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Gotthard G, Mous S, Weinert T, Maia RNA, James D, Dworkowski F, Gashi D, Furrer A, Ozerov D, Panepucci E, Wang M, Schertler GFX, Heberle J, Standfuss J, Nogly P. Capturing the blue-light activated state of the Phot-LOV1 domain from Chlamydomonas reinhardtii using time-resolved serial synchrotron crystallography. IUCRJ 2024; 11:792-808. [PMID: 39037420 PMCID: PMC11364019 DOI: 10.1107/s2052252524005608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 06/11/2024] [Indexed: 07/23/2024]
Abstract
Light-oxygen-voltage (LOV) domains are small photosensory flavoprotein modules that allow the conversion of external stimuli (sunlight) into intracellular signals responsible for various cell behaviors (e.g. phototropism and chloroplast relocation). This ability relies on the light-induced formation of a covalent thioether adduct between a flavin chromophore and a reactive cysteine from the protein environment, which triggers a cascade of structural changes that result in the activation of a serine/threonine (Ser/Thr) kinase. Recent developments in time-resolved crystallography may allow the activation cascade of the LOV domain to be observed in real time, which has been elusive. In this study, we report a robust protocol for the production and stable delivery of microcrystals of the LOV domain of phototropin Phot-1 from Chlamydomonas reinhardtii (CrPhotLOV1) with a high-viscosity injector for time-resolved serial synchrotron crystallography (TR-SSX). The detailed process covers all aspects, from sample optimization to data collection, which may serve as a guide for soluble protein preparation for TR-SSX. In addition, we show that the crystals obtained preserve the photoreactivity using infrared spectroscopy. Furthermore, the results of the TR-SSX experiment provide high-resolution insights into structural alterations of CrPhotLOV1 from Δt = 2.5 ms up to Δt = 95 ms post-photoactivation, including resolving the geometry of the thioether adduct and the C-terminal region implicated in the signal transduction process.
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Affiliation(s)
- Guillaume Gotthard
- Institute of Molecular Biology and Biophysics, Department of BiologyETH Zurich8093ZürichSwitzerland
- Laboratory of Biomolecular Research, Division of Biology and ChemistryPaul Scherrer Institute5232Villigen PSISwitzerland
| | - Sandra Mous
- Institute of Molecular Biology and Biophysics, Department of BiologyETH Zurich8093ZürichSwitzerland
| | - Tobias Weinert
- Laboratory of Biomolecular Research, Division of Biology and ChemistryPaul Scherrer Institute5232Villigen PSISwitzerland
| | - Raiza Nara Antonelli Maia
- Experimental Molecular Biophysics, Department of PhysicsFreie Universität BerlinArnimallee 1414195BerlinGermany
| | - Daniel James
- Laboratory of Biomolecular Research, Division of Biology and ChemistryPaul Scherrer Institute5232Villigen PSISwitzerland
| | - Florian Dworkowski
- Macromolecular Crystallography, Swiss Light SourcePaul Scherrer Institute5232Villigen PSISwitzerland
| | - Dardan Gashi
- Laboratory of Biomolecular Research, Division of Biology and ChemistryPaul Scherrer Institute5232Villigen PSISwitzerland
- Laboratory of Femtochemistry, Photon Science DivisionPaul Scherrer Institute5232Villigen PSISwitzerland
| | - Antonia Furrer
- Laboratory of Biomolecular Research, Division of Biology and ChemistryPaul Scherrer Institute5232Villigen PSISwitzerland
| | - Dmitry Ozerov
- Science ITPaul Scherrer Institute5232Villigen PSISwitzerland
| | - Ezequiel Panepucci
- Laboratory for Macromolecules and Bioimaging, Photon Science DivisionPaul Scherrer Institute5232Villigen PSISwitzerland
| | - Meitian Wang
- Laboratory for Macromolecules and Bioimaging, Photon Science DivisionPaul Scherrer Institute5232Villigen PSISwitzerland
| | - Gebhard F. X. Schertler
- Laboratory of Biomolecular Research, Division of Biology and ChemistryPaul Scherrer Institute5232Villigen PSISwitzerland
- Department of BiologyETH Zürich8093ZürichSwitzerland
| | - Joachim Heberle
- Experimental Molecular Biophysics, Department of PhysicsFreie Universität BerlinArnimallee 1414195BerlinGermany
| | - Joerg Standfuss
- Laboratory of Biomolecular Research, Division of Biology and ChemistryPaul Scherrer Institute5232Villigen PSISwitzerland
| | - Przemyslaw Nogly
- Institute of Molecular Biology and Biophysics, Department of BiologyETH Zurich8093ZürichSwitzerland
- Dioscuri Center For Structural Dynamics of Receptors, Faculty of Biochemistry, Biophysics and BiotechnologyJagiellonian University in Kraków30-387KrakówPoland
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2
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Schuhmacher L, Heck S, Pitz M, Mathey E, Lamparter T, Blumhofer A, Leister K, Fischer R. The LOV-domain blue-light receptor LreA of the fungus Alternaria alternata binds predominantly FAD as chromophore and acts as a light and temperature sensor. J Biol Chem 2024; 300:107238. [PMID: 38552736 PMCID: PMC11061223 DOI: 10.1016/j.jbc.2024.107238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 03/16/2024] [Accepted: 03/20/2024] [Indexed: 05/04/2024] Open
Abstract
Light and temperature sensing are important features of many organisms. Light may provide energy but may also be used by non-photosynthetic organisms for orientation in the environment. Recent evidence suggests that plant and fungal phytochrome and plant phototropin serve dual functions as light and temperature sensors. Here we characterized the fungal LOV-domain blue-light receptor LreA of Alternaria alternata and show that it predominantly contains FAD as chromophore. Blue-light illumination induced ROS production followed by protein agglomeration in vitro. In vivo ROS may control LreA activity. LreA acts as a blue-light photoreceptor but also triggers temperature-shift-induced gene expression. Both responses required the conserved amino acid cysteine 421. We therefore propose that temperature mimics the photoresponse, which could be the ancient function of the chromoprotein. Temperature-dependent gene expression control with LreA was distinct from the response with phytochrome suggesting fine-tuned, photoreceptor-specific gene regulation.
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Affiliation(s)
- Lars Schuhmacher
- Department of Microbiology, Institute for Applied Biosciences, Karlsruhe Institute of Technology (KIT) - South Campus, Karlsruhe, Germany
| | - Steffen Heck
- Department of Microbiology, Institute for Applied Biosciences, Karlsruhe Institute of Technology (KIT) - South Campus, Karlsruhe, Germany
| | - Michael Pitz
- Department of Microbiology, Institute for Applied Biosciences, Karlsruhe Institute of Technology (KIT) - South Campus, Karlsruhe, Germany
| | - Elena Mathey
- Department of Microbiology, Institute for Applied Biosciences, Karlsruhe Institute of Technology (KIT) - South Campus, Karlsruhe, Germany
| | - Tilman Lamparter
- Joseph Kölreuter Institute for Plant Research, Karlsruhe Institute of Technology (KIT) - South Campus, Karlsruhe, Germany
| | - Alexander Blumhofer
- Department of Microbiology, Institute for Applied Biosciences, Karlsruhe Institute of Technology (KIT) - South Campus, Karlsruhe, Germany
| | - Kai Leister
- Department of Microbiology, Institute for Applied Biosciences, Karlsruhe Institute of Technology (KIT) - South Campus, Karlsruhe, Germany
| | - Reinhard Fischer
- Department of Microbiology, Institute for Applied Biosciences, Karlsruhe Institute of Technology (KIT) - South Campus, Karlsruhe, Germany.
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3
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Elahi Y, Baker MAB. Light Control in Microbial Systems. Int J Mol Sci 2024; 25:4001. [PMID: 38612810 PMCID: PMC11011852 DOI: 10.3390/ijms25074001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 03/27/2024] [Accepted: 03/28/2024] [Indexed: 04/14/2024] Open
Abstract
Light is a key environmental component influencing many biological processes, particularly in prokaryotes such as archaea and bacteria. Light control techniques have revolutionized precise manipulation at molecular and cellular levels in recent years. Bacteria, with adaptability and genetic tractability, are promising candidates for light control studies. This review investigates the mechanisms underlying light activation in bacteria and discusses recent advancements focusing on light control methods and techniques for controlling bacteria. We delve into the mechanisms by which bacteria sense and transduce light signals, including engineered photoreceptors and light-sensitive actuators, and various strategies employed to modulate gene expression, protein function, and bacterial motility. Furthermore, we highlight recent developments in light-integrated methods of controlling microbial responses, such as upconversion nanoparticles and optical tweezers, which can enhance the spatial and temporal control of bacteria and open new horizons for biomedical applications.
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4
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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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5
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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: 0.7] [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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6
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Smolentseva A, Goncharov IM, Yudenko A, Bogorodskiy A, Semenov O, Nazarenko VV, Borshchevskiy V, Fonin AV, Remeeva A, Jaeger KE, Krauss U, Gordeliy V, Gushchin I. Extreme dependence of Chloroflexus aggregans LOV domain thermo- and photostability on the bound flavin species. Photochem Photobiol Sci 2021; 20:1645-1656. [PMID: 34796467 DOI: 10.1007/s43630-021-00138-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 11/08/2021] [Indexed: 01/10/2023]
Abstract
Light-oxygen-voltage (LOV) domains are common photosensory modules that found many applications in fluorescence microscopy and optogenetics. Here, we show that the Chloroflexus aggregans LOV domain can bind different flavin species (lumichrome, LC; riboflavin, RF; flavin mononucleotide, FMN; flavin adenine dinucleotide, FAD) during heterologous expression and that its physicochemical properties depend strongly on the nature of the bound flavin. We show that whereas the dissociation constants for different chromophores are similar, the melting temperature of the protein reconstituted with single flavin species varies from ~ 60 °C for LC to ~ 81 °C for FMN, and photobleaching half-times vary almost 100-fold. These observations serve as a caution for future studies of LOV domains in non-native conditions yet raise the possibility of fine-tuning various properties of LOV-based fluorescent probes and optogenetic tools by manipulating the chromophore composition.
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Affiliation(s)
- Anastasia Smolentseva
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Ivan M Goncharov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Anna Yudenko
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Andrey Bogorodskiy
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Oleg Semenov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Vera V Nazarenko
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Valentin Borshchevskiy
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia.,Institute of Biological Information Processing IBI-7: Structural Biochemistry, Forschungszentrum Jülich, 52428, Jülich, Germany
| | - Alexander V Fonin
- Institute of Cytology, Russian Academy of Sciences, 194064, Saint Petersburg, Russia
| | - Alina Remeeva
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Karl-Erich Jaeger
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich, Jülich, Germany.,Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Ulrich Krauss
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich, Jülich, Germany.,Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Valentin Gordeliy
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia.,Institut de Biologie Structurale J.-P. Ebel, Université Grenoble Alpes-CEA-CNRS, 38000, Grenoble, France.,Institute of Biological Information Processing IBI-7: Structural Biochemistry, Forschungszentrum Jülich, 52428, Jülich, Germany
| | - Ivan Gushchin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia.
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7
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Remeeva A, Nazarenko VV, Kovalev K, Goncharov IM, Yudenko A, Astashkin R, Gordeliy V, Gushchin I. Insights into the mechanisms of light-oxygen-voltage domain color tuning from a set of high-resolution X-ray structures. Proteins 2021; 89:1005-1016. [PMID: 33774867 DOI: 10.1002/prot.26078] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 03/16/2021] [Indexed: 01/01/2023]
Abstract
Light-oxygen-voltage (LOV) domains are widespread photosensory modules that can be used in fluorescence microscopy, optogenetics and controlled production of reactive oxygen species. All of the currently known LOV domains have absorption maxima in the range of ~440 to ~450 nm, and it is not clear whether they can be shifted significantly using mutations. Here, we have generated a panel of LOV domain variants by mutating the key chromophore-proximal glutamine aminoacid of a thermostable flavin based fluorescent protein CagFbFP (Gln148) to asparagine, aspartate, glutamate, histidine, lysine and arginine. Absorption spectra of all of the mutants are blue-shifted, with the maximal shift of 8 nm observed for the Q148H variant. While CagFbFP and its Q148N/D/E variants are not sensitive to pH, Q148H/K/R reveal a moderate red shift induced byacidic pH. To gain further insight, we determined high resolution crystal structures of all of the mutants studied at the resolutions from 1.07 Å for Q148D to 1.63 Å for Q148R. Whereas in some of the variants, the aminoacid 148 remains in the vicinity of the flavin, in Q148K, Q148R and partially Q148D, the C-terminus of the protein unlatches and the side chain of the residue 148 is reoriented away from the chromophore. Our results explain the absence of color shifts from replacing Gln148 with charged aminoacids and pave the way for rational design of color-shifted flavin based fluorescent proteins.
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Affiliation(s)
- Alina Remeeva
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Vera V Nazarenko
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Kirill Kovalev
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
- Institut de Biologie Structurale J.-P. Ebel, Université Grenoble Alpes-CEA-CNRS, Grenoble, France
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, Jülich, Germany
- Institute of Crystallography, RWTH Aachen University, Aachen, Germany
| | - Ivan M Goncharov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Anna Yudenko
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Roman Astashkin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
- Institut de Biologie Structurale J.-P. Ebel, Université Grenoble Alpes-CEA-CNRS, Grenoble, France
| | - Valentin Gordeliy
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
- Institut de Biologie Structurale J.-P. Ebel, Université Grenoble Alpes-CEA-CNRS, Grenoble, France
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, Jülich, Germany
| | - Ivan Gushchin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
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8
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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: 1.8] [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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9
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Tian H, Tao P. ivis Dimensionality Reduction Framework for Biomacromolecular Simulations. J Chem Inf Model 2020; 60:4569-4581. [PMID: 32820912 DOI: 10.1021/acs.jcim.0c00485] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Molecular dynamics (MD) simulations have been widely applied to study macromolecules including proteins. However, the high dimensionality of the data sets produced by simulations makes thorough analysis difficult and further hinders a deeper understanding of biomacromolecules. To gain more insights into the protein structure-function relations, appropriate dimensionality reduction methods are needed to project simulations onto low-dimensional spaces. Linear dimensionality reduction methods, such as principal component analysis (PCA) and time-structure-based independent component analysis (t-ICA), could not preserve sufficient structural information. Though better than linear methods, nonlinear methods, such as t-distributed stochastic neighbor embedding (t-SNE), still suffer from the limitations in avoiding system noise and keeping inter-cluster relations. ivis is a novel deep learning-based dimensionality reduction method originally developed for single-cell data sets. Here, we applied this framework for the study of light, oxygen, and voltage (LOV) domains of diatom Phaeodactylum tricornutum aureochrome 1a (PtAu1a). Compared with other methods, ivis is shown to be superior in constructing a Markov state model (MSM), preserving information of both local and global distances, and maintaining similarity between high and low dimensions with the least information loss. Moreover, the ivis framework is capable of providing new perspectives for deciphering residue-level protein allostery through the feature weights in the neural network. Overall, ivis is a promising member of the analysis toolbox for proteins.
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Affiliation(s)
- Hao Tian
- Department of Chemistry, Center for Research Computing, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, Texas 75205, United States
| | - Peng Tao
- Department of Chemistry, Center for Research Computing, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, Texas 75205, United States
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10
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Ganesh I, Gwon DA, Lee JW. Gas-Sensing Transcriptional Regulators. Biotechnol J 2020; 15:e1900345. [PMID: 32362055 DOI: 10.1002/biot.201900345] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 04/08/2020] [Indexed: 11/10/2022]
Abstract
Gas molecules are ubiquitous in the environment and are used as nutrient and energy sources for living organisms. Many organisms, therefore, have developed gas-sensing systems to respond efficiently to changes in the atmospheric environment. In microorganisms and plants, two-component systems (TCSs) and transcription factors (TFs) are two primary mechanisms to sense gas molecules. In this review, gas-sensing transcriptional regulators, TCSs, and TFs, focusing on protein structures, mechanisms of gas molecule interaction, DNA binding regions of transcriptional regulators, signal transduction mechanisms, and gene expression regulation are discussed. At first, transcriptional regulators that directly sense gas molecules with the help of a prosthetic group is described and then gas-sensing systems that indirectly recognize the presence of gas molecules is explained. Overall, this review provides a comprehensive understanding of gas-sensing transcriptional regulators in microorganisms and plants, and proposes a future perspective on the use of gas-sensing transcriptional regulators.
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Affiliation(s)
- Irisappan Ganesh
- Department of Chemical Engineering, Pohang University of Science and Technology, Pohang, 37673, Republic of Korea
| | - Da-Ae Gwon
- Department of Chemical Engineering, Pohang University of Science and Technology, Pohang, 37673, Republic of Korea
| | - Jeong Wook Lee
- Department of Chemical Engineering, Pohang University of Science and Technology, Pohang, 37673, Republic of Korea.,School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang, 37673, Republic of Korea
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11
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Petrenčáková M, Varhač R, Kožár T, Nemergut M, Jancura D, Schwer MS, Sedlák E. Conformational properties of LOV2 domain and its C450A variant within broad pH region. Biophys Chem 2020; 259:106337. [PMID: 32126442 DOI: 10.1016/j.bpc.2020.106337] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Revised: 02/03/2020] [Accepted: 02/24/2020] [Indexed: 11/28/2022]
Abstract
LOV2 (Light-Oxygen-Voltage) domain from Avena sativa phototropin 1 (AsLOV2) belongs to the superfamily of PAS (Per-Arnt-Sim) domains, members of which function as signaling sensors. AsLOV2 undergoes a conformational change upon blue-light absorption by its FMN cofactor. AsLOV2 wild type (wt) is intensively studied as a photo-switchable element in conjugation with various proteins. On the other hand, its variant AsLOV2 with replaced cysteinyl residue C450, which is critical for the forming a covalent adduct with FMN upon irradiation, forms a precursor for some recently developed genetically encoded photosensitizers. In the presented work, we investigated conformational properties of AsLOV2 wt and its variant C450A by circular dichroism, tryptophan and FMN fluorescence, and differential scanning calorimetry in dependence on pH and temperature. We show that both variants are similarly sensitive towards pH of solvent. On the other hand, the mutation C450A leads to a more stable AsLOV2 variant in comparison with the wild type. Thermal transitions of the AsLOV2 proteins monitored by circular dichroism indicate the presence of significant residual structure in thermally-denatured states of both proteins in the pH range from 4 to 9. Both pH- and thermal- transitions of AsLOV2 are accompanied by FMN leaching to solvent. Higher stability, reversibility of thermal transitions, and efficiency of FMN rebinding in the case of C450A variant suggest that the cofactor release may be modulated by suitable mutations in combination with a suitable physicochemical perturbation. These findings can have implications for a design of genetically encoded photosensitizers.
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Affiliation(s)
- Martina Petrenčáková
- Department of Biophysics, Faculty of Science, P.J. Šafárik University, Jesenná 5, 041 54 Košice, Slovakia
| | - Rastislav Varhač
- Department of Biochemistry, Faculty of Science, P.J. Šafárik University, Moyzesova 11, 041 54 Košice, Slovakia
| | - Tibor Kožár
- Center for Interdisciplinary Biosciences, Technology and Innovation Park, P.J. Šafárik University, Jesenná 5, 041 54 Košice, Slovakia
| | - Michal Nemergut
- Center for Interdisciplinary Biosciences, Technology and Innovation Park, P.J. Šafárik University, Jesenná 5, 041 54 Košice, Slovakia
| | - Daniel Jancura
- Department of Biophysics, Faculty of Science, P.J. Šafárik University, Jesenná 5, 041 54 Košice, Slovakia; Center for Interdisciplinary Biosciences, Technology and Innovation Park, P.J. Šafárik University, Jesenná 5, 041 54 Košice, Slovakia
| | - Marc-Simon Schwer
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Erik Sedlák
- Department of Biochemistry, Faculty of Science, P.J. Šafárik University, Moyzesova 11, 041 54 Košice, Slovakia; Center for Interdisciplinary Biosciences, Technology and Innovation Park, P.J. Šafárik University, Jesenná 5, 041 54 Košice, Slovakia.
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12
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Nazarenko VV, Remeeva A, Yudenko A, Kovalev K, Dubenko A, Goncharov IM, Kuzmichev P, Rogachev AV, Buslaev P, Borshchevskiy V, Mishin A, Dhoke GV, Schwaneberg U, Davari MD, Jaeger KE, Krauss U, Gordeliy V, Gushchin I. A thermostable flavin-based fluorescent protein from Chloroflexus aggregans: a framework for ultra-high resolution structural studies. Photochem Photobiol Sci 2019; 18:1793-1805. [DOI: 10.1039/c9pp00067d] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
A new thermostable fluorescent protein is shown to be a promising model for ultra-high resolution structural studies of LOV domains and for application as a fluorescent reporter.
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13
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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: 1.4] [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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14
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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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15
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Foley BJ, Stutts H, Schmitt SL, Lokhandwala J, Nagar A, Zoltowski BD. Characterization of a Vivid Homolog in Botrytis cinerea. Photochem Photobiol 2018; 94:985-993. [PMID: 29682744 DOI: 10.1111/php.12927] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2017] [Accepted: 04/04/2018] [Indexed: 01/15/2023]
Abstract
Blue light-signaling pathways regulated by members of the light-oxygen-voltage (LOV) domain family integrate stress responses, circadian rhythms and pathogenesis in fungi. The canonical signaling mechanism involves two LOV-containing proteins that maintain homology to Neurospora crassa Vivid (NcVVD) and White Collar 1 (NcWC1). These proteins engage in homo- and heterodimerization events that modulate gene transcription in response to light. Here, we clone and characterize the VVD homolog in Botrytis cinerea (BcVVD). BcVVD retains divergent photocycle kinetics and is incapable of LOV mediated homodimerization, indicating modification of the classical hetero/homodimerization mechanism of photoadaptation in fungi.
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Affiliation(s)
- Brandon J Foley
- Department of Chemistry, Center for Drug Discovery, Design and Delivery, Southern Methodist University, Dallas, TX
| | - Haley Stutts
- Department of Chemistry, Center for Drug Discovery, Design and Delivery, Southern Methodist University, Dallas, TX
| | - Sydney L Schmitt
- Department of Chemistry, Center for Drug Discovery, Design and Delivery, Southern Methodist University, Dallas, TX
| | - Jameela Lokhandwala
- Department of Chemistry, Center for Drug Discovery, Design and Delivery, Southern Methodist University, Dallas, TX
| | - Aditi Nagar
- Department of Chemistry, Center for Drug Discovery, Design and Delivery, Southern Methodist University, Dallas, TX
| | - Brian D Zoltowski
- Department of Chemistry, Center for Drug Discovery, Design and Delivery, Southern Methodist University, Dallas, TX
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