruzzetti S, Losi A, Mandalari C, Bedotti R, Viappiani C, Zanacchi FC, Diaspro A, Gärtner W. The dark recovery rate in the photocycle of the bacterial photoreceptor YtvA is affected by the cellular environment and by hydration. PLoS One 2014; 9:e107489. [PMID: 25211155 PMCID: PMC4161478 DOI: 10.1371/journal.pone.0107489] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Accepted: 08/10/2014] [Indexed: 11/19/2022] Open
Abstract
We report thermal recovery kinetics of the lit state into the parental dark state, measured for the blue light-sensing photoreceptor YtvA inside overexpressing E. coli and B. subtilis bacterial cells, performed for the wild type and several mutated proteins. Recovery was followed as a recovery of the fluorescence, as this property is only found for the parental but not for the photochemically generated lit state. When cells were deposited onto a microscope glass plate, the observed thermal recovery rate in the photocycle was found ca. ten times faster in comparison to purified YtvA in solution. When the E. coli or B. subtilis colonies were soaked in an isotonic buffer, the dark relaxation became again much slower and was very similar to that observed for YtvA in solution. The observed effects show that rate constants can be tuned by the cellular environment through factors such as hydration.
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Affiliation(s)
| | - Stefania Abbruzzetti
- Dipartimento di Fisica e Scienze della Terra, Università di Parma, Parma, Italy
- NEST, Istituto Nanoscienze, Consiglio Nazionale delle Ricerche, Pisa, Italy
| | - Aba Losi
- Dipartimento di Fisica e Scienze della Terra, Università di Parma, Parma, Italy
| | - Carmen Mandalari
- Dipartimento di Fisica e Scienze della Terra, Università di Parma, Parma, Italy
| | - Roberta Bedotti
- Dipartimento di Fisica e Scienze della Terra, Università di Parma, Parma, Italy
| | - Cristiano Viappiani
- Dipartimento di Fisica e Scienze della Terra, Università di Parma, Parma, Italy
- NEST, Istituto Nanoscienze, Consiglio Nazionale delle Ricerche, Pisa, Italy
- * E-mail:
| | | | | | - Wolfgang Gärtner
- Max-Planck-Institute for Chemical Energy Conversion (CEC), Mülheim a.d. Ruhr, Germany
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15
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Pudasaini A, Zoltowski BD. Zeitlupe senses blue-light fluence to mediate circadian timing in Arabidopsis thaliana. Biochemistry 2013; 52:7150-8. [PMID: 24033190 DOI: 10.1021/bi401027n] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Plants employ a variety of light, oxygen, voltage (LOV) domain photoreceptors to regulate diverse aspects of growth and development. The Zeitlupe (ZTL), Flavin-Kelch-Fbox-1 (FKF1), and LOV-Kelch-Protein-2 (LKP2) proteins dictate measurement of the day length, flowering time, and regulation of the circadian clock by blue-light regulation of protein complex formation. Previous reports indicated that ZTL photochemistry was irreversible, which is inconsistent with its role in marking the day-night transition. A kinetic model of LOV domain function predicts that ZTL has evolved unique photochemical parameters to allow it to function as a sensor of environmental light intensity. Moreover, our model indicates that a photocatalyzed reverse reaction is required for the sensitivity of LOV domains to light fluence. Inclusion of a photocatalyzed rate constant allows the establishment of a photostationary steady state of light-activated proteins, whose relative population is sensitive to daily (circadian) or positional (phototropism) oscillations in light intensity. Photochemical characterization confirms that ZTL undergoes adduct decay on a time scale of hours in contrast to previous reports. The fast photocycle allows detection of the day-night transition facilitating circadian timing. ZTL kinetics reflect an evolutionary adaptation of the ZTL/FKF1/LKP2 family to function in distinct aspects of blue-light signaling.
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Affiliation(s)
- Ashutosh Pudasaini
- Department of Chemistry, Southern Methodist University , Dallas, Texas 75275, United States
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16
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Okajima K, Kashojiya S, Tokutomi S. Photosensitivity of kinase activation by blue light involves the lifetime of a cysteinyl-flavin adduct intermediate, S390, in the photoreaction cycle of the LOV2 domain in phototropin, a plant blue light receptor. J Biol Chem 2012; 287:40972-81. [PMID: 23066024 DOI: 10.1074/jbc.m112.406512] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Phototropin (phot) is a light-regulated protein kinase that mediates a variety of photoresponses in plants, such as phototropism, chloroplast positioning, and stomata opening. Arabidopsis has two homologues, phot1 and phot2, that share physiological functions depending on light intensity. A phot molecule has two photoreceptive light oxygen voltage-sensing domains, LOV1 and LOV2, and a Ser/Thr kinase domain. The LOV domains undergo a photocycle upon blue light (BL) stimulation, including transient adduct formation between the chromophore and a conserved cysteine (S390 intermediate) that leads to activation of the kinase. To uncover the mechanism underlying the photoactivation of the kinase, we have introduced a kinase assay system composed of a phot1 LOV2-linker-kinase polypeptide as a light-regulated kinase and its N-terminal polypeptide as an artificial substrate (Okajima, K., Matsuoka, D., and Tokutomi, S. (2011) LOV2-linker-kinase phosphorylates LOV1-containing N-terminal polypeptide substrate via photoreaction of LOV2 in Arabidopsis phototropin1. FEBS Lett. 585, 3391-3395). In the present study, we extended the assay system to phot2 and compared the photochemistry and kinase activation by BL between phot1 and phot2 to gain insight into the molecular basis for the different photosensitivities of phot1 and phot2. Photosensitivity of kinase activation by BL and the lifetime of S390 of phot1 were 10 times higher and longer, respectively, than those of phot2. This correlation was confirmed by an amino acid substitution experiment with phot1 to shorten the lifetime of S390. The present results demonstrated that the photosensitivity of kinase activation in phot involves the lifetime of S390 in LOV2, suggesting that the lifetime is one of the key factors for the different photosensitivities observed for phot1 and phot2.
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Affiliation(s)
- Koji Okajima
- Department of Biological Sciences, Graduate School of Science, Osaka Prefecture University, Gakuen-cho 1-1, Nakaku, Sakai, Osaka 599-8531, Japan
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17
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Kraiselburd I, Alet AI, Tondo ML, Petrocelli S, Daurelio LD, Monzón J, Ruiz OA, Losi A, Orellano EG. A LOV protein modulates the physiological attributes of Xanthomonas axonopodis pv. citri relevant for host plant colonization. PLoS One 2012; 7:e38226. [PMID: 22675525 PMCID: PMC3366940 DOI: 10.1371/journal.pone.0038226] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2011] [Accepted: 05/02/2012] [Indexed: 01/04/2023] Open
Abstract
Recent studies have demonstrated that an appropriate light environment is required for the establishment of efficient vegetal resistance responses in several plant-pathogen interactions. The photoreceptors implicated in such responses are mainly those belonging to the phytochrome family. Data obtained from bacterial genome sequences revealed the presence of photosensory proteins of the BLUF (Blue Light sensing Using FAD), LOV (Light, Oxygen, Voltage) and phytochrome families with no known functions. Xanthomonas axonopodis pv. citri is a Gram-negative bacterium responsible for citrus canker. The in silico analysis of the X. axonopodis pv. citri genome sequence revealed the presence of a gene encoding a putative LOV photoreceptor, in addition to two genes encoding BLUF proteins. This suggests that blue light sensing could play a role in X. axonopodis pv. citri physiology. We obtained the recombinant Xac-LOV protein by expression in Escherichia coli and performed a spectroscopic analysis of the purified protein, which demonstrated that it has a canonical LOV photochemistry. We also constructed a mutant strain of X. axonopodis pv. citri lacking the LOV protein and found that the loss of this protein altered bacterial motility, exopolysaccharide production and biofilm formation. Moreover, we observed that the adhesion of the mutant strain to abiotic and biotic surfaces was significantly diminished compared to the wild-type. Finally, inoculation of orange (Citrus sinensis) leaves with the mutant strain of X. axonopodis pv. citri resulted in marked differences in the development of symptoms in plant tissues relative to the wild-type, suggesting a role for the Xac-LOV protein in the pathogenic process. Altogether, these results suggest the novel involvement of a photosensory system in the regulation of physiological attributes of a phytopathogenic bacterium. A functional blue light receptor in Xanthomonas spp. has been described for the first time, showing an important role in virulence during citrus canker disease.
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Affiliation(s)
- Ivana Kraiselburd
- Molecular Biology Division, Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Analía I. Alet
- Molecular Biology Division, Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - María Laura Tondo
- Molecular Biology Division, Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Silvana Petrocelli
- Molecular Biology Division, Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Lucas D. Daurelio
- Molecular Biology Division, Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Jesica Monzón
- Molecular Biology Division, Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Oscar A. Ruiz
- IIB-INTECH, Unidad de Biotecnología, Chascomús, Buenos Aires, Argentina
| | - Aba Losi
- Department of Physics, University of Parma, Parma, Italy
| | - Elena G. Orellano
- Molecular Biology Division, Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
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18
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Penzkofer A. Photoluminescence behavior of riboflavin and lumiflavin in liquid solutions and solid films. Chem Phys 2012. [DOI: 10.1016/j.chemphys.2012.03.017] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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19
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Losi A, Gärtner W. The evolution of flavin-binding photoreceptors: an ancient chromophore serving trendy blue-light sensors. ANNUAL REVIEW OF PLANT BIOLOGY 2012; 63:49-72. [PMID: 22136567 DOI: 10.1146/annurev-arplant-042811-105538] [Citation(s) in RCA: 140] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Photoreceptor flavoproteins of the LOV, BLUF, and cryptochrome families are ubiquitous among the three domains of life and are configured as UVA/blue-light systems not only in plants-their original arena-but also in prokaryotes and microscopic algae. Here, we review these proteins' structure and function, their biological roles, and their evolution and impact in the living world, and underline their growing application in biotechnologies. We present novel developments such as the interplay of light and redox stimuli, emerging enzymatic and biological functions, lessons on evolution from picoalgae, metagenomics analysis, and optogenetics applications.
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Affiliation(s)
- Aba Losi
- Department of Physics, University of Parma, Parma, Italy.
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20
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Peter E, Dick B, Baeurle SA. Signals of LOV1: a computer simulation study on the wildtype LOV1-domain of Chlamydomonas reinhardtii and its mutants. J Mol Model 2011; 18:1375-88. [PMID: 21761179 DOI: 10.1007/s00894-011-1165-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2011] [Accepted: 06/24/2011] [Indexed: 01/12/2023]
Abstract
Phototropins are photoreceptors regulating the blue-light response in plants and bacteria. They consist of two LOV (light oxygen voltage sensitive) domains each containing a non-covalently bound flavin-mononucleotide (FMN) chromophore, which are connected to a serine/threonine-kinase. Upon illumination, the LOV-domains undergo conformational changes, triggering a signal cascade in the organism through kinase activation. Here, we present results from molecular dynamics simulations in which we investigate the signal transduction pathway of the wildtype LOV1-domain of Chlamydomonas reinhardtii and a methyl-mercaptan (MM) adduct of its Cys57Gly-mutant at the molecular level. In particular, we analyzed the effect of covalent-bond formation between the reactive cysteine Cys57 and the FMN-reaction center, as well as the subsequent charge redistribution, on the spatio-dynamical behavior of the LOV1-domain. We compare the calculation results with experimental data and demonstrate that these adduct state characteristics have an important influence on the response of this photosensor. The light-induced changes implicate primarily an alteration of the surface charge distribution through rearrangement of the highly flexible Cα-, Dα- and Eα-helices including the Glu51-Lys91-salt bridge on the hydrophilic side of the protein domain and a β-sheet tightening process via coupling of the Aβ- and Bβ-strands. Our findings confirm the aptitude of the LOV1-domain to function as a dimerization partner, allowing the green alga to adapt its reproduction and growth speed to the environmental conditions.
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Affiliation(s)
- Emanuel Peter
- Department of Chemistry and Pharmacy, Institute of Physical and Theoretical Chemistry, University of Regensburg, 93040 Regensburg, Germany
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21
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Structural basis of photosensitivity in a bacterial light-oxygen-voltage/helix-turn-helix (LOV-HTH) DNA-binding protein. Proc Natl Acad Sci U S A 2011; 108:9449-54. [PMID: 21606338 DOI: 10.1073/pnas.1100262108] [Citation(s) in RCA: 140] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Light-oxygen-voltage (LOV) domains are blue light-activated signaling modules integral to a wide range of photosensory proteins. Upon illumination, LOV domains form internal protein-flavin adducts that generate conformational changes which control effector function. Here we advance our understanding of LOV regulation with structural, biophysical, and biochemical studies of EL222, a light-regulated DNA-binding protein. The dark-state crystal structure reveals interactions between the EL222 LOV and helix-turn-helix domains that we show inhibit DNA binding. Solution biophysical data indicate that illumination breaks these interactions, freeing the LOV and helix-turn-helix domains of each other. This conformational change has a key functional effect, allowing EL222 to bind DNA in a light-dependent manner. Our data reveal a conserved signaling mechanism among diverse LOV-containing proteins, where light-induced conformational changes trigger activation via a conserved interaction surface.
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22
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Losi A, Gärtner W. Old Chromophores, New Photoactivation Paradigms, Trendy Applications: Flavins in Blue Light-Sensing Photoreceptors†. Photochem Photobiol 2011; 87:491-510. [DOI: 10.1111/j.1751-1097.2011.00913.x] [Citation(s) in RCA: 120] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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23
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Raffelberg S, Mansurova M, Gärtner W, Losi A. Modulation of the photocycle of a LOV domain photoreceptor by the hydrogen-bonding network. J Am Chem Soc 2011; 133:5346-56. [PMID: 21410163 DOI: 10.1021/ja1097379] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
An extended hydrogen-bonding (HB) network stabilizes the isoalloxazine ring of the flavin mononucleotide (FMN) chromophore within the photosensing LOV domain of blue-light protein receptors, via interactions between the C(2)═O, N(3)H, C(4)═O, and N(5) groups and conserved glutamine and asparagine residues. In this work we studied the influence of the HB network on the efficiency, kinetics, and energetics of a LOV protein photocycle, involving the reversible formation of a FMN-cysteine covalent adduct. The following results were found for mutations of the conserved amino acids N94, N104, and Q123 in the Bacillus subtilis LOV protein YtvA: (i) Increased (N104D, N94D) or strongly reduced (N94A) rate of adduct formation; this latter mutation extends the lifetime of the flavin triplet state, i.e., adduct formation, more than 60-fold, from 2 μs for the wild-type (WT) protein to 129 μs. (ii) Acceleration of the overall photocycle for N94S, N94A, and Q123N, with recovery lifetimes 20, 45, and 85 times faster than for YtvA-WT, respectively. (iii) Slight modifications of FMN spectral features, correlated with the polarization of low-energy transitions. (iv) Strongly reduced (N94S) or suppressed (Q123N) structural volume changes accompanying adduct formation, as determined by optoacoustic spectroscopy. (v) Minor effects on the quantum yield, with the exception of a considerable reduction for Q123N, i.e., 0.22 vs 0.49 for YtvA-WT. The data stress the importance of the HB network in modulating the photocycle of LOV domains, while at the same time establishing a link with functional responses.
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Affiliation(s)
- Sarah Raffelberg
- Max-Planck-Institute for Bioinorganic Chemistry, Stiftstrasse 34-36, 45470 Mülheim, Germany
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Peter E, Dick B, Baeurle SA. Effect of computational methodology on the conformational dynamics of the protein photosensor LOV1 from Chlamydomonas reinhardtii. J Chem Biol 2011; 4:167-84. [PMID: 22408688 DOI: 10.1007/s12154-011-0060-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2010] [Accepted: 02/17/2011] [Indexed: 12/22/2022] Open
Abstract
UNLABELLED LOV domains are the light-sensitive protein domains of plant phototropins and bacteria. They photochemically form a covalent bond between a flavin mononucleotide (FMN) chromophore and a cysteine, attached to the apo-protein, upon irradiation with blue light, which triggers a signal in the adjacent kinase. Although their signaling state has been well characterized through experimental means, their signal transduction pathway as well as dark-state activity are generally only poorly understood. Here we show results from molecular dynamics simulations where we investigated the effect of thermostating and long-range electrostatics on the solution structure and dynamical behavior of the wild-type LOV1 domain from the green algae Chlamydomonas reinhardtii in the dark. We demonstrate that these computational issues can dramatically affect the conformational fluctuations of such protein domains by suppressing configurations far from equilibrium or destabilizing local configurations, leading to artificial changes of the protein secondary structure as well as the H-bond network formed by the amino acids and the FMN. By comparing our calculation results with recent experimental data, we show that the non-invasive thermostating strategy, where the protein solute is only indirectly coupled to the thermostat via the solvent, in conjunction with the particle-mesh Ewald technique, provides dark-state conformers, which are in consistency with experimental observations. Moreover, our calculations indicate that the LOV1 domains can alter the intersystem crossing rate and rate of adduct formation by adjusting the population distribution of these dark-state conformers. This might permit them to function as a modulator of the signal intensity under low light conditions. ELECTRONIC SUPPLEMENTARY MATERIAL The online version of this article (doi:10.1007/s12154-011-0060-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Emanuel Peter
- Department of Chemistry and Pharmacy, Institute of Physical and Theoretical Chemistry, University of Regensburg, 93040 Regensburg, Germany
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25
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Nakasone Y, Zikihara K, Tokutomi S, Terazima M. Kinetics of conformational changes of the FKF1-LOV domain upon photoexcitation. Biophys J 2011; 99:3831-9. [PMID: 21112308 DOI: 10.1016/j.bpj.2010.10.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2010] [Revised: 10/01/2010] [Accepted: 10/06/2010] [Indexed: 01/16/2023] Open
Abstract
The photochemical reaction dynamics of a light-oxygen-voltage (LOV) domain from the blue light sensor protein, FKF1 (flavin-binding Kelch repeat F-box) was studied by means of the pulsed laser-induced transient grating method. The observed absorption spectral changes upon photoexcitation were similar to the spectral changes observed for typical LOV domain proteins (e.g., phototropins). The adduct formation took place with a time constant of 6 μs. After this reaction, a significant conformational change with a time constant of 6 ms was observed as a change in the diffusion coefficient. An FKF1-LOV mutant without the conserved loop connecting helices E and F, which is present only in the FKF1/LOV Kelch protein 2/ZEITLUPE family, did not show these slow phase dynamics. This result indicates that the conformational change in the loop region represents a major change in the FKF1-LOV photoreaction.
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Affiliation(s)
- Yusuke Nakasone
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto, Japan
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26
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Terazima M. Studies of photo-induced protein reactions by spectrally silent reaction dynamics detection methods: applications to the photoreaction of the LOV2 domain of phototropin from Arabidopsis thaliana. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2011; 1814:1093-105. [PMID: 21211575 DOI: 10.1016/j.bbapap.2010.12.011] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2010] [Revised: 12/06/2010] [Accepted: 12/22/2010] [Indexed: 01/28/2023]
Abstract
Biological function involves a series of chemical reactions of biological molecules, and during these reactions, there are numerous spectrally silent dynamic events that cannot be monitored by absorption or emission spectroscopic techniques. Such spectrally silent dynamics include changes in conformation, intermolecular interactions (hydrogen bonding, hydrophobic interactions), inter-protein interactions (oligomer formation, dissociation reactions) and conformational fluctuations. These events might be associated with biological function. To understand the molecular mechanisms of reactions, time-resolved detection of such dynamics is essential. Recently, it has been shown that time-resolved detection of the refractive index is a powerful tool for measuring dynamic events. This technique is complementary to optical absorption detection methods and the signal contains many unique properties, which are difficult to obtain by other methods. The advantages and methods for signal analyses are described in detail in this review. A typical example of an application of time-resolved refractive index change detection is given in the second part: The photoreaction of the LOV2 domain of a blue light photoreceptor from Arabidopsis Thaliana (phototropin). This article is part of a Special Issue entitled: Protein Dynamics: Experimental and Computational Approaches.
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Affiliation(s)
- Masahide Terazima
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan.
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27
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Kritsky MS, Telegina TA, Vechtomova YL, Kolesnikov MP, Lyudnikova TA, Golub OA. Excited flavin and pterin coenzyme molecules in evolution. BIOCHEMISTRY (MOSCOW) 2010; 75:1200-16. [DOI: 10.1134/s0006297910100020] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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28
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Alexandre MT, Purcell EB, van Grondelle R, Robert B, Kennis JT, Crosson S. Electronic and protein structural dynamics of a photosensory histidine kinase. Biochemistry 2010; 49:4752-9. [PMID: 20459101 PMCID: PMC2882989 DOI: 10.1021/bi100527a] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The bacterium Caulobacter crescentus encodes a two-component signaling protein, LovK, that contains an N-terminal photosensory LOV domain coupled to a C-terminal histidine kinase. LovK binds a flavin cofactor, undergoes a reversible photocycle, and displays regulated ATPase and autophosphorylation activity in response to visible light. Femtosecond to nanosecond visible absorption spectroscopy demonstrates congruence between full-length LovK and isolated LOV domains in the mechanism and kinetics of light-dependent cysteinyl-C4(a) adduct formation and rupture, while steady-state absorption and fluorescence line narrowing (FLN) spectroscopies reveal unique features in the electronic structure of the LovK flavin cofactor. In agreement with other sensor histidine kinases, ATP binds specifically to LovK with micromolar affinity. However, ATP binding to the histidine kinase domain of LovK has no apparent effect on global protein structure as assessed by differential Fourier transform infrared (FTIR) spectroscopy. Cysteinyl adduct formation results in only minor changes in the structure of LovK as determined by differential FTIR. This study provides insight into the structural underpinnings of LOV-mediated signal transduction in the context of a full-length histidine kinase. In particular, the data provide evidence for a model in which small changes in the tertiary/quaternary structure of LovK, as triggered by photon detection in the N-terminal LOV sensory domain, are sufficient to regulate histidine kinase activity.
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Affiliation(s)
- Maxime T.A. Alexandre
- Biophysics Group, Department of Physics and Astronomy, Faculty of Sciences, Vrije Universiteit, Amsterdam, The Netherlands
| | - Erin B. Purcell
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
| | - Rienk van Grondelle
- Biophysics Group, Department of Physics and Astronomy, Faculty of Sciences, Vrije Universiteit, Amsterdam, The Netherlands
| | - Bruno Robert
- Commissariat à l’Énergie Atomique, Institut de Biologie et de Technologie de Saclay, F-91191, Gif-sur-Yvette Cedex, France
| | - John T.M. Kennis
- Biophysics Group, Department of Physics and Astronomy, Faculty of Sciences, Vrije Universiteit, Amsterdam, The Netherlands
| | - Sean Crosson
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
- The Committee on Microbiology, University of Chicago, Chicago, IL, USA
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Tang Y, Cao Z, Livoti E, Krauss U, Jaeger KE, Gärtner W, Losi A. Interdomain signalling in the blue-light sensing and GTP-binding protein YtvA: a mutagenesis study uncovering the importance of specific protein sites. Photochem Photobiol Sci 2009; 9:47-56. [PMID: 20062844 DOI: 10.1039/b9pp00075e] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
YtvA from Bacillus subtilis is a blue-light responsive, flavin-binding photoreceptor, built of a light-sensing LOV domain (aa 25-126) and an NTP (nucleoside triphosphate)-binding STAS domain (aa 147-261). The STAS domain is supposed to be the effector part of the protein or a secondary switch. Both domains are connected by a linker polypeptide. The active form of YtvA is generated upon light excitation, causing the formation of a covalent bond between a cysteine residue (Cys62) in the LOV domain and the position 4a of the flavin chromophore. This photoadduct formation within the LOV domain results in a conformational change of the NTP-binding cavity, evidencing intra-protein signal transmission. We have previously shown that Glu105, localized on the beta-scaffold of the LOV-core, is involved in this process. Here, we extend this work by the identification of further residues that upon mutation supress or strongly impair signal transmission by interfering with the communication between the two domains. These comprise L106 and D109 on the LOV domain; K130 and K134 on the linker region; D193, L194 and G196 within the DLSG GTP-binding motif (switch region) and N201 on the STAS domain. Furthermore in the mutated S195A and D193A proteins, GTP affinity is diminished. Other mutations investigated have little or no effect on signal transmission and GTP-binding affinity: R63K that was found to accelerate the thermal recovery of the parent state ca. ten-fold; K128A, Q129A and Y132A within the linker region, and S183A and S212A on the STAS domain. The results show a key role of the LOV domain beta-scaffold and of positively charged residues within the linker for intra-protein signal transmission. Furthermore they evidence the conformational switch function of a structurally conserved strand-loop-helix region (bearing the DLSG GTP-binding motif and N201) within the STAS domain that constitutes a novel GTP-binding fold.
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Affiliation(s)
- Yifen Tang
- Max-Planck-Institute for Bioinorganic Chemistry, Stifstrasse 34-36 45470, Mülheim, Germany
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Jentzsch K, Wirtz A, Circolone F, Drepper T, Losi A, Gärtner W, Jaeger KE, Krauss U. Mutual exchange of kinetic properties by extended mutagenesis in two short LOV domain proteins from Pseudomonas putida. Biochemistry 2009; 48:10321-33. [PMID: 19772355 DOI: 10.1021/bi901115z] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
We previously characterized a LOV protein PpSB2-LOV, present in the common soil bacterium Pseudomonas putida, that exhibits a plant phototropin LOV-like photochemistry [Krauss, U., Losi, A., Gartner, W., Jaeger, K. E., and Eggert, T. (2005) Phys. Chem. Chem. Phys. 7, 2804-2811]. Now, we have identified a second LOV homologue, PpSB1-LOV, found in the same organism with approximately 66% identical amino acids. Both proteins consist of a conserved LOV core flanked by short N- and C-terminal extensions but lack a fused effector domain. Although both proteins are highly similar in sequence, they display drastically different dark recovery kinetics. At 20 degrees C, PpSB2-LOV reverts with an average time constant of 137 s from the photoequilibrium to the dark state, whereas PpSB1-LOV exhibits an average dark recovery time constant of 1.48 x 10(5) s. Irrespective of the significant differences in their dark recovery behavior, both proteins showed nearly identical kinetics for the photochemically induced adduct formation. In order to elucidate the structural and mechanistic basis of these extremely different dark recovery time constants, we performed a mutational analysis. Six amino acids in a distance of up to 6 A from the flavin chromophore, which differ between the two proteins, were identified and interchanged by site-directed mutagenesis. The amino acid substitution R66I located near the FMN phosphate in LOV domains was identified in PpSB1-LOV to accelerate the dark recovery by 2 orders of magnitude. Vice versa, the corresponding substitution I66R slowed down the dark recovery in PpSB2-LOV by a factor of 10. Interestingly, the interchange of the C-terminal extensions between the two proteins also had a pronounced effect on the dark recovery time constants, thus highlighting a coupling of these protein regions to the chromophore binding pocket.
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Affiliation(s)
- Katrin Jentzsch
- Institut für Molekulare Enzymtechnologie, Heinrich-Heine Universität Düsseldorf, FZ-Julich, Stetternicher Forst D-52426 Jülich, Germany
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Losi A, Gensch T, van der Horst MA, Hellingwerf KJ, Braslavsky SE. Hydrogen-bond network probed by time-resolved optoacoustic spectroscopy: photoactive yellow protein and the effect of E46Q and E46A mutations. Phys Chem Chem Phys 2009; 7:2229-36. [PMID: 19791418 DOI: 10.1039/b419079c] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The enthalpy and structural volume changes (delta Hi and delta Vi) produced upon photoinduced formation and decay of the red-shifted intermediate (pR = I1) in the photoactive yellow protein (WT-PYP) from Halorhodospira halophila and the mutated E46Q-PYP and E46A-PYP, were determined by laser-induced optoacoustic spectroscopy (LIOAS) using the two-temperatures method, at pH 8.5. These mutations alter the hydrogen bond between the phenolate oxygen of the chromophore and the residue at position 46. Hydrogen bonding is still possible in E46Q-PYP via the delta-NH2 group of glutamine, whereas it is no longer possible with the methyl group of alanine in E46A-PYP. In all three proteins, pR decays within hundreds of ns to micros into the next intermediate, pR'. The delta H values for the formation of pR (delta H pR) and for its decay into pR'(delta H pR-->pR') are negligibly affected by the E46Q and the E46A substitution. In all three proteins the large delta H pR value drives the photocycle. Whereas delta V pR is a similar contraction of ca. 15 ml mol(-1) for E46Q-PYP and WT-PYP, attributed to strengthening the hydrogen bond network (between 4 and 5 hydrogen bonds) inside the protein chromophore cavity, an expansion is observed for E46A-PYP, indicating just an enlargement of the chromophore cavity upon chromophore isomerization. The results are discussed in the light of the recent time-resolved room temperature, crystallographic studies with WT-PYP and E46Q-PYP. Formation of pR' is somewhat slower for E46Q-PYP and much slower for E46A-PYP. The structural volume change for this transition, delta V pR-->pR', is relatively small and positive for WT-PYP, slightly larger for E46Q-PYP, and definitely larger for the hydrogen-bond lacking E46A-PYP. This indicates a larger entropic change for this transition in E46A-PYP, reflected in the large pre-exponential factor for the pR to pR' decay rate constant determined in the 5-30 degrees C temperature range. This decay also shows an activation entropy that compensates the larger activation energy in E46A-PYP, as compared to the values for WT-PYP and E46Q-PYP.
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Affiliation(s)
- Aba Losi
- Max-Planck-Institut für Bioanorganische Chemie (formerly Strahlenchemie), Postfach 101365, D-45413 Mülheim an der Ruhr, Germany
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Alexandre MT, Domratcheva T, Bonetti C, van Wilderen LJ, van Grondelle R, Groot ML, Hellingwerf KJ, Kennis JT. Primary reactions of the LOV2 domain of phototropin studied with ultrafast mid-infrared spectroscopy and quantum chemistry. Biophys J 2009; 97:227-37. [PMID: 19580760 PMCID: PMC2711383 DOI: 10.1016/j.bpj.2009.01.066] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2008] [Revised: 01/09/2009] [Accepted: 01/21/2009] [Indexed: 11/20/2022] Open
Abstract
Phototropins, major blue-light receptors in plants, are sensitive to blue light through a pair of flavin mononucleotide (FMN)-binding light oxygen and voltage (LOV) domains, LOV1 and LOV2. LOV2 undergoes a photocycle involving light-driven covalent adduct formation between a conserved cysteine and the FMN C(4a) atom. Here, the primary reactions of Avena sativa phototropin 1 LOV2 (AsLOV2) were studied using ultrafast mid-infrared spectroscopy and quantum chemistry. The singlet excited state (S1) evolves into the triplet state (T1) with a lifetime of 1.5 ns at a yield of approximately 50%. The infrared signature of S1 is characterized by absorption bands at 1657 cm(-1), 1495-1415 cm(-1), and 1375 cm(-1). The T1 state shows infrared bands at 1657 cm(-1), 1645 cm(-1), 1491-1438 cm(-1), and 1390 cm(-1). For both electronic states, these bands are assigned principally to C=O, C=N, C-C, and C-N stretch modes. The overall downshifting of C=O and C=N bond stretch modes is consistent with an overall bond-order decrease of the conjugated isoalloxazine system upon a pi-pi* transition. The configuration interaction singles (CIS) method was used to calculate the vibrational spectra of the S1 and T1 excited pipi* states, as well as respective electronic energies, structural parameters, electronic dipole moments, and intrinsic force constants. The harmonic frequencies of S1 and T1, as calculated by the CIS method, are in satisfactory agreement with the evident band positions and intensities. On the other hand, CIS calculations of a T1 cation that was protonated at the N(5) site did not reproduce the experimental FMN T1 spectrum. We conclude that the FMN T1 state remains nonprotonated on a nanosecond timescale, which rules out an ionic mechanism for covalent adduct formation involving cysteine-N(5) proton transfer on this timescale. Finally, we observed a heterogeneous population of singly and doubly H-bonded FMN C(4)=O conformers in the dark state, with stretch frequencies at 1714 cm(-1) and 1694 cm(-1), respectively.
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Affiliation(s)
- Maxime T.A. Alexandre
- Biophysics Group, Department of Physics and Astronomy, Faculty of Sciences, Vrije Universiteit, Amsterdam, The Netherlands
| | | | - Cosimo Bonetti
- Biophysics Group, Department of Physics and Astronomy, Faculty of Sciences, Vrije Universiteit, Amsterdam, The Netherlands
| | - Luuk J.G.W. van Wilderen
- Biophysics Group, Department of Physics and Astronomy, Faculty of Sciences, Vrije Universiteit, Amsterdam, The Netherlands
| | - Rienk van Grondelle
- Biophysics Group, Department of Physics and Astronomy, Faculty of Sciences, Vrije Universiteit, Amsterdam, The Netherlands
| | - Marie-Louise Groot
- Biophysics Group, Department of Physics and Astronomy, Faculty of Sciences, Vrije Universiteit, Amsterdam, The Netherlands
| | - Klaas J. Hellingwerf
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - John T.M. Kennis
- Biophysics Group, Department of Physics and Astronomy, Faculty of Sciences, Vrije Universiteit, Amsterdam, The Netherlands
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Pathak GP, Ehrenreich A, Losi A, Streit WR, Gärtner W. Novel blue light-sensitive proteins from a metagenomic approach. Environ Microbiol 2009; 11:2388-99. [PMID: 19538504 DOI: 10.1111/j.1462-2920.2009.01967.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A microarray-based approach was used to screen a soil metagenome for the presence of blue light (BL) photoreceptor-encoding genes. The microarray carried 149 different 54-mer oligonucleotides, derived from consensus sequences of light, oxygen and voltage (LOV) domain BL photoreceptor genes. Calibration of the microarrays allowed the detection of minimally 50 ng of genomic DNA against a background of 2-5 microg of genomic DNA. Identification of a positive cosmid clone was still possible for an amount of 0.25 ng against a background of 10 microg of labelled DNA clones. The array could readily identify targets carrying 4% sequence mismatch. Using the LOV microarray, up to 1200 library clones in concentrations of c. 20 ng each with a c. 40 kb insert size could be screened in a single batch. After calibration and reliability controls, the microarray was probed with cosmid-cloned DNA from the thermophilic fraction of a soil sample. From this approach, a novel gene was isolated that encodes a protein consisting of several Per-Arnt-Sim domains, a LOV domain associated to a histidine kinase and a response regulator domain. The novel gene showed highest similarity to a known sequence from Kineococcus radiotolerans SRS30216 (58% identity for the LOV domain only) and to a gene from Methylibium petroleiphilum PM1 (57% identity). The gene, designated as ht-met1 (Hamburg Thermophile Metagenome 1), was isolated and fully sequenced (3615 bp). ht-met1 is followed by a second open reading frame encoding a Fe-chelatase, an arrangement quite frequent for BL photoreceptors. The LOV domain region of ht-met1 was subcloned and expressed yielding a fully functional, flavin-containing LOV domain. Irradiation generated the typical LOV photochemistry, with the transient formation of a flavin-protein photoadduct. The dark recovery lifetime was found as tau(REC) = 120 s (20 degrees C) and is among the fastest ones determined so far for bacterial LOV domains.
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Affiliation(s)
- G P Pathak
- Max-Planck-Institute for Bioinorganic Chemistry, Mülheim, Germany
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Nash AI, Ko WH, Harper SM, Gardner KH. A conserved glutamine plays a central role in LOV domain signal transmission and its duration. Biochemistry 2009; 47:13842-9. [PMID: 19063612 DOI: 10.1021/bi801430e] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Light is a key stimulus for plant biological functions, several of which are controlled by light-activated kinases known as phototropins, a group of kinases that contain two light-sensing domains (LOV, light-oxygen-voltage domains) and a C-terminal serine/threonine kinase domain. The second sensory domain, LOV2, plays a key role in regulating kinase enzymatic activity via the photochemical formation of a covalent adduct between a LOV2 cysteine residue and an internally bound flavin mononucleotide (FMN) chromophore. Subsequent conformational changes in LOV2 lead to the unfolding of a peripheral Jalpha helix and, ultimately, phototropin kinase activation. To date, the mechanism coupling bond formation and helix dissociation has remained unclear. Previous studies found that a conserved glutamine residue [Q513 in the Avena sativa phototropin 1 LOV2 (AsLOV2) domain] switches its hydrogen bonding pattern with FMN upon light stimulation. Located in the immediate vicinity of the FMN binding site, this Gln residue is provided by the Ibeta strand that interacts with the Jalpha helix, suggesting a route for signal propagation from the core of the LOV domain to its peripheral Jalpha helix. To test whether Q513 plays a key role in tuning the photochemical and transduction properties of AsLOV2, we designed two point mutations, Q513L and Q513N, and monitored the effects on the chromophore and protein using a combination of UV-visible absorbance and circular dichroism spectroscopy, limited proteolysis, and solution NMR. The results show that these mutations significantly dampen the changes between the dark and lit state AsLOV2 structures, leaving the protein in a pseudodark state (Q513L) or a pseudolit state (Q513N). Further, both mutations changed the photochemical properties of this receptor, in particular the lifetime of the photoexcited signaling states. Together, these data establish that this residue plays a central role in both spectral tuning and signal propagation from the core of the LOV domain through the Ibeta strand to the peripheral Jalpha helix.
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Affiliation(s)
- Abigail I Nash
- Departments of Biochemistry and Pharmacology, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390-8816, USA
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Alexandre MTA, van Grondelle R, Hellingwerf KJ, Robert B, Kennis JTM. Perturbation of the ground-state electronic structure of FMN by the conserved cysteine in phototropin LOV2 domains. Phys Chem Chem Phys 2008; 10:6693-702. [PMID: 18989482 DOI: 10.1039/b810040c] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In LOV2, the blue-light sensitive domain of phototropin, the primary photophysical event involves intersystem crossing (ISC) from the singlet-excited state to the triplet state. The ISC rate is enhanced in LOV2 as compared to flavin mononucleotide (FMN) in solution, which likely results from a heavy-atom effect of a nearby conserved cysteine, C450. Here, we applied fluorescence line narrowing (FLN), resonance Raman (RR) and Fourier-transform infrared (FTIR) spectroscopy to investigate the electronic structure of FMN bound to Avena sativa LOV2 (AsLOV2), its C450A mutant and Adiantum LOV2 (Phy3LOV2). We demonstrate that FLN is the method of choice to obtain accurate vibrational spectra on highly fluorescent flavoproteins. The vibrational spectrum of AsLOV2-C450A showed small but significant shifts with respect to those of wild type AsLOV2 and Phy3LOV2, with a systematic down-shift of Ring I vibrations, upshifts of Ring II and III vibrations and an upshift of the C2=O mode. These trends are similar to those in FMN model systems with an electron-donating group substituted at Ring I, known to induce a quinoid character to the electronic structure of oxidized flavin. Thus, enhancement of the ISC rate in LOV2 is induced through weak electron donation by the cysteine which mixes the FMN pi-electrons with the heavy sulfur orbitals, manifesting itself in a quinoid character of the ground electronic state of oxidized FMN. The proximity of the cysteine to FMN thus not only enables formation of a covalent adduct between FMN and cysteine, but also facilitates the rapid electronic formation of the reactive FMN triplet state.
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Affiliation(s)
- Maxime T A Alexandre
- Department of Biophysics, Faculty of Sciences, Vrije Universiteit, De Boelelaan 1081, 1081HV, Amsterdam, The Netherlands.
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Cao Z, Buttani V, Losi A, Gärtner W. A blue light inducible two-component signal transduction system in the plant pathogen Pseudomonas syringae pv. tomato. Biophys J 2008; 94:897-905. [PMID: 17905842 PMCID: PMC2186247 DOI: 10.1529/biophysj.107.108977] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2007] [Accepted: 08/23/2007] [Indexed: 11/18/2022] Open
Abstract
The open reading frame PSPTO2896 from the plant pathogen Pseudomonas syringae pv. tomato encodes a protein of 534 amino acids showing all salient features of a blue light-driven two-component system. The N-terminal LOV (light, oxygen, voltage) domain, potentially binding a flavin chromophore, is followed by a histidine kinase (HK) motif and a response regulator (RR). The full-length protein (PST-LOV) and, separately, the RR and the LOV+HK part (PST-LOV(DeltaRR)) were heterologously expressed and functionally characterized. The two LOV proteins showed typical LOV-like spectra and photochemical reactions, with the blue light-driven, reversible formation of a covalent flavin-cysteine bond. The fluorescence changes in the lit state of full-length PST-LOV, but not in PST-LOV(DeltaRR), indicating a direct interaction between the LOV core and the RR module. Experiments performed with radioactive ATP uncover the light-driven kinase activity. For both PST-LOV and PST-LOV(DeltaRR), much more radioactivity is incorporated when the protein is in the lit state. Furthermore, addition of the RR domain to the fully phosphorylated PST-LOV(DeltaRR) leads to a very fast transfer of radioactivity, indicating a highly efficient HK activity and a tight interaction between PST-LOV(DeltaRR) and RR, possibly facilitated by the LOV core itself.
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Affiliation(s)
- Z. Cao
- Max-Planck-Institut für Bioanorganische Chemie, D-45470 Mülheim, Germany
| | - V. Buttani
- Department of Physics, University of Parma, Italy
| | - A. Losi
- Department of Physics, University of Parma, Italy
| | - W. Gärtner
- Max-Planck-Institut für Bioanorganische Chemie, D-45470 Mülheim, Germany
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Hazra P, Inoue K, Laan W, Hellingwerf KJ, Terazima M. Energetics and role of the hydrophobic interaction during photoreaction of the BLUF domain of AppA. J Phys Chem B 2008; 112:1494-501. [PMID: 18189382 DOI: 10.1021/jp0767314] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A recently developed method for time-resolved thermodynamic measurements was used to study the photochemical reaction(s) of the BLUF domain of AppA (AppA-BLUF), which has a dimeric form in the ground state, in terms of the energetics and heat capacity changes (DeltaC(p)) in different time domains. The enthalpy change (DeltaH) of the first intermediate that forms within 1 ns after photoexcitation was 38 (+/-8) kJ mol(-1) at 298 K. The heat capacity change (DeltaC(p)) upon formation of this intermediate was positive [1.4 (+/-0.3) kJ mol(-1) K(-1)]. This positive DeltaC(p) suggests that the hydrophobic surface area of AppA-BLUF exposed to the bulk solvent increased. After this initial transition, a dimerization reaction with another ground-state dimer (i.e., tetramer formation) takes place. Upon this reaction, the energy was stabilized to 26 (+/-6) kJ mol(-1) at 298 K. Interestingly, the dimer formation was accompanied by a larger but negative DeltaC(p) [-6.0 (+/-1) kJ mol(-1) K(-1)]. This negative DeltaC(p) might indicate buried hydrophobic residues at the interface of the dimer and/or the existence of trapped water at the interface. We suggest that hydrophobic interactions are the main driving force for the formation of the dimer upon photoactivation of AppA-BLUF.
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Affiliation(s)
- Partha Hazra
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
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Zenichowski K, Gothe M, Saalfrank P. Exciting flavins: Absorption spectra and spin–orbit coupling in light–oxygen–voltage (LOV) domains. J Photochem Photobiol A Chem 2007. [DOI: 10.1016/j.jphotochem.2007.02.007] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Matsuoka D, Iwata T, Zikihara K, Kandori H, Tokutomi S. Primary processes during the light-signal transduction of phototropin. Photochem Photobiol 2007; 83:122-30. [PMID: 16802859 DOI: 10.1562/2006-03-29-ra-861] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Phototropin is a blue-light photoreceptor in plants that mediates phototropism, chloroplast relocation, stomata opening and leaf expansion. Phototropin molecule has two photoreceptive domains named LOV1 (light-oxygen-voltage) and LOV2 in the N-terminus and a serine/threonine kinase domain in the C-terminus, and acts as a blue light-regulated kinase. Each LOV domain binds a flavin mononucleotide as a chromophore and undergoes unique cyclic reactions upon blue-light absorption that comprises a cysteinyl-flavin adduct formation through a triplet-excited state and a successive adduct break to revert to the initial ground state. The molecular reactions underlying the photocycle are reviewed and one of the probable molecular schemes is presented. Adduct formation alters the secondary protein structure of the LOV domains. This structural change could be transferred to the linker between the kinase domain and involved in the photoregulation of the kinase activity. The structural changes as well as the oligomeric structures seem to differ between LOV1 and LOV2, which may explain the proposed roles of each domain in the photoregulation of the kinase activity. The photoregulation mechanism of phototropin kinase is reviewed and discussed in reference to the regulation mechanism of protein kinase A, which it resembles.
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Affiliation(s)
- Daisuke Matsuoka
- Department of Biological Science, Graduate School of Science, Osaka Prefecture University, Naka-ku, Sakai, Osaka, Japan
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Dittrich M, Freddolino PL, Schulten K. When light falls in LOV: a quantum mechanical/molecular mechanical study of photoexcitation in Phot-LOV1 of Chlamydomonas reinhardtii. J Phys Chem B 2007; 109:13006-13. [PMID: 16852614 PMCID: PMC2453334 DOI: 10.1021/jp050943o] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Plants use sophisticated photosensing mechanisms to maximize their utilization of the available sunlight and to control developmental processes. The plant blue-light receptors of the Phot family mediate plant phototropism and contain two light, oxygen, and voltage (LOV)-sensitive domains as photoactive elements. Here, we report combined quantum mechanical/molecular mechanical simulations of the photocycle of a complete Phot-LOV1 domain from Chlamydomonas reinhardtii. We have investigated the electronic properties and structural changes that follow blue-light absorption. This permitted us to characterize the pathway for flavin-cysteinyl adduct formation, which was found to proceed via a neutral radical state generated by hydrogen atom transfer from the reactive cysteine residue, Cys57, to the chromophore flavin mononucleotide. Interestingly, we find that adduct formation does not cause any larger scale conformational changes in Phot-LOV1, which suggests that dynamic effects mediate signal transmission following the initial photoexcitation event.
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Affiliation(s)
- Markus Dittrich
- Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Peter L. Freddolino
- Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Klaus Schulten
- Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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Zoltowski BD, Schwerdtfeger C, Widom J, Loros JJ, Bilwes AM, Dunlap JC, Crane BR. Conformational switching in the fungal light sensor Vivid. Science 2007; 316:1054-7. [PMID: 17510367 PMCID: PMC3682417 DOI: 10.1126/science.1137128] [Citation(s) in RCA: 287] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
The Neurospora crassa photoreceptor Vivid tunes blue-light responses and modulates gating of the circadian clock. Crystal structures of dark-state and light-state Vivid reveal a light, oxygen, or voltage Per-Arnt-Sim domain with an unusual N-terminal cap region and a loop insertion that accommodates the flavin cofactor. Photoinduced formation of a cystein-flavin adduct drives flavin protonation to induce an N-terminal conformational change. A cysteine-to-serine substitution remote from the flavin adenine dinucleotide binding site decouples conformational switching from the flavin photocycle and prevents Vivid from sending signals in Neurospora. Key elements of this activation mechanism are conserved by other photosensors such as White Collar-1, ZEITLUPE, ENVOY, and flavin-binding, kelch repeat, F-BOX 1 (FKF1).
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Affiliation(s)
- Brian D. Zoltowski
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | | | - Joanne Widom
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Jennifer J. Loros
- Department of Genetics, Dartmouth Medical School, Hanover, NH 03755, USA
- Department of Biochemistry, Dartmouth Medical School, Hanover, NH 03755, USA
| | - Alexandrine M. Bilwes
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Jay C. Dunlap
- Department of Genetics, Dartmouth Medical School, Hanover, NH 03755, USA
| | - Brian R. Crane
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
- To whom correspondence should be addressed.
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Celaya RB, Liscum E. Phototropins and Associated Signaling: Providing the Power of Movement in Higher Plants¶. Photochem Photobiol 2007. [DOI: 10.1111/j.1751-1097.2005.tb01524.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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Buttani V, Gärtner W, Losi A. NTP-binding properties of the blue-light receptor YtvA and effects of the E105L mutation. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2007; 36:831-9. [PMID: 17443319 DOI: 10.1007/s00249-007-0155-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2006] [Revised: 03/02/2007] [Accepted: 03/15/2007] [Indexed: 11/28/2022]
Abstract
YtvA is a blue-light-sensing protein from Bacillus subtilis related to plant phototropins. It carries a LOV (light, oxygen and voltage) domain, binding FMN (flavin mononucleotide) as chromophore, and a STAS (sulphate transporters and antisigma-factor antagonists) domain with poorly characterized function. We have recently shown that YtvA binds triphosphate nucleotides (NTP) and highlighted a structural similarity between the STAS domain and small GTP-binding proteins. In this work we further investigated the NTP-binding properties of YtvA, employing a fluorescent derivative of GTP (GTP(TR)) and mutagenesis experiments. The main results are as follows: (a) competition experiments indicate that the affinity of YtvA for GTP is much higher than that for GDP and GMP. (b) Blue-light-induced structural changes are transmitted from the LOV core to the NTP-binding cavity, establishing a possible intraprotein signal-transduction pathway. (c) A mutation in the central beta-scaffold of the LOV core, E105L, impairs the light-driven spectroscopic changes of bound GTP(TR). This result is supported by circular dichroism data, in that YtvA-E105L does not show the light-induced conformational change in the turn fraction that characterizes YtvA, implying that E105 is functionally important. (d) In the structural model of the LOV-STAS complex, based on docking algorithms, the interface includes the Ibeta-Hbeta loop on the LOV core, as well as parts of the central beta-scaffold. E105 is predicted to interact with the LOV-STAS linker region, suggested to play a role in phototropin signaling.
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Affiliation(s)
- Valentina Buttani
- Department of Physics, University of Parma, viale G.P. Usberti 7/A, Parma, Italy
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Alexandre MTA, Arents JC, van Grondelle R, Hellingwerf KJ, Kennis JTM. A base-catalyzed mechanism for dark state recovery in the Avena sativa phototropin-1 LOV2 domain. Biochemistry 2007; 46:3129-37. [PMID: 17311415 DOI: 10.1021/bi062074e] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Phototropins are autophosphorylating serine/threonine kinases responsible for blue-light perception in plants; their action gives rise to phototropism, chloroplast relocation, and opening of stomatal guard cells. The kinase domain constitutes the C-terminal part of Avena sativa phototropin 1. The N-terminal part contains two light, oxygen, or voltage (LOV) sensing domains, LOV1 and LOV2; each binds a flavin mononucleotide (FMN) chromophore (lambdamax = 447 nm, termed D447) and forms the light-sensitive domains, of which LOV2 is the principal component. Blue-light absorption produces a covalent adduct between a very conserved nearby cysteine residue and the C(4a) atom of the FMN moiety via the triplet state of the flavin. The covalent adduct thermally decays to regenerate the D447 dark state, with a rate that may vary by several orders of magnitude between different species. We report that the imidazole base can act as a very efficient enhancer of the dark recovery of A. sativa phot1 LOV2 (AsLOV2) and some other well-characterized LOV domains. Imidazole accelerates the thermal decay of AsLOV2 by 3 orders of magnitude in the submolar concentration range, via a base-catalyzed mechanism involving base abstraction of the FMN N(5)-H adduct state and subsequent reprotonation of the reactive cysteine. The LOV2 crystal structure suggests that the imidazole molecules may act from a cavity located in the vicinity of the FMN, explaining its high efficiency, populated through a channel connecting the cavity to the protein surface. Use of pH titration and chemical inactivation by diethyl pyrocarbonate (DEPC) suggests that histidines located at the surface of the LOV domain act as base catalysts via an as yet unidentified H-bond network, operating at a rate of (55 s)-1 at pH 8. In addition, molecular processes other than histidine-mediated base catalysis contibute significantly to the total thermal decay rate of the adduct and operate at a rate constant of (65 s)-1, leading to a net adduct decay time constant of 30 s at pH 8.
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Affiliation(s)
- Maxime T A Alexandre
- Department of Biophysics, Faculty of Sciences, Vrije Universiteit, De Boelelaan 1081, 1081HV Amsterdam, The Netherlands.
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Freddolino PL, Dittrich M, Schulten K. Dynamic switching mechanisms in LOV1 and LOV2 domains of plant phototropins. Biophys J 2006; 91:3630-9. [PMID: 16935961 PMCID: PMC1630464 DOI: 10.1529/biophysj.106.088609] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
LOV domains are the light-sensitive portion of plant phototropins. They absorb light through a flavin cofactor, photochemically form a covalent bond between the chromophore and a cysteine residue in the protein, and proceed to mediate activation of an attached kinase domain. Although the photoreaction itself is now well-characterized experimentally and computationally, it is still unclear how the formation of the adduct leads to kinase activation. We have performed molecular dynamics simulations on the LOV1 domain of Chlamydomonas reinhardtii and the LOV2 domain of Avena sativa, both before and after the photoreaction, to answer this question. The extensive simulations, over 240 ns in duration, reveal significant differences in how the LOV1 and LOV2 domains respond to photoactivation. The simulations indicate that LOV1 activation is likely caused by a change in hydrogen bonding between protein and ligand that destabilizes a highly conserved salt bridge, whereas LOV2 activation seems to result from a change in the flexibility of a set of protein loops. Results of electrostatics calculations, principal component analysis, sequence alignments, and root mean-square deviation analysis corroborate the above findings.
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Affiliation(s)
- Peter L Freddolino
- Center for Biophysics and Computational Biology, Beckman Institute, and Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
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Kottke T, Hegemann P, Dick B, Heberle J. The photochemistry of the light-, oxygen-, and voltage-sensitive domains in the algal blue light receptor phot. Biopolymers 2006; 82:373-8. [PMID: 16552739 DOI: 10.1002/bip.20510] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Phot proteins are blue light photoreceptors in plants and algae that mainly regulate photomovement responses. They contain two light-, oxygen-, and voltage-sensitive (LOV) domains and a serine/threonine kinase domain. Both LOV domains noncovalently bind a flavin mononucleotide (FMN) as chromophore. Upon blue light illumination, the LOV domains undergo a photocycle, transiently forming a covalent adduct of the FMN moiety with a nearby cysteine residue. The presence of two light-sensitive domains in the photoreceptor raises the question about the differences in properties and function between LOV1 and LOV2. As a model system, the photocycles of the LOV1 and LOV2 domains from phot of the green alga Chlamydomonas reinhardtii have been studied in detail, both separately and in a tandem construct. Here we give an overview about the results on the individual behavior of the domains and their interaction. Furthermore, the current status in the understanding of the role of LOV1 in phot in general is presented.
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Affiliation(s)
- Tilman Kottke
- Research Center Jülich, IBI-2, Structural Biology, 52425 Jülich, Germany
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Crovetto L, Martínez-Junza V, Braslavsky SE. Entropy changes drive the electron transfer reaction of triplet flavin mononucleotide from aromatic amino acids in cation-organized aqueous media. A laser-induced optoacoustic study. Photochem Photobiol 2006; 82:281-90. [PMID: 15901210 DOI: 10.1562/2005-03-22-ra-468] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The thermodynamic parameters for the formation of the free radicals upon electron transfer quenching of the flavin triplet state (3FMN) by tryptophan and tyrosine, Delta(FR)H and Delta(FR)V, were obtained in aqueous solution by the application of laser-induced optoacoustic spectroscopy at various temperatures. The Delta(FR)H and Delta(FR)V values include the electron transfer and charge separation steps plus the protonation of the FMN anion radical and the deprotonation of the amino-acid cation radical. A linear correlation was found between the Delta(FR)H and Delta(FR)V values for each of the amino acids in phosphate buffers of [CH3(CH2)3]4N+, Li+, NH4+, K+ and Cs+. The compensation between Delta(FR)H and Delta(FR)V within the salt series, and the independent evaluation of the Gibbs energy for electron transfer Delta(ET)G(o) afforded the entropy change, Delta(FR)S, for the reaction, different for the two amino acids. The values of Delta(FR)H, Delta(FR)V and Delta(FR)S in each buffer are mainly determined by the changes in strength and probably number of hydrogen bonds between the reacting partners and water produced along all steps leading to the radicals FMNH* and A*. The Delta(FR)V values linearly correlate with the tabulated entropy of organization of the water structure for the five cations, DeltaS(o)(cat). The entropy change upon formation of the free radicals, Delta(FR)S, quantitatively correlated to the Delta(FR)V value, drives the separation of the ion pair after the electron transfer reaction in the case of highly organizing cations. The ratio X = T Delta(FR)S/Delta(FR)V = (55 +/- 9) kJ cm(-3) for Trp as 3FMN quencher is smaller than X = (83 +/- 9) kJ cm(-3) for Tyr as quencher. These values are discussed in conjunction with the Marcus reorganization energy, as calculated from the Gibbs activation energy of the electron transfer process, which is independent of the salt present but different for each of the two quenchers.
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Affiliation(s)
- Luis Crovetto
- Max-Planck-Institut für Bioanorganische Chemie (formerly Strahlenchemie), Mülheim an der Ruhr, Germany
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Nakasone Y, Eitoku T, Matsuoka D, Tokutomi S, Terazima M. Kinetic measurement of transient dimerization and dissociation reactions of Arabidopsis phototropin 1 LOV2 domain. Biophys J 2006; 91:645-53. [PMID: 16679373 PMCID: PMC1483119 DOI: 10.1529/biophysj.106.084772] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Photochemical reaction of a plant blue-light photoreceptor, Arabidopsis phototropin 1-LOV (light-oxygen-voltage sensing) domain 2, was studied with a view to the diffusion coefficients (D) using the pulsed-laser-induced transient grating method. Although the reaction dynamics completes at a rate of several microseconds as long as it is monitored by the absorption change, the diffusion coefficient was found to be time-dependent in a time range of submilliseconds to seconds. The observed signal can be analyzed by the two-state model, which includes the D-value decrease from D of the reactant (9.8 +/- 0.4) x 10(-11) m2/s to D of the product (8.0 +/- 0.4) x 10(-11) m2/s. The D-value of the reactant implies that the dominant form in the ground state of phototropin 1 LOV2 is the monomeric form in a concentration range of 50-200 microM. According to the Stokes-Einstein relationship, the D-change can be explained by a volume increase of 1.8 times. Furthermore, the rate of the D-change was roughly proportional to the concentration of the sample. These two observations indicate that the LOV2 domain transiently forms a dimer upon photoexcitation. When the sample concentration is increased (>180 microM), a new signal component appears within a few milliseconds. This signal represents a D increase from 8.0 x 10(-11) m2/s to 9.8 x 10(-11) m2/s with a time constant of 300 micros. The completely opposite D-change from that observed in a lower concentration, as well as the concentration dependence, implies that a dimer is formed in the ground state in a higher concentration range, even though the fraction of the dimer is still minor in this range. This dimer is photodissociated, with a time constant of 300 micros. This research clearly shows that the time-resolved diffusion measurement is a very powerful tool for detecting spectrally silent association/dissociation processes during chemical reactions. The photoreaction of the LOV2 domain is discussed.
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Affiliation(s)
- Yusuke Nakasone
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto, Japan
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