1
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Sineshchekov VA. Applications of fluorescence spectroscopy in the investigation of plant phytochrome invivo. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 208:108434. [PMID: 38412703 DOI: 10.1016/j.plaphy.2024.108434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 02/08/2024] [Accepted: 02/10/2024] [Indexed: 02/29/2024]
Abstract
Fluorometry is an effective research tool in biology and medicine; it is widely used in the study of the photosynthetic pigment apparatus in vivo. This method can be applied to the key plant photoreceptor phytochrome (phy). The fluorescence of phytochrome in plants was recorded for the first time in the group of the author, and a spectrofluorometric technique for its in vivo study was developed. The photophysical and photochemical properties of the pigment were described, and the photoreceptor was shown to be present in plants as two phenomenological types-active (at cryogenic temperatures) and water-soluble (Pr') and inactive and amphiphilic (Pr″). The scheme of the photoreaction explaining their photochemical distinctions was proposed. Phytochrome A was shown to comprise both types (phyA' and phyA″), whereas phytochrome B was only the second type. For phyA', distinct conformers have been detected. phyA' and phyA″ differ by the N-terminus of the molecule, possibly by serine phosphorylation. They mediate, respectively, the very low fluence and high irradiance photoresponses. Light, internal factors (kinase/phosphatase balance, pH), and hormones (jasmonate) were shown to affect the content and functions of the two phyA pools. All this points to the effectiveness of the developed method for invivo investigations of the phytochrome system. The data obtained can be applied in practical terms in agrobiology and light culture, as well as in the use of phytochrome as a new nanotool and a fluorescent probe.
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Affiliation(s)
- V A Sineshchekov
- Biology Department, M. V. Lomonosov Moscow State University, Moscow, 119234, Russia.
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2
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Flores-Ibarra A, Maia RNA, Olasz B, Church JR, Gotthard G, Schapiro I, Heberle J, Nogly P. Light-Oxygen-Voltage (LOV)-sensing Domains: Activation Mechanism and Optogenetic Stimulation. J Mol Biol 2024; 436:168356. [PMID: 37944792 DOI: 10.1016/j.jmb.2023.168356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 10/11/2023] [Accepted: 11/02/2023] [Indexed: 11/12/2023]
Abstract
The light-oxygen-voltage (LOV) domains of phototropins emerged as essential constituents of light-sensitive proteins, helping initiate blue light-triggered responses. Moreover, these domains have been identified across all kingdoms of life. LOV domains utilize flavin nucleotides as co-factors and undergo structural rearrangements upon exposure to blue light, which activates an effector domain that executes the final output of the photoreaction. LOV domains are versatile photoreceptors that play critical roles in cellular signaling and environmental adaptation; additionally, they can noninvasively sense and control intracellular processes with high spatiotemporal precision, making them ideal candidates for use in optogenetics, where a light signal is linked to a cellular process through a photoreceptor. The ongoing development of LOV-based optogenetic tools, driven by advances in structural biology, spectroscopy, computational methods, and synthetic biology, has the potential to revolutionize the study of biological systems and enable the development of novel therapeutic strategies.
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Affiliation(s)
- Andrea Flores-Ibarra
- Dioscuri Center for Structural Dynamics of Receptors, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Krakow, Poland
| | - Raiza N A Maia
- Department of Chemistry, The University of Texas at Austin, 78712-1224 Austin, TX, USA
| | - Bence Olasz
- Dioscuri Center for Structural Dynamics of Receptors, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Krakow, Poland
| | - Jonathan R Church
- Institute of Chemistry, The Hebrew University of Jerusalem, 91905 Jerusalem, Israel
| | | | - Igor Schapiro
- Institute of Chemistry, The Hebrew University of Jerusalem, 91905 Jerusalem, Israel
| | - Joachim Heberle
- Department of Physics, Freie Universität Berlin, 14195 Berlin, Germany
| | - Przemyslaw Nogly
- Dioscuri Center for Structural Dynamics of Receptors, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Krakow, Poland.
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3
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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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4
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Marchetti M, Ronda L, Cozzi M, Bettati S, Bruno S. Genetically Encoded Biosensors for the Fluorescence Detection of O 2 and Reactive O 2 Species. SENSORS (BASEL, SWITZERLAND) 2023; 23:8517. [PMID: 37896609 PMCID: PMC10611200 DOI: 10.3390/s23208517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 10/07/2023] [Accepted: 10/14/2023] [Indexed: 10/29/2023]
Abstract
The intracellular concentrations of oxygen and reactive oxygen species (ROS) in living cells represent critical information for investigating physiological and pathological conditions. Real-time measurement often relies on genetically encoded proteins that are responsive to fluctuations in either oxygen or ROS concentrations. The direct binding or chemical reactions that occur in their presence either directly alter the fluorescence properties of the binding protein or alter the fluorescence properties of fusion partners, mostly consisting of variants of the green fluorescent protein. Oxygen sensing takes advantage of several mechanisms, including (i) the oxygen-dependent hydroxylation of a domain of the hypoxia-inducible factor-1, which, in turn, promotes its cellular degradation along with fluorescent fusion partners; (ii) the naturally oxygen-dependent maturation of the fluorophore of green fluorescent protein variants; and (iii) direct oxygen binding by proteins, including heme proteins, expressed in fusion with fluorescent partners, resulting in changes in fluorescence due to conformational alterations or fluorescence resonance energy transfer. ROS encompass a group of highly reactive chemicals that can interconvert through various chemical reactions within biological systems, posing challenges for their selective detection through genetically encoded sensors. However, their general reactivity, and particularly that of the relatively stable oxygen peroxide, can be exploited for ROS sensing through different mechanisms, including (i) the ROS-induced formation of disulfide bonds in engineered fluorescent proteins or fusion partners of fluorescent proteins, ultimately leading to fluorescence changes; and (ii) conformational changes of naturally occurring ROS-sensing domains, affecting the fluorescence properties of fusion partners. In this review, we will offer an overview of these genetically encoded biosensors.
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Affiliation(s)
- Marialaura Marchetti
- Department of Medicine and Surgery, University of Parma, 43125 Parma, Italy; (M.M.); (L.R.); (M.C.)
| | - Luca Ronda
- Department of Medicine and Surgery, University of Parma, 43125 Parma, Italy; (M.M.); (L.R.); (M.C.)
- Institute of Biophysics, Italian National Research Council (CNR), 56124 Pisa, Italy
| | - Monica Cozzi
- Department of Medicine and Surgery, University of Parma, 43125 Parma, Italy; (M.M.); (L.R.); (M.C.)
| | - Stefano Bettati
- Department of Medicine and Surgery, University of Parma, 43125 Parma, Italy; (M.M.); (L.R.); (M.C.)
- Institute of Biophysics, Italian National Research Council (CNR), 56124 Pisa, Italy
| | - Stefano Bruno
- Department of Food and Drug, University of Parma, 43124 Parma, Italy;
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5
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Reynolds JA, Vishweshwaraiah YL, Chirasani VR, Pritchard JR, Dokholyan NV. An engineered N-acyltransferase-LOV2 domain fusion protein enables light-inducible allosteric control of enzymatic activity. J Biol Chem 2023; 299:103069. [PMID: 36841477 PMCID: PMC10060751 DOI: 10.1016/j.jbc.2023.103069] [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: 12/16/2022] [Revised: 02/21/2023] [Accepted: 02/22/2023] [Indexed: 02/27/2023] Open
Abstract
Transferases are ubiquitous across all known life. While much work has been done to understand and describe these essential enzymes, there have been minimal efforts to exert tight and reversible control over their activity for various biotechnological applications. Here, we apply a rational, computation-guided methodology to design and test a transferase-class enzyme allosterically regulated by light-oxygen-voltage 2 sensing domain. We utilize computational techniques to determine the intrinsic allosteric networks within N-acyltransferase (Orf11/∗Dbv8) and identify potential allosteric sites on the protein's surface. We insert light-oxygen-voltage 2 sensing domain at the predicted allosteric site, exerting reversible control over enzymatic activity. We demonstrate blue-light regulation of N-acyltransferase (Orf11/∗Dbv8) function. Our study for the first time demonstrates optogenetic regulation of a transferase-class enzyme as a proof-of-concept for controllable transferase design. This successful design opens the door for many future applications in metabolic engineering and cellular programming.
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Affiliation(s)
- J A Reynolds
- Department of Biomedical Engineering, Penn State University, University Park, Pennsylvania, USA
| | - Y L Vishweshwaraiah
- Department of Pharmacology, Penn State College of Medicine, Hershey, Pennsylvania, USA
| | - V R Chirasani
- Department of Pharmacology, Penn State College of Medicine, Hershey, Pennsylvania, USA
| | - J R Pritchard
- Department of Biomedical Engineering, Penn State University, University Park, Pennsylvania, USA
| | - N V Dokholyan
- Department of Biomedical Engineering, Penn State University, University Park, Pennsylvania, USA; Department of Pharmacology, Penn State College of Medicine, Hershey, Pennsylvania, USA; Department of Biochemistry & Molecular Biology, Penn State College of Medicine, Hershey, Pennsylvania, USA; Department of Chemistry, Penn State University, University Park, Pennsylvania, USA.
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6
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Rojas V, Larrondo LF. Coupling Cell Communication and Optogenetics: Implementation of a Light-Inducible Intercellular System in Yeast. ACS Synth Biol 2023; 12:71-82. [PMID: 36534043 PMCID: PMC9872819 DOI: 10.1021/acssynbio.2c00338] [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: 06/28/2022] [Indexed: 12/23/2022]
Abstract
Cell communication is a widespread mechanism in biology, allowing the transmission of information about environmental conditions. In order to understand how cell communication modulates relevant biological processes such as survival, division, differentiation, and apoptosis, different synthetic systems based on chemical induction have been successfully developed. In this work, we coupled cell communication and optogenetics in the budding yeast Saccharomyces cerevisiae. Our approach is based on two strains connected by the light-dependent production of α-factor pheromone in one cell type, which induces gene expression in the other type. After the individual characterization of the different variants of both strains, the optogenetic intercellular system was evaluated by combining the cells under contrasting illumination conditions. Using luciferase as a reporter gene, specific co-cultures at a 1:1 ratio displayed activation of the response upon constant blue light, which was not observed for the same cell mixtures grown in darkness. Then, the system was assessed at several dark/blue-light transitions, where the response level varies depending on the moment in which illumination was delivered. Furthermore, we observed that the amplitude of response can be tuned by modifying the initial ratio between both strains. Finally, the two-population system showed higher fold inductions in comparison with autonomous strains. Altogether, these results demonstrated that external light information is propagated through a diffusible signaling molecule to modulate gene expression in a synthetic system involving microbial cells, which will pave the road for studies allowing optogenetic control of population-level dynamics.
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Affiliation(s)
- Vicente Rojas
- Departamento
de Genética Molecular y Microbiología, Facultad de Ciencias
Biológicas, Pontificia Universidad
Católica de Chile, Santiago 8331150, Chile
- Millennium
Institute for Integrative Biology (iBio), Santiago 8331150, Chile
| | - Luis F. Larrondo
- Departamento
de Genética Molecular y Microbiología, Facultad de Ciencias
Biológicas, Pontificia Universidad
Católica de Chile, Santiago 8331150, Chile
- Millennium
Institute for Integrative Biology (iBio), Santiago 8331150, Chile
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7
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Castillo O, Mancillas J, Hughes W, Brancaleon L. Characterization of the interaction of metal-protoporphyrins photosensitizers with β- lactoglobulin. Biophys Chem 2023; 292:106918. [PMID: 36399946 DOI: 10.1016/j.bpc.2022.106918] [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: 07/26/2022] [Revised: 10/24/2022] [Accepted: 10/27/2022] [Indexed: 11/17/2022]
Abstract
We investigated the interaction of a series of metal-protoporphyrins (PPIXs) with bovine β- lactoglobulin (BLG) using a combination of optical spectroscopy and computational simulations. Unlike other studies, the simulations were not merely used to rationalize the experimental data but were employed to refine the experimental data itself. The study was carried out at two pH values, 5 and 9, where BLG is known to have different conformation dictated by the so-called Tanford transition which occurs near pH 7.5. The transition is postulated to regulate access to the interior binding cavity of the protein, thus the pH variation was used as a parameter to investigate whether PPIXs access the central cavity of BLG. The results of our study show that indeed binding increases significantly at alkaline pH, however, the increased affinity is not due to the accessibility of the central cavity. Instead, binding appears to be determined by the tendency of PPIXs to form large inhomogeneous aggregates at acidic pH which hinders interactions with proteins. The binding site determined through a combination of experimental and computational methods is located at the interface between two BLG monomers where the long α-helix segment of the protein face each other. This region is rich in positively charged Lys residues that interact with the propionic acid chains of the protoporphyrins. Establishing the modality of binding between protoporphyrins and BLG would have important consequences for the use of BLG:PPIX complexes in applications such as artificial photoreceptors, artificial metallo-enzymes, delivery of photosensitizers for phototherapy and even solar energy conversion.
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Affiliation(s)
- Omar Castillo
- Department of Physics and Astronomy, University of Texas at San Antonio, San Antonio, TX 78249, USA
| | - James Mancillas
- Department of Physics and Astronomy, University of Texas at San Antonio, San Antonio, TX 78249, USA
| | - William Hughes
- Department of Physics and Astronomy, University of Texas at San Antonio, San Antonio, TX 78249, USA
| | - Lorenzo Brancaleon
- Department of Physics and Astronomy, University of Texas at San Antonio, San Antonio, TX 78249, USA.
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8
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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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9
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Protein control of photochemistry and transient intermediates in phytochromes. Nat Commun 2022; 13:6838. [PMID: 36369284 PMCID: PMC9652276 DOI: 10.1038/s41467-022-34640-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 11/01/2022] [Indexed: 11/13/2022] Open
Abstract
Phytochromes are ubiquitous photoreceptors responsible for sensing light in plants, fungi and bacteria. Their photoactivation is initiated by the photoisomerization of the embedded chromophore, triggering large conformational changes in the protein. Despite numerous experimental and computational studies, the role of chromophore-protein interactions in controlling the mechanism and timescale of the process remains elusive. Here, we combine nonadiabatic surface hopping trajectories and adiabatic molecular dynamics simulations to reveal the molecular details of such control for the Deinococcus radiodurans bacteriophytochrome. Our simulations reveal that chromophore photoisomerization proceeds through a hula-twist mechanism whose kinetics is mainly determined by the hydrogen bond of the chromophore with a close-by histidine. The resulting photoproduct relaxes to an early intermediate stabilized by a tyrosine, and finally evolves into a late intermediate, featuring a more disordered binding pocket and a weakening of the aspartate-to-arginine salt-bridge interaction, whose cleavage is essential to interconvert the phytochrome to the active state.
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10
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Multamäki E, García de Fuentes A, Sieryi O, Bykov A, Gerken U, Ranzani A, Köhler J, Meglinski I, Möglich A, Takala H. Optogenetic Control of Bacterial Expression by Red Light. ACS Synth Biol 2022; 11:3354-3367. [PMID: 35998606 PMCID: PMC9594775 DOI: 10.1021/acssynbio.2c00259] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
In optogenetics, as in nature, sensory photoreceptors serve to control cellular processes by light. Bacteriophytochrome (BphP) photoreceptors sense red and far-red light via a biliverdin chromophore and, in response, cycle between the spectroscopically, structurally, and functionally distinct Pr and Pfr states. BphPs commonly belong to two-component systems that control the phosphorylation of cognate response regulators and downstream gene expression through histidine kinase modules. We recently demonstrated that the paradigm BphP from Deinococcus radiodurans exclusively acts as a phosphatase but that its photosensory module can control the histidine kinase activity of homologous receptors. Here, we apply this insight to reprogram two widely used setups for bacterial gene expression from blue-light to red-light control. The resultant pREDusk and pREDawn systems allow gene expression to be regulated down and up, respectively, uniformly under red light by 100-fold or more. Both setups are realized as portable, single plasmids that encode all necessary components including the biliverdin-producing machinery. The triggering by red light affords high spatial resolution down to the single-cell level. As pREDusk and pREDawn respond sensitively to red light, they support multiplexing with optogenetic systems sensitive to other light colors. Owing to the superior tissue penetration of red light, the pREDawn system can be triggered at therapeutically safe light intensities through material layers, replicating the optical properties of the skin and skull. Given these advantages, pREDusk and pREDawn enable red-light-regulated expression for diverse use cases in bacteria.
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Affiliation(s)
- Elina Multamäki
- Department
of Anatomy, University of Helsinki, Helsinki 00014, Finland
| | | | - Oleksii Sieryi
- Optoelectronics
and Measurement Techniques, University of
Oulu, Oulu 90014, Finland
| | - Alexander Bykov
- Optoelectronics
and Measurement Techniques, University of
Oulu, Oulu 90014, Finland
| | - Uwe Gerken
- Lehrstuhl
für Spektroskopie weicher Materie, Universität Bayreuth, Bayreuth 95447, Germany
| | | | - Jürgen Köhler
- Lehrstuhl
für Spektroskopie weicher Materie, Universität Bayreuth, Bayreuth 95447, Germany
| | - Igor Meglinski
- Optoelectronics
and Measurement Techniques, University of
Oulu, Oulu 90014, Finland,College
of Engineering and Physical Sciences, Aston
University, Birmingham B4 7ET, U.K.
| | - Andreas Möglich
- Lehrstuhl
für Biochemie, Photobiochemie, Universität
Bayreuth, Bayreuth 95447, Germany,. Phone: +49 921 55
7835
| | - Heikki Takala
- Department
of Anatomy, University of Helsinki, Helsinki 00014, Finland,Department
of Biological and Environmental Science, Nanoscience Center, University of Jyvaskyla, Jyvaskyla 40014, Finland,. Phone: +358 46 923 6211
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11
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Optogenetic tools for microbial synthetic biology. Biotechnol Adv 2022; 59:107953. [DOI: 10.1016/j.biotechadv.2022.107953] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 03/09/2022] [Accepted: 04/04/2022] [Indexed: 12/22/2022]
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12
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Kneuttinger AC. A guide to designing photocontrol in proteins: methods, strategies and applications. Biol Chem 2022; 403:573-613. [PMID: 35355495 DOI: 10.1515/hsz-2021-0417] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 03/08/2022] [Indexed: 12/20/2022]
Abstract
Light is essential for various biochemical processes in all domains of life. In its presence certain proteins inside a cell are excited, which either stimulates or inhibits subsequent cellular processes. The artificial photocontrol of specifically proteins is of growing interest for the investigation of scientific questions on the organismal, cellular and molecular level as well as for the development of medicinal drugs or biocatalytic tools. For the targeted design of photocontrol in proteins, three major methods have been developed over the last decades, which employ either chemical engineering of small-molecule photosensitive effectors (photopharmacology), incorporation of photoactive non-canonical amino acids by genetic code expansion (photoxenoprotein engineering), or fusion with photoreactive biological modules (hybrid protein optogenetics). This review compares the different methods as well as their strategies and current applications for the light-regulation of proteins and provides background information useful for the implementation of each technique.
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Affiliation(s)
- Andrea C Kneuttinger
- Institute of Biophysics and Physical Biochemistry and Regensburg Center for Biochemistry, University of Regensburg, D-93040 Regensburg, Germany
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13
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Rydzewski J, Walczewska-Szewc K, Czach S, Nowak W, Kuczera K. Enhancing the Inhomogeneous Photodynamics of Canonical Bacteriophytochrome. J Phys Chem B 2022; 126:2647-2657. [PMID: 35357137 PMCID: PMC9014414 DOI: 10.1021/acs.jpcb.2c00131] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
The ability of phytochromes
to act as photoswitches in plants and
microorganisms depends on interactions between a bilin-like chromophore
and a host protein. The interconversion occurs between the spectrally
distinct red (Pr) and far-red (Pfr) conformers. This conformational
change is triggered by the photoisomerization of the chromophore D-ring
pyrrole. In this study, as a representative example of a phytochrome-bilin
system, we consider biliverdin IXα (BV) bound to bacteriophytochrome
(BphP) from Deinococcus radiodurans. In the absence
of light, we use an enhanced sampling molecular dynamics (MD) method
to overcome the photoisomerization energy barrier. We find that the
calculated free energy (FE) barriers between essential metastable
states agree with spectroscopic results. We show that the enhanced
dynamics of the BV chromophore in BphP contributes to triggering nanometer-scale
conformational movements that propagate by two experimentally determined
signal transduction pathways. Most importantly, we describe how the
metastable states enable a thermal transition known as the dark reversion
between Pfr and Pr, through a previously unknown intermediate state
of Pfr. We present the heterogeneity of temperature-dependent Pfr
states at the atomistic level. This work paves a way toward understanding
the complete mechanism of the photoisomerization of a bilin-like chromophore
in phytochromes.
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Affiliation(s)
- Jakub Rydzewski
- Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University, Grudziadzka 5, 87-100, Torun, Poland
| | - Katarzyna Walczewska-Szewc
- Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University, Grudziadzka 5, 87-100, Torun, Poland
| | - Sylwia Czach
- Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University, Grudziadzka 5, 87-100, Torun, Poland
| | - Wieslaw Nowak
- Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University, Grudziadzka 5, 87-100, Torun, Poland
| | - Krzysztof Kuczera
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66047, United States.,Department of Chemistry, University of Kansas, Lawrence, Kansas 66045, United States
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14
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Crossman SH, Janovjak H. Light-activated receptor tyrosine kinases: Designs and applications. Curr Opin Pharmacol 2022; 63:102197. [PMID: 35245796 DOI: 10.1016/j.coph.2022.102197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Revised: 01/28/2022] [Accepted: 01/30/2022] [Indexed: 11/03/2022]
Abstract
Receptor tyrosine kinases (RTKs) are a large and essential membrane receptor family. The molecular mechanisms and physiological consequences of RTK activation depend on, for example, ligand identity, subcellular localization, and developmental or disease stage. In the past few years, genetically-encoded light-activated RTKs (Opto-RTKs) have been developed to dissect these complexities by providing reversible and spatio-temporal control over cell signaling. These methods have very recently matured to include highly-sensitive multi-color actuators. The new ability to regulate RTK activity with high precision has been recently harnessed to gain mechanistic insights in subcellular, tissue, and animal models. Because of their sophisticated engineering, Opto-RTKs may only mirror some aspects of natural activation mechanisms but nevertheless offer unique opportunities to study RTK signaling and physiology.
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Affiliation(s)
- Samuel H Crossman
- Australian Regenerative Medicine Institute (ARMI), Faculty of Medicine, Nursing and Health Sciences, Monash University, 15 Innovation Walk, Clayton, Victoria 3800, Australia; European Molecular Biology Laboratory Australia (EMBL Australia), Monash University, 15 Innovation Walk, Clayton, Victoria 3800, Australia
| | - Harald Janovjak
- Australian Regenerative Medicine Institute (ARMI), Faculty of Medicine, Nursing and Health Sciences, Monash University, 15 Innovation Walk, Clayton, Victoria 3800, Australia; European Molecular Biology Laboratory Australia (EMBL Australia), Monash University, 15 Innovation Walk, Clayton, Victoria 3800, Australia; Flinders Health and Medical Research Institute, College of Medicine and Public Health, Flinders University, Sturt Road, Bedford Park, South Australia 5042, Australia.
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15
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Kaur P, Chua EHZ, Lim WK, Liu J, Harmston N, Tolwinski NS. Wnt Signaling Rescues Amyloid Beta-Induced Gut Stem Cell Loss. Cells 2022; 11:cells11020281. [PMID: 35053396 PMCID: PMC8774390 DOI: 10.3390/cells11020281] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 01/12/2022] [Accepted: 01/13/2022] [Indexed: 02/05/2023] Open
Abstract
Patients with Alzheimer’s disease suffer from a decrease in brain mass and a prevalence of amyloid-β plaques. These plaques are thought to play a role in disease progression, but their exact role is not entirely established. We developed an optogenetic model to induce amyloid-β intracellular oligomerization to model distinct disease etiologies. Here, we examine the effect of Wnt signaling on amyloid in an optogenetic, Drosophila gut stem cell model. We observe that Wnt activation rescues the detrimental effects of amyloid expression and oligomerization. We analyze the gene expression changes downstream of Wnt that contribute to this rescue and find changes in aging related genes, protein misfolding, metabolism, and inflammation. We propose that Wnt expression reduces inflammation through repression of Toll activating factors. We confirm that chronic Toll activation reduces lifespan, but a decrease in the upstream activator Persephone extends it. We propose that the protective effect observed for lithium treatment functions, at least in part, through Wnt activation and the inhibition of inflammation.
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Affiliation(s)
- Prameet Kaur
- Division of Science, Yale-NUS College, Singapore 138527, Singapore; (P.K.); (E.H.Z.C.); (W.K.L.); (J.L.); (N.H.)
| | - Ellora Hui Zhen Chua
- Division of Science, Yale-NUS College, Singapore 138527, Singapore; (P.K.); (E.H.Z.C.); (W.K.L.); (J.L.); (N.H.)
| | - Wen Kin Lim
- Division of Science, Yale-NUS College, Singapore 138527, Singapore; (P.K.); (E.H.Z.C.); (W.K.L.); (J.L.); (N.H.)
| | - Jiarui Liu
- Division of Science, Yale-NUS College, Singapore 138527, Singapore; (P.K.); (E.H.Z.C.); (W.K.L.); (J.L.); (N.H.)
| | - Nathan Harmston
- Division of Science, Yale-NUS College, Singapore 138527, Singapore; (P.K.); (E.H.Z.C.); (W.K.L.); (J.L.); (N.H.)
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Nicholas S. Tolwinski
- Division of Science, Yale-NUS College, Singapore 138527, Singapore; (P.K.); (E.H.Z.C.); (W.K.L.); (J.L.); (N.H.)
- Correspondence: ; Tel.: +65-66013092
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16
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Time-resolved detection of association/dissociation reactions and conformation changes in photosensor proteins for application in optogenetics. Biophys Rev 2021; 13:1053-1059. [DOI: 10.1007/s12551-021-00868-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 10/22/2021] [Indexed: 11/27/2022] Open
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17
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Lindner F, Diepold A. Optogenetics in bacteria - applications and opportunities. FEMS Microbiol Rev 2021; 46:6427354. [PMID: 34791201 PMCID: PMC8892541 DOI: 10.1093/femsre/fuab055] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 11/11/2021] [Indexed: 12/12/2022] Open
Abstract
Optogenetics holds the promise of controlling biological processes with superb temporal and spatial resolution at minimal perturbation. Although many of the light-reactive proteins used in optogenetic systems are derived from prokaryotes, applications were largely limited to eukaryotes for a long time. In recent years, however, an increasing number of microbiologists use optogenetics as a powerful new tool to study and control key aspects of bacterial biology in a fast and often reversible manner. After a brief discussion of optogenetic principles, this review provides an overview of the rapidly growing number of optogenetic applications in bacteria, with a particular focus on studies venturing beyond transcriptional control. To guide future experiments, we highlight helpful tools, provide considerations for successful application of optogenetics in bacterial systems, and identify particular opportunities and challenges that arise when applying these approaches in bacteria.
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Affiliation(s)
- Florian Lindner
- Max-Planck-Institute for Terrestrial Microbiology, Department of Ecophysiology, Karl-von-Frisch-Str. 10, 35043 Marburg, Germany
| | - Andreas Diepold
- Max-Planck-Institute for Terrestrial Microbiology, Department of Ecophysiology, Karl-von-Frisch-Str. 10, 35043 Marburg, Germany.,SYNMIKRO, LOEWE Center for Synthetic Microbiology, Marburg, Germany
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18
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Blain-Hartung M, Rockwell NC, Lagarias JC. Natural diversity provides a broad spectrum of cyanobacteriochrome-based diguanylate cyclases. PLANT PHYSIOLOGY 2021; 187:632-645. [PMID: 34608946 PMCID: PMC8491021 DOI: 10.1093/plphys/kiab240] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 05/02/2021] [Indexed: 05/03/2023]
Abstract
Cyanobacteriochromes (CBCRs) are spectrally diverse photosensors from cyanobacteria distantly related to phytochromes that exploit photoisomerization of linear tetrapyrrole (bilin) chromophores to regulate associated signaling output domains. Unlike phytochromes, a single CBCR domain is sufficient for photoperception. CBCR domains that regulate the production or degradation of cyclic nucleotide second messengers are becoming increasingly well characterized. Cyclic di-guanosine monophosphate (c-di-GMP) is a widespread small-molecule regulator of bacterial motility, developmental transitions, and biofilm formation whose biosynthesis is regulated by CBCRs coupled to GGDEF (diguanylate cyclase) output domains. In this study, we compare the properties of diverse CBCR-GGDEF proteins with those of synthetic CBCR-GGDEF chimeras. Our investigation shows that natural diversity generates promising candidates for robust, broad spectrum optogenetic applications in live cells. Since light quality is constantly changing during plant development as upper leaves begin to shade lower leaves-affecting elongation growth, initiation of flowering, and responses to pathogens, these studies presage application of CBCR-GGDEF sensors to regulate orthogonal, c-di-GMP-regulated circuits in agronomically important plants for robust mitigation of such deleterious responses under natural growing conditions in the field.
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Affiliation(s)
- Matthew Blain-Hartung
- Department of Molecular and Cellular Biology, University of California, Davis, California 95616
| | - Nathan C. Rockwell
- Department of Molecular and Cellular Biology, University of California, Davis, California 95616
| | - J. Clark Lagarias
- Department of Molecular and Cellular Biology, University of California, Davis, California 95616
- Author for communication:
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19
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Wichert N, Witt M, Blume C, Scheper T. Clinical applicability of optogenetic gene regulation. Biotechnol Bioeng 2021; 118:4168-4185. [PMID: 34287844 DOI: 10.1002/bit.27895] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 05/27/2021] [Accepted: 07/13/2021] [Indexed: 11/10/2022]
Abstract
The field of optogenetics is rapidly growing in relevance and number of developed tools. Among other things, the optogenetic repertoire includes light-responsive ion channels and methods for gene regulation. This review will be confined to the optogenetic control of gene expression in mammalian cells as suitable models for clinical applications. Here optogenetic gene regulation might offer an excellent method for spatially and timely regulated gene and protein expression in cell therapeutic approaches. Well-known systems for gene regulation, such as the LOV-, CRY2/CIB-, PhyB/PIF-systems, as well as other, in mammalian cells not yet fully established systems, will be described. Advantages and disadvantages with regard to clinical applications are outlined in detail. Among the many unanswered questions concerning the application of optogenetics, we discuss items such as the use of exogenous chromophores and their effects on the biology of the cells and methods for a gentle, but effective gene transfection method for optogenetic tools for in vivo applications.
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Affiliation(s)
- Nina Wichert
- Insitute of Technical Chemistry, Leibniz University of Hannover, Hannover, Germany
| | - Martin Witt
- Insitute of Technical Chemistry, Leibniz University of Hannover, Hannover, Germany
| | - Cornelia Blume
- Insitute of Technical Chemistry, Leibniz University of Hannover, Hannover, Germany
| | - Thomas Scheper
- Insitute of Technical Chemistry, Leibniz University of Hannover, Hannover, Germany
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20
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Ariyanti D, Ikebukuro K, Sode K. Artificial complementary chromatic acclimation gene expression system in Escherichia coli. Microb Cell Fact 2021; 20:128. [PMID: 34225717 PMCID: PMC8256508 DOI: 10.1186/s12934-021-01621-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 06/26/2021] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND The development of multiple gene expression systems, especially those based on the physical signals, such as multiple color light irradiations, is challenging. Complementary chromatic acclimation (CCA), a photoreversible process that facilitates the control of cellular expression using light of different wavelengths in cyanobacteria, is one example. In this study, an artificial CCA systems, inspired by type III CCA light-regulated gene expression, was designed by employing a single photosensor system, the CcaS/CcaR green light gene expression system derived from Synechocystis sp. PCC6803, combined with G-box (the regulator recognized by activated CcaR), the cognate cpcG2 promoter, and the constitutively transcribed promoter, the PtrcΔLacO promoter. RESULTS One G-box was inserted upstream of the cpcG2 promoter and a reporter gene, the rfp gene (green light-induced gene expression), and the other G-box was inserted between the PtrcΔLacO promoter and a reporter gene, the bfp gene (red light-induced gene expression). The Escherichia coli transformants with plasmid-encoded genes were evaluated at the transcriptional and translational levels under red or green light illumination. Under green light illumination, the transcription and translation of the rfp gene were observed, whereas the expression of the bfp gene was repressed. Under red light illumination, the transcription and translation of the bfp gene were observed, whereas the expression of the rfp gene was repressed. During the red and green light exposure cycles at every 6 h, BFP expression increased under red light exposure while RFP expression was repressed, and RFP expression increased under green light exposure while BFP expression was repressed. CONCLUSION An artificial CCA system was developed to realize a multiple gene expression system, which was regulated by two colors, red and green lights, using a single photosensor system, the CcaS/CcaR system derived from Synechocystis sp. PCC6803, in E. coli. The artificial CCA system functioned repeatedly during red and green light exposure cycles. These results demonstrate the potential application of this CCA gene expression system for the production of multiple metabolites in a variety of microorganisms, such as cyanobacteria.
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Affiliation(s)
- Dwi Ariyanti
- Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo, 184-8588, Japan
- Faculty of Biotechnology, Sumbawa University of Technology, Olat Maras, Moyo Hulu, Sumbawa, West Nusa Tenggara, 84371, Indonesia
| | - Kazunori Ikebukuro
- Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo, 184-8588, Japan.
| | - Koji Sode
- Joint Department of Biomedical Engineering, The University of North Carolina at Chapel Hill and North Carolina State University, Chapel Hill, NC, 27599, USA.
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21
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Cavanaugh KE, Oakes PW, Gardel ML. Optogenetic Control of RhoA to Probe Subcellular Mechanochemical Circuitry. ACTA ACUST UNITED AC 2021; 86:e102. [PMID: 32031760 DOI: 10.1002/cpcb.102] [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] [Indexed: 01/01/2023]
Abstract
Spatiotemporal localization of protein function is essential for physiological processes from subcellular to tissue scales. Genetic and pharmacological approaches have played instrumental roles in isolating molecular components necessary for subcellular machinery. However, these approaches have limited capabilities to reveal the nature of the spatiotemporal regulation of subcellular machineries like those of cytoskeletal organelles. With the recent advancement of optogenetic probes, the field now has a powerful tool to localize cytoskeletal stimuli in both space and time. Here, we detail the use of tunable light-controlled interacting protein tags (TULIPs) to manipulate RhoA signaling in vivo. This is an optogenetic dimerization system that rapidly, reversibly, and efficiently directs a cytoplasmic RhoGEF to the plasma membrane for activation of RhoA using light. We first compare this probe to other available optogenetic systems and outline the engineering logic for the chosen recruitable RhoGEFs. We also describe how to generate the cell line, spatially control illumination, confirm optogenetic control of RhoA, and mechanically induce cell-cell junction deformation in cultured tissues. Together, these protocols detail how to probe the mechanochemical circuitry downstream of RhoA signaling. © 2020 by John Wiley & Sons, Inc. Basic Protocol 1: Generation of a stable cell line expressing TULIP constructs Basic Protocol 2: Preparation of collagen substrate for imaging Basic Protocol 3: Transient transfection for visualization of downstream effectors Basic Protocol 4: Calibration of spatial illumination Basic Protocol 5: Optogenetic activation of a region of interest.
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Affiliation(s)
- Kate E Cavanaugh
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, Illinois
| | - Patrick W Oakes
- Department of Cell & Molecular Physiology, Stritch School of Medicine, Loyola University Chicago, Maywood, Illinois
| | - Margaret L Gardel
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, Illinois
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22
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Takala H, Edlund P, Ihalainen JA, Westenhoff S. Tips and turns of bacteriophytochrome photoactivation. Photochem Photobiol Sci 2021; 19:1488-1510. [PMID: 33107538 DOI: 10.1039/d0pp00117a] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Phytochromes are ubiquitous photosensor proteins, which control the growth, reproduction and movement in plants, fungi and bacteria. Phytochromes switch between two photophysical states depending on the light conditions. In analogy to molecular machines, light absorption induces a series of structural changes that are transduced from the bilin chromophore, through the protein, and to the output domains. Recent progress towards understanding this structural mechanism of signal transduction has been manifold. We describe this progress with a focus on bacteriophytochromes. We describe the mechanism along three structural tiers, which are the chromophore-binding pocket, the photosensory module, and the output domains. We discuss possible interconnections between the tiers and conclude by presenting future directions and open questions. We hope that this review may serve as a compendium to guide future structural and spectroscopic studies designed to understand structural signaling in phytochromes.
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Affiliation(s)
- Heikki Takala
- Department of Biological and Environmental Science, Nanoscience Center, University of Jyvaskyla, Box 35, 40014 Jyvaskyla, Finland. and Department of Anatomy, Faculty of Medicine, University of Helsinki, Box 63, 00014 Helsinki, Finland
| | - Petra Edlund
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden.
| | - Janne A Ihalainen
- Department of Biological and Environmental Science, Nanoscience Center, University of Jyvaskyla, Box 35, 40014 Jyvaskyla, Finland.
| | - Sebastian Westenhoff
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden.
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23
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Forlani G, Di Ventura B. A light way for nuclear cell biologists. J Biochem 2021; 169:273-286. [PMID: 33245128 PMCID: PMC8053400 DOI: 10.1093/jb/mvaa139] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 11/12/2020] [Indexed: 12/11/2022] Open
Abstract
The nucleus is a very complex organelle present in eukaryotic cells. Having the crucial task to safeguard, organize and manage the genetic information, it must tightly control its molecular constituents, its shape and its internal architecture at any given time. Despite our vast knowledge of nuclear cell biology, much is yet to be unravelled. For instance, only recently we came to appreciate the existence of a dynamic nuclear cytoskeleton made of actin filaments that regulates processes such as gene expression, DNA repair and nuclear expansion. This suggests further exciting discoveries ahead of us. Modern cell biologists embrace a new methodology relying on precise perturbations of cellular processes that require a reversible, highly spatially confinable, rapid, inexpensive and tunEable external stimulus: light. In this review, we discuss how optogenetics, the state-of-the-art technology that uses genetically encoded light-sensitive proteins to steer biological processes, can be adopted to specifically investigate nuclear cell biology.
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Affiliation(s)
- Giada Forlani
- Spemann Graduate School of Biology and Medicine (SGBM)
- Centers for Biological Signalling Studies BIOSS and CIBSS
- Faculty of Biology, Institute of Biology II, Albert Ludwigs University of Freiburg, Freiburg, Germany
| | - Barbara Di Ventura
- Centers for Biological Signalling Studies BIOSS and CIBSS
- Faculty of Biology, Institute of Biology II, Albert Ludwigs University of Freiburg, Freiburg, Germany
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Kaur P, Kibat C, Teo E, Gruber J, Mathuru A, Tolwinski ANS. Use of Optogenetic Amyloid-β to Monitor Protein Aggregation in Drosophila melanogaster, Danio rerio and Caenorhabditis elegans. Bio Protoc 2020; 10:e3856. [PMID: 33659494 PMCID: PMC7842303 DOI: 10.21769/bioprotoc.3856] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 10/20/2020] [Accepted: 11/22/2020] [Indexed: 12/31/2022] Open
Abstract
Alzheimer's Disease (AD) has long been associated with accumulation of extracellular amyloid plaques (Aβ) originating from the Amyloid Precursor Protein. Plaques have, however, been discovered in healthy individuals and not all AD brains show plaques, suggesting that extracellular Aβ aggregates may play a smaller role than anticipated. One limitation to studying Aβ peptide in vivo during disease progression is the inability to induce aggregation in a controlled manner. We developed an optogenetic method to induce Aβ aggregation and tested its biological influence in three model organisms-D. melanogaster, C. elegans and D. rerio. We generated a fluorescently labeled, optogenetic Aβ peptide that oligomerizes rapidly in vivo in the presence of blue light in all organisms. Here, we detail the procedures for expressing this fusion protein in animal models, investigating the effects on the nervous system using time lapse light-sheet microscopy, and performing metabolic assays to measure changes due to intracellular Aβ aggregation. This method, employing optogenetics to study the pathology of AD, allows spatial and temporal control in vivo that cannot be achieved by any other method at present.
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Affiliation(s)
| | - Caroline Kibat
- Institute of Molecular and Cell Biology (IMCB), Singapore
| | - Emelyne Teo
- Science Division, Yale-NUS College, Singapore
| | - Jan Gruber
- Science Division, Yale-NUS College, Singapore
- Department of Biochemistry, National University of Singapore, Singapore
| | - Ajay Mathuru
- Science Division, Yale-NUS College, Singapore
- Department of Physiology, YLL School of Medicine, National University of Singapore, Singapore
- Institute of Molecular and Cell Biology (IMCB), Singapore
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25
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Jenkins AJ, Gottlieb SM, Chang CW, Kim PW, Hayer RJ, Hanke SJ, Martin SS, Lagarias JC, Larsen DS. Conservation and Diversity in the Primary Reverse Photodynamics of the Canonical Red/Green Cyanobacteriochrome Family. Biochemistry 2020; 59:4015-4028. [PMID: 33021375 DOI: 10.1021/acs.biochem.0c00454] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In this report, we compare the femtosecond to nanosecond primary reverse photodynamics (15EPg → 15ZPr) of eight tetrapyrrole binding photoswitching cyanobacteriochromes in the canonical red/green family from the cyanobacterium Nostoc punctiforme. Three characteristic classes were identified on the basis of the diversity of excited-state and ground-state properties, including the lifetime, photocycle initiation quantum yield, photointermediate stability, spectra, and temporal properties. We observed a correlation between the excited-state lifetime and peak wavelength of the electronic absorption spectrum with higher-energy-absorbing representatives exhibiting both faster excited-state decay times and higher photoisomerization quantum yields. The latter was attributed to both an increased number of structural restraints and differences in H-bonding networks that facilitate photoisomerization. All three classes exhibited primary Lumi-Go intermediates, with class II and III representatives evolving to a secondary Meta-G photointermediate. Class II Meta-GR intermediates were orange absorbing, whereas class III Meta-G had structurally relaxed, red-absorbing chromophores that resemble their dark-adapted 15ZPr states. Differences in the reverse and forward reaction mechanisms are discussed within the context of structural constraints.
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Affiliation(s)
- Adam J Jenkins
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - Sean Marc Gottlieb
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - Che-Wei Chang
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - Peter W Kim
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - Randeep J Hayer
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - Samuel J Hanke
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - Shelley S Martin
- Department of Molecular and Cellular Biology, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - J Clark Lagarias
- Department of Molecular and Cellular Biology, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - Delmar S Larsen
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
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Iuliano JN, Hall CR, Green D, Jones GA, Lukacs A, Illarionov B, Bacher A, Fischer M, French JB, Tonge PJ, Meech SR. Excited State Vibrations of Isotopically Labeled FMN Free and Bound to a Light-Oxygen-Voltage (LOV) Protein. J Phys Chem B 2020; 124:7152-7165. [PMID: 32786715 PMCID: PMC7533957 DOI: 10.1021/acs.jpcb.0c04943] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Flavoproteins are important blue light sensors in photobiology and play a key role in optogenetics. The characterization of their excited state structure and dynamics is thus an important objective. Here, we present a detailed study of excited state vibrational spectra of flavin mononucleotide (FMN), in solution and bound to the LOV-2 (Light-Oxygen-Voltage) domain of Avena sativa phototropin. Vibrational frequencies are determined for the optically excited singlet state and the reactive triplet state, through resonant ultrafast femtosecond stimulated Raman spectroscopy (FSRS). To assign the observed spectra, vibrational frequencies of the excited states are calculated using density functional theory, and both measurement and theory are applied to four different isotopologues of FMN. Excited state mode assignments are refined in both states, and their sensitivity to deuteration and protein environment are investigated. We show that resonant FSRS provides a useful tool for characterizing photoactive flavoproteins and is able to highlight chromophore localized modes and to record hydrogen/deuterium exchange.
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Affiliation(s)
- James N. Iuliano
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400, United States
| | | | - Dale Green
- School of Chemistry, University of East Anglia, Norwich NR4 7TJ, U.K
| | - Garth A. Jones
- School of Chemistry, University of East Anglia, Norwich NR4 7TJ, U.K
| | - Andras Lukacs
- Department of Biophysics, Medical School, University of Pecs, Szigeti ut 12, 7624 Pecs, Hungary
| | - Boris Illarionov
- Institut für Biochemie und Lebensmittelchemie, Universität Hamburg, Grindelallee 117, D-20146 Hamburg, Germany
| | - Adelbert Bacher
- Institut für Biochemie und Lebensmittelchemie, Universität Hamburg, Grindelallee 117, D-20146 Hamburg, Germany
- Department of Chemistry, Technical University of Munich, 85747 Garching, Germany
| | - Markus Fischer
- Institut für Biochemie und Lebensmittelchemie, Universität Hamburg, Grindelallee 117, D-20146 Hamburg, Germany
| | - Jarrod B. French
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400, United States
| | - Peter J. Tonge
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400, United States
| | - Stephen R. Meech
- School of Chemistry, University of East Anglia, Norwich NR4 7TJ, U.K
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27
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Lim CH, Kaur P, Teo E, Lam VYM, Zhu F, Kibat C, Gruber J, Mathuru AS, Tolwinski NS. Application of optogenetic Amyloid-β distinguishes between metabolic and physical damages in neurodegeneration. eLife 2020; 9:52589. [PMID: 32228858 PMCID: PMC7145416 DOI: 10.7554/elife.52589] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 03/18/2020] [Indexed: 12/14/2022] Open
Abstract
The brains of Alzheimer’s disease patients show a decrease in brain mass and a preponderance of extracellular Amyloid-β plaques. These plaques are formed by aggregation of polypeptides that are derived from the Amyloid Precursor Protein (APP). Amyloid-β plaques are thought to play either a direct or an indirect role in disease progression, however the exact role of aggregation and plaque formation in the aetiology of Alzheimer’s disease (AD) is subject to debate as the biological effects of soluble and aggregated Amyloid-β peptides are difficult to separate in vivo. To investigate the consequences of formation of Amyloid-β oligomers in living tissues, we developed a fluorescently tagged, optogenetic Amyloid-β peptide that oligomerizes rapidly in the presence of blue light. We applied this system to the crucial question of how intracellular Amyloid-β oligomers underlie the pathologies of A. We use Drosophila, C. elegans and D. rerio to show that, although both expression and induced oligomerization of Amyloid-β were detrimental to lifespan and healthspan, we were able to separate the metabolic and physical damage caused by light-induced Amyloid-β oligomerization from Amyloid-β expression alone. The physical damage caused by Amyloid-β oligomers also recapitulated the catastrophic tissue loss that is a hallmark of late AD. We show that the lifespan deficit induced by Amyloid-β oligomers was reduced with Li+ treatment. Our results present the first model to separate different aspects of disease progression. Alzheimer's disease is a progressive condition that damages the brain over time. The cause is not clear, but a toxic molecule called Amyloid-β peptide seems to play a part. It builds up in the brains of people with Alzheimer's disease, forming hard clumps called plaques. Yet, though the plaques are a hallmark of the disease, experimental treatments designed to break them down do not seem to help. This raises the question – do Amyloid-β plaques actually cause Alzheimer's disease? Answering this question is not easy. One way to study the effect of amyloid plaques is to inject clumps of Amyloid-β peptides into model organisms. This triggers Alzheimer's-like brain damage, but it is not clear why. It remains difficult to tell the difference between the damage caused by the injected Amyloid-β peptides and the damage caused by the solid plaques that they form. For this, researchers need a way to trigger plaque formation directly inside animal brains. This would make it possible to test the effects of plaque-targeting treatments, like the drug lithium. Optogenetics is a technique that uses light to control molecules in living animals. Hsien, Kaur et al. have now used this approach to trigger plaque formation by fusing light-sensitive proteins to Amyloid-β peptides in worms, fruit flies and zebrafish. This meant that the peptides clumped together to form plaques whenever the animals were exposed to blue light. This revealed that, while both the Amyloid-β peptides and the plaques caused damage, the plaques were much more toxic. They damaged cell metabolism and caused tissue loss that resembled late Alzheimer's disease in humans. To find out whether it was possible to test Alzheimer's treatments in these animals, Hsien, Kaur et al. treated them with the drug, lithium. This increased their lifespan, reversing some of the damage caused by the plaques. Alzheimer's disease affects more than 46.8 million people worldwide and is the sixth leading cause of death in the USA. But, despite over 50 years of research, there is no cure. This new plaque-formation technique allows researchers to study the effects of amyloid plaques in living animals, providing a new way to test Alzheimer's treatments. This could be of particular help in studies of experimental drugs that aim to reduce plaque formation.
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Affiliation(s)
- Chu Hsien Lim
- Science Division, Yale- NUS College, Singapore, Singapore
| | - Prameet Kaur
- Science Division, Yale- NUS College, Singapore, Singapore
| | - Emelyne Teo
- Science Division, Yale- NUS College, Singapore, Singapore
| | | | - Fangchen Zhu
- Science Division, Yale- NUS College, Singapore, Singapore
| | - Caroline Kibat
- Science Division, Yale- NUS College, Singapore, Singapore.,Institute of Molecular and Cell Biology (IMCB), Singapore, Singapore.,Department of Physiology, YLL School of Medicine, Singapore, Singapore
| | - Jan Gruber
- Science Division, Yale- NUS College, Singapore, Singapore.,Department of Biochemistry, National University of Singapore, Singapore, Singapore
| | - Ajay S Mathuru
- Science Division, Yale- NUS College, Singapore, Singapore.,Institute of Molecular and Cell Biology (IMCB), Singapore, Singapore.,Department of Physiology, YLL School of Medicine, Singapore, Singapore
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28
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Elucidating cyclic AMP signaling in subcellular domains with optogenetic tools and fluorescent biosensors. Biochem Soc Trans 2020; 47:1733-1747. [PMID: 31724693 DOI: 10.1042/bst20190246] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 10/17/2019] [Accepted: 10/17/2019] [Indexed: 12/16/2022]
Abstract
The second messenger 3',5'-cyclic nucleoside adenosine monophosphate (cAMP) plays a key role in signal transduction across prokaryotes and eukaryotes. Cyclic AMP signaling is compartmentalized into microdomains to fulfil specific functions. To define the function of cAMP within these microdomains, signaling needs to be analyzed with spatio-temporal precision. To this end, optogenetic approaches and genetically encoded fluorescent biosensors are particularly well suited. Synthesis and hydrolysis of cAMP can be directly manipulated by photoactivated adenylyl cyclases (PACs) and light-regulated phosphodiesterases (PDEs), respectively. In addition, many biosensors have been designed to spatially and temporarily resolve cAMP dynamics in the cell. This review provides an overview about optogenetic tools and biosensors to shed light on the subcellular organization of cAMP signaling.
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29
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Rotstan KA, Abdelsayed MM, Passalacqua LFM, Chizzolini F, Sudarshan K, Chamberlin AR, Míšek J, Luptak A. Regulation of mRNA translation by a photoriboswitch. eLife 2020; 9:e51737. [PMID: 32053109 PMCID: PMC7051177 DOI: 10.7554/elife.51737] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 02/12/2020] [Indexed: 12/15/2022] Open
Abstract
Optogenetic tools have revolutionized the study of receptor-mediated processes, but such tools are lacking for RNA-controlled systems. In particular, light-activated regulatory RNAs are needed for spatiotemporal control of gene expression. To fill this gap, we used in vitro selection to isolate a novel riboswitch that selectively binds the trans isoform of a stiff-stilbene (amino-tSS)-a rapidly and reversibly photoisomerizing small molecule. Structural probing revealed that the RNA binds amino-tSS about 100-times stronger than the cis photoisoform (amino-cSS). In vitro and in vivo functional analysis showed that the riboswitch, termed Werewolf-1 (Were-1), inhibits translation of a downstream open reading frame when bound to amino-tSS. Photoisomerization of the ligand with a sub-millisecond pulse of light induced the protein expression. In contrast, amino-cSS supported protein expression, which was inhibited upon photoisomerization to amino-tSS. Reversible photoregulation of gene expression using a genetically encoded RNA will likely facilitate high-resolution spatiotemporal analysis of complex RNA processes.
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Affiliation(s)
- Kelly A Rotstan
- Department of Pharmaceutical Sciences, University of CaliforniaIrvineUnited States
| | - Michael M Abdelsayed
- Department of Molecular Biology and Biochemistry, University of CaliforniaIrvineUnited States
| | - Luiz FM Passalacqua
- Department of Pharmaceutical Sciences, University of CaliforniaIrvineUnited States
| | - Fabio Chizzolini
- Department of Pharmaceutical Sciences, University of CaliforniaIrvineUnited States
| | | | - A Richard Chamberlin
- Department of Pharmaceutical Sciences, University of CaliforniaIrvineUnited States
- Department of Chemistry, University of CaliforniaIrvineUnited States
| | - Jiří Míšek
- Department of Pharmaceutical Sciences, University of CaliforniaIrvineUnited States
- Department of Organic Chemistry, Charles UniversityPragueCzech Republic
| | - Andrej Luptak
- Department of Pharmaceutical Sciences, University of CaliforniaIrvineUnited States
- Department of Molecular Biology and Biochemistry, University of CaliforniaIrvineUnited States
- Department of Chemistry, University of CaliforniaIrvineUnited States
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30
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Buhrke D, Gourinchas G, Müller M, Michael N, Hildebrandt P, Winkler A. Distinct chromophore-protein environments enable asymmetric activation of a bacteriophytochrome-activated diguanylate cyclase. J Biol Chem 2020; 295:539-551. [PMID: 31801828 PMCID: PMC6956517 DOI: 10.1074/jbc.ra119.011915] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 12/04/2019] [Indexed: 01/31/2023] Open
Abstract
Sensing of red and far-red light by bacteriophytochromes involves intricate interactions between their bilin chromophore and the protein environment. The light-triggered rearrangements of the cofactor configuration and eventually the protein conformation enable bacteriophytochromes to interact with various protein effector domains for biological modulation of diverse physiological functions. Excitation of the holoproteins by red or far-red light promotes the photoconversion to their far-red light-absorbing Pfr state or the red light-absorbing Pr state, respectively. Because prototypical bacteriophytochromes have a parallel dimer architecture, it is generally assumed that symmetric activation with two Pfr state protomers constitutes the signaling-active species. However, the bacteriophytochrome from Idiomarina species A28L (IsPadC) has recently been reported to enable long-range signal transduction also in asymmetric dimers containing only one Pfr protomer. By combining crystallography, hydrogen-deuterium exchange coupled to MS, and vibrational spectroscopy, we show here that Pfr of IsPadC is in equilibrium with an intermediate "Pfr-like" state that combines features of Pfr and Meta-R states observed in other bacteriophytochromes. We also show that structural rearrangements in the N-terminal segment (NTS) can stabilize this Pfr-like state and that the PHY-tongue conformation of IsPadC is partially uncoupled from the initial changes in the NTS. This uncoupling enables structural asymmetry of the overall homodimeric assembly and allows signal transduction to the covalently linked physiological diguanylate cyclase output module in which asymmetry might play a role in the enzyme-catalyzed reaction. The functional differences to other phytochrome systems identified here highlight opportunities for using additional red-light sensors in artificial sensor-effector systems.
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Affiliation(s)
- David Buhrke
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Straβe des 17. Juni 135, D-10623 Berlin, Germany.
| | - Geoffrey Gourinchas
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/II, 8010 Graz, Austria
| | - Melanie Müller
- Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Norbert Michael
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Straβe des 17. Juni 135, D-10623 Berlin, Germany
| | - Peter Hildebrandt
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Straβe des 17. Juni 135, D-10623 Berlin, Germany
| | - Andreas Winkler
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/II, 8010 Graz, Austria; BioTechMed-Graz, 8010 Graz, Austria.
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31
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Banerjee S, Mitra D. Structural Basis of Design and Engineering for Advanced Plant Optogenetics. TRENDS IN PLANT SCIENCE 2020; 25:35-65. [PMID: 31699521 DOI: 10.1016/j.tplants.2019.10.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 09/12/2019] [Accepted: 10/03/2019] [Indexed: 06/10/2023]
Abstract
In optogenetics, light-sensitive proteins are specifically expressed in target cells and light is used to precisely control the activity of these proteins at high spatiotemporal resolution. Optogenetics initially used naturally occurring photoreceptors to control neural circuits, but has expanded to include carefully designed and engineered photoreceptors. Several optogenetic constructs are based on plant photoreceptors, but their application to plant systems has been limited. Here, we present perspectives on the development of plant optogenetics, considering different levels of design complexity. We discuss how general principles of light-driven signal transduction can be coupled with approaches for engineering protein folding to develop novel optogenetic tools. Finally, we explore how the use of computation, networks, circular permutation, and directed evolution could enrich optogenetics.
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Affiliation(s)
- Sudakshina Banerjee
- Department of Life Sciences, Presidency University, 86/1 College Street, Kolkata 700073, India
| | - Devrani Mitra
- Department of Life Sciences, Presidency University, 86/1 College Street, Kolkata 700073, India.
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32
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Polverini E, Schackert FK, Losi A. Interplay among the “flipping” glutamine, a conserved phenylalanine, water and hydrogen bonds within a blue-light sensing LOV domain. Photochem Photobiol Sci 2020; 19:892-904. [DOI: 10.1039/d0pp00082e] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
A combined photoacoustics and molecular dynamics approach highlights the crucial role of a conserved phenyalanine in photosensing LOV domains.
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Affiliation(s)
- Eugenia Polverini
- Department of Mathematical
- Physical and Computer Sciences
- University of Parma
- 43124 Parma
- Italy
| | - Florian Karl Schackert
- Department of Mathematical
- Physical and Computer Sciences
- University of Parma
- 43124 Parma
- Italy
| | - Aba Losi
- Department of Mathematical
- Physical and Computer Sciences
- University of Parma
- 43124 Parma
- Italy
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33
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Modular Diversity of the BLUF Proteins and Their Potential for the Development of Diverse Optogenetic Tools. APPLIED SCIENCES-BASEL 2019. [DOI: 10.3390/app9183924] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Organisms can respond to varying light conditions using a wide range of sensory photoreceptors. These photoreceptors can be standalone proteins or represent a module in multidomain proteins, where one or more modules sense light as an input signal which is converted into an output response via structural rearrangements in these receptors. The output signals are utilized downstream by effector proteins or multiprotein clusters to modulate their activity, which could further affect specific interactions, gene regulation or enzymatic catalysis. The blue-light using flavin (BLUF) photosensory module is an autonomous unit that is naturally distributed among functionally distinct proteins. In this study, we identified 34 BLUF photoreceptors of prokaryotic and eukaryotic origin from available bioinformatics sequence databases. Interestingly, our analysis shows diverse BLUF-effector arrangements with a functional association that was previously unknown or thought to be rare among the BLUF class of sensory proteins, such as endonucleases, tet repressor family (tetR), regulators of G-protein signaling, GAL4 transcription family and several other previously unidentified effectors, such as RhoGEF, Phosphatidyl-Ethanolamine Binding protein (PBP), ankyrin and leucine-rich repeats. Interaction studies and the indexing of BLUF domains further show the diversity of BLUF-effector combinations. These diverse modular architectures highlight how the organism’s behaviour, cellular processes, and distinct cellular outputs are regulated by integrating BLUF sensing modules in combination with a plethora of diverse signatures. Our analysis highlights the modular diversity of BLUF containing proteins and opens the possibility of creating a rational design of novel functional chimeras using a BLUF architecture with relevant cellular effectors. Thus, the BLUF domain could be a potential candidate for the development of powerful novel optogenetic tools for its application in modulating diverse cell signaling.
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Formation Mechanism of Ion Channel in Channelrhodopsin-2: Molecular Dynamics Simulation and Steering Molecular Dynamics Simulations. Int J Mol Sci 2019; 20:ijms20153780. [PMID: 31382458 PMCID: PMC6695816 DOI: 10.3390/ijms20153780] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 07/30/2019] [Indexed: 01/19/2023] Open
Abstract
Channelrhodopsin-2 (ChR2) is a light-activated and non-selective cationic channel protein that can be easily expressed in specific neurons to control neuronal activity by light. Although ChR2 has been extensively used as an optogenetic tool in neuroscience research, the molecular mechanism of cation channel formation following retinal photoisomerization in ChR2 is not well understood. In this paper, studies of the closed and opened state ChR2 structures are presented. The formation of the cationic channel is elucidated in atomic detail using molecular dynamics simulations on the all-trans-retinal (ChR2-trans) configuration of ChR2 and its isomerization products, 13-cis-retinal (ChR2-cis) configuration, respectively. Photoisomerization of the retinal-chromophore causes the destruction of interactions among the crucial residues (e.g., E90, E82, N258, and R268) around the channel and the extended H-bond network mediated by numerous water molecules, which opens the pore. Steering molecular dynamics (SMD) simulations show that the electrostatic interactions at the binding sites in intracellular gate (ICG) and central gate (CG) can influence the transmembrane transport of Na+ in ChR2-cis obviously. Potential of mean force (PMF) constructed by SMD and umbrella sampling also found the existing energy wells at these two binding sites during the transportation of Na+. These wells partly hinder the penetration of Na+ into cytoplasm through the ion channel. This investigation provides a theoretical insight on the formation mechanism of ion channels and the mechanism of ion permeation.
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Schmermund L, Jurkaš V, Özgen FF, Barone GD, Büchsenschütz HC, Winkler CK, Schmidt S, Kourist R, Kroutil W. Photo-Biocatalysis: Biotransformations in the Presence of Light. ACS Catal 2019. [DOI: 10.1021/acscatal.9b00656] [Citation(s) in RCA: 147] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Luca Schmermund
- Institute of Chemistry, University of Graz, NAWI Graz, BioTechMed Graz, BioHealth, Heinrichstrasse 28, 8010 Graz, Austria
| | - Valentina Jurkaš
- Institute of Chemistry, University of Graz, NAWI Graz, BioTechMed Graz, BioHealth, Heinrichstrasse 28, 8010 Graz, Austria
| | - F. Feyza Özgen
- Institute of Molecular Biotechnology, Graz University of Technology, NAWI Graz, Petersgasse 14, 8010 Graz, Austria
| | - Giovanni D. Barone
- Institute of Molecular Biotechnology, Graz University of Technology, NAWI Graz, Petersgasse 14, 8010 Graz, Austria
| | - Hanna C. Büchsenschütz
- Institute of Molecular Biotechnology, Graz University of Technology, NAWI Graz, Petersgasse 14, 8010 Graz, Austria
| | - Christoph K. Winkler
- Institute of Chemistry, University of Graz, NAWI Graz, BioTechMed Graz, BioHealth, Heinrichstrasse 28, 8010 Graz, Austria
| | - Sandy Schmidt
- Institute of Molecular Biotechnology, Graz University of Technology, NAWI Graz, Petersgasse 14, 8010 Graz, Austria
| | - Robert Kourist
- Institute of Molecular Biotechnology, Graz University of Technology, NAWI Graz, Petersgasse 14, 8010 Graz, Austria
| | - Wolfgang Kroutil
- Institute of Chemistry, University of Graz, NAWI Graz, BioTechMed Graz, BioHealth, Heinrichstrasse 28, 8010 Graz, Austria
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36
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Schmidt M. Time-Resolved Macromolecular Crystallography at Pulsed X-ray Sources. Int J Mol Sci 2019; 20:ijms20061401. [PMID: 30897736 PMCID: PMC6470897 DOI: 10.3390/ijms20061401] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 03/14/2019] [Accepted: 03/18/2019] [Indexed: 11/30/2022] Open
Abstract
The focus of structural biology is shifting from the determination of static structures to the investigation of dynamical aspects of macromolecular function. With time-resolved macromolecular crystallography (TRX), intermediates that form and decay during the macromolecular reaction can be investigated, as well as their reaction dynamics. Time-resolved crystallographic methods were initially developed at synchrotrons. However, about a decade ago, extremely brilliant, femtosecond-pulsed X-ray sources, the free electron lasers for hard X-rays, became available to a wider community. TRX is now possible with femtosecond temporal resolution. This review provides an overview of methodological aspects of TRX, and at the same time, aims to outline the frontiers of this method at modern pulsed X-ray sources.
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Affiliation(s)
- Marius Schmidt
- Physics Department, University of Wisconsin-Milwaukee, Milwaukee, WI 53211, USA.
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37
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Abstract
Many proteins can be split into fragments that spontaneously reassemble, without covalent linkage, into a functional protein. For split green fluorescent proteins (GFPs), fragment reassembly leads to a fluorescent readout, which has been widely used to investigate protein-protein interactions. We review the scope and limitations of this approach as well as other diverse applications of split GFPs as versatile sensors, molecular glues, optogenetic tools, and platforms for photophysical studies.
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Affiliation(s)
- Matthew G Romei
- Department of Chemistry, Stanford University, Stanford, California 94305, USA; ,
| | - Steven G Boxer
- Department of Chemistry, Stanford University, Stanford, California 94305, USA; ,
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38
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Optogenetic Navigation of Routes Leading to Protein Amyloidogenesis in Bacteria. J Mol Biol 2019; 431:1186-1202. [PMID: 30721672 DOI: 10.1016/j.jmb.2019.01.037] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 01/24/2019] [Accepted: 01/28/2019] [Indexed: 01/10/2023]
Abstract
Modulation of liquid-liquid and liquid-hydrogel phase transitions is central to avoid the cytotoxic aggregation of proteins in eukaryotic cells, but knowledge on its relevance in bacteria is limited. Here the power of optogenetics to engineer proteins as light-responsive switches has been used to control the balance between solubility and aggregation for LOV2-WH1, a chimera between the plant blue light-responsive domain LOV2 and the bacterial prion-like protein RepA-WH1. These proteins were first linked by fusing, as a continuous α-helix, the C-terminal photo-transducer Jα helix in LOV2 with the N-terminal domain-closure α1 helix in RepA-WH1, and then improved for light-responsiveness by including mutations in the Jα moiety. In the darkness and in a crowded solution in vitro, LOV2-WH1 nucleates the irreversible assembly of amyloid fibers into a hydrogel. However, under blue light illumination, LOV2-WH1 assembles as soluble oligomers. When expressed in Escherichia coli, LOV2-WH1 forms in the darkness large intracellular amyloid inclusions compatible with bacterial proliferation. Strikingly, under blue light, LOV2-WH1 aggregates decrease in size, while they become detrimental for bacterial growth. LOV2-WH1 optogenetics governs the assembly of mutually exclusive inert amyloid fibers or cytotoxic oligomers, thus enabling the navigation of the conformational landscape of protein amyloidogenesis to generate potential photo-activated anti-bacterial devices (optobiotics).
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39
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Zayner JP, Mathes T, Sosnick TR, Kennis JTM. Helical Contributions Mediate Light-Activated Conformational Change in the LOV2 Domain of Avena sativa Phototropin 1. ACS OMEGA 2019; 4:1238-1243. [PMID: 31459397 PMCID: PMC6648828 DOI: 10.1021/acsomega.8b02872] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 01/02/2019] [Indexed: 06/10/2023]
Abstract
Algae, plants, bacteria, and fungi contain flavin-binding light-oxygen-voltage (LOV) domains that function as blue light sensors to control cellular responses to light. In the second LOV domain of phototropins, called LOV2 domains, blue light illumination leads to covalent bond formation between protein and flavin that induces the dissociation and unfolding of a C-terminally attached α helix (Jα) and the N-terminal helix (A'α). To date, the majority of studies on these domains have focused on versions that contain truncations in the termini, which creates difficulties when extrapolating to the much larger proteins that contain these domains. Here, we study the influence of deletions and extensions of the A'α helix of the LOV2 domain of Avena sativa phototropin 1 (AsLOV2) on the light-triggered structural response of the protein by Fourier-transform infrared difference spectroscopy. Deletion of the A'α helix abolishes the light-induced unfolding of Jα, whereas extensions of the A'α helix lead to an attenuated structural change of Jα. These results are different from shorter constructs, indicating that the conformational changes in full-length phototropin LOV domains might not be as large as previously assumed, and that the well-characterized full unfolding of the Jα helix in AsLOV2 with short A'α helices may be considered a truncation artifact. It also suggests that the N- and C-terminal helices of phot-LOV2 domains are necessary for allosteric regulation of the phototropin kinase domain and may provide a basis for signal integration of LOV1 and LOV2 domains in phototropins.
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Affiliation(s)
- Josiah P. Zayner
- Department of Biochemistry
and Molecular Biology, The University of
Chicago, Chicago 60637, United States
| | - Tilo Mathes
- Biophysics
Section, Department of Physics and Astronomy, Faculty of Sciences, Vrije Universiteit, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
| | - Tobin R. Sosnick
- Department of Biochemistry
and Molecular Biology, The University of
Chicago, Chicago 60637, United States
- Institute
for Biophysical Dynamics, The University
of Chicago, Chicago, Illinois 60637 United States
| | - John T. M. Kennis
- Biophysics
Section, Department of Physics and Astronomy, Faculty of Sciences, Vrije Universiteit, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
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Applications of molecular modeling to flavoproteins: Insights and challenges. Methods Enzymol 2019; 620:277-314. [DOI: 10.1016/bs.mie.2019.03.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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41
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Liu L, Shadish JA, Arakawa CK, Shi K, Davis J, DeForest CA. Cyclic Stiffness Modulation of Cell-Laden Protein-Polymer Hydrogels in Response to User-Specified Stimuli including Light. ADVANCED BIOSYSTEMS 2018; 2:1800240. [PMID: 34316509 PMCID: PMC8312699 DOI: 10.1002/adbi.201800240] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Indexed: 11/10/2022]
Abstract
Although mechanical signals presented by the extracellular matrix are known to regulate many essential cell functions, the specific effects of these interactions, particularly in response to dynamic and heterogeneous cues, remain largely unknown. Here, we introduce a modular semisynthetic approach to create protein-polymer hydrogel biomaterials that undergo reversible stiffening in response to user-specified inputs. Employing a novel dual-chemoenzymatic modification strategy, we create fusion protein-based gel crosslinkers that exhibit stimuli-dependent intramolecular association. Linkers based on calmodulin yield calcium-sensitive materials, while those containing the photosensitive LOV2 (light, oxygen, and voltage sensing domain 2) protein give phototunable constructs whose moduli can be cycled on demand with spatiotemporal control about living cells. We exploit these unique materials to demonstrate the significant role that cyclic mechanical loading plays on fibroblast-to-myofibroblast transdifferentiation in three-dimensional (3D) space. Our moduli-switchable materials should prove useful for studies in mechanobiology, providing new avenues to probe and direct matrix-driven changes in 4D cell physiology.
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Affiliation(s)
- Luman Liu
- Department of Chemical Engineering, University of Washington, 3781 Okanogan Lane NE, Seattle, WA, 98195, USA
| | - Jared A Shadish
- Department of Chemical Engineering, University of Washington, 3781 Okanogan Lane NE, Seattle, WA, 98195, USA
| | - Christopher K Arakawa
- Department of Bioengineering, University of Washington, 3720 15th Ave NE, Seattle, WA, 98105, USA
| | - Kevin Shi
- Department of Bioengineering, University of Washington, 3720 15th Ave NE, Seattle, WA, 98105, USA
| | - Jennifer Davis
- Department of Bioengineering, University of Washington, 3720 15th Ave NE, Seattle, WA, 98105, USA; Department of Pathology, University of Washington, 1959 NE Pacific St., Seattle, WA, 98195, USA; Institute of Stem Cell & Regenerative Medicine, University of Washington, 850 Republican St., Seattle, WA, 98109, USA
| | - Cole A DeForest
- Department of Chemical Engineering, University of Washington, 3781 Okanogan Lane NE, Seattle, WA, 98195, USA; Department of Bioengineering, University of Washington, 3720 15th Ave NE, Seattle, WA, 98105, USA; Institute of Stem Cell & Regenerative Medicine, University of Washington, 850 Republican St., Seattle, WA, 98109, USA; Molecular Engineering & Sciences Institute, University of Washington, 3946 W Stevens Way NE, Seattle, WA, 98195, USA
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Snell NE, Rao VP, Seckinger KM, Liang J, Leser J, Mancini AE, Rizzo MA. Homotransfer of FRET Reporters for Live Cell Imaging. BIOSENSORS-BASEL 2018; 8:bios8040089. [PMID: 30314323 PMCID: PMC6316388 DOI: 10.3390/bios8040089] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 09/27/2018] [Accepted: 10/10/2018] [Indexed: 01/01/2023]
Abstract
Förster resonance energy transfer (FRET) between fluorophores of the same species was recognized in the early to mid-1900s, well before modern heterotransfer applications. Recently, homotransfer FRET principles have re-emerged in biosensors that incorporate genetically encoded fluorescent proteins. Homotransfer offers distinct advantages over the standard heterotransfer FRET method, some of which are related to the use of fluorescence polarization microscopy to quantify FRET between two fluorophores of identical color. These include enhanced signal-to-noise, greater compatibility with other optical sensors and modulators, and new design strategies based upon the clustering or dimerization of singly-labeled sensors. Here, we discuss the theoretical basis for measuring homotransfer using polarization microscopy, procedures for data collection and processing, and we review the existing genetically-encoded homotransfer biosensors.
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Affiliation(s)
- Nicole E Snell
- Department of Physiology, University of Maryland School of Medicine, 660 W Redwood St/HH525B, Baltimore, MD 21201, USA.
| | - Vishnu P Rao
- Department of Physiology, University of Maryland School of Medicine, 660 W Redwood St/HH525B, Baltimore, MD 21201, USA.
| | - Kendra M Seckinger
- Department of Physiology, University of Maryland School of Medicine, 660 W Redwood St/HH525B, Baltimore, MD 21201, USA.
| | - Junyi Liang
- Department of Physiology, University of Maryland School of Medicine, 660 W Redwood St/HH525B, Baltimore, MD 21201, USA.
| | - Jenna Leser
- Department of Physiology, University of Maryland School of Medicine, 660 W Redwood St/HH525B, Baltimore, MD 21201, USA.
| | - Allison E Mancini
- Department of Physiology, University of Maryland School of Medicine, 660 W Redwood St/HH525B, Baltimore, MD 21201, USA.
| | - M A Rizzo
- Department of Physiology, University of Maryland School of Medicine, 660 W Redwood St/HH525B, Baltimore, MD 21201, USA.
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Pérez-García F, Wendisch VF. Transport and metabolic engineering of the cell factory Corynebacterium glutamicum. FEMS Microbiol Lett 2018; 365:5047308. [DOI: 10.1093/femsle/fny166] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 06/28/2018] [Indexed: 12/16/2022] Open
Affiliation(s)
- Fernando Pérez-García
- Genetics of Prokaryotes, Faculty of Biology and Center for Biotechnology (CeBiTec), Bielefeld University, Universitaetsstr. 25, 33615, Bielefeld, Germany
| | - Volker F Wendisch
- Genetics of Prokaryotes, Faculty of Biology and Center for Biotechnology (CeBiTec), Bielefeld University, Universitaetsstr. 25, 33615, Bielefeld, Germany
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Kirpich JS, Mix LT, Martin SS, Rockwell NC, Lagarias JC, Larsen DS. Protonation Heterogeneity Modulates the Ultrafast Photocycle Initiation Dynamics of Phytochrome Cph1. J Phys Chem Lett 2018; 9:3454-3462. [PMID: 29874080 PMCID: PMC6247788 DOI: 10.1021/acs.jpclett.8b01133] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Phytochrome proteins utilize ultrafast photoisomerization of a linear tetrapyrrole chromophore to detect the ratio of red to far-red light. Femtosecond photodynamics in the PAS-GAF-PHY photosensory core of the Cph1 phytochrome from Synechocystis sp. PCC6803 (Cph1Δ) were resolved with a dual-excitation-wavelength-interleaved pump-probe (DEWI) approach with two excitation wavelengths (600 and 660 nm) at three pH values (6.5, 8.0, and 9.0). Observed spectral and kinetic heterogeneity in the excited-state dynamics were described with a self-consistent model comprised of three spectrally distinct populations with different protonation states (Pr-I, Pr-II, and Pr-III), each composed of multiple kinetically distinct subpopulations. Apparent partitioning among these populations is dictated by pH, temperature, and excitation wavelength. Our studies provide insight into photocycle initiation dynamics at physiological temperatures, implicate the low-pH/low-temperature Pr-I state as the photoactive state in vitro, and implicate an internal hydrogen-bonding network in regulating the photochemical quantum yield.
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Affiliation(s)
- Julia S. Kirpich
- Department of Chemistry, University of California, Davis, One Shields Ave, Davis, 95616
| | - L. Tyler Mix
- Department of Chemistry, University of California, Davis, One Shields Ave, Davis, 95616
| | - Shelley S. Martin
- Department of Molecular and Cell Biology, University of California, Davis, One Shields Ave, Davis, CA, 95616
| | - Nathan C. Rockwell
- Department of Molecular and Cell Biology, University of California, Davis, One Shields Ave, Davis, CA, 95616
| | - J. Clark Lagarias
- Department of Molecular and Cell Biology, University of California, Davis, One Shields Ave, Davis, CA, 95616
| | - Delmar S. Larsen
- Department of Chemistry, University of California, Davis, One Shields Ave, Davis, 95616
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Kirpich JS, Chang CW, Madsen D, Gottlieb SM, Martin SS, Rockwell NC, Lagarias JC, Larsen DS. Noncanonical Photodynamics of the Orange/Green Cyanobacteriochrome Power Sensor NpF2164g7 from the PtxD Phototaxis Regulator of Nostoc punctiforme. Biochemistry 2018; 57:2636-2648. [PMID: 29633829 DOI: 10.1021/acs.biochem.7b01252] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Forward and reverse primary (<10 ns) and secondary (>10 ns) photodynamics of cyanobacteriochrome (CBCR) NpF2164g7 were characterized by global analysis of ultrafast broadband transient absorption measurements. NpF2164g7 is the most C-terminal bilin-binding GAF domain in the Nostoc punctiforme phototaxis sensor PtxD (locus Npun_F2164). Although a member of the canonical red/green CBCR subfamily phylogenetically, NpF2164g7 exhibits an orange-absorbing 15ZPo dark-adapted state instead of the typical red-absorbing 15ZPr dark-adapted state characteristic of this subfamily. The green-absorbing 15EPg photoproduct of NpF2164g7 is unstable, allowing this CBCR domain to function as a power sensor. Photoexcitation of the 15ZPo state triggers inhomogeneous excited-state dynamics with three spectrally and temporally distinguishable pathways to generate the light-adapted 15EPg state in high yield (estimated at 25-30%). Although observed in other CBCR domains, the inhomogeneity in NpF2164g7 extends far into secondary relaxation dynamics (10 ns -1 ms) through to formation of 15EPg. In the reverse direction, the primary dynamics after photoexcitation of 15EPg are qualitatively similar to those of other red/green CBCRs, but secondary dynamics involve a "pre-equilibrium" step before regenerating 15ZPo. The anomalous photodynamics of NpF2164g7 may reflect an evolutionary adaptation of CBCR sensors that function as broadband light intensity sensors.
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Leopold AV, Chernov KG, Verkhusha VV. Optogenetically controlled protein kinases for regulation of cellular signaling. Chem Soc Rev 2018; 47:2454-2484. [PMID: 29498733 DOI: 10.1039/c7cs00404d] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Protein kinases are involved in the regulation of many cellular processes including cell differentiation, survival, migration, axon guidance and neuronal plasticity. A growing set of optogenetic tools, termed opto-kinases, allows activation and inhibition of different protein kinases with light. The optogenetic regulation enables fast, reversible and non-invasive manipulation of protein kinase activities, complementing traditional methods, such as treatment with growth factors, protein kinase inhibitors or chemical dimerizers. In this review, we summarize the properties of the existing optogenetic tools for controlling tyrosine kinases and serine-threonine kinases. We discuss how the opto-kinases can be applied for studies of spatial and temporal aspects of protein kinase signaling in cells and organisms. We compare approaches for chemical and optogenetic regulation of protein kinase activity and present guidelines for selection of opto-kinases and equipment to control them with light. We also describe strategies to engineer novel opto-kinases on the basis of various photoreceptors.
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Affiliation(s)
- Anna V Leopold
- Department of Biochemistry and Developmental Biology, Faculty of Medicine, University of Helsinki, Helsinki 00290, Finland
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Bury A, Hellingwerf KJ. Design, characterization and in vivo functioning of a light-dependent histidine protein kinase in the yeast Saccharomyces cerevisiae. AMB Express 2018; 8:53. [PMID: 29611000 PMCID: PMC5880792 DOI: 10.1186/s13568-018-0582-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 03/25/2018] [Indexed: 01/24/2023] Open
Abstract
Helical alignment of the α-helical linker of the LOV (light-oxygen-voltage) domain of YtvA from Bacillus subtilis with the α-helical linker of the histidine-protein kinase domain of the Sln1 kinase of the phospho-relay system for osmoregulation of Saccharomyces cerevisiae has been used to construct a light-modulatable histidine protein kinase. In vitro, illumination with blue light inhibits both the ATP-dependent phosphorylation of this hybrid kinase, as well as the phosphoryl transfer to Ypd1, the phosphoryl transfer domain of the Sln1 system. The helical alignment was carried out with conservation of the complete Jα helix of YtvA, as well as of the phosphorylatable histidine residue of the Sln1 kinase, with conservation of the hepta-helical motive of coiled-coil structures, recognizable in the helices of the two separate, constituent, proteins. Introduction of the gene encoding this hybrid histidine protein kinase into cells of S. cerevisiae in which the endogenous Sln1 kinase had been deleted, allowed us to modulate gene expression in the yeast cells with (blue) light. This was first demonstrated via the light-induced alteration of the expression level of the mannosyl-transferase OCH1, via a translational-fusion approach. As expected, illumination decreased the expression level of OCH1; the steady state decrease in saturating levels of blue light was about 40%. To visualize the in vivo functionality of this light-dependent regulation system, we fused the green fluorescent protein (GFP) to another regulatory protein, HOG1, which is also responsive to the Sln1 kinase. HOG1 is phosphorylated by the MAP-kinase-kinase Pbs2, which in turn is under control of the Sln1 kinase, via the phosphoryl transfer domain Ypd1. Fluorescence microscopy was used to show that illumination of cells that contained the combination of the hybrid kinase and the HOG1::GFP fusion protein, led to a persistent increase in the level of nuclear accumulation of HOG1, in contrast to salt stress, which-as expected-showed the well-characterized transient response. The system described in this study will be valuable in future studies on the role of cytoplasmic diffusion in signal transduction in eukaryotic cells.
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Magerl K, Stambolic I, Dick B. Switching from adduct formation to electron transfer in a light-oxygen-voltage domain containing the reactive cysteine. Phys Chem Chem Phys 2018; 19:10808-10819. [PMID: 28271102 DOI: 10.1039/c6cp08370f] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
LOV (light-, oxygen- or voltage-sensitive) domains act as photosensory units of many prokaryotic and eukaryotic proteins. Upon blue light excitation they undergo a photocycle via the excited triplet state of their flavin chromophore yielding the flavin-cysteinyl adduct. Adduct formation is highly conserved among all LOV domains and constitutes the primary step of LOV domain signaling. But recently, it has been shown that signal propagation can also be triggered by flavin photoreduction to the neutral semiquinone offering new prospects for protein engineering. This, however, requires mutation of the photo-active Cys. Here, we report on LOV1 mutants of C. reinhardtii phototropin in which adduct formation is suppressed although the photo-active Cys is present. Introduction of a Tyr into the LOV core induces a proton coupled electron transfer towards the flavin chromophore. Flavin radical species are formed via either the excited flavin singlet or triplet state depending on the geometry of donor and acceptor. This photoreductive pathway resembles the photoreaction observed in other blue light photoreceptors, e.g. blue-light sensors using flavin adenine dinucleotide (BLUF) domains or cryptochromes. The ability to tune the photoreactivity of the flavin chromophore inside the LOV core has implications for the mechanism of adduct formation in the wild type and may be of use for protein engineering.
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Affiliation(s)
- Kathrin Magerl
- Institute of Physical and Theoretical Chemistry, University of Regensburg, Universitaetsstrasse 31, 93053 Regensburg, Germany.
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49
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Hall CR, Heisler IA, Jones GA, Frost JE, Gil AA, Tonge PJ, Meech SR. Femtosecond stimulated Raman study of the photoactive flavoprotein AppABLUF. Chem Phys Lett 2017. [DOI: 10.1016/j.cplett.2017.03.030] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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50
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Lechno-Yossef S, Melnicki MR, Bao H, Montgomery BL, Kerfeld CA. Synthetic OCP heterodimers are photoactive and recapitulate the fusion of two primitive carotenoproteins in the evolution of cyanobacterial photoprotection. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 91:646-656. [PMID: 28503830 DOI: 10.1111/tpj.13593] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2017] [Revised: 04/25/2017] [Accepted: 05/03/2017] [Indexed: 06/07/2023]
Abstract
The orange carotenoid protein (OCP) governs photoprotection in the majority of cyanobacteria. It is structurally and functionally modular, comprised of a C-terminal regulatory domain (CTD), an N-terminal effector domain (NTD) and a ketocarotenoid; the chromophore spans the two domains in the ground state and translocates fully into the NTD upon illumination. Using both the canonical OCP1 from Fremyella diplosiphon and the presumably more primitive OCP2 paralog from the same organism, we show that an NTD-CTD heterodimer forms when the domains are expressed as separate polypeptides. The carotenoid is required for the heterodimeric association, assembling an orange complex which is stable in the dark. Both OCP1 and OCP2 heterodimers are photoactive, undergoing light-driven heterodimer dissociation, but differ in their ability to reassociate in darkness, setting the stage for bioengineering photoprotection in cyanobacteria as well as for developing new photoswitches for biotechnology. Additionally, we reveal that homodimeric CTD can bind carotenoid in the absence of NTD, and name this truncated variant the C-terminal domain-like carotenoid protein (CCP). This finding supports the hypothesis that the OCP evolved from an ancient fusion event between genes for two different carotenoid-binding proteins ancestral to the NTD and CTD. We suggest that the CCP and its homologs constitute a new family of carotenoproteins within the NTF2-like superfamily found across all kingdoms of life.
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Affiliation(s)
- Sigal Lechno-Yossef
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, 48824, USA
| | - Matthew R Melnicki
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, 48824, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Han Bao
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, 48824, USA
| | - Beronda L Montgomery
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, 48824, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, 48824, USA
| | - Cheryl A Kerfeld
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, 48824, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
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