1
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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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2
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Hemmer S, Schulte M, Knieps-Grünhagen E, Granzin J, Willbold D, Jaeger KE, Batra-Safferling R, Panwalkar V, Krauss U. Residue alterations within a conserved hydrophobic pocket influence light, oxygen, voltage photoreceptor dark recovery. Photochem Photobiol Sci 2022; 22:713-727. [PMID: 36480084 DOI: 10.1007/s43630-022-00346-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 11/18/2022] [Indexed: 12/14/2022]
Abstract
AbstractLight, oxygen, voltage (LOV) photoreceptors are widely distributed throughout all kingdoms of life, and have in recent years, due to their modular nature, been broadly used as sensor domains for the construction of optogenetic tools. For understanding photoreceptor function as well as for optogenetic tool design and fine-tuning, a detailed knowledge of the photophysics, photochemistry, and structural changes underlying the LOV signaling paradigm is instrumental. Mutations that alter the lifetime of the photo-adduct signaling state represent a convenient handle to tune LOV sensor on/off kinetics and, thus, steady-state on/off equilibria of the photoreceptor (or optogenetic switch). Such mutations, however, should ideally only influence sensor kinetics, while being benign with regard to the nature of the structural changes that are induced by illumination, i.e., they should not result in a disruption of signal transduction. In the present study, we identify a conserved hydrophobic pocket for which mutations have a strong impact on the adduct-state lifetime across different LOV photoreceptor families. Using the slow cycling bacterial short LOV photoreceptor PpSB1-LOV, we show that the I48T mutation within this pocket, which accelerates adduct rupture, is otherwise structurally and mechanistically benign, i.e., light-induced structural changes, as probed by NMR spectroscopy and X-ray crystallography, are not altered in the variant. Additional mutations within the pocket of PpSB1-LOV and the introduction of homologous mutations in the LOV photoreceptor YtvA of Bacillus subtilis and the Avena sativa LOV2 domain result in similarly altered kinetics. Given the conserved nature of the corresponding structural region, the here identified mutations should find application in dark-recovery tuning of optogenetic tools and LOV photoreceptors, alike.
Graphical abstract
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Affiliation(s)
- Stefanie Hemmer
- Institut Für Molekulare Enzymtechnologie, Heinrich-Heine-Universität Düsseldorf, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
- IBG-1: Biotechnology IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Marianne Schulte
- IBI-7: Structural Biochemistry, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
- Institut Für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225, Düsseldorf, Germany
| | - Esther Knieps-Grünhagen
- Institut Für Molekulare Enzymtechnologie, Heinrich-Heine-Universität Düsseldorf, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Joachim Granzin
- IBI-7: Structural Biochemistry, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52428, Jülich, Germany
| | - Dieter Willbold
- IBI-7: Structural Biochemistry, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
- Institut Für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225, Düsseldorf, Germany
| | - Karl-Erich Jaeger
- Institut Für Molekulare Enzymtechnologie, Heinrich-Heine-Universität Düsseldorf, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
- IBG-1: Biotechnology IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Renu Batra-Safferling
- IBI-7: Structural Biochemistry, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52428, Jülich, Germany
| | - Vineet Panwalkar
- IBI-7: Structural Biochemistry, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
- Institut Für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225, Düsseldorf, Germany
- Biozentrum University of Basel, CH-4056, Basel, Switzerland
| | - Ulrich Krauss
- Institut Für Molekulare Enzymtechnologie, Heinrich-Heine-Universität Düsseldorf, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany.
- IBG-1: Biotechnology IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany.
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3
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Mix LT, Hara M, Fuzell J, Kumauchi M, Kaledhonkar S, Xie A, Hoff WD, Larsen DS. Not All Photoactive Yellow Proteins Are Built Alike: Surprises and Insights into Chromophore Photoisomerization, Protonation, and Thermal Reisomerization of the Photoactive Yellow Protein Isolated from Salinibacter ruber. J Am Chem Soc 2021; 143:19614-19628. [PMID: 34780163 DOI: 10.1021/jacs.1c08910] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
We demonstrate that the Halorhodospira halophila (Hhal) photoactive yellow protein (PYP) is not representative of the greater PYP family. The photodynamics of the PYP isolated from Salinibacter ruber (Srub) is characterized with a comprehensive range of spectroscopic techniques including ultrafast transient absorption, photostationary light titrations, Fourier transform infrared, and cryokinetics spectroscopies. We demonstrate that the dark-adapted pG state consists of two subpopulations differing in the protonation state of the chromophore and that both are photoactive, with the protonated species undergoing excited-state proton transfer. However, the primary I0 photoproduct observed in the Hhal PYP photocycle is absent in the Srub PYP photodynamics, which indicates that this intermediate, while important in Hhal photodynamics, is not a critical intermediate in initiating all PYP photocycles. The excited-state lifetime of Srub PYP is the longest of any PYP resolved to date (∼30 ps), which we ascribe to the more constrained chromophore binding pocket of Srub PYP and the absence of the critical Arg52 residue found in Hhal PYP. The final stage of the Srub PYP photocycle involves the slowest known thermal dark reversion of a PYP (∼40 min vs 350 ms in Hhal PYP). This property allowed the characterization of a pH-dependent equilibrium between the light-adapted pB state with a protonated cis chromophore and a newly resolved pG' intermediate with a deprotonated cis chromophore and pG-like protein conformation. This result demonstates that protein conformational changes and chromophore deprotonation precede chromophore reisomerization during the thermal recovery of the PYP photocycle.
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Affiliation(s)
- L Tyler Mix
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - Miwa Hara
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma 74078, United States
| | - Jack Fuzell
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - Masato Kumauchi
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma 74078, United States
| | - Sandip Kaledhonkar
- Department of Physics, Oklahoma State University, Stillwater, Oklahoma 74078, United States
| | - Aihua Xie
- Department of Physics, Oklahoma State University, Stillwater, Oklahoma 74078, United States.,Center for Advanced Infrared Biology College of Arts and Sciences, Oklahoma State University, Stillwater, Oklahoma 74078, United States
| | - Wouter D Hoff
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma 74078, United States.,Center for Advanced Infrared Biology College of Arts and Sciences, Oklahoma State University, Stillwater, Oklahoma 74078, United States
| | - Delmar S Larsen
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
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4
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Cheng X, Pu L, Fu S, Xia A, Huang S, Ni L, Xing X, Yang S, Jin F. Engineering Gac/Rsm Signaling Cascade for Optogenetic Induction of the Pathogenicity Switch in Pseudomonas aeruginosa. ACS Synth Biol 2021; 10:1520-1530. [PMID: 34076414 DOI: 10.1021/acssynbio.1c00075] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Bacterial pathogens operate by tightly controlling the pathogenicity to facilitate invasion and survival in host. While small molecule inducers can be designed to modulate pathogenicity to perform studies of pathogen-host interaction, these approaches, due to the diffusion property of chemicals, may have unintended, or pleiotropic effects that can impose limitations on their use. By contrast, light provides superior spatial and temporal resolution. Here, using optogenetics we reengineered GacS of the opportunistic pathogen Pseudomonas aeruginosa, signal transduction protein of the global regulatory Gac/Rsm cascade which is of central importance for the regulation of infection factors. The resultant protein (termed YGS24) displayed significant light-dependent activity of GacS kinases in Pseudomonas aeruginosa. When introduced in the Caenorhabditis elegans host systems, YGS24 stimulated the pathogenicity of the Pseudomonas aeruginosa strain PAO1 in a brain-heart infusion and of another strain, PA14, in slow killing media progressively upon blue-light exposure. This optogenetic system provides an accessible way to spatiotemporally control bacterial pathogenicity in defined hosts, even specific tissues, to develop new pathogenesis systems, which may in turn expedite development of innovative therapeutics.
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Affiliation(s)
- Xinyi Cheng
- Hefei National Laboratory for Physical Sciences at the Microscale; Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei, 230026, China
| | - Lu Pu
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Shengwei Fu
- Hefei National Laboratory for Physical Sciences at the Microscale; Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei, 230026, China
| | - Aiguo Xia
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Shuqiang Huang
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Lei Ni
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Xiaochen Xing
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Shuai Yang
- Hefei National Laboratory for Physical Sciences at the Microscale; Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei, 230026, China
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Fan Jin
- Hefei National Laboratory for Physical Sciences at the Microscale; Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei, 230026, China
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
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5
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Yee EF, Oldemeyer S, Böhm E, Ganguly A, York DM, Kottke T, Crane BR. Peripheral Methionine Residues Impact Flavin Photoreduction and Protonation in an Engineered LOV Domain Light Sensor. Biochemistry 2021; 60:1148-1164. [PMID: 33787242 PMCID: PMC8107827 DOI: 10.1021/acs.biochem.1c00064] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Proton-coupled electron transfer reactions play critical roles in many aspects of sensory phototransduction. In the case of flavoprotein light sensors, reductive quenching of flavin excited states initiates chemical and conformational changes that ultimately transmit light signals to downstream targets. These reactions generally require neighboring aromatic residues and proton-donating side chains for rapid and coordinated electron and proton transfer to flavin. Although photoreduction of flavoproteins can produce either the anionic (ASQ) or neutral semiquinone (NSQ), the factors that favor one over the other are not well understood. Here we employ a biologically active variant of the light-oxygen-voltage (LOV) domain protein VVD devoid of the adduct-forming Cys residue (VVD-III) to probe the mechanism of flavin photoreduction and protonation. A series of isosteric and conservative residue replacements studied by rate measurements, fluorescence quantum yields, FTIR difference spectroscopy, and molecular dynamics simulations indicate that tyrosine residues facilitate charge recombination reactions that limit sustained flavin reduction, whereas methionine residues facilitate radical propagation and quenching and also gate solvent access for flavin protonation. Replacement of a single surface Met residue with Leu favors formation of the ASQ over the NSQ and desensitizes photoreduction to oxidants. In contrast, increasing site hydrophilicity by Gln substitution promotes rapid NSQ formation and weakens the influence of the redox environment. Overall, the photoreactivity of VVD-III can be understood in terms of redundant electron donors, internal hole quenching, and coupled proton transfer reactions that all depend upon protein conformation, dynamics, and solvent penetration.
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Affiliation(s)
- Estella F. Yee
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Sabine Oldemeyer
- Physical and Biophysical Chemistry, Department of Chemistry, Bielefeld University, 33615 Bielefeld, Germany
| | - Elena Böhm
- Physical and Biophysical Chemistry, Department of Chemistry, Bielefeld University, 33615 Bielefeld, Germany
| | - Abir Ganguly
- Laboratory for Biomolecular Simulation Research, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Darrin M. York
- Laboratory for Biomolecular Simulation Research, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Tilman Kottke
- Physical and Biophysical Chemistry, Department of Chemistry, Bielefeld University, 33615 Bielefeld, Germany
| | - Brian R. Crane
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
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6
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Arinkin V, Granzin J, Krauss U, Jaeger KE, Willbold D, Batra-Safferling R. Structural determinants underlying the adduct lifetime in the LOV proteins of Pseudomonas putida. FEBS J 2021; 288:4955-4972. [PMID: 33621443 DOI: 10.1111/febs.15785] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Revised: 01/22/2021] [Accepted: 02/22/2021] [Indexed: 11/30/2022]
Abstract
The primary photochemistry is similar among the flavin-bound sensory domains of light-oxygen-voltage (LOV) photoreceptors, where upon blue-light illumination a covalent adduct is formed on the microseconds time scale between the flavin chromophore and a strictly conserved cysteine residue. In contrast, the adduct-state decay kinetics vary from seconds to days or longer. The molecular basis for this variation among structurally conserved LOV domains is not fully understood. Here, we selected PpSB2-LOV, a fast-cycling (τrec 3.5 min, 20 °C) short LOV protein from Pseudomonas putida that shares 67% sequence identity with a slow-cycling (τrec 2467 min, 20 °C) homologous protein PpSB1-LOV. Based on the crystal structure of the PpSB2-LOV in the dark state reported here, we used a comparative approach, in which we combined structure and sequence information with molecular dynamic (MD) simulations to address the mechanistic basis for the vastly different adduct-state lifetimes in the two homologous proteins. MD simulations pointed toward dynamically distinct structural region, which were subsequently targeted by site-directed mutagenesis of PpSB2-LOV, where we introduced single- and multisite substitutions exchanging them with the corresponding residues from PpSB1-LOV. Collectively, the data presented identify key amino acids on the Aβ-Bβ, Eα-Fα loops, and the Fα helix, such as E27 and I66, that play a decisive role in determining the adduct lifetime. Our results additionally suggest a correlation between the solvent accessibility of the chromophore pocket and adduct-state lifetime. The presented results add to our understanding of LOV signaling and will have important implications in tuning the signaling behavior (on/off kinetics) of LOV-based optogenetic tools.
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Affiliation(s)
- Vladimir Arinkin
- IBI-7: Structural Biochemistry, Forschungszentrum Jülich, Germany
| | - Joachim Granzin
- IBI-7: Structural Biochemistry, Forschungszentrum Jülich, Germany
| | - Ulrich Krauss
- Institut für Molekulare Enzymtechnologie, Heinrich-Heine-Universität Düsseldorf, Forschungszentrum Jülich GmbH, Germany.,IBG-1: Biotechnologie, Forschungszentrum Jülich GmbH, Germany
| | - Karl-Erich Jaeger
- Institut für Molekulare Enzymtechnologie, Heinrich-Heine-Universität Düsseldorf, Forschungszentrum Jülich GmbH, Germany.,IBG-1: Biotechnologie, Forschungszentrum Jülich GmbH, Germany
| | - Dieter Willbold
- IBI-7: Structural Biochemistry, Forschungszentrum Jülich, Germany.,Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Germany.,Jülich Centre for Structural Biology (JuStruct), Forschungszentrum Jülich, Germany
| | - Renu Batra-Safferling
- IBI-7: Structural Biochemistry, Forschungszentrum Jülich, Germany.,Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Germany
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7
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Fettweiss T, Röllen K, Granzin J, Reiners O, Endres S, Drepper T, Willbold D, Jaeger KE, Batra-Safferling R, Krauss U. Mechanistic Basis of the Fast Dark Recovery of the Short LOV Protein DsLOV from Dinoroseobacter shibae. Biochemistry 2018; 57:4833-4847. [DOI: 10.1021/acs.biochem.8b00645] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Timo Fettweiss
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - Katrin Röllen
- Institute of Complex Systems, ICS-6: Structural Biochemistry, Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - Joachim Granzin
- Institute of Complex Systems, ICS-6: Structural Biochemistry, Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - Oliver Reiners
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - Stephan Endres
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - Thomas Drepper
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - Dieter Willbold
- Institute of Complex Systems, ICS-6: Structural Biochemistry, Forschungszentrum Jülich, D-52425 Jülich, Germany
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, D-40225 Düsseldorf, Germany
| | - Karl-Erich Jaeger
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich, D-52425 Jülich, Germany
- IBG-1: Biotechnology, Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - Renu Batra-Safferling
- Institute of Complex Systems, ICS-6: Structural Biochemistry, Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - Ulrich Krauss
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich, D-52425 Jülich, Germany
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8
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Abstract
Sensory photoreceptors underpin light-dependent adaptations of organismal physiology, development, and behavior in nature. Adapted for optogenetics, sensory photoreceptors become genetically encoded actuators and reporters to enable the noninvasive, spatiotemporally accurate and reversible control by light of cellular processes. Rooted in a mechanistic understanding of natural photoreceptors, artificial photoreceptors with customized light-gated function have been engineered that greatly expand the scope of optogenetics beyond the original application of light-controlled ion flow. As we survey presently, UV/blue-light-sensitive photoreceptors have particularly allowed optogenetics to transcend its initial neuroscience applications by unlocking numerous additional cellular processes and parameters for optogenetic intervention, including gene expression, DNA recombination, subcellular localization, cytoskeleton dynamics, intracellular protein stability, signal transduction cascades, apoptosis, and enzyme activity. The engineering of novel photoreceptors benefits from powerful and reusable design strategies, most importantly light-dependent protein association and (un)folding reactions. Additionally, modified versions of these same sensory photoreceptors serve as fluorescent proteins and generators of singlet oxygen, thereby further enriching the optogenetic toolkit. The available and upcoming UV/blue-light-sensitive actuators and reporters enable the detailed and quantitative interrogation of cellular signal networks and processes in increasingly more precise and illuminating manners.
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Affiliation(s)
- Aba Losi
- Department of Mathematical, Physical and Computer Sciences , University of Parma , Parco Area delle Scienze 7/A-43124 Parma , Italy
| | - Kevin H Gardner
- Structural Biology Initiative, CUNY Advanced Science Research Center , New York , New York 10031 , United States.,Department of Chemistry and Biochemistry, City College of New York , New York , New York 10031 , United States.,Ph.D. Programs in Biochemistry, Chemistry, and Biology , The Graduate Center of the City University of New York , New York , New York 10016 , United States
| | - Andreas Möglich
- Lehrstuhl für Biochemie , Universität Bayreuth , 95447 Bayreuth , Germany.,Research Center for Bio-Macromolecules , Universität Bayreuth , 95447 Bayreuth , Germany.,Bayreuth Center for Biochemistry & Molecular Biology , Universität Bayreuth , 95447 Bayreuth , Germany
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9
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Iuliano JN, Gil AA, Laptenok SP, Hall CR, Collado JT, Lukacs A, Hag Ahmed SA, Abyad J, Daryaee T, Greetham GM, Sazanovich IV, Illarionov B, Bacher A, Fischer M, Towrie M, French JB, Meech SR, Tonge PJ. Variation in LOV Photoreceptor Activation Dynamics Probed by Time-Resolved Infrared Spectroscopy. Biochemistry 2018; 57:620-630. [PMID: 29239168 PMCID: PMC5801046 DOI: 10.1021/acs.biochem.7b01040] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
The light, oxygen, voltage (LOV) domain proteins are blue light photoreceptors that utilize a noncovalently bound flavin mononucleotide (FMN) cofactor as the chromophore. The modular nature of these proteins has led to their wide adoption in the emerging fields of optogenetics and optobiology, where the LOV domain has been fused to a variety of output domains leading to novel light-controlled applications. In this work, we extend our studies of the subpicosecond to several hundred microsecond transient infrared spectroscopy of the isolated LOV domain AsLOV2 to three full-length photoreceptors in which the LOV domain is fused to an output domain: the LOV-STAS protein, YtvA, the LOV-HTH transcription factor, EL222, and the LOV-histidine kinase, LovK. Despite differences in tertiary structure, the overall pathway leading to cysteine adduct formation from the FMN triplet state is highly conserved, although there are slight variations in rate. However, significant differences are observed in the vibrational spectra and kinetics after adduct formation, which are directly linked to the specific output function of the LOV domain. While the rate of adduct formation varies by only 3.6-fold among the proteins, the subsequent large-scale structural changes in the full-length LOV photoreceptors occur over the micro- to submillisecond time scales and vary by orders of magnitude depending on the different output function of each LOV domain.
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Affiliation(s)
- James N. Iuliano
- Department of Chemistry, Stony Brook University, New York, 11794, United States
| | - Agnieszka A. Gil
- Department of Chemistry, Stony Brook University, New York, 11794, United States
| | | | | | | | - Andras Lukacs
- School of Chemistry, University of East Anglia, Norwich, NR4 7TJ, U.K
- Department of Biophysics, Medical School, University of Pecs, Szigeti út 12, 7624 Pecs, Hungary
| | - Safaa A. Hag Ahmed
- Department of Chemistry, Stony Brook University, New York, 11794, United States
| | - Jenna Abyad
- Department of Chemistry, Stony Brook University, New York, 11794, United States
| | - Taraneh Daryaee
- Department of Chemistry, Stony Brook University, New York, 11794, United States
| | - Gregory M. Greetham
- Central Laser Facility, Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, OX11 0QX, U.K
| | - Igor V. Sazanovich
- Central Laser Facility, Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, OX11 0QX, U.K
| | - Boris Illarionov
- Institut für Biochemie und Lebensmittelchemie, Universität Hamburg, Grindelallee 117, D-20146 Hamburg, Germany
| | - Adelbert Bacher
- Department Chemie, Technische Universität München, D-85747 Garching, Germany
| | - Markus Fischer
- Institut für Biochemie und Lebensmittelchemie, Universität Hamburg, Grindelallee 117, D-20146 Hamburg, Germany
| | - Michael Towrie
- Central Laser Facility, Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, OX11 0QX, U.K
| | - Jarrod B. French
- Department of Chemistry, Stony Brook University, New York, 11794, United States
| | - Stephen R. Meech
- School of Chemistry, University of East Anglia, Norwich, NR4 7TJ, U.K
| | - Peter J. Tonge
- Department of Chemistry, Stony Brook University, New York, 11794, United States
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10
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Nakagawa S, Weingart O, Marian CM. Dual Photochemical Reaction Pathway in Flavin-Based Photoreceptor LOV Domain: A Combined Quantum-Mechanics/Molecular-Mechanics Investigation. J Phys Chem B 2017; 121:9583-9596. [PMID: 28926259 DOI: 10.1021/acs.jpcb.7b09207] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The primary photochemical reaction of the light, oxygen, and voltage (LOV) domain of the blue-light photosensor YtvA of Bacillus subtilis were investigated using high-level QM(DFT/MRCI)/MM methods. After blue-light excitation, the Sγ atom of the reactive cysteine forms a covalent bond with the C4a of the flavin mononucleotide (FMN) ring. Two conformations for the side chain of reactive cysteine with occupancies of 70% (conf A) and 30% (conf B) are observed in the X-ray crystallographic structures of the YtvA-LOV ( Möglich , A. ; Moffat , K. J. Mol. Biol. 2007 , 373 , 112 - 126 ). In conf A, the thiol group is directed toward the dimethylbenzene moiety of the FMN ring whereas it is placed directly above the N5 atom of the FMN ring in conf B. Starting from both conformations, the singlet and triplet excited pathways were evaluated. The singlet states excited from conf A decay nonradiatively to the triplet states by intersystem crossing (ISC). After the formation of a neutral biradical, the triplet states cross over to the electronic ground state by a second ISC and the adducts are efficiently formed. The singlet states excited from conf B are located near the S1/S0 conical intersection (CIn). A major fraction returns to the initial states through the CIn. The rest may directly reach the adduct state. Thus, the photoexcitation has a dual reaction pathway. In YtvA-LOV, it is inferred that the efficient triplet excitation from conf A was chosen by bypassing the less efficient singlet excitation from conf B.
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Affiliation(s)
- Setsuko Nakagawa
- Department of Human Life and Environment, Kinjo Gakuin University , Omori, Moriyama-ku, Nagoya 463-8521, Japan
| | - Oliver Weingart
- Institute of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf , Universitätsstrasse 1, D-40225 Düsseldorf, Germany
| | - Christel M Marian
- Institute of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf , Universitätsstrasse 1, D-40225 Düsseldorf, Germany
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11
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Chang XP, Gao YJ, Fang WH, Cui G, Thiel W. Quantum Mechanics/Molecular Mechanics Study on the Photoreactions of Dark- and Light-Adapted States of a Blue-Light YtvA LOV Photoreceptor. Angew Chem Int Ed Engl 2017. [PMID: 28632317 DOI: 10.1002/anie.201703487] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The dark- and light-adapted states of YtvA LOV domains exhibit distinct excited-state behavior. We have employed high-level QM(MS-CASPT2)/MM calculations to study the photochemical reactions of the dark- and light-adapted states. The photoreaction from the dark-adapted state starts with an S1 →T1 intersystem crossing followed by a triplet-state hydrogen transfer from the thiol to the flavin moiety that produces a diradical intermediate, and a subsequent internal conversion that triggers a barrierless C-S bond formation in the S0 state. The energy profiles for these transformations are different for the four conformers of the dark-adapted state considered. The photochemistry of the light-adapted state does not involve the triplet state: photoexcitation to the S1 state triggers C-S bond cleavage followed by recombination in the S0 state; both these processes are essentially barrierless and thus ultrafast. The present work offers new mechanistic insights into the photoresponse of flavin-containing blue-light photoreceptors.
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Affiliation(s)
- Xue-Ping Chang
- College of Chemistry, Beijing Normal University, Xin-Jie-Kou Outer St. 19, 100875, Beijing, China
| | - Yuan-Jun Gao
- College of Chemistry, Beijing Normal University, Xin-Jie-Kou Outer St. 19, 100875, Beijing, China
| | - Wei-Hai Fang
- College of Chemistry, Beijing Normal University, Xin-Jie-Kou Outer St. 19, 100875, Beijing, China
| | - Ganglong Cui
- College of Chemistry, Beijing Normal University, Xin-Jie-Kou Outer St. 19, 100875, Beijing, China
| | - Walter Thiel
- Max-Planck-Institut für Kohlenforschung, 45470, Mülheim an der Ruhr, Germany
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12
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Chang XP, Gao YJ, Fang WH, Cui G, Thiel W. Quantum Mechanics/Molecular Mechanics Study on the Photoreactions of Dark- and Light-Adapted States of a Blue-Light YtvA LOV Photoreceptor. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201703487] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Xue-Ping Chang
- College of Chemistry; Beijing Normal University; Xin-Jie-Kou Outer St. 19 100875 Beijing China
| | - Yuan-Jun Gao
- College of Chemistry; Beijing Normal University; Xin-Jie-Kou Outer St. 19 100875 Beijing China
| | - Wei-Hai Fang
- College of Chemistry; Beijing Normal University; Xin-Jie-Kou Outer St. 19 100875 Beijing China
| | - Ganglong Cui
- College of Chemistry; Beijing Normal University; Xin-Jie-Kou Outer St. 19 100875 Beijing China
| | - Walter Thiel
- Max-Planck-Institut für Kohlenforschung; 45470 Mülheim an der Ruhr Germany
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13
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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: 45] [Impact Index Per Article: 6.4] [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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14
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Zhu J, Mathes T, Hontani Y, Alexandre MTA, Toh KC, Hegemann P, Kennis JTM. Photoadduct Formation from the FMN Singlet Excited State in the LOV2 Domain of Chlamydomonas reinhardtii Phototropin. J Phys Chem Lett 2016; 7:4380-4384. [PMID: 27766868 DOI: 10.1021/acs.jpclett.6b02075] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
The two light, oxygen, and voltage domains of phototropin are blue-light photoreceptor domains that control various functions in plants and green algae. The key step of the light-driven reaction is the formation of a photoadduct between its FMN chromophore and a conserved cysteine, where the canonical reaction proceeds through the FMN triplet state. Here, complete photoreaction mapping of CrLOV2 from Chlamydomonas reinhardtii phototropin and AsLOV2 from Avena sativa phototropin-1 was realized by ultrafast broadband spectroscopy from femtoseconds to microseconds. We demonstrate that in CrLOV2, a direct photoadduct formation channel originates from the initially excited singlet state, in addition to the canonical reaction through the triplet state. This direct photoadduct reaction is coupled by a proton or hydrogen transfer process, as indicated by a significant kinetic isotope effect of 1.4 on the fluorescence lifetime. Kinetic model analyses showed that 38% of the photoadducts are generated from the singlet excited state.
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Affiliation(s)
- Jingyi Zhu
- Department of Physics and Astronomy, Faculty of Sciences, Vrije Universiteit , 1081 De Boelelaan, 1081 HV Amsterdam, The Netherlands
| | - Tilo Mathes
- Department of Physics and Astronomy, Faculty of Sciences, Vrije Universiteit , 1081 De Boelelaan, 1081 HV Amsterdam, The Netherlands
| | - Yusaku Hontani
- Department of Physics and Astronomy, Faculty of Sciences, Vrije Universiteit , 1081 De Boelelaan, 1081 HV Amsterdam, The Netherlands
| | - Maxime T A Alexandre
- Department of Physics and Astronomy, Faculty of Sciences, Vrije Universiteit , 1081 De Boelelaan, 1081 HV Amsterdam, The Netherlands
| | - K C Toh
- Department of Physics and Astronomy, Faculty of Sciences, Vrije Universiteit , 1081 De Boelelaan, 1081 HV Amsterdam, The Netherlands
| | - Peter Hegemann
- Department of Biology, Experimental Biophysics, Humboldt-Universität zu Berlin , Invalidenstraße 42, 10115 Berlin, Germany
| | - John T M Kennis
- Department of Physics and Astronomy, Faculty of Sciences, Vrije Universiteit , 1081 De Boelelaan, 1081 HV Amsterdam, The Netherlands
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15
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Tracking the secondary photodynamics of the green/red cyanobacteriochrome RcaE from Fremyella diplosiphon. Chem Phys Lett 2016. [DOI: 10.1016/j.cplett.2015.11.059] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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16
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Lee R, Gam J, Moon J, Lee SG, Suh YG, Lee BJ, Lee J. A critical element of the light-induced quaternary structural changes in YtvA-LOV. Protein Sci 2015; 24:1997-2007. [PMID: 26402155 DOI: 10.1002/pro.2810] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Revised: 09/18/2015] [Accepted: 09/19/2015] [Indexed: 01/27/2023]
Abstract
YtvA, a photosensory LOV (light-oxygen-voltage) protein from Bacillus subtilis, exists as a dimer that previously appeared to undergo surprisingly small structural changes after light illumination compared with other light-sensing proteins. However, we now report that light induces significant structural perturbations in a series of YtvA-LOV domain derivatives in which the Jα helix has been truncated or replaced. Results from native gel analysis showed significant mobility changes in these derivatives after light illumination; YtvA-LOV without the Jα helix dimerized in the dark state but existed as a monomer in the light state. The absence of the Jα helix also affected the dark regeneration kinetics and the stability of the flavin mononucleotide (FMN) binding to its binding site. Our results demonstrate an alternative way of photo-induced signal propagation that leads to a bigger functional response through dimer/monomer conversions of the YtvA-LOV than the local disruption of Jα helix in the As-LOV domain.
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Affiliation(s)
- Rang Lee
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul, 151-742, Korea
| | - Jongsik Gam
- Department of Medicinal Bioscience, College of Interdisciplinary & Creative Studies, Konyang University, Nonsan-Si, 320-711, Korea
| | - Jayoung Moon
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul, 151-742, Korea
| | - Seung-Goo Lee
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 305-806, Korea
| | - Young-Ger Suh
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul, 151-742, Korea
| | - Bong-Jin Lee
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul, 151-742, Korea
| | - Jeeyeon Lee
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul, 151-742, Korea
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17
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Kutta RJ, Magerl K, Kensy U, Dick B. A search for radical intermediates in the photocycle of LOV domains. Photochem Photobiol Sci 2015; 14:288-99. [PMID: 25380177 DOI: 10.1039/c4pp00155a] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
LOV domains are the light sensitive parts of phototropins and many other light-activated enzymes that regulate the response to blue light in plants and algae as well as some fungi and bacteria. Unlike all other biological photoreceptors known so far, the photocycle of LOV domains involves the excited triplet state of the chromophore. This chromophore is flavin mononucleotide (FMN) which forms a covalent adduct with a cysteine residue in the signaling state. Since the formation of this adduct from the triplet state involves breaking and forming of two bonds as well as a change from the triplet to the singlet spin state, various intermediates have been proposed, e.g. a protonated triplet state (3)FMNH(+), the radical anion (2)FMN˙(-), or the neutral semiquinone radical (2)FMNH˙. We performed an extensive search for these intermediates by two-dimensional transient absorption (2D-TA) with a streak camera. However, no transient with a rate constant between the decay of fluorescence and the decay of the triplet state could be detected. Analysis of the decay associated difference spectra results in quantum yields for the formation of the adduct from the triplet of ΦA(LOV1) ≈ 0.75 and ΦA(LOV2) ≈ 0.80. This is lower than the values ΦA(LOV1) ≈ 0.95 and ΦA(LOV2) ≈ 0.99 calculated from the rate constants, giving indirect evidence of an intermediate that reacts either to form the adduct or to decay back to the ground state. Since there is no measurable delay between the decay of the triplet and the formation of the adduct, we conclude that this intermediate reacts much faster than it is formed. The LOV1-C57S mutant shows a weak and slowly decaying (τ > 100 μs) transient whose decay associated spectrum has bands at 375 and 500 nm, with a shoulder at 400 nm. This transient is insensitive to the pH change in the range 6.5-10.0 but increases on addition of β-mercaptoethanol as the reducing agent. We assign this intermediate to the radical anion which is protected from protonation by the protein. We propose that the adduct is formed via the same intermediate by combination of the radical ion pair.
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Affiliation(s)
- Roger Jan Kutta
- Institut für Physikalische und Theoretische Chemie, Universität Regensburg, 93053 Regensburg, Germany.
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18
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van der Steen JB, Hellingwerf KJ. Activation of the General Stress Response of Bacillus subtilis by Visible Light. Photochem Photobiol 2015; 91:1032-45. [PMID: 26189730 DOI: 10.1111/php.12499] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2015] [Accepted: 06/25/2015] [Indexed: 12/20/2022]
Abstract
A key challenge for microbiology is to understand how evolution has shaped the wiring of regulatory networks. This is amplified by the paucity of information of power-spectra of physicochemical stimuli to which microorganisms are exposed. Future studies of genome evolution, driven by altered stimulus regimes, will therefore require a versatile signal transduction system that allows accurate signal dosing. Here, we review the general stress response of Bacillus subtilis, and its upstream signal transduction network, as a candidate system. It can be activated by red and blue light, and by many additional stimuli. Signal integration therefore is an intricate function of this system. The blue-light response is elicited via the photoreceptor YtvA, which forms an integral part of stressosomes, to activate expression of the stress regulon of B. subtilis. Signal transfer through this network can be assayed with reporter enzymes, while intermediate steps can be studied with live-cell imaging of fluorescently tagged proteins. Different parts of this system have been studied in vitro, such that its computational modeling has made significant progress. One can directly relate the microscopic characteristics of YtvA with activation of the general stress regulon, making this system a very well-suited system for network evolution studies.
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Affiliation(s)
- Jeroen B van der Steen
- Molecular Microbial Physiology Group, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Klaas J Hellingwerf
- Molecular Microbial Physiology Group, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
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19
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Losi A, Mandalari C, Gärtner W. The Evolution and Functional Role of Flavin-based Prokaryotic Photoreceptors. Photochem Photobiol 2015; 91:1021-31. [DOI: 10.1111/php.12489] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Accepted: 06/15/2015] [Indexed: 12/12/2022]
Affiliation(s)
- Aba Losi
- Department of Physics and Earth Sciences; University of Parma; Parma Italy
| | - Carmen Mandalari
- 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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20
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Nudel CB, Hellingwerf KJ. Photoreceptors in Chemotrophic Prokaryotes: The Case of Acinetobacter spp. Revisited. Photochem Photobiol 2015; 91:1012-20. [PMID: 26147719 DOI: 10.1111/php.12491] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 06/08/2015] [Indexed: 12/23/2022]
Abstract
A comprehensive description of blue light using flavin (BLUF) photosensory proteins, including preferred domain architectures and the molecular mechanism of their light activation and signal generation, among chemotrophic prokaryotes is presented. Light-regulated physiological responses in Acinetobacter spp. from environmental and clinically relevant strains are discussed. The twitching motility response in A. baylyi sp. ADP1 and the joint involvement of three of the four putative BLUF-domain-containing proteins in this response, in this species, is presented as an example of remarkable photoreceptor redundancy.
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Affiliation(s)
- Clara B Nudel
- Nanobiotec Institute, Faculty of Pharmacy and Biochemistry, University of Buenos Aires, Ciudad de Buenos Aires, Argentina
| | - Klaas J Hellingwerf
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
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21
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Diensthuber RP, Engelhard C, Lemke N, Gleichmann T, Ohlendorf R, Bittl R, Möglich A. Biophysical, mutational, and functional investigation of the chromophore-binding pocket of light-oxygen-voltage photoreceptors. ACS Synth Biol 2014; 3:811-9. [PMID: 24926890 DOI: 10.1021/sb400205x] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
As light-regulated actuators, sensory photoreceptors underpin optogenetics and numerous applications in synthetic biology. Protein engineering has been applied to fine-tune the properties of photoreceptors and to generate novel actuators. For the blue-light-sensitive light-oxygen-voltage (LOV) photoreceptors, mutations near the flavin chromophore modulate response kinetics and the effective light responsiveness. To probe for potential, inadvertent effects on receptor activity, we introduced these mutations into the engineered LOV photoreceptor YF1 and determined their impact on light regulation. While several mutations severely impaired the dynamic range of the receptor (e.g., I39V, R63K, and N94A), residue substitutions in a second group were benign with little effect on regulation (e.g., V28T, N37C, and L82I). Electron paramagnetic resonance and absorption spectroscopy identified correlated effects for certain of the latter mutations on chromophore environment and response kinetics in YF1 and the LOV2 domain from Avena sativa phototropin 1. Carefully chosen mutations provide a powerful means to adjust the light-response function of photoreceptors as demanded for diverse applications.
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Affiliation(s)
- Ralph P. Diensthuber
- Humboldt-Universität zu Berlin, Institut für Biologie,
Biophysikalische Chemie, 10115 Berlin, Germany
| | - Christopher Engelhard
- Freie Universität Berlin, Fachbereich Physik,
Institut für Experimentalphysik, 14195 Berlin, Germany
| | - Nora Lemke
- Humboldt-Universität zu Berlin, Institut für Biologie,
Biophysikalische Chemie, 10115 Berlin, Germany
| | - Tobias Gleichmann
- Humboldt-Universität zu Berlin, Institut für Biologie,
Biophysikalische Chemie, 10115 Berlin, Germany
| | - Robert Ohlendorf
- Humboldt-Universität zu Berlin, Institut für Biologie,
Biophysikalische Chemie, 10115 Berlin, Germany
| | - Robert Bittl
- Freie Universität Berlin, Fachbereich Physik,
Institut für Experimentalphysik, 14195 Berlin, Germany
| | - Andreas Möglich
- Humboldt-Universität zu Berlin, Institut für Biologie,
Biophysikalische Chemie, 10115 Berlin, Germany
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22
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From Plant Infectivity to Growth Patterns: The Role of Blue-Light Sensing in the Prokaryotic World. PLANTS 2014; 3:70-94. [PMID: 27135492 PMCID: PMC4844311 DOI: 10.3390/plants3010070] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Revised: 01/14/2014] [Accepted: 01/15/2014] [Indexed: 01/15/2023]
Abstract
Flavin-based photoreceptor proteins of the LOV (Light, Oxygen, and Voltage) and BLUF (Blue Light sensing Using Flavins) superfamilies are ubiquitous among the three life domains and are essential blue-light sensing systems, not only in plants and algae, but also in prokaryotes. Here we review their biological roles in the prokaryotic world and their evolution pathways. An unexpected large number of bacterial species possess flavin-based photosensors, amongst which are important human and plant pathogens. Still, few cases are reported where the activity of blue-light sensors could be correlated to infectivity and/or has been shown to be involved in the activation of specific genes, resulting in selective growth patterns. Metagenomics and bio-informatic analysis have only recently been initiated, but signatures are beginning to emerge that allow definition of a bona fide LOV or BLUF domain, aiming at better selection criteria for novel blue-light sensors. We also present here, for the first time, the phylogenetic tree for archaeal LOV domains that have reached a statistically significant number but have not at all been investigated thus far.
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