1
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Meier SSM, Multamäki E, Ranzani AT, Takala H, Möglich A. Leveraging the histidine kinase-phosphatase duality to sculpt two-component signaling. Nat Commun 2024; 15:4876. [PMID: 38858359 PMCID: PMC11164954 DOI: 10.1038/s41467-024-49251-8] [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: 02/07/2024] [Accepted: 05/29/2024] [Indexed: 06/12/2024] Open
Abstract
Bacteria must constantly probe their environment for rapid adaptation, a crucial need most frequently served by two-component systems (TCS). As one component, sensor histidine kinases (SHK) control the phosphorylation of the second component, the response regulator (RR). Downstream responses hinge on RR phosphorylation and can be highly stringent, acute, and sensitive because SHKs commonly exert both kinase and phosphatase activity. With a bacteriophytochrome TCS as a paradigm, we here interrogate how this catalytic duality underlies signal responses. Derivative systems exhibit tenfold higher red-light sensitivity, owing to an altered kinase-phosphatase balance. Modifications of the linker intervening the SHK sensor and catalytic entities likewise tilt this balance and provide TCSs with inverted output that increases under red light. These TCSs expand synthetic biology and showcase how deliberate perturbations of the kinase-phosphatase duality unlock altered signal-response regimes. Arguably, these aspects equally pertain to the engineering and the natural evolution of TCSs.
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Affiliation(s)
| | - Elina Multamäki
- Department of Anatomy, University of Helsinki, Helsinki, Finland
| | - Américo T Ranzani
- Department of Biochemistry, University of Bayreuth, Bayreuth, Germany
| | - Heikki Takala
- Department of Anatomy, University of Helsinki, Helsinki, Finland.
- Department of Biological and Environmental Science, Nanoscience Center, University of Jyvaskyla, Jyvaskyla, Finland.
| | - Andreas Möglich
- Department of Biochemistry, University of Bayreuth, Bayreuth, Germany.
- Bayreuth Center for Biochemistry & Molecular Biology, Universität Bayreuth, Bayreuth, Germany.
- North-Bavarian NMR Center, Universität Bayreuth, Bayreuth, Germany.
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2
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Kannan P, Oh J, Yeon YJ, Park YI, Seo MH, Park K. Computational identification of key residues regulating fluorescence emission in a red/green cyanobacteriochrome. Proteins 2024; 92:106-116. [PMID: 37646483 DOI: 10.1002/prot.26586] [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: 05/22/2023] [Revised: 08/03/2023] [Accepted: 08/16/2023] [Indexed: 09/01/2023]
Abstract
Cyanobacteriochromes (CBCRs) are linear tetrapyrrole bilin-binding photoreceptors of cyanobacteria that exhibit high spectral diversity, gaining attention in optogenetics and bioimaging applications. Several engineering studies on CBCRs were attempted, especially for designing near-infrared (NIR) fluorescent proteins with longer fluorescence wavelengths. However, despite continuous efforts, a key component regulating fluorescence emission property in CBCRs is still poorly understood. As a model system, we focused on red/green CBCR Slr1393g3, from the unicellular cyanobacterium Synechocystis sp. PCC 6803 to engineer Pr to get far-red light-emitting property. Energy profiling and pairwise structural comparison of Slr1393g3 variants effectively reveal the mutations that are critical to the fluorescence changes. H497 seems to play a key role in stabilizing the chromophore environment, especially the α3 helix, while H495, T499, and Q502 are potential key residues determining fluorescence emission peak wavelength. We also found that mutations of α2 and α4 helical regions are closely related to the chromophore binding stability and likely affect fluorescence properties. Taken together, our computational analysis suggests that the fluorescence of Slr1393g3 is mainly controlled by the stabilization of the chromophore binding pocket. The predicted key residues potentially regulating the fluorescence emission property of a red/green CBCR will be advantageous for designing improved NIR fluorescent protein when combined with in vitro molecular evolution approaches.
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Affiliation(s)
- Priyadharshini Kannan
- Natural Product Informatics Research Center, Korea Institute of Science and Technology, Gangneung, Republic of Korea
- Department of Biochemical Engineering, Gangneung-Wonju National University, Gangneung, Republic of Korea
| | - Jisung Oh
- Department of Biochemical Engineering, Gangneung-Wonju National University, Gangneung, Republic of Korea
- Natural Product Research Center, Korea Institute of Science and Technology, Gangneung, Republic of Korea
| | - Young Joo Yeon
- Department of Biochemical Engineering, Gangneung-Wonju National University, Gangneung, Republic of Korea
| | - Youn-Il Park
- Department of Biological Sciences, Chungnam National University, Daejeon, Republic of Korea
| | - Moon-Hyeong Seo
- Natural Product Research Center, Korea Institute of Science and Technology, Gangneung, Republic of Korea
- Department of Convergence Medicine, Wonju Severance Christian Hospital, Yonsei University Wonju College of Medicine, Wonju, Republic of Korea
- Department of YM-KIST Bio-Health Convergence, Yonsei University, Wonju, Republic of Korea
| | - Keunwan Park
- Natural Product Informatics Research Center, Korea Institute of Science and Technology, Gangneung, Republic of Korea
- Department of YM-KIST Bio-Health Convergence, Yonsei University, Wonju, Republic of Korea
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3
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Influence of the PHY domain on the ms-photoconversion dynamics of a knotless phytochrome. Photochem Photobiol Sci 2022; 21:1627-1636. [PMID: 35687310 DOI: 10.1007/s43630-022-00245-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 05/11/2022] [Indexed: 10/18/2022]
Abstract
The ability of some knotless phytochromes to photoconvert without the PHY domain allows evaluation of the distinct effect of the PHY domain on their photodynamics. Here, we compare the ms dynamics of the single GAF domain (g1) and the GAF-PHY (g1g2) construct of the knotless phytochrome All2699 from cyanobacterium Nostoc punctiforme. While the spectral signatures and occurrence of the intermediates are mostly unchanged by the domain composition, the presence of the PHY domain slows down the early forward and reverse dynamics involving chromophore and protein binding pocket relaxation. We assign this effect to a more restricted binding pocket imprinted by the PHY domain. The photoproduct formation is also slowed down by the presence of the PHY domain but to a lesser extent than the early dynamics. This indicates a rate limiting step within the GAF and not the PHY domain. We further identify a pH dependence of the biphasic photoproduct formation hinting towards a pKa dependent tuning mechanism. Our findings add to the understanding of the role of the individual domains in the photocycle dynamics and provide a basis for engineering of phytochromes towards biotechnological applications.
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4
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Garzella F, Bianchini P, Diaspro A, Losi A, Gärtner W, Abbruzzetti S, Viappiani C. A red-green photochromic bacterial protein as a new contrast agent for improved photoacoustic imaging. PHOTOACOUSTICS 2022; 26:100358. [PMID: 35656384 PMCID: PMC9152790 DOI: 10.1016/j.pacs.2022.100358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 04/14/2022] [Indexed: 06/15/2023]
Abstract
The GAF3 domain of the cyanobacteriochrome Slr1393 from Synechocystis sp. PCC6803, binding phycocyanobilin as a chromophore, shows photochromicity between two stable, green- and red-absorbing states, characterized by relatively high photoconversion yields. Using nanosecond-pulsed excitation by red or green light, respectively, and suitable cw photoconversion beams, we demonstrate that the light-modulatable photoacoustic waveforms arising from GAF3 can be easily distinguished from background signals originating from non-modulatable competitive absorbers and scattering media. It is demonstrated that this effect can be exploited to identify the position of the photochromic molecule by using as a phantom a cylindrical capillary tube filled with either a GAF3 solution or with an E.coli suspension overexpressing GAF3. These properties identify the high potential of GAF3 to be included in the palette of genetically encoded photochromic probes for photoacoustic imaging.
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Affiliation(s)
- Francesco Garzella
- Dipartimento di Scienze Matematiche, Fisiche e Informatiche, Università di Parma, Italy
- Nanoscopy @ Istituto Italiano di Tecnologia, Genova, Italy
| | - Paolo Bianchini
- Dipartimento di Scienze Matematiche, Fisiche e Informatiche, Università di Parma, Italy
- Nanoscopy @ Istituto Italiano di Tecnologia, Genova, Italy
- DIFILAB, Dipartimento di Fisica, Università di Genova, Genova, Italy
| | - Alberto Diaspro
- Nanoscopy @ Istituto Italiano di Tecnologia, Genova, Italy
- DIFILAB, Dipartimento di Fisica, Università di Genova, Genova, Italy
| | - Aba Losi
- Dipartimento di Scienze Matematiche, Fisiche e Informatiche, Università di Parma, Italy
| | - Wolfgang Gärtner
- Institut für Analytische Chemie - Universität Leipzig, Leipzig, Germany
| | - Stefania Abbruzzetti
- Dipartimento di Scienze Matematiche, Fisiche e Informatiche, Università di Parma, Italy
| | - Cristiano Viappiani
- Dipartimento di Scienze Matematiche, Fisiche e Informatiche, Università di Parma, Italy
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5
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Lee SJ, Kim TW, Kim JG, Yang C, Yun SR, Kim C, Ren Z, Kumarapperuma I, Kuk J, Moffat K, Yang X, Ihee H. Light-induced protein structural dynamics in bacteriophytochrome revealed by time-resolved x-ray solution scattering. SCIENCE ADVANCES 2022; 8:eabm6278. [PMID: 35622911 PMCID: PMC9140987 DOI: 10.1126/sciadv.abm6278] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 04/13/2022] [Indexed: 05/25/2023]
Abstract
Bacteriophytochromes (BphPs) are photoreceptors that regulate a wide range of biological mechanisms via red light-absorbing (Pr)-to-far-red light-absorbing (Pfr) reversible photoconversion. The structural dynamics underlying Pfr-to-Pr photoconversion in a liquid solution phase are not well understood. We used time-resolved x-ray solution scattering (TRXSS) to capture light-induced structural transitions in the bathy BphP photosensory module of Pseudomonas aeruginosa. Kinetic analysis of the TRXSS data identifies three distinct structural species, which are attributed to lumi-F, meta-F, and Pr, connected by time constants of 95 μs and 21 ms. Structural analysis based on molecular dynamics simulations shows that the light activation of PaBphP accompanies quaternary structural rearrangements from an "II"-framed close form of the Pfr state to an "O"-framed open form of the Pr state in terms of the helical backbones. This study provides mechanistic insights into how modular signaling proteins such as BphPs transmit structural signals over long distances and regulate their downstream biological responses.
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Affiliation(s)
- Sang Jin Lee
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- Center for Advanced Reaction Dynamics, Institute for Basic Science (IBS), Daejeon 34141, Republic of Korea
| | - Tae Wu Kim
- Department of Chemistry, Mokpo National University, Muan-gun, Jeollanam-do, 58554, Republic of Korea
| | - Jong Goo Kim
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- Center for Advanced Reaction Dynamics, Institute for Basic Science (IBS), Daejeon 34141, Republic of Korea
| | - Cheolhee Yang
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- Center for Advanced Reaction Dynamics, Institute for Basic Science (IBS), Daejeon 34141, Republic of Korea
| | - So Ri Yun
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- Center for Advanced Reaction Dynamics, Institute for Basic Science (IBS), Daejeon 34141, Republic of Korea
| | - Changin Kim
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- Center for Advanced Reaction Dynamics, Institute for Basic Science (IBS), Daejeon 34141, Republic of Korea
| | - Zhong Ren
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Indika Kumarapperuma
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Jane Kuk
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
| | - Keith Moffat
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
| | - Xiaojing Yang
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL 60607, USA
- Department of Ophthalmology and Vision Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Hyotcherl Ihee
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- Center for Advanced Reaction Dynamics, Institute for Basic Science (IBS), Daejeon 34141, Republic of Korea
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6
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Broser M. Far-Red Absorbing Rhodopsins, Insights From Heterodimeric Rhodopsin-Cyclases. Front Mol Biosci 2022; 8:806922. [PMID: 35127823 PMCID: PMC8815786 DOI: 10.3389/fmolb.2021.806922] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 12/27/2021] [Indexed: 11/13/2022] Open
Abstract
The recently discovered Rhodopsin-cyclases from Chytridiomycota fungi show completely unexpected properties for microbial rhodopsins. These photoreceptors function exclusively as heterodimers, with the two subunits that have very different retinal chromophores. Among them is the bimodal photoswitchable Neorhodopsin (NeoR), which exhibits a near-infrared absorbing, highly fluorescent state. These are features that have never been described for any retinal photoreceptor. Here these properties are discussed in the context of color-tuning approaches of retinal chromophores, which have been extensively studied since the discovery of the first microbial rhodopsin, bacteriorhodopsin, in 1971 (Oesterhelt et al., Nature New Biology, 1971, 233 (39), 149–152). Further a brief review about the concept of heterodimerization is given, which is widely present in class III cyclases but is unknown for rhodopsins. NIR-sensitive retinal chromophores have greatly expanded our understanding of the spectral range of natural retinal photoreceptors and provide a novel perspective for the development of optogenetic tools.
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7
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Tang K, Beyer HM, Zurbriggen MD, Gärtner W. The Red Edge: Bilin-Binding Photoreceptors as Optogenetic Tools and Fluorescence Reporters. Chem Rev 2021; 121:14906-14956. [PMID: 34669383 PMCID: PMC8707292 DOI: 10.1021/acs.chemrev.1c00194] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Indexed: 12/15/2022]
Abstract
This review adds the bilin-binding phytochromes to the Chemical Reviews thematic issue "Optogenetics and Photopharmacology". The work is structured into two parts. We first outline the photochemistry of the covalently bound tetrapyrrole chromophore and summarize relevant spectroscopic, kinetic, biochemical, and physiological properties of the different families of phytochromes. Based on this knowledge, we then describe the engineering of phytochromes to further improve these chromoproteins as photoswitches and review their employment in an ever-growing number of different optogenetic applications. Most applications rely on the light-controlled complex formation between the plant photoreceptor PhyB and phytochrome-interacting factors (PIFs) or C-terminal light-regulated domains with enzymatic functions present in many bacterial and algal phytochromes. Phytochrome-based optogenetic tools are currently implemented in bacteria, yeast, plants, and animals to achieve light control of a wide range of biological activities. These cover the regulation of gene expression, protein transport into cell organelles, and the recruitment of phytochrome- or PIF-tagged proteins to membranes and other cellular compartments. This compilation illustrates the intrinsic advantages of phytochromes compared to other photoreceptor classes, e.g., their bidirectional dual-wavelength control enabling instant ON and OFF regulation. In particular, the long wavelength range of absorption and fluorescence within the "transparent window" makes phytochromes attractive for complex applications requiring deep tissue penetration or dual-wavelength control in combination with blue and UV light-sensing photoreceptors. In addition to the wide variability of applications employing natural and engineered phytochromes, we also discuss recent progress in the development of bilin-based fluorescent proteins.
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Affiliation(s)
- Kun Tang
- Institute
of Synthetic Biology, Heinrich-Heine-University
Düsseldorf, Universitätsstrasse 1, D-40225 Düsseldorf, Germany
| | - Hannes M. Beyer
- Institute
of Synthetic Biology, Heinrich-Heine-University
Düsseldorf, Universitätsstrasse 1, D-40225 Düsseldorf, Germany
| | - Matias D. Zurbriggen
- Institute
of Synthetic Biology and CEPLAS, Heinrich-Heine-University
Düsseldorf, Universitätsstrasse
1, D-40225 Düsseldorf, Germany
| | - Wolfgang Gärtner
- Retired: Max Planck Institute
for Chemical Energy Conversion. At present: Institute for Analytical Chemistry, University
Leipzig, Linnéstrasse
3, 04103 Leipzig, Germany
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8
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Merga G, Lopez MF, Fischer P, Piwowarski P, Nogacz Ż, Kraskov A, Buhrke D, Escobar FV, Michael N, Siebert F, Scheerer P, Bartl F, Hildebrandt P. Light- and temperature-dependent dynamics of chromophore and protein structural changes in bathy phytochrome Agp2. Phys Chem Chem Phys 2021; 23:18197-18205. [PMID: 34612283 DOI: 10.1039/d1cp02494a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Bacterial phytochromes are sensoric photoreceptors that transform light absorbed by the photosensor core module (PCM) to protein structural changes that eventually lead to the activation of the enzymatic output module. The underlying photoinduced reaction cascade in the PCM starts with the isomerization of the tetrapyrrole chromophore, followed by conformational relaxations, proton transfer steps, and a secondary structure transition of a peptide segment (tongue) that is essential for communicating the signal to the output module. In this work, we employed various static and time-resolved IR and resonance Raman spectroscopic techniques to study the structural and reaction dynamics of the Meta-F intermediate of both the PCM and the full-length (PCM and output module) variant of the bathy phytochrome Agp2 from Agrobacterium fabrum. In both cases, this intermediate represents a branching point of the phototransformation, since it opens an unproductive reaction channel back to the initial state and a productive pathway to the final active state, including the functional protein structural changes. It is shown that the functional quantum yield, i.e. the events of tongue refolding per absorbed photons, is lower by a factor of ca. two than the quantum yield of the primary photochemical process. However, the kinetic data derived from the spectroscopic experiments imply an increased formation of the final active state upon increasing photon flux or elevated temperature under photostationary conditions. Accordingly, the branching mechanism does not only account for the phytochrome's function as a light intensity sensor but may also modulate its temperature sensitivity.
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Affiliation(s)
- Galaan Merga
- Humboldt Universität zu Berlin, Institut für Biologie, Biophysikalische Chemie, Invalidenstr. 42, D-10115 Berlin, Germany
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9
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Ding Y, Zhao Z, Matysik J, Gärtner W, Losi A. Mapping the role of aromatic amino acids within a blue-light sensing LOV domain. Phys Chem Chem Phys 2021; 23:16767-16775. [PMID: 34319324 DOI: 10.1039/d1cp02217b] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Photosensing LOV (Light, Oxygen, Voltage) domains detect and respond to UVA/Blue (BL) light by forming a covalent adduct between the flavin chromophore and a nearby cysteine, via the decay of the flavin triplet excited state. LOV domains where the reactive cysteine has been mutated are valuable fluorescent tools for microscopy and as genetically encoded photosensitisers for reactive oxygen species. Besides being convenient tools for applications, LOV domains without the reactive cysteine (naturally occurring or engineered) can still be functionally photoactivated via formation of a neutral flavin radical. Tryptophans and tyrosines are held as the main partners as potential electron donors to the flavin excited states. In this work, we explore the relevance of aromatic amino acids in determining the photophysical features of the LOV protein Mr4511 from Methylobacterium radiotolerans by introducing point mutations into the C71S variant that does not form the covalent adduct. By using an array of spectroscopic techniques we measured the fluorescence quantum yields and lifetimes, the triplet yields and lifetimes, and the efficiency of singlet oxygen (SO) formation for eleven Mr4511 variants. Insertion of Trp residues at distances between 0.6 and 1.5 nm from the flavin chromophore results in strong quenching of the flavin excited triplet state and, at the shorter distances even of the singlet excited state. The mutation F130W (ca. 0.6 nm) completely quenches the singlet excited state, preventing triplet formation: in this case, even if the cysteine is present, the photo-adduct is not formed. Tyrosines are also quenchers for the flavin excited states, although not as efficient as Trp residues, as demonstrated with their substitution with the inert phenylalanine. For one of these variants, C71S/Y116F, we found that the quantum yield of formation for singlet oxygen is 0.44 in aqueous aerobic solution, vs 0.17 for C71S. Based on our study with Mr4511 and on literature data for other LOV domains we suggest that Trp and Tyr residues too close to the flavin chromophore (at distances less than 0.9 nm) reduce the yield of photoproduct formation and that introduction of inert Phe residues in key positions can help in developing efficient, LOV-based photosensitisers.
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Affiliation(s)
- Yonghong Ding
- Institute for Analytical Chemistry, University of Leipzig, Linnéstrasse 3, 04103 Leipzig, Germany
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10
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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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11
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Fathi P, Roslend A, Mehta K, Moitra P, Zhang K, Pan D. UV-trained and metal-enhanced fluorescence of biliverdin and biliverdin nanoparticles. NANOSCALE 2021; 13:4785-4798. [PMID: 33434263 PMCID: PMC9297654 DOI: 10.1039/d0nr08485a] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Increasing the fluorescence quantum yield of fluorophores is of great interest for in vitro and in vivo biomedical imaging applications. At the same time, photobleaching and photodegradation resulting from continuous exposure to light are major considerations in the translation of fluorophores from research applications to industrial or healthcare applications. A number of tetrapyrrolic compounds, such as heme and its derivatives, are known to provide fluorescence contrast. In this work, we found that biliverdin (BV), a naturally-occurring tetrapyrrolic fluorophore, exhibits an increase in fluorescence quantum yield, without exhibiting photobleaching or degradation, in response to continuous ultraviolet (UV) irradiation. We attribute this increased fluorescence quantum yield to photoisomerization and conformational changes in BV in response to UV irradiation. This enhanced fluorescence can be further altered by chelating BV with metals. UV irradiation of BV led to an approximately 10-fold increase in its 365 nm fluorescence quantum yield, and the most favorable combination of UV irradiation and metal chelation led to an approximately 18.5-fold increase in its 365 nm fluorescence quantum yield. We also evaluated these stimuli-responsive behaviors in biliverdin nanoparticles (BVNPs) at the bulk-state and single-particle level. We determined that UV irradiation led to an approximately 2.4-fold increase in BVNP 365 nm quantum yield, and the combination of UV irradiation and metal chelation led to up to a 6.75-fold increase in BVNP 365 nm quantum yield. Altogether, these findings suggest that UV irradiation and metal chelation can be utilized alone or in combination to tailor the fluorescence behavior of imaging probes such as BV and BVNPs at selected wavelengths.
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Affiliation(s)
- Parinaz Fathi
- Departments of Bioengineering, Materials Science and Engineering, and Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.
| | - Ayman Roslend
- Departments of Bioengineering, Materials Science and Engineering, and Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.
| | - Kritika Mehta
- Department of Biochemistry, School of Molecular and Cellular Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Parikshit Moitra
- Department of Pediatrics, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Kai Zhang
- Department of Biochemistry, School of Molecular and Cellular Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Dipanjan Pan
- Departments of Bioengineering, Materials Science and Engineering, and Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA. and Departments of Diagnostic Radiology Nuclear Medicine, Pediatrics, and Chemical and Biomolecular Engineering, University of Maryland School of Medicine and University of Maryland Baltimore County, Baltimore, MD 21201, USA
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12
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Losi A, Gärtner W. A light life together: photosensing in the plant microbiota. Photochem Photobiol Sci 2021; 20:451-473. [PMID: 33721277 DOI: 10.1007/s43630-021-00029-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 02/17/2021] [Indexed: 12/12/2022]
Abstract
Bacteria and fungi of the plant microbiota can be phytopathogens, parasites or symbionts that establish mutually advantageous relationships with plants. They are often rich in photoreceptors for UVA-Visible light, and in many cases, they exhibit light regulation of growth patterns, infectivity or virulence, reproductive traits, and production of pigments and of metabolites. In addition to the light-driven effects, often demonstrated via the generation of photoreceptor gene knock-outs, microbial photoreceptors can exert effects also in the dark. Interestingly, some fungi switch their attitude towards plants in dependence of illumination or dark conditions in as much as they may be symbiotic or pathogenic. This review summarizes the current knowledge about the roles of light and photoreceptors in plant-associated bacteria and fungi aiming at the identification of common traits and general working ideas. Still, reports on light-driven infection of plants are often restricted to the description of macroscopically observable phenomena, whereas detailed information on the molecular level, e.g., protein-protein interaction during signal transduction or induction mechanisms of infectivity/virulence initiation remains sparse. As it becomes apparent from still only few molecular studies, photoreceptors, often from the red- and the blue light sensitive groups interact and mutually modulate their individual effects. The topic is of great relevance, even in economic terms, referring to plant-pathogen or plant-symbionts interactions, considering the increasing usage of artificial illumination in greenhouses, the possible light-regulation of the synthesis of plant-growth stimulating substances or herbicides by certain symbionts, and the biocontrol of pests by selected fungi and bacteria in a sustainable agriculture.
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Affiliation(s)
- Aba Losi
- Department of Mathematical, Physical and Computer Sciences, University of Parma, Parco Area delle Scienze 7/A, 43124, Parma, Italy.
| | - Wolfgang Gärtner
- Institute for Analytical Chemistry, University of Leipzig, Linnéstrasse 3, 04103, Leipzig, Germany
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13
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Consiglieri E, Xu QZ, Zhao KH, Gärtner W, Losi A. The first molecular characterisation of blue- and red-light photoreceptors from Methylobacterium radiotolerans. Phys Chem Chem Phys 2020; 22:12434-12446. [PMID: 32458860 DOI: 10.1039/d0cp02014a] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Methylobacteria are facultative methylotrophic phytosymbionts of great industrial and agronomical interest, and they are considered as opportunistic pathogens posing a health threat to humans. So far only a few reports mention photoreceptor coding sequences in Methylobacteria genomes, but no investigation at the molecular level has been performed yet. We here present comprehensive in silico research into potential photoreceptors in this bacterial phylum and report the photophysical and photochemical characterisation of two representatives of the most widespread photoreceptor classes, a blue-light sensing LOV (light, oxygen, voltage) protein and a red/far red light sensing BphP (biliverdin-binding bacterial phytochrome) from M. radiotolerans JCM 2831. Overall, both proteins undergo the expected light-triggered reactions, but peculiar features were also identified. The LOV protein Mr4511 has an extremely long photocycle and lacks a tryptophan conserved in ca. 75% of LOV domains. Mutation I37V accelerates the photocycle by one order of magnitude, while the Q112W change underscores the ability of tryptophan in this position to perform efficient energy transfer to the flavin chromophore. Time-resolved photoacoustic experiments showed that Mr4511 has a higher triplet quantum yield than other LOV domains and that the formation of the photoproduct results in a volume expansion, in sharp contrast to other LOV proteins. Mr4511 was found to be astonishingly resistant to denaturation by urea, still showing light-triggered reactions after incubation in urea for more than 20 h. The phytochrome MrBphP1 exhibits the so far most red-shifted absorption maxima for its Pr- and Pfr forms (λmax = 707 nm and 764 nm for the Pr and Pfr forms). The light-driven conversions in both directions occur with relatively high quantum yields of 0.2. Transient ns absorption spectroscopy (μs-ms time range) identifies the decay of the instantaneously formed lumi-intermediate, followed by only one additional intermediate before the formation of the respective final photoproducts for Pr-to-Pfr or Pfr-to-Pr photoconversion, in contrast to other BphPs. The relatively simple photoconversion patterns suggest the absence of the shunt pathways reported for other bacterial phytochromes.
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Affiliation(s)
- Eleonora Consiglieri
- Department of Mathematical, Physical and Computer Sciences, University of Parma, Parco Area delle Scienze 7/A, 43124 Parma, Italy.
| | - Qian-Zhao Xu
- Institute for Analytical Chemistry, University of Leipzig, Linnéstrasse 3, 04103 Leipzig, Germany and State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Kai-Hong Zhao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Wolfgang Gärtner
- Institute for Analytical Chemistry, University of Leipzig, Linnéstrasse 3, 04103 Leipzig, Germany
| | - Aba Losi
- Department of Mathematical, Physical and Computer Sciences, University of Parma, Parco Area delle Scienze 7/A, 43124 Parma, Italy.
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Yao Q, Lan QH, Jiang X, Du CC, Zhai YY, Shen X, Xu HL, Xiao J, Kou L, Zhao YZ. Bioinspired biliverdin/silk fibroin hydrogel for antiglioma photothermal therapy and wound healing. Theranostics 2020; 10:11719-11736. [PMID: 33052243 PMCID: PMC7545989 DOI: 10.7150/thno.47682] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 09/13/2020] [Indexed: 12/11/2022] Open
Abstract
Rationale: Photothermal therapy employs the photoabsorbers to generate heat under the near-infrared (NIR) irradiation for thermal tumor ablation. However, NIR irradiation might damage the adjacent tissue due to the leakage of the photoabsorbers and the residual materials after treatment might hinder the local healing process. A bifunctional hydrogel that holds both photothermal property and potent pro-healing ability provides a viable option to resolve this issue. Methods: In this study, we developed a bioinspired green hydrogel (BVSF) with the integration of bioproduct biliverdin into natural derived silk fibroin matrix for antiglioma photothermal therapy and wound healing. Results: The BVSF hydrogel possessed excellent and controllable photothermal activity under NIR irradiation and resulted in effective tumor ablation both in vitro and in vivo. Additionally, the BVSF hydrogel exerted anti-inflammatory effects both in vitro and in vivo, and stimulated angiogenesis and wound healing in a full-thickness defect rat model. Conclusion: Overall, this proof-of-concept study was aimed to determine the feasibility and reliability of using an all-natural green formulation for photothermal therapy and post-treatment care.
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Velazquez Escobar F, Kneip C, Michael N, Hildebrandt T, Tavraz N, Gärtner W, Hughes J, Friedrich T, Scheerer P, Mroginski MA, Hildebrandt P. The Lumi-R Intermediates of Prototypical Phytochromes. J Phys Chem B 2020; 124:4044-4055. [PMID: 32330037 DOI: 10.1021/acs.jpcb.0c01059] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Phytochromes are photoreceptors that upon light absorption initiate a physiological reaction cascade. The starting point is the photoisomerization of the tetrapyrrole cofactor in the parent Pr state, followed by thermal relaxation steps culminating in activation of the physiological signal. Here we have employed resonance Raman (RR) spectroscopy to study the chromophore structure in the primary photoproduct Lumi-R, trapped between 130 and 200 K. The investigations covered phytochromes from plants (phyA) and prokaryotes (Cph1, Agp1, CphB, and RpBphP2) including phytochromobilin (PΦB), phycocyanobilin (PCB), and biliverdin (BV). In PΦB- and PCB-binding phyA and Cph1, two Lumi-R states (Lumi-R1, Lumi-R2) were identified and discussed in terms of sequential and parallel reaction models. In Lumi-R1, the chromophore structural changes are restricted to the C-D methine bridge isomerization site but extended throughout the chromophore in Lumi-R2. Formation and decay kinetics as well as photochemical activity depend on the specific protein-chromophore interactions and thus account for the different distribution between Lumi-R1 and Lumi-R2 in the photostationary mixtures of the various PΦB(PCB)-binding phytochromes. For BV-binding bacteriophytochromes, only a single Lumi-R(BV) state was found. In this state, which is similar for Agp1, CphB, and RpBphP2, the chromophore structural changes comprise major torsions of the C-D methine bridge but also perturbations at the A-B methine bridge remote from the isomerization site. The different structures of the photoproducts in PΦB(PCB)-binding phytochromes and BV-binding bacteriophytochromes are attributed to the different disposition of ring D upon isomerization, which leads to distinct protein-chromophore interactions in the Lumi-R states of these two classes of phytochromes.
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Affiliation(s)
- Francisco Velazquez Escobar
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Straße des 17 Juni 135, D-10623 Berlin, Germany
| | - Christa Kneip
- Grünenthal GmbH, Zieglerstraße 6, D-52078 Aachen, Germany
| | - Norbert Michael
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Straße des 17 Juni 135, D-10623 Berlin, Germany
| | - Thomas Hildebrandt
- Universitätsklinikum Düsseldorf, Klinik für Neurologie, Moorenstr. 5, D-40225 Düsseldorf, Germany
| | - Neslihan Tavraz
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Straße des 17 Juni 135, D-10623 Berlin, Germany
| | - Wolfgang Gärtner
- Universität Leipzig, Institut für Analytische Chemie, Linnéstr. 3, D-04103 Leipzig, Germany
| | - Jon Hughes
- Plant Physiology, Justus-Liebig University Gießen, Senckenbergstrasse 3, D-35390 Giessen, Germany
| | - Thomas Friedrich
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Straße des 17 Juni 135, D-10623 Berlin, Germany
| | - Patrick Scheerer
- Group Protein X-ray Crystallography and Signal Transduction, Institute of Medical Physics and Biophysics, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, D-10117 Berlin, Germany
| | - Maria Andrea Mroginski
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Straße des 17 Juni 135, D-10623 Berlin, Germany
| | - Peter Hildebrandt
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Straße des 17 Juni 135, D-10623 Berlin, Germany
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16
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Hassan F, Khan FI, Song H, Lai D, Juan F. Effects of reverse genetic mutations on the spectral and photochemical behavior of a photoactivatable fluorescent protein PAiRFP1. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 228:117807. [PMID: 31806482 DOI: 10.1016/j.saa.2019.117807] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 10/29/2019] [Accepted: 11/15/2019] [Indexed: 06/10/2023]
Abstract
Bacteriophytochrome photoreceptors (BphPs) containing biliverdin (BV) have great potential for the development of genetically engineered near-infrared fluorescent proteins (NIR FPs). We investigated a photoactivatable fluorescent protein PAiRFP1, was engineered through directed molecular evolution. The coexistence of both red light absorbing (Pr) and far-red light absorbing (Pfr) states in dark is essential for the photoactivation of PAiRFP1. The PCR based site-directed reverse mutagenesis, spectroscopic measurements and molecular dynamics (MD) simulations were performed on three targeted sites V386A, V480A and Y498H in PHY domain to explore their potential effects during molecular evolution of PAiRFP1. We found that these substitutions did not affect the coexistence of Pr and Pfr states but led to slight changes in the photophysical parameters. The covalent docking of biliverdin (cis and trans form) with PAiRFP1 was followed by several 100 ns MD simulations to provide some theoretical explanations for the coexistence of Pr and pfr states. The results suggested that experimentally observed coexistence of Pr and Pfr states in both PAiRFP1 and mutants were resulted from the improved stability of Pr state. The use of experimental and computational work provided useful understanding of Pr and Pfr states and the effects of these mutations on the photophysical properties of PAiRFP1.
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Affiliation(s)
- Fakhrul Hassan
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
| | - Faez Iqbal Khan
- School of Electronic Science and Engineering, University of Electronic Science and Technology of China, Chengdu, China.
| | - Honghong Song
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
| | - Dakun Lai
- School of Electronic Science and Engineering, University of Electronic Science and Technology of China, Chengdu, China.
| | - Feng Juan
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China.
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Competing excited-state deactivation processes in bacteriophytochromes. ADVANCES IN QUANTUM CHEMISTRY 2020. [DOI: 10.1016/bs.aiq.2020.05.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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