1
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Bódizs S, Mészáros P, Grunewald L, Takala H, Westenhoff S. Cryo-EM structures of a bathy phytochrome histidine kinase reveal a unique light-dependent activation mechanism. Structure 2024:S0969-2126(24)00325-3. [PMID: 39216473 DOI: 10.1016/j.str.2024.08.008] [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: 05/13/2024] [Revised: 07/05/2024] [Accepted: 08/06/2024] [Indexed: 09/04/2024]
Abstract
Phytochromes are photoreceptor proteins in plants, fungi, and bacteria. They can adopt two photochromic states with differential biochemical responses. The structural changes transducing the signal from the chromophore to the biochemical output modules are poorly understood due to challenges in capturing structures of the dynamic, full-length protein. Here, we present cryoelectron microscopy (cryo-EM) structures of the phytochrome from Pseudomonas aeruginosa (PaBphP) in its resting (Pfr) and photoactivated (Pr) state. The kinase-active Pr state has an asymmetric, dimeric structure, whereas the kinase-inactive Pfr state opens up. This behavior is different from other known phytochromes and we explain it with the unusually short connection between the photosensory and output modules. Multiple sequence alignment of this region suggests evolutionary optimization for different modes of signal transduction in sensor proteins. The results establish a new mechanism for light-sensing by phytochrome histidine kinases and provide input for the design of optogenetic phytochrome variants.
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Affiliation(s)
- Szabolcs Bódizs
- Department of Chemistry - BMC, Biochemistry, Uppsala University, 75123 Uppsala, Sweden
| | - Petra Mészáros
- Department of Chemistry - BMC, Biochemistry, Uppsala University, 75123 Uppsala, Sweden
| | - Lukas Grunewald
- Department of Chemistry - BMC, Biochemistry, Uppsala University, 75123 Uppsala, Sweden
| | - Heikki Takala
- Nanoscience Center, Department of Biological and Environmental Science, University of Jyväskylä, 40014 Jyväskylä, Finland
| | - Sebastian Westenhoff
- Department of Chemistry - BMC, Biochemistry, Uppsala University, 75123 Uppsala, Sweden.
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2
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Malla TN, Hernandez C, Muniyappan S, Menendez D, Bizhga D, Mendez JH, Schwander P, Stojković EA, Schmidt M. Photoreception and signaling in bacterial phytochrome revealed by single-particle cryo-EM. SCIENCE ADVANCES 2024; 10:eadq0653. [PMID: 39121216 PMCID: PMC11313861 DOI: 10.1126/sciadv.adq0653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Accepted: 07/08/2024] [Indexed: 08/11/2024]
Abstract
Phytochromes are red-light photoreceptors discovered in plants with homologs in bacteria and fungi that regulate a variety of physiological responses. They display a reversible photocycle between two distinct states: a red-light-absorbing Pr state and a far-red light-absorbing Pfr state. The photoconversion regulates the activity of an enzymatic domain, usually a histidine kinase (HK). The molecular mechanism that explains how light controls the HK activity is not understood because structures of unmodified bacterial phytochromes with HK activity are missing. Here, we report three cryo-electron microscopy structures of a wild-type bacterial phytochrome with HK activity determined as Pr and Pfr homodimers and as a Pr/Pfr heterodimer with individual subunits in distinct states. We propose that the Pr/Pfr heterodimer is a physiologically relevant signal transduction intermediate. Our results offer insight into the molecular mechanism that controls the enzymatic activity of the HK as part of a bacterial two-component system that perceives and transduces light signals.
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Affiliation(s)
- Tek Narsingh Malla
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, WI 53211, USA
| | | | | | - David Menendez
- Department of Biology, Northeastern Illinois University, Chicago, IL 60625, USA
| | - Dorina Bizhga
- Department of Biology, Northeastern Illinois University, Chicago, IL 60625, USA
| | - Joshua H. Mendez
- New York Structural Biology Center (NYSBC), New York, NY 10027, USA
| | - Peter Schwander
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, WI 53211, USA
| | - Emina A. Stojković
- Department of Biology, Northeastern Illinois University, Chicago, IL 60625, USA
| | - Marius Schmidt
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, WI 53211, USA
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3
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Hughes J, Winkler A. New Insight Into Phytochromes: Connecting Structure to Function. ANNUAL REVIEW OF PLANT BIOLOGY 2024; 75:153-183. [PMID: 39038250 DOI: 10.1146/annurev-arplant-070623-110636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/24/2024]
Abstract
Red and far-red light-sensing phytochromes are widespread in nature, occurring in plants, algae, fungi, and prokaryotes. Despite at least a billion years of evolution, their photosensory modules remain structurally and functionally similar. Conversely, nature has found remarkably different ways of transmitting light signals from the photosensor to diverse physiological responses. We summarize key features of phytochrome structure and function and discuss how these are correlated, from how the bilin environment affects the chromophore to how light induces cellular signals. Recent advances in the structural characterization of bacterial and plant phytochromes have resulted in paradigm changes in phytochrome research that we discuss in the context of present-day knowledge. Finally, we highlight questions that remain to be answered and suggest some of the benefits of understanding phytochrome structure and function.
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Affiliation(s)
- Jon Hughes
- Department of Plant Physiology, Justus Liebig University, Giessen, Germany;
- Department of Physics, Free University of Berlin, Berlin, Germany
| | - Andreas Winkler
- Institute of Biochemistry, Graz University of Technology, Graz, Austria;
- BioTechMed-Graz, Graz, Austria
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4
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Santra S, Manna RN, Chakrabarty S, Ghosh D. Conformational Effects on the Absorption Spectra of Phytochromes. J Phys Chem B 2024; 128:3614-3620. [PMID: 38581077 DOI: 10.1021/acs.jpcb.4c00859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2024]
Abstract
Bacteriophytochrome is a photoreceptor protein that contains the biliverdin (BV) chromophore as its active component. The spectra of BV upon mutation remain remarkably unchanged, as far as spectral positions are concerned. This points toward the minimal effect of electrostatic effects on the electronic structure of the chromophore. However, the relative intensities of the Q and Soret bands of the chromophore change dramatically upon mutation. In this work, we delve into the molecular origin of this unusual intensity modulation. Using extensive classical MD and QM/MM calculations, we show that due to mutation, the conformational population of the chromophore changes significantly. The noncovalent interactions, especially the stacking interactions, lead to extra stabilization of the cyclic form in the D207H mutated species as opposed to the open form in the wild-type BV. Thus, unlike the commonly observed direct electrostatic effect on the spectral shift, in the case of BV the difference observed is in varying intensities, and this in turn is driven by a conformational shift due to enhanced stacking interaction.
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Affiliation(s)
- Supriyo Santra
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Rabindra Nath Manna
- Department of Chemical and Biological Sciences, S. N. Bose National Centre for Basic Sciences, Salt Lake, Kolkata 700106, India
| | - Suman Chakrabarty
- Department of Chemical and Biological Sciences, S. N. Bose National Centre for Basic Sciences, Salt Lake, Kolkata 700106, India
| | - Debashree Ghosh
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
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5
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Salvadori G, Mazzeo P, Accomasso D, Cupellini L, Mennucci B. Deciphering Photoreceptors Through Atomistic Modeling from Light Absorption to Conformational Response. J Mol Biol 2024; 436:168358. [PMID: 37944793 DOI: 10.1016/j.jmb.2023.168358] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 10/28/2023] [Accepted: 11/02/2023] [Indexed: 11/12/2023]
Abstract
In this review, we discuss the successes and challenges of the atomistic modeling of photoreceptors. Throughout our presentation, we integrate explanations of the primary methodological approaches, ranging from quantum mechanical descriptions to classical enhanced sampling methods, all while providing illustrative examples of their practical application to specific systems. To enhance the effectiveness of our analysis, our primary focus has been directed towards the examination of applications across three distinct photoreceptors. These include an example of Blue Light-Using Flavin (BLUF) domains, a bacteriophytochrome, and the orange carotenoid protein (OCP) employed by cyanobacteria for photoprotection. Particular emphasis will be placed on the pivotal role played by the protein matrix in fine-tuning the initial photochemical event within the embedded chromophore. Furthermore, we will investigate how this localized perturbation initiates a cascade of events propagating from the binding pocket throughout the entire protein structure, thanks to the intricate network of interactions between the chromophore and the protein.
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Affiliation(s)
- Giacomo Salvadori
- Department of Chemistry and Industrial Chemistry, University of Pisa, 56124 Pisa, Italy
| | - Patrizia Mazzeo
- Department of Chemistry and Industrial Chemistry, University of Pisa, 56124 Pisa, Italy
| | - Davide Accomasso
- Department of Chemistry and Industrial Chemistry, University of Pisa, 56124 Pisa, Italy
| | - Lorenzo Cupellini
- Department of Chemistry and Industrial Chemistry, University of Pisa, 56124 Pisa, Italy
| | - Benedetta Mennucci
- Department of Chemistry and Industrial Chemistry, University of Pisa, 56124 Pisa, Italy
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6
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Malla TN, Hernandez C, Menendez D, Bizhga D, Mendez JH, Muniyappan S, Schwander P, Stojković EA, Schmidt M. Signal Transduction in an Enzymatic Photoreceptor Revealed by Cryo-Electron Microscopy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.08.566274. [PMID: 37986774 PMCID: PMC10659365 DOI: 10.1101/2023.11.08.566274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Phytochromes are essential photoreceptor proteins in plants with homologs in bacteria and fungi that regulate a variety of important environmental responses. They display a reversible photocycle between two distinct states, the red-light absorbing Pr and the far-red light absorbing Pfr, each with its own structure. The reversible Pr to Pfr photoconversion requires covalently bound bilin chromophore and regulates the activity of a C-terminal enzymatic domain, which is usually a histidine kinase (HK). In plants, phytochromes translocate to nucleus where the C-terminal effector domain interacts with protein interaction factors (PIFs) to induce gene expression. In bacteria, the HK phosphorylates a response-regulator (RR) protein triggering downstream gene expression through a two-component signaling pathway. Although plant and bacterial phytochromes share similar structural composition, they have contrasting activity in the presence of light with most BphPs being active in the dark. The molecular mechanism that explains bacterial and plant phytochrome signaling has not been well understood due to limited structures of full-length phytochromes with enzymatic domain resolved at or near atomic resolution in both Pr and Pfr states. Here, we report the first Cryo-EM structures of a wild-type bacterial phytochrome with a HK enzymatic domain, determined in both Pr and Pfr states, between 3.75 and 4.13 Å resolution, respectively. Furthermore, we capture a distinct Pr/Pfr heterodimer of the same protein as potential signal transduction intermediate at 3.75 Å resolution. Our three Cryo-EM structures of the distinct signaling states of BphPs are further reinforced by Cryo-EM structures of the truncated PCM of the same protein determined for the Pr/Pfr heterodimer as well as Pfr state. These structures provide insight into the different light-signaling mechanisms that could explain how bacteria and plants see the light.
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7
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Ramírez Martínez C, Gómez-Pérez LS, Ordaz A, Torres-Huerta AL, Antonio-Perez A. Current Trends of Bacterial and Fungal Optoproteins for Novel Optical Applications. Int J Mol Sci 2023; 24:14741. [PMID: 37834188 PMCID: PMC10572898 DOI: 10.3390/ijms241914741] [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: 08/31/2023] [Revised: 09/13/2023] [Accepted: 09/15/2023] [Indexed: 10/15/2023] Open
Abstract
Photoproteins, luminescent proteins or optoproteins are a kind of light-response protein responsible for the conversion of light into biochemical energy that is used by some bacteria or fungi to regulate specific biological processes. Within these specific proteins, there are groups such as the photoreceptors that respond to a given light wavelength and generate reactions susceptible to being used for the development of high-novel applications, such as the optocontrol of metabolic pathways. Photoswitchable proteins play important roles during the development of new materials due to their capacity to change their conformational structure by providing/eliminating a specific light stimulus. Additionally, there are bioluminescent proteins that produce light during a heatless chemical reaction and are useful to be employed as biomarkers in several fields such as imaging, cell biology, disease tracking and pollutant detection. The classification of these optoproteins from bacteria and fungi as photoreceptors or photoresponse elements according to the excitation-emission spectrum (UV-Vis-IR), as well as their potential use in novel applications, is addressed in this article by providing a structured scheme for this broad area of knowledge.
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Affiliation(s)
| | | | | | | | - Aurora Antonio-Perez
- Escuela de Ingeniería y Ciencias, Tecnológico de Monterrey, Campus Estado de México, Av. Lago de Guadalupe KM 3.5, Margarita Maza de Juárez, Ciudad López Mateos, Atizapán de Zaragoza 52926, Estado de México, Mexico; (C.R.M.); (L.S.G.-P.); (A.O.); (A.L.T.-H.)
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8
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Kurttila M, Rumfeldt J, Takala H, Ihalainen JA. The interconnecting hairpin extension "arm": An essential allosteric element of phytochrome activity. Structure 2023; 31:1100-1108.e4. [PMID: 37392739 DOI: 10.1016/j.str.2023.06.007] [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: 03/23/2023] [Revised: 05/23/2023] [Accepted: 06/06/2023] [Indexed: 07/03/2023]
Abstract
In red-light sensing phytochromes, isomerization of the bilin chromophore triggers structural and dynamic changes across multiple domains, ultimately leading to control of the output module (OPM) activity. In between, a hairpin structure, "arm", extends from an interconnecting domain to the chromophore region. Here, by removing this protein segment in a bacteriophytochrome from Deinococcus radiodurans (DrBphP), we show that the arm is crucial for signal transduction. Crystallographic, spectroscopic, and biochemical data indicate that this variant maintains the properties of DrBphP in the resting state. Spectroscopic data also reveal that the armless systems maintain the ability to respond to light. However, there is no subsequent regulation of OPM activity without the arms. Thermal denaturation reveals that the arms stabilize the DrBphP structure. Our results underline the importance of the structurally flexible interconnecting hairpin extensions and describe their central role in the allosteric coupling of phytochromes.
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Affiliation(s)
- Moona Kurttila
- University of Jyvaskyla, Nanoscience Center, Department of Biological and Environmental Science, 40014 Jyvaskyla, Finland
| | - Jessica Rumfeldt
- University of Jyvaskyla, Nanoscience Center, Department of Biological and Environmental Science, 40014 Jyvaskyla, Finland
| | - Heikki Takala
- University of Jyvaskyla, Nanoscience Center, Department of Biological and Environmental Science, 40014 Jyvaskyla, Finland.
| | - Janne A Ihalainen
- University of Jyvaskyla, Nanoscience Center, Department of Biological and Environmental Science, 40014 Jyvaskyla, Finland.
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9
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Balke J, Díaz Gutiérrez P, Rafaluk-Mohr T, Proksch J, Koksch B, Alexiev U. Osmolytes Modulate Photoactivation of Phytochrome: Probing Protein Hydration. Molecules 2023; 28:6121. [PMID: 37630372 PMCID: PMC10457786 DOI: 10.3390/molecules28166121] [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: 06/13/2023] [Revised: 07/23/2023] [Accepted: 07/26/2023] [Indexed: 08/27/2023] Open
Abstract
Phytochromes are bistable red/far-red light-responsive photoreceptor proteins found in plants, fungi, and bacteria. Light-activation of the prototypical phytochrome Cph1 from the cyanobacterium Synechocystis sp. PCC 6803 allows photoisomerization of the bilin chromophore in the photosensory module and a subsequent series of intermediate states leading from the red absorbing Pr to the far-red-absorbing Pfr state. We show here via osmotic and hydrostatic pressure-based measurements that hydration of the photoreceptor modulates the photoconversion kinetics in a controlled manner. While small osmolytes like sucrose accelerate Pfr formation, large polymer osmolytes like PEG 4000 delay the formation of Pfr. Thus, we hypothesize that an influx of mobile water into the photosensory domain is necessary for proceeding to the Pfr state. We suggest that protein hydration changes are a molecular event that occurs during photoconversion to Pfr, in addition to light activation, ultrafast electric field changes, photoisomerization, proton release and uptake, and the major conformational change leading to signal transmission, or simultaneously with one of these events. Moreover, we discuss this finding in light of the use of Cph1-PGP as a hydration sensor, e.g., for the characterization of novel hydrogel biomaterials.
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Affiliation(s)
- Jens Balke
- Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Paula Díaz Gutiérrez
- Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Timm Rafaluk-Mohr
- Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Jonas Proksch
- Department of Biology, Chemistry, Pharmacy, Institute of Chemistry and Biochemistry–Organic Chemistry, Freie Universität Berlin, Takustr. 3, 14195 Berlin, Germany; (J.P.); (B.K.)
| | - Beate Koksch
- Department of Biology, Chemistry, Pharmacy, Institute of Chemistry and Biochemistry–Organic Chemistry, Freie Universität Berlin, Takustr. 3, 14195 Berlin, Germany; (J.P.); (B.K.)
| | - Ulrike Alexiev
- Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
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10
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Bacteria phototaxis optimizer. Neural Comput Appl 2023. [DOI: 10.1007/s00521-023-08391-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2023]
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11
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Peña-Medina RL, Fimbres-Olivarría D, Enríquez-Ocaña LF, Martínez-Córdova LR, Del-Toro-Sánchez CL, López-Elías JA, González-Vega RI. Erythroprotective Potential of Phycobiliproteins Extracted from Porphyridium cruentum. Metabolites 2023; 13:metabo13030366. [PMID: 36984806 PMCID: PMC10057957 DOI: 10.3390/metabo13030366] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 02/22/2023] [Accepted: 02/25/2023] [Indexed: 03/06/2023] Open
Abstract
There are multiple associations between the different blood groups (ABO and RhD) and the incidence of oxidative stress-related diseases, such as certain carcinomas and COVID-19. Bioactive compounds represent an alternative to its prevention and treatment. Phycobiliproteins (PBP) are bioactive compounds present in the microalga Porphyridium cruentum and, despite its antioxidant activity, their inhibitory effect on hemolysis has not been reported. The aim of this work was to evaluate the erythroprotective potential of phycobiliproteins from P. cruentum in different blood groups. The microalga was cultured in F/2 medium under controlled laboratory conditions. Day 10 of culture was determined as the harvest point. The microalgal biomass was lyophilized and a methanolic (MetOH), Tris HCl (T-HCl), and a physiological solution (PS) ultrasound-assisted extraction were performed. Extract pigments were quantified by spectrophotometry. The antioxidant activity of the extracts was evaluated with the ABTS+•, DPPH•, and FRAP methods, finding that the main antioxidant mechanism on the aqueous extracts was HAT (hydrogen atom transfer), while for MetOH it was SET (single electron transfer). The results of the AAPH, hypotonicity, and heat-induced hemolysis revealed a probable relationship between the different antigens (ABO and RhD) with the antihemolytic effect, highlighting the importance of bio-directed drugs.
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Affiliation(s)
- Rubria Lucía Peña-Medina
- Department of Scientific and Technological Research, University of Sonora, Blvd Luis Encinas y Reforma S/N, Col. Centro, Hermosillo 83000, Mexico
| | - Diana Fimbres-Olivarría
- Department of Scientific and Technological Research, University of Sonora, Blvd Luis Encinas y Reforma S/N, Col. Centro, Hermosillo 83000, Mexico
- Correspondence: (D.F.-O.); (R.I.G.-V.)
| | - Luis Fernando Enríquez-Ocaña
- Department of Scientific and Technological Research, University of Sonora, Blvd Luis Encinas y Reforma S/N, Col. Centro, Hermosillo 83000, Mexico
| | - Luis Rafael Martínez-Córdova
- Department of Scientific and Technological Research, University of Sonora, Blvd Luis Encinas y Reforma S/N, Col. Centro, Hermosillo 83000, Mexico
| | - Carmen Lizette Del-Toro-Sánchez
- Department of Research and Postgraduate in Food, University of Sonora, Blvd Luis Encinas y Rosales S/N, Col. Centro, Hermosillo 83000, Mexico
| | - José Antonio López-Elías
- Department of Scientific and Technological Research, University of Sonora, Blvd Luis Encinas y Reforma S/N, Col. Centro, Hermosillo 83000, Mexico
| | - Ricardo Iván González-Vega
- Department of Medical and Life Sciences, Cienega University Center (CUCIÉNEGA), University of Guadalajara, Av. Universidad 1115, Lindavista, Ocotlán 47820, Mexico
- Correspondence: (D.F.-O.); (R.I.G.-V.)
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12
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Chenchiliyan M, Kübel J, Ooi SA, Salvadori G, Mennucci B, Westenhoff S, Maj M. Ground-state heterogeneity and vibrational energy redistribution in bacterial phytochrome observed with femtosecond 2D IR spectroscopy. J Chem Phys 2023; 158:085103. [PMID: 36859103 DOI: 10.1063/5.0135268] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023] Open
Abstract
Phytochromes belong to a group of photoreceptor proteins containing a covalently bound biliverdin chromophore that inter-converts between two isomeric forms upon photoexcitation. The existence and stability of the photocycle products are largely determined by the protein sequence and the presence of conserved hydrogen-bonding interactions in the vicinity of the chromophore. The vibrational signatures of biliverdin, however, are often weak and obscured under more intense protein bands, limiting spectroscopic studies of its non-transient signals. In this study, we apply isotope-labeling techniques to isolate the vibrational bands from the protein-bound chromophore of the bacterial phytochrome from Deinococcus radiodurans. We elucidate the structure and ultrafast dynamics of the chromophore with 2D infra-red (IR) spectroscopy and molecular dynamics simulations. The carbonyl stretch vibrations of the pyrrole rings show the heterogeneous distribution of hydrogen-bonding structures, which exhibit distinct ultrafast relaxation dynamics. Moreover, we resolve a previously undetected 1678 cm-1 band that is strongly coupled to the A- and D-ring of biliverdin and demonstrate the presence of complex vibrational redistribution pathways between the biliverdin modes with relaxation-assisted measurements of 2D IR cross peaks. In summary, we expect 2D IR spectroscopy to be useful in explaining how point mutations in the protein sequence affect the hydrogen-bonding structure around the chromophore and consequently its ability to photoisomerize to the light-activated states.
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Affiliation(s)
- Manoop Chenchiliyan
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden
| | - Joachim Kübel
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden
| | - Saik Ann Ooi
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden
| | - Giacomo Salvadori
- Department of Chemistry and Industrial Chemistry, University of Pisa, Via G. Moruzzi 13, 56126 Pisa, Italy
| | - Benedetta Mennucci
- Department of Chemistry and Industrial Chemistry, University of Pisa, Via G. Moruzzi 13, 56126 Pisa, Italy
| | - Sebastian Westenhoff
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden
| | - Michał Maj
- Department of Chemistry-Ångström Laboratory, Uppsala University, SE-75120 Uppsala, Sweden
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13
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Wahlgren WY, Claesson E, Tuure I, Trillo-Muyo S, Bódizs S, Ihalainen JA, Takala H, Westenhoff S. Structural mechanism of signal transduction in a phytochrome histidine kinase. Nat Commun 2022; 13:7673. [PMID: 36509762 PMCID: PMC9744887 DOI: 10.1038/s41467-022-34893-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 11/10/2022] [Indexed: 12/14/2022] Open
Abstract
Phytochrome proteins detect red/far-red light to guide the growth, motion, development and reproduction in plants, fungi, and bacteria. Bacterial phytochromes commonly function as an entrance signal in two-component sensory systems. Despite the availability of three-dimensional structures of phytochromes and other two-component proteins, the conformational changes, which lead to activation of the protein, are not understood. We reveal cryo electron microscopy structures of the complete phytochrome from Deinoccocus radiodurans in its resting and photoactivated states at 3.6 Å and 3.5 Å resolution, respectively. Upon photoactivation, the photosensory core module hardly changes its tertiary domain arrangement, but the connector helices between the photosensory and the histidine kinase modules open up like a zipper, causing asymmetry and disorder in the effector domains. The structures provide a framework for atom-scale understanding of signaling in phytochromes, visualize allosteric communication over several nanometers, and suggest that disorder in the dimeric arrangement of the effector domains is important for phosphatase activity in a two-component system. The results have implications for the development of optogenetic applications.
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Affiliation(s)
- Weixiao Yuan Wahlgren
- grid.8761.80000 0000 9919 9582Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Elin Claesson
- grid.8761.80000 0000 9919 9582Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Iida Tuure
- grid.9681.60000 0001 1013 7965Department of Biological and Environmental Science, Nanoscience Center, University of Jyvaskyla, Jyvaskyla, Finland
| | - Sergio Trillo-Muyo
- grid.8761.80000 0000 9919 9582Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Gothenburg, Sweden
| | - Szabolcs Bódizs
- grid.8761.80000 0000 9919 9582Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Janne A. Ihalainen
- grid.9681.60000 0001 1013 7965Department of Biological and Environmental Science, Nanoscience Center, University of Jyvaskyla, Jyvaskyla, Finland
| | - Heikki Takala
- grid.9681.60000 0001 1013 7965Department of Biological and Environmental Science, Nanoscience Center, University of Jyvaskyla, Jyvaskyla, Finland ,grid.7737.40000 0004 0410 2071Faculty of Medicine, Anatomy, University of Helsinki, Helsinki, Finland
| | - Sebastian Westenhoff
- grid.8761.80000 0000 9919 9582Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden ,grid.8993.b0000 0004 1936 9457Department of Chemistry—BMC, Biochemistry, Uppsala University, Uppsala, Sweden
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14
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Sadeghi M, Balke J, Rafaluk-Mohr T, Alexiev U. Long-Distance Protonation-Conformation Coupling in Phytochrome Species. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27238395. [PMID: 36500486 PMCID: PMC9737838 DOI: 10.3390/molecules27238395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 11/25/2022] [Accepted: 11/27/2022] [Indexed: 12/04/2022]
Abstract
Phytochromes are biological red/far-red light sensors found in many organisms. The connection between photoconversion and the cellular output signal involves light-mediated global structural changes in the interaction between the photosensory module (PAS-GAF-PHY, PGP) and the C-terminal transmitter (output) module. We recently showed a direct correlation of chromophore deprotonation with pH-dependent conformational changes in the various domains of the prototypical phytochrome Cph1 PGP. These results suggested that the transient phycocyanobilin (PCB) chromophore deprotonation is closely associated with a higher protein mobility both in proximal and distal protein sites, implying a causal relationship that might be important for the global large-scale protein rearrangements. Here, we investigate the prototypical biliverdin (BV)-binding phytochrome Agp1. The structural changes at various positions in Agp1 PGP were investigated as a function of pH using picosecond time-resolved fluorescence anisotropy and site-directed fluorescence labeling of cysteine variants of Agp1 PGP. We show that the direct correlation of chromophore deprotonation with pH-dependent conformational changes does not occur in Agp1. Together with the absence of long-range effects between the PHY domain and chromophore pKa, in contrast to the findings in Cph1, our results imply phytochrome species-specific correlations between transient chromophore deprotonation and intramolecular signal transduction.
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15
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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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16
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Kurttila M, Etzl S, Rumfeldt J, Takala H, Galler N, Winkler A, Ihalainen JA. The structural effect between the output module and chromophore-binding domain is a two-way street via the hairpin extension. Photochem Photobiol Sci 2022; 21:1881-1894. [PMID: 35984631 PMCID: PMC9630206 DOI: 10.1007/s43630-022-00265-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 06/30/2022] [Indexed: 11/23/2022]
Abstract
Signal transduction typically starts with either ligand binding or cofactor activation, eventually affecting biological activities in the cell. In red light-sensing phytochromes, isomerization of the bilin chromophore results in regulation of the activity of diverse output modules. During this process, several structural elements and chemical events influence signal propagation. In our study, we have studied the full-length bacteriophytochrome from Deinococcus radiodurans as well as a previously generated optogenetic tool where the native histidine kinase output module has been replaced with an adenylate cyclase. We show that the composition of the output module influences the stability of the hairpin extension. The hairpin, often referred as the PHY tongue, is one of the central structural elements for signal transduction. It extends from a distinct domain establishing close contacts with the chromophore binding site. If the coupling between these interactions is disrupted, the dynamic range of the enzymatic regulation is reduced. Our study highlights the complex conformational properties of the hairpin extension as a bidirectional link between the chromophore-binding site and the output module, as well as functional properties of diverse output modules.
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Affiliation(s)
- Moona Kurttila
- Nanoscience Center, Department of Biological and Environmental Science, University of Jyväskylä, 40014, Jyväskylä, Finland
| | - Stefan Etzl
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/II, 8010, Graz, Austria
| | - Jessica Rumfeldt
- Nanoscience Center, Department of Biological and Environmental Science, University of Jyväskylä, 40014, Jyväskylä, Finland
| | - Heikki Takala
- Nanoscience Center, Department of Biological and Environmental Science, University of Jyväskylä, 40014, Jyväskylä, Finland
| | - Nadine Galler
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/II, 8010, Graz, Austria
| | - Andreas Winkler
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/II, 8010, Graz, Austria.
| | - Janne A Ihalainen
- Nanoscience Center, Department of Biological and Environmental Science, University of Jyväskylä, 40014, Jyväskylä, Finland.
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17
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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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18
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Böhm C, Gourinchas G, Zweytick S, Hujdur E, Reiter M, Trstenjak S, Sensen CW, Winkler A. Characterisation of sequence-structure-function space in sensor-effector integrators of phytochrome-regulated diguanylate cyclases. Photochem Photobiol Sci 2022; 21:1761-1779. [PMID: 35788917 PMCID: PMC9587094 DOI: 10.1007/s43630-022-00255-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 06/08/2022] [Indexed: 11/21/2022]
Abstract
Understanding the relationship between protein sequence, structure and function is one of the fundamental challenges in biochemistry. A direct correlation, however, is often not trivial since protein dynamics also play an important functional role-especially in signal transduction processes. In a subfamily of bacterial light sensors, phytochrome-activated diguanylate cyclases (PadCs), a characteristic coiled-coil linker element connects photoreceptor and output module, playing an essential role in signal integration. Combining phylogenetic analyses with biochemical characterisations, we were able to show that length and composition of this linker determine sensor-effector function and as such are under considerable evolutionary pressure. The linker length, together with the upstream PHY-specific domain, influences the dynamic range of effector activation and can even cause light-induced enzyme inhibition. We demonstrate phylogenetic clustering according to linker length, and the development of new linker lengths as well as new protein function within linker families. The biochemical characterisation of PadC homologs revealed that the functional coupling of PHY dimer interface and linker element defines signal integration and regulation of output functionality. A small subfamily of PadCs, characterised by a linker length breaking the coiled-coil pattern, shows a markedly different behaviour from other homologs. The effect of the central helical spine on PadC function highlights its essential role in signal integration as well as direct regulation of diguanylate cyclase activity. Appreciation of sensor-effector linkers as integrator elements and their coevolution with sensory modules is a further step towards the use of functionally diverse homologs as building blocks for rationally designed optogenetic tools.
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Affiliation(s)
- Cornelia Böhm
- Institute of Biochemistry, Graz University of Technology, 8010, Graz, Austria
- BioTechMed-Graz, 8010, Graz, Austria
| | - Geoffrey Gourinchas
- Institute of Biochemistry, Graz University of Technology, 8010, Graz, Austria
- Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67404, Illkirch, France
| | - Sophie Zweytick
- Institute of Biochemistry, Graz University of Technology, 8010, Graz, Austria
| | - Elvira Hujdur
- Institute of Biochemistry, Graz University of Technology, 8010, Graz, Austria
| | - Martina Reiter
- Institute of Biochemistry, Graz University of Technology, 8010, Graz, Austria
| | - Sara Trstenjak
- Institute of Biochemistry, Graz University of Technology, 8010, Graz, Austria
| | - Christoph Wilhelm Sensen
- BioTechMed-Graz, 8010, Graz, Austria
- Hungarian Centre of Excellence for Molecular Medicine, Római körút 21, 6723, Szeged, Hungary
| | - Andreas Winkler
- Institute of Biochemistry, Graz University of Technology, 8010, Graz, Austria.
- BioTechMed-Graz, 8010, Graz, Austria.
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19
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Sarabi D, Ostojić L, Bosman R, Vallejos A, Linse JB, Wulff M, Levantino M, Neutze R. Modeling difference x-ray scattering observations from an integral membrane protein within a detergent micelle. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2022; 9:054102. [PMID: 36329868 PMCID: PMC9625836 DOI: 10.1063/4.0000157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 09/15/2022] [Indexed: 06/16/2023]
Abstract
Time-resolved x-ray solution scattering (TR-XSS) is a sub-field of structural biology, which observes secondary structural changes in proteins as they evolve along their functional pathways. While the number of distinct conformational states and their rise and decay can be extracted directly from TR-XSS experimental data recorded from light-sensitive systems, structural modeling is more challenging. This step often builds from complementary structural information, including secondary structural changes extracted from crystallographic studies or molecular dynamics simulations. When working with integral membrane proteins, another challenge arises because x-ray scattering from the protein and the surrounding detergent micelle interfere and these effects should be considered during structural modeling. Here, we utilize molecular dynamics simulations to explicitly incorporate the x-ray scattering cross term between a membrane protein and its surrounding detergent micelle when modeling TR-XSS data from photoactivated samples of detergent solubilized bacteriorhodopsin. This analysis provides theoretical foundations in support of our earlier approach to structural modeling that did not explicitly incorporate this cross term and improves agreement between experimental data and theoretical predictions at lower x-ray scattering angles.
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Affiliation(s)
- Daniel Sarabi
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden
| | - Lucija Ostojić
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden
| | - Robert Bosman
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden
| | - Adams Vallejos
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden
| | - Johanna-Barbara Linse
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden
| | - Michael Wulff
- European Synchrotron Radiation Facility, 38043 Grenoble Cedex 9, France
| | - Matteo Levantino
- European Synchrotron Radiation Facility, 38043 Grenoble Cedex 9, France
| | - Richard Neutze
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden
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20
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Conserved histidine and tyrosine determine spectral responses through the water network in Deinococcus radiodurans phytochrome. PHOTOCHEMICAL & PHOTOBIOLOGICAL SCIENCES : OFFICIAL JOURNAL OF THE EUROPEAN PHOTOCHEMISTRY ASSOCIATION AND THE EUROPEAN SOCIETY FOR PHOTOBIOLOGY 2022; 21:1975-1989. [PMID: 35906527 DOI: 10.1007/s43630-022-00272-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 07/12/2022] [Indexed: 10/16/2022]
Abstract
Phytochromes are red light-sensing photoreceptor proteins that bind a bilin chromophore. Here, we investigate the role of a conserved histidine (H260) and tyrosine (Y263) in the chromophore-binding domain (CBD) of Deinococcus radiodurans phytochrome (DrBphP). Using crystallography, we show that in the H260A variant, the missing imidazole side chain leads to increased water content in the binding pocket. On the other hand, Y263F mutation reduces the water occupancy around the chromophore. Together, these changes in water coordination alter the protonation and spectroscopic properties of the biliverdin. These results pinpoint the importance of this conserved histidine and tyrosine, and the related water network, for the function and applications of phytochromes.
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21
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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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22
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Leopold AV, Thankachan S, Yang C, Gerashchenko D, Verkhusha VV. A general approach for engineering RTKs optically controlled with far-red light. Nat Methods 2022; 19:871-880. [PMID: 35681062 DOI: 10.1038/s41592-022-01517-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Accepted: 05/06/2022] [Indexed: 11/09/2022]
Abstract
Regulation of receptor tyrosine kinase (RTK) activity is necessary for studying cell signaling pathways in health and disease. We developed a generalized approach for engineering RTKs optically controlled with far-red light. We targeted the bacterial phytochrome DrBphP to the cell surface and allowed its light-induced conformational changes to be transmitted across the plasma membrane via transmembrane helices to intracellular RTK domains. Systematic optimization of these constructs has resulted in optically regulated epidermal growth factor receptor, HER2, TrkA, TrkB, FGFR1, IR1, cKIT and cMet, named eDrRTKs. eDrRTKs induced downstream signaling in mammalian cells in tens of seconds. The ability to activate eDrRTKs with far-red light enabled spectral multiplexing with fluorescent probes operating in a shorter spectral range, allowing for all-optical assays. We validated eDrTrkB performance in mice and found that minimally invasive stimulation in the neocortex with penetrating via skull far-red light-induced neural activity, early immediate gene expression and affected sleep patterns.
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Affiliation(s)
- Anna V Leopold
- Medicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | | | - Chun Yang
- Department of Psychiatry, Harvard Medical School, West Roxbury, MA, USA
| | | | - Vladislav V Verkhusha
- Medicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland. .,Department of Genetics and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY, USA.
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23
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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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24
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Morozov D, Modi V, Mironov V, Groenhof G. The Photocycle of Bacteriophytochrome Is Initiated by Counterclockwise Chromophore Isomerization. J Phys Chem Lett 2022; 13:4538-4542. [PMID: 35576453 PMCID: PMC9150100 DOI: 10.1021/acs.jpclett.2c00899] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Photoactivation of bacteriophytochrome involves a cis-trans photoisomerization of a biliverdin chromophore, but neither the precise sequence of events nor the direction of the isomerization is known. Here, we used nonadiabatic molecular dynamics simulations on the photosensory protein dimer to resolve the isomerization mechanism in atomic detail. In our simulations the photoisomerization of the D ring occurs in the counterclockwise direction. On a subpicosecond time scale, the photoexcited chromophore adopts a short-lived intermediate with a highly twisted configuration stabilized by an extended hydrogen-bonding network. Within tens of picoseconds, these hydrogen bonds break, allowing the chromophore to adopt a more planar configuration, which we assign to the early Lumi-R state. The isomerization process is completed via helix inversion of the biliverdin chromophore to form the late Lumi-R state. The mechanistic insights into the photoisomerization process are essential to understand how bacteriophytochrome has evolved to mediate photoactivation and to engineer this protein for new applications.
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Affiliation(s)
- Dmitry Morozov
- Nanoscience
Center and Department of Chemistry, University
of Jyväskylä, P.O. Box 35, 40014 Jyväskylä, Finland
| | - Vaibhav Modi
- Nanoscience
Center and Department of Chemistry, University
of Jyväskylä, P.O. Box 35, 40014 Jyväskylä, Finland
| | - Vladimir Mironov
- Department
of Chemistry, Kyungpook National University, Daegu 702-701, South Korea
| | - Gerrit Groenhof
- Nanoscience
Center and Department of Chemistry, University
of Jyväskylä, P.O. Box 35, 40014 Jyväskylä, Finland
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25
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Berntsson O, Terry AE, Plivelic TS. A setup for millisecond time-resolved X-ray solution scattering experiments at the CoSAXS beamline at the MAX IV Laboratory. JOURNAL OF SYNCHROTRON RADIATION 2022; 29:555-562. [PMID: 35254321 PMCID: PMC8900842 DOI: 10.1107/s1600577522000996] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 01/28/2022] [Indexed: 06/14/2023]
Abstract
The function of biomolecules is tightly linked to their structure, and changes therein. Time-resolved X-ray solution scattering has proven a powerful technique for interrogating structural changes and signal transduction in photoreceptor proteins. However, these only represent a small fraction of the biological macromolecules of interest. More recently, laser-induced temperature jumps have been introduced as a more general means of initiating structural changes in biomolecules. Here we present the development of a setup for millisecond time-resolved X-ray solution scattering experiments at the CoSAXS beamline, primarily using infrared laser light to trigger a temperature increase, and structural changes. We present results that highlight the characteristics of this setup along with data showing structural changes in lysozyme caused by a temperature jump. Further developments and applications of the setup are also discussed.
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Affiliation(s)
| | - Ann E. Terry
- MAX IV Laboratory, Lund University, Lund, Sweden
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26
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Jeong H, Ki H, Kim JG, Kim J, Lee Y, Ihee H. Sensitivity of
time‐resolved
diffraction data to changes in internuclear distances and atomic positions. B KOREAN CHEM SOC 2022. [DOI: 10.1002/bkcs.12494] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Haeyun Jeong
- Department of Chemistry and KI for the BioCentury Korea Advanced Institute of Science and Technology (KAIST) Daejeon Republic of Korea
| | - Hosung Ki
- Department of Chemistry and KI for the BioCentury Korea Advanced Institute of Science and Technology (KAIST) Daejeon Republic of Korea
- Center for Advanced Reaction Dynamics Institute for Basic Science (IBS) Daejeon Republic of Korea
| | - Jong Goo Kim
- Department of Chemistry and KI for the BioCentury Korea Advanced Institute of Science and Technology (KAIST) Daejeon Republic of Korea
- Center for Advanced Reaction Dynamics Institute for Basic Science (IBS) Daejeon Republic of Korea
| | - Jungmin Kim
- Department of Chemistry and KI for the BioCentury Korea Advanced Institute of Science and Technology (KAIST) Daejeon Republic of Korea
- Center for Advanced Reaction Dynamics Institute for Basic Science (IBS) Daejeon Republic of Korea
| | - Yunbeom Lee
- Department of Chemistry and KI for the BioCentury Korea Advanced Institute of Science and Technology (KAIST) Daejeon Republic of Korea
- Center for Advanced Reaction Dynamics Institute for Basic Science (IBS) Daejeon Republic of Korea
| | - Hyotcherl Ihee
- Department of Chemistry and KI for the BioCentury Korea Advanced Institute of Science and Technology (KAIST) Daejeon Republic of Korea
- Center for Advanced Reaction Dynamics Institute for Basic Science (IBS) Daejeon Republic of Korea
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27
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Lehtinen K, Nokia MS, Takala H. Red Light Optogenetics in Neuroscience. Front Cell Neurosci 2022; 15:778900. [PMID: 35046775 PMCID: PMC8761848 DOI: 10.3389/fncel.2021.778900] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 12/02/2021] [Indexed: 12/25/2022] Open
Abstract
Optogenetics, a field concentrating on controlling cellular functions by means of light-activated proteins, has shown tremendous potential in neuroscience. It possesses superior spatiotemporal resolution compared to the surgical, electrical, and pharmacological methods traditionally used in studying brain function. A multitude of optogenetic tools for neuroscience have been created that, for example, enable the control of action potential generation via light-activated ion channels. Other optogenetic proteins have been used in the brain, for example, to control long-term potentiation or to ablate specific subtypes of neurons. In in vivo applications, however, the majority of optogenetic tools are operated with blue, green, or yellow light, which all have limited penetration in biological tissues compared to red light and especially infrared light. This difference is significant, especially considering the size of the rodent brain, a major research model in neuroscience. Our review will focus on the utilization of red light-operated optogenetic tools in neuroscience. We first outline the advantages of red light for in vivo studies. Then we provide a brief overview of the red light-activated optogenetic proteins and systems with a focus on new developments in the field. Finally, we will highlight different tools and applications, which further facilitate the use of red light optogenetics in neuroscience.
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Affiliation(s)
- Kimmo Lehtinen
- Department of Biological and Environmental Science, Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
| | - Miriam S. Nokia
- Department of Psychology, University of Jyväskylä, Jyväskylä, Finland
- Centre for Interdisciplinary Brain Research, University of Jyväskylä, Jyväskylä, Finland
| | - Heikki Takala
- Department of Biological and Environmental Science, Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
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28
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Choi EH, Lee Y, Heo J, Ihee H. Reaction dynamics studied via femtosecond X-ray liquidography at X-ray free-electron lasers. Chem Sci 2022; 13:8457-8490. [PMID: 35974755 PMCID: PMC9337737 DOI: 10.1039/d2sc00502f] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 06/06/2022] [Indexed: 02/04/2023] Open
Abstract
X-ray free-electron lasers (XFELs) provide femtosecond X-ray pulses suitable for pump–probe time-resolved studies with a femtosecond time resolution. Since the advent of the first XFEL in 2009, recent years have witnessed a great number of applications with various pump–probe techniques at XFELs. Among these, time-resolved X-ray liquidography (TRXL) is a powerful method for visualizing structural dynamics in the liquid solution phase. Here, we classify various chemical and biological molecular systems studied via femtosecond TRXL (fs-TRXL) at XFELs, depending on the focus of the studied process, into (i) bond cleavage and formation, (ii) charge distribution and electron transfer, (iii) orientational dynamics, (iv) solvation dynamics, (v) coherent nuclear wavepacket dynamics, and (vi) protein structural dynamics, and provide a brief review on each category. We also lay out a plausible roadmap for future fs-TRXL studies for areas that have not been explored yet. Femtosecond X-ray liquidography using X-ray free-electron lasers (XFELs) visualizes various aspects of reaction dynamics.![]()
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Affiliation(s)
- Eun Hyuk Choi
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
- 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
| | - Yunbeom Lee
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
- 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
| | - Jun Heo
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
- 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
| | - Hyotcherl Ihee
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
- 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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29
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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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30
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Otero LH, Foscaldi S, Antelo GT, Rosano GL, Sirigu S, Klinke S, Defelipe LA, Sánchez-Lamas M, Battocchio G, Conforte V, Vojnov AA, Chavas LMG, Goldbaum FA, Mroginski MA, Rinaldi J, Bonomi HR. Structural basis for the Pr-Pfr long-range signaling mechanism of a full-length bacterial phytochrome at the atomic level. SCIENCE ADVANCES 2021; 7:eabh1097. [PMID: 34818032 PMCID: PMC8612531 DOI: 10.1126/sciadv.abh1097] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 09/22/2021] [Indexed: 06/13/2023]
Abstract
Phytochromes constitute a widespread photoreceptor family that typically interconverts between two photostates called Pr (red light–absorbing) and Pfr (far-red light–absorbing). The lack of full-length structures solved at the (near-)atomic level in both pure Pr and Pfr states leaves gaps in the structural mechanisms involved in the signal transmission pathways during the photoconversion. Here, we present the crystallographic structures of three versions from the plant pathogen Xanthomonas campestris virulence regulator XccBphP bacteriophytochrome, including two full-length proteins, in the Pr and Pfr states. The structures show a reorganization of the interaction networks within and around the chromophore-binding pocket, an α-helix/β-sheet tongue transition, and specific domain reorientations, along with interchanging kinks and breaks at the helical spine as a result of the photoswitching, which subsequently affect the quaternary assembly. These structural findings, combined with multidisciplinary studies, allow us to describe the signaling mechanism of a full-length bacterial phytochrome at the atomic level.
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Affiliation(s)
- Lisandro H. Otero
- Fundación Instituto Leloir, IIBBA-CONICET, Av. Patricias Argentinas 435 (C1405BWE), Buenos Aires, Argentina
- Plataforma Argentina de Biología Estructural y Metabolómica PLABEM, Av. Patricias Argentinas 435 (C1405BWE), Buenos Aires, Argentina
| | - Sabrina Foscaldi
- Fundación Instituto Leloir, IIBBA-CONICET, Av. Patricias Argentinas 435 (C1405BWE), Buenos Aires, Argentina
| | - Giuliano T. Antelo
- Fundación Instituto Leloir, IIBBA-CONICET, Av. Patricias Argentinas 435 (C1405BWE), Buenos Aires, Argentina
| | - Germán L. Rosano
- Unidad de Espectrometría de Masa, Instituto de Biología Molecular y Celular de Rosario, UEM-IBR, CONICET, Bv. 27 de Febrero (S2000EZP), Rosario, Argentina
| | - Serena Sirigu
- Proxima-1, Synchrotron SOLEIL, L’Orme des Merisiers, Saint-Aubin, BP 48 (91192), Gif-sur-Yvette Cedex, France
| | - Sebastián Klinke
- Fundación Instituto Leloir, IIBBA-CONICET, Av. Patricias Argentinas 435 (C1405BWE), Buenos Aires, Argentina
- Plataforma Argentina de Biología Estructural y Metabolómica PLABEM, Av. Patricias Argentinas 435 (C1405BWE), Buenos Aires, Argentina
| | - Lucas A. Defelipe
- European Molecular Biology Laboratory (EMBL), Hamburg Unit, Notkestrasse 85 (22607), Hamburg, Germany
| | - Maximiliano Sánchez-Lamas
- Fundación Instituto Leloir, IIBBA-CONICET, Av. Patricias Argentinas 435 (C1405BWE), Buenos Aires, Argentina
| | - Giovanni Battocchio
- Technische Universität Berlin, Institute of Chemistry, Strasse des 17. Juni 135 (D-10623), Berlin, Germany
| | - Valeria Conforte
- Instituto de Ciencia y Tecnología Dr. César Milstein, Fundación Pablo Cassará, CONICET, Saladillo 2468 (C1440FFX), Buenos Aires, Argentina
| | - Adrián A. Vojnov
- Instituto de Ciencia y Tecnología Dr. César Milstein, Fundación Pablo Cassará, CONICET, Saladillo 2468 (C1440FFX), Buenos Aires, Argentina
| | - Leonard M. G. Chavas
- Proxima-1, Synchrotron SOLEIL, L’Orme des Merisiers, Saint-Aubin, BP 48 (91192), Gif-sur-Yvette Cedex, France
- Synchrotron Radiation Research Center, Nagoya University, Nagoya 464-8603, Japan
| | - Fernando A. Goldbaum
- Fundación Instituto Leloir, IIBBA-CONICET, Av. Patricias Argentinas 435 (C1405BWE), Buenos Aires, Argentina
- Plataforma Argentina de Biología Estructural y Metabolómica PLABEM, Av. Patricias Argentinas 435 (C1405BWE), Buenos Aires, Argentina
| | - Maria-Andrea Mroginski
- Technische Universität Berlin, Institute of Chemistry, Strasse des 17. Juni 135 (D-10623), Berlin, Germany
| | - Jimena Rinaldi
- Fundación Instituto Leloir, IIBBA-CONICET, Av. Patricias Argentinas 435 (C1405BWE), Buenos Aires, Argentina
| | - Hernán R. Bonomi
- Fundación Instituto Leloir, IIBBA-CONICET, Av. Patricias Argentinas 435 (C1405BWE), Buenos Aires, Argentina
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31
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Orädd F, Ravishankar H, Goodman J, Rogne P, Backman L, Duelli A, Nors Pedersen M, Levantino M, Wulff M, Wolf-Watz M, Andersson M. Tracking the ATP-binding response in adenylate kinase in real time. SCIENCE ADVANCES 2021; 7:eabi5514. [PMID: 34788091 PMCID: PMC8597995 DOI: 10.1126/sciadv.abi5514] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 09/27/2021] [Indexed: 05/25/2023]
Abstract
The biological function of proteins is critically dependent on dynamics inherent to the native structure. Such structural dynamics obey a predefined order and temporal timing to execute the specific reaction. Determination of the cooperativity of key structural rearrangements requires monitoring protein reactions in real time. In this work, we used time-resolved x-ray solution scattering (TR-XSS) to visualize structural changes in the Escherichia coli adenylate kinase (AdK) enzyme upon laser-induced activation of a protected ATP substrate. A 4.3-ms transient intermediate showed partial closing of both the ATP- and AMP-binding domains, which indicates a cooperative closing mechanism. The ATP-binding domain also showed local unfolding and breaking of an Arg131-Asp146 salt bridge. Nuclear magnetic resonance spectroscopy data identified similar unfolding in an Arg131Ala AdK mutant, which refolded in a closed, substrate-binding conformation. The observed structural dynamics agree with a “cracking mechanism” proposed to underlie global structural transformation, such as allostery, in proteins.
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Affiliation(s)
- Fredrik Orädd
- Department of Chemistry, Umeå University, Linnaeus Väg 10, 901 87 Umeå, Sweden
| | - Harsha Ravishankar
- Department of Chemistry, Umeå University, Linnaeus Väg 10, 901 87 Umeå, Sweden
| | - Jack Goodman
- Department of Chemistry, Umeå University, Linnaeus Väg 10, 901 87 Umeå, Sweden
| | - Per Rogne
- Department of Chemistry, Umeå University, Linnaeus Väg 10, 901 87 Umeå, Sweden
| | - Lars Backman
- Department of Chemistry, Umeå University, Linnaeus Väg 10, 901 87 Umeå, Sweden
| | - Annette Duelli
- Department of Biomedical Sciences, University of Copenhagen, Blegdamsvej 3, 2200 Copenhagen, Denmark
| | - Martin Nors Pedersen
- ESRF—The European Synchrotron, 71 Avenue des Martyrs, CS40220, 38043 Grenoble, Cedex 9, France
| | - Matteo Levantino
- ESRF—The European Synchrotron, 71 Avenue des Martyrs, CS40220, 38043 Grenoble, Cedex 9, France
| | - Michael Wulff
- ESRF—The European Synchrotron, 71 Avenue des Martyrs, CS40220, 38043 Grenoble, Cedex 9, France
| | - Magnus Wolf-Watz
- Department of Chemistry, Umeå University, Linnaeus Väg 10, 901 87 Umeå, Sweden
| | - Magnus Andersson
- Department of Chemistry, Umeå University, Linnaeus Väg 10, 901 87 Umeå, Sweden
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32
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Brändén G, Neutze R. Advances and challenges in time-resolved macromolecular crystallography. Science 2021; 373:373/6558/eaba0954. [PMID: 34446579 DOI: 10.1126/science.aba0954] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Conformational changes within biological macromolecules control a vast array of chemical reactions in living cells. Time-resolved crystallography can reveal time-dependent structural changes that occur within protein crystals, yielding chemical insights in unparalleled detail. Serial crystallography approaches developed at x-ray free-electron lasers are now routinely used for time-resolved diffraction studies of macromolecules. These techniques are increasingly being applied at synchrotron radiation sources and to a growing diversity of macromolecules. Here, we review recent progress in the field, including visualizing ultrafast structural changes that guide the initial trajectories of light-driven reactions as well as capturing biologically important conformational changes on slower time scales, for which bacteriorhodopsin and photosystem II are presented as illustrative case studies.
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Affiliation(s)
- Gisela Brändén
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Richard Neutze
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden.
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33
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Lee SJ, Kim Y, Kim TW, Yang C, Thamilselvan K, Jeong H, Hyun J, Ihee H. Reversible molecular motional switch based on circular photoactive protein oligomers exhibits unexpected photo-induced contraction. CELL REPORTS. PHYSICAL SCIENCE 2021; 2:100512. [PMID: 35509376 PMCID: PMC9062587 DOI: 10.1016/j.xcrp.2021.100512] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Molecular switches alterable between two stable states by environmental stimuli, such as light and temperature, offer the potential for controlling biological functions. Here, we report a circular photoswitchable protein complex made of multiple protein molecules that can rapidly and reversibly switch with significant conformational changes. The structural and photochromic properties of photoactive yellow protein (PYP) are harnessed to construct circular oligomer PYPs (coPYPs) of desired sizes. Considering the light-induced N-terminal protrusion of monomer PYP, we expected coPYPs would expand upon irradiation, but time-resolved X-ray scattering data reveal that the late intermediate has a pronounced light-induced contraction motion. This work not only provides an approach to engineering a novel protein-based molecular switch based on circular oligomers of well-known protein units but also demonstrates the importance of characterizing the structural dynamics of designed molecular switches.
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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 Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon 34141, Republic of Korea
- These authors contributed equally
| | - Youngmin Kim
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon 34141, Republic of Korea
- These authors contributed equally
| | - Tae Wu Kim
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- Center for Nanomaterials and Chemical Reactions, 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 Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon 34141, Republic of Korea
| | - Kamatchi Thamilselvan
- Department of Chemistry and KI for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon 34141, Republic of Korea
| | - Hyeongseop Jeong
- Center for Research Equipment, Korea Basic Science Institute (KBSI), Cheongju-si, Chungcheongbuk-do 28119, Republic of Korea
| | - Jaekyung Hyun
- Center for Research Equipment, Korea Basic Science Institute (KBSI), Cheongju-si, Chungcheongbuk-do 28119, Republic of Korea
- Molecular Cryo-Electron Microscopy Unit, Okinawa Institute of Science and Technology (OIST), Okinawa 904-0495, Japan
| | - 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 Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon 34141, Republic of Korea
- Lead contact
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34
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Böhm C, Todorović N, Balasso M, Gourinchas G, Winkler A. The PHY Domain Dimer Interface of Bacteriophytochromes Mediates Cross-talk between Photosensory Modules and Output Domains. J Mol Biol 2021; 433:167092. [PMID: 34116122 PMCID: PMC7615318 DOI: 10.1016/j.jmb.2021.167092] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 05/21/2021] [Accepted: 06/01/2021] [Indexed: 10/21/2022]
Abstract
Protein dynamics play a major role for the catalytic function of enzymes, the interaction of protein complexes or signal integration in regulatory proteins. In the context of multi-domain proteins involved in light-regulation of enzymatic effectors, the central role of conformational dynamics is well established. Light activation of sensory modules is followed by long-range signal transduction to different effectors; rather than domino-style structural rearrangements, a complex interplay of functional elements is required to maintain functionality. One family of such sensor-effector systems are red-light-regulated phytochromes that control diguanylate cyclases involved in cyclic-dimeric-GMP formation. Based on structural and functional studies of one prototypic family member, the central role of the coiled-coil sensor-effector linker was established. Interestingly, subfamilies with different linker lengths feature strongly varying biochemical characteristics. The dynamic interplay of the domains involved, however, is presently not understood. Here we show that the PHY domain dimer interface plays an essential role in signal integration, and that a functional coupling with the coiled-coil linker element is crucial. Chimaeras of two biochemically different family members highlight the phytochrome-spanning helical spine as an essential structural element involved in light-dependent upregulation of enzymatic turnover. However, isolated structural elements can frequently not be assigned to individual characteristics, which further emphasises the importance of global conformational dynamics. Our results provide insights into the intricate processes at play during light signal integration and transduction in these photosensory systems and thus provide additional guidelines for a more directed design of novel sensor-effector combinations with potential applications as optogenetic tools.
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Affiliation(s)
- Cornelia Böhm
- Institute of Biochemistry, Graz University of Technology, 8010 Graz, Austria; BioTechMed-Graz, 8010 Graz, Austria
| | - Nikolina Todorović
- Institute of Biochemistry, Graz University of Technology, 8010 Graz, Austria
| | - Marco Balasso
- Institute of Biochemistry, Graz University of Technology, 8010 Graz, Austria
| | - Geoffrey Gourinchas
- Institute of Biochemistry, Graz University of Technology, 8010 Graz, Austria
| | - Andreas Winkler
- Institute of Biochemistry, Graz University of Technology, 8010 Graz, Austria; BioTechMed-Graz, 8010 Graz, Austria.
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35
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Multamäki E, Nanekar R, Morozov D, Lievonen T, Golonka D, Wahlgren WY, Stucki-Buchli B, Rossi J, Hytönen VP, Westenhoff S, Ihalainen JA, Möglich A, Takala H. Comparative analysis of two paradigm bacteriophytochromes reveals opposite functionalities in two-component signaling. Nat Commun 2021; 12:4394. [PMID: 34285211 PMCID: PMC8292422 DOI: 10.1038/s41467-021-24676-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 06/30/2021] [Indexed: 02/06/2023] Open
Abstract
Bacterial phytochrome photoreceptors usually belong to two-component signaling systems which transmit environmental stimuli to a response regulator through a histidine kinase domain. Phytochromes switch between red light-absorbing and far-red light-absorbing states. Despite exhibiting extensive structural responses during this transition, the model bacteriophytochrome from Deinococcus radiodurans (DrBphP) lacks detectable kinase activity. Here, we resolve this long-standing conundrum by comparatively analyzing the interactions and output activities of DrBphP and a bacteriophytochrome from Agrobacterium fabrum (Agp1). Whereas Agp1 acts as a conventional histidine kinase, we identify DrBphP as a light-sensitive phosphatase. While Agp1 binds its cognate response regulator only transiently, DrBphP does so strongly, which is rationalized at the structural level. Our data pinpoint two key residues affecting the balance between kinase and phosphatase activities, which immediately bears on photoreception and two-component signaling. The opposing output activities in two highly similar bacteriophytochromes suggest the use of light-controllable histidine kinases and phosphatases for optogenetics.
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Affiliation(s)
- Elina Multamäki
- grid.7737.40000 0004 0410 2071Faculty of Medicine, Anatomy, University of Helsinki, Helsinki, Finland
| | - Rahul Nanekar
- grid.9681.60000 0001 1013 7965Department of Biological and Environmental Science, Nanoscience Center, University of Jyvaskyla, Jyvaskyla, Finland
| | - Dmitry Morozov
- grid.9681.60000 0001 1013 7965Department of Chemistry, Nanoscience Center, University of Jyvaskyla, Jyvaskyla, Finland
| | - Topias Lievonen
- grid.9681.60000 0001 1013 7965Department of Biological and Environmental Science, Nanoscience Center, University of Jyvaskyla, Jyvaskyla, Finland
| | - David Golonka
- grid.7384.80000 0004 0467 6972Lehrstuhl für Biochemie, Universität Bayreuth, Bayreuth, Germany
| | - Weixiao Yuan Wahlgren
- grid.8761.80000 0000 9919 9582Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Brigitte Stucki-Buchli
- grid.9681.60000 0001 1013 7965Department of Biological and Environmental Science, Nanoscience Center, University of Jyvaskyla, Jyvaskyla, Finland
| | - Jari Rossi
- grid.7737.40000 0004 0410 2071Faculty of Medicine, Anatomy, University of Helsinki, Helsinki, Finland
| | - Vesa P. Hytönen
- grid.502801.e0000 0001 2314 6254Faculty of Medicine and Health Technology, BioMediTech, Tampere University, Tampere, Finland ,grid.511163.10000 0004 0518 4910Fimlab Laboratories, Tampere, Finland
| | - Sebastian Westenhoff
- grid.8761.80000 0000 9919 9582Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Janne A. Ihalainen
- grid.9681.60000 0001 1013 7965Department of Biological and Environmental Science, Nanoscience Center, University of Jyvaskyla, Jyvaskyla, Finland
| | - Andreas Möglich
- grid.7384.80000 0004 0467 6972Lehrstuhl für Biochemie, Universität Bayreuth, Bayreuth, Germany
| | - Heikki Takala
- grid.7737.40000 0004 0410 2071Faculty of Medicine, Anatomy, University of Helsinki, Helsinki, Finland ,grid.9681.60000 0001 1013 7965Department of Biological and Environmental Science, Nanoscience Center, University of Jyvaskyla, Jyvaskyla, Finland
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36
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Kurttila M, Stucki-Buchli B, Rumfeldt J, Schroeder L, Häkkänen H, Liukkonen A, Takala H, Kottke T, Ihalainen JA. Site-by-site tracking of signal transduction in an azidophenylalanine-labeled bacteriophytochrome with step-scan FTIR spectroscopy. Phys Chem Chem Phys 2021; 23:5615-5628. [PMID: 33656023 DOI: 10.1039/d0cp06553f] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Signal propagation in photosensory proteins is a complex and multidimensional event. Unraveling such mechanisms site-specifically in real time is an eligible but a challenging goal. Here, we elucidate the site-specific events in a red-light sensing phytochrome using the unnatural amino acid azidophenylalanine, vibrationally distinguishable from all other protein signals. In canonical phytochromes, signal transduction starts with isomerization of an excited bilin chromophore, initiating a multitude of processes in the photosensory unit of the protein, which eventually control the biochemical activity of the output domain, nanometers away from the chromophore. By implementing the label in prime protein locations and running two-color step-scan FTIR spectroscopy on the Deinococcus radiodurans bacteriophytochrome, we track the signal propagation at three specific sites in the photosensory unit. We show that a structurally switchable hairpin extension, a so-called tongue region, responds to the photoconversion already in microseconds and finalizes its structural changes concomitant with the chromophore, in milliseconds. In contrast, kinetics from the other two label positions indicate that the site-specific changes deviate from the chromophore actions, even though the labels locate in the chromophore vicinity. Several other sites for labeling resulted in impaired photoswitching, low structural stability, or no changes in the difference spectrum, which provides additional information on the inner dynamics of the photosensory unit. Our work enlightens the multidimensionality of the structural changes of proteins under action. The study also shows that the signaling mechanism of phytochromes is accessible in a time-resolved and site-specific approach by azido probes and demonstrates challenges in using these labels.
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Affiliation(s)
- Moona Kurttila
- University of Jyväskylä, Nanoscience Center, Department of Biological and Environmental Science, 40014 Jyväskylä, Finland.
| | - Brigitte Stucki-Buchli
- University of Jyväskylä, Nanoscience Center, Department of Biological and Environmental Science, 40014 Jyväskylä, Finland.
| | - Jessica Rumfeldt
- University of Jyväskylä, Nanoscience Center, Department of Biological and Environmental Science, 40014 Jyväskylä, Finland.
| | - Lea Schroeder
- Physical and Biophysical Chemistry, Department of Chemistry, Bielefeld University, Universitätsstr. 25, 33615 Bielefeld, Germany.
| | - Heikki Häkkänen
- University of Jyväskylä, Nanoscience Center, Department of Biological and Environmental Science, 40014 Jyväskylä, Finland.
| | - Alli Liukkonen
- University of Jyväskylä, Nanoscience Center, Department of Biological and Environmental Science, 40014 Jyväskylä, Finland.
| | - Heikki Takala
- University of Jyväskylä, Nanoscience Center, Department of Biological and Environmental Science, 40014 Jyväskylä, Finland.
| | - Tilman Kottke
- Physical and Biophysical Chemistry, Department of Chemistry, Bielefeld University, Universitätsstr. 25, 33615 Bielefeld, Germany.
| | - Janne A Ihalainen
- University of Jyväskylä, Nanoscience Center, Department of Biological and Environmental Science, 40014 Jyväskylä, Finland.
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Abstract
The perception of light signals by the phytochrome family of photoreceptors has a crucial influence on almost all aspects of growth and development throughout a plant's life cycle. The holistic regulatory networks orchestrated by phytochromes, including conformational switching, subcellular localization, direct protein-protein interactions, transcriptional and posttranscriptional regulations, and translational and posttranslational controls to promote photomorphogenesis, are highly coordinated and regulated at multiple levels. During the past decade, advances using innovative approaches have substantially broadened our understanding of the sophisticated mechanisms underlying the phytochrome-mediated light signaling pathways. This review discusses and summarizes these discoveries of the role of the modular structure of phytochromes, phytochrome-interacting proteins, and their functions; the reciprocal modulation of both positive and negative regulators in phytochrome signaling; the regulatory roles of phytochromes in transcriptional activities, alternative splicing, and translational regulation; and the kinases and E3 ligases that modulate PHYTOCHROME INTERACTING FACTORs to optimize photomorphogenesis.
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Affiliation(s)
- Mei-Chun Cheng
- Department of Biochemical Science and Technology, National Taiwan University, Taipei 10617, Taiwan
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, USA;
| | - Praveen Kumar Kathare
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, USA;
| | - Inyup Paik
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, USA;
| | - Enamul Huq
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, USA;
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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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39
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Wahlgren WY, Golonka D, Westenhoff S, Möglich A. Cryo-Electron Microscopy of Arabidopsis thaliana Phytochrome A in Its Pr State Reveals Head-to-Head Homodimeric Architecture. FRONTIERS IN PLANT SCIENCE 2021; 12:663751. [PMID: 34108981 PMCID: PMC8182759 DOI: 10.3389/fpls.2021.663751] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 03/29/2021] [Indexed: 06/12/2023]
Abstract
Phytochrome photoreceptors regulate vital adaptations of plant development, growth, and physiology depending on the ratio of red and far-red light. The light-triggered Z/E isomerization of a covalently bound bilin chromophore underlies phytochrome photoconversion between the red-absorbing Pr and far-red-absorbing Pfr states. Compared to bacterial phytochromes, the molecular mechanisms of signal propagation to the C-terminal module and its regulation are little understood in plant phytochromes, not least owing to a dearth of structural information. To address this deficit, we studied the Arabidopsis thaliana phytochrome A (AtphyA) at full length by cryo-electron microscopy (cryo-EM). Following heterologous expression in Escherichia coli, we optimized the solvent conditions to overcome protein aggregation and thus obtained photochemically active, near-homogenous AtphyA. We prepared grids for cryo-EM analysis of AtphyA in its Pr state and conducted single-particle analysis. The resulting two-dimensional class averages and the three-dimensional electron density map at 17 Å showed a homodimeric head-to-head assembly of AtphyA. Docking of domain structures into the electron density revealed a separation of the AtphyA homodimer at the junction of its photosensor and effector modules, as reflected in a large void in the middle of map. The overall architecture of AtphyA resembled that of bacterial phytochromes, thus hinting at commonalities in signal transduction and mechanism between these receptors. Our work paves the way toward future studies of the structure, light response, and interactions of full-length phytochromes by cryo-EM.
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Affiliation(s)
- Weixiao Yuan Wahlgren
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - David Golonka
- Lehrstuhl fur Biochemie, Universität Bayreuth, Bayreuth, Germany
| | - Sebastian Westenhoff
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Andreas Möglich
- Lehrstuhl fur Biochemie, Universität Bayreuth, Bayreuth, Germany
- Bayreuth Center for Biochemistry and Molecular Biology, Universität Bayreuth, Bayreuth, Germany
- North-Bavarian NMR Center, Universität Bayreuth, Bayreuth, Germany
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40
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Conforte V, Otero LH, Toum L, Sirigu S, Antelo GT, Rinaldi J, Foscaldi S, Klinke S, Chavas LMG, Vojnov AA, Goldbaum FA, Malamud F, Bonomi HR. Pr-favoured variants of the bacteriophytochrome from the plant pathogen Xanthomonas campestris hint on light regulation of virulence-associated mechanisms. FEBS J 2021; 288:5986-6002. [PMID: 33864705 DOI: 10.1111/febs.15883] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 02/25/2021] [Accepted: 04/14/2021] [Indexed: 11/29/2022]
Abstract
Red/far-red light-sensing bacteriophytochrome photoreceptor (BphP) pathways play key roles in bacterial physiology and ecology. These bilin-binding proteins photoswitch between two states, Pr (red absorbing) and Pfr (far-red absorbing). The isomerization of the chromophore and the downstream structural changes result in the light signal transduction. The agricultural pathogen Xanthomonas campestris pv. campestris (Xcc) code for a single bathy-like type BphP (XccBphP), previously shown to negatively regulate several light-mediated biological processes involved in virulence. Here, we generated three different full-length variants with single amino acid changes within its GAF domain that affect the XccBphP photocycle favouring its Pr state: L193Q, L193N and D199A. While D199A recombinant protein locks XccBphP in a Pr-like state, L193Q and L193N exhibit a significant enrichment of the Pr form in thermal equilibrium. The X-ray crystal structures of the three variants were solved, resembling the wild-type protein in the Pr state. Finally, we studied the effects of altering the XccBphP photocycle on the exopolysaccharide xanthan production and stomatal aperture assays as readouts of its bacterial signalling pathway. Null-mutant complementation assays show that the photoactive Pr-favoured XccBphP variants L193Q and L193N tend to negatively regulate xanthan production in vivo. In addition, our results indicate that strains expressing these variants also promote stomatal apertures in challenged plant epidermal peels, compared to wild-type Xcc. The findings presented in this work provide new evidence on the Pr state of XccBphP as a negative regulator of the virulence-associated mechanisms by light in Xcc.
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Affiliation(s)
- Valeria Conforte
- Instituto de Ciencia y Tecnología Dr. César Milstein, Fundación Pablo Cassará, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad de Autónoma de Buenos Aires, Argentina
| | - Lisandro Horacio Otero
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires, Argentina.,Plataforma Argentina de Biología Estructural y Metabolómica PLABEM, Ciudad Autónoma de Buenos Aires, Argentina
| | - Laila Toum
- Instituto de Ciencia y Tecnología Dr. César Milstein, Fundación Pablo Cassará, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad de Autónoma de Buenos Aires, Argentina
| | - Serena Sirigu
- Synchrotron SOLEIL, L'Orme des Merisiers Saint-Aubin, Gif sur Yvette, France
| | - Giuliano Tomás Antelo
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires, Argentina
| | - Jimena Rinaldi
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires, Argentina
| | - Sabrina Foscaldi
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires, Argentina
| | - Sebastián Klinke
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires, Argentina.,Plataforma Argentina de Biología Estructural y Metabolómica PLABEM, Ciudad Autónoma de Buenos Aires, Argentina
| | - Leonard Michel Gabriel Chavas
- Synchrotron SOLEIL, L'Orme des Merisiers Saint-Aubin, Gif sur Yvette, France.,Synchrotron Radiation Research Center, Nagoya University, Nagoya, Japan
| | - Adrián Alberto Vojnov
- Instituto de Ciencia y Tecnología Dr. César Milstein, Fundación Pablo Cassará, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad de Autónoma de Buenos Aires, Argentina
| | - Fernando Alberto Goldbaum
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires, Argentina.,Plataforma Argentina de Biología Estructural y Metabolómica PLABEM, Ciudad Autónoma de Buenos Aires, Argentina
| | - Florencia Malamud
- Departamento de Ciencias Básicas, Universidad Nacional de Luján, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Luján, Buenos Aires, Argentina
| | - Hernán Ruy Bonomi
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires, Argentina
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41
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Poddar H, Heyes DJ, Schirò G, Weik M, Leys D, Scrutton NS. A guide to time-resolved structural analysis of light-activated proteins. FEBS J 2021; 289:576-595. [PMID: 33864718 DOI: 10.1111/febs.15880] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 04/03/2021] [Accepted: 04/13/2021] [Indexed: 01/08/2023]
Abstract
Dynamical changes in protein structures are essential for protein function and occur over femtoseconds to seconds timescales. X-ray free electron lasers have facilitated investigations of structural dynamics in proteins with unprecedented temporal and spatial resolution. Light-activated proteins are attractive targets for time-resolved structural studies, as the reaction chemistry and associated protein structural changes can be triggered by short laser pulses. Proteins with different light-absorbing centres have evolved to detect light and harness photon energy to bring about downstream chemical and biological output responses. Following light absorption, rapid chemical/small-scale structural changes are typically localised around the chromophore. These localised changes are followed by larger structural changes propagated throughout the photoreceptor/photocatalyst that enables the desired chemical and/or biological output response. Time-resolved serial femtosecond crystallography (SFX) and solution scattering techniques enable direct visualisation of early chemical change in light-activated proteins on timescales previously inaccessible, whereas scattering gives access to slower timescales associated with more global structural change. Here, we review how advances in time-resolved SFX and solution scattering techniques have uncovered mechanisms of photochemistry and its coupling to output responses. We also provide a prospective on how these time-resolved structural approaches might impact on other photoreceptors/photoenzymes that have not yet been studied by these methods.
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Affiliation(s)
- Harshwardhan Poddar
- Manchester Institute of Biotechnology, Department of Chemistry, University of Manchester, UK
| | - Derren J Heyes
- Manchester Institute of Biotechnology, Department of Chemistry, University of Manchester, UK
| | - Giorgio Schirò
- Institut de Biologie Structurale, Univ. Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - Martin Weik
- Institut de Biologie Structurale, Univ. Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - David Leys
- Manchester Institute of Biotechnology, Department of Chemistry, University of Manchester, UK
| | - Nigel S Scrutton
- Manchester Institute of Biotechnology, Department of Chemistry, University of Manchester, UK
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42
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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: 10] [Impact Index Per Article: 3.3] [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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43
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Clinger JA, Chen E, Kliger DS, Phillips GN. Pump-Probe Circular Dichroism Spectroscopy of Cyanobacteriochrome TePixJ Yields: Insights into Its Photoconversion. J Phys Chem B 2021; 125:202-210. [PMID: 33355472 DOI: 10.1021/acs.jpcb.0c04822] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The bilin-containing photoreceptor TePixJ, a member of the cyanobacteriochrome (CBCR) family of phytochromes, switches between blue-light-absorbing and green-light-absorbing states in order to drive phototaxis in Thermosynechococcus elongatus. Its photoswitching process involves the formation of a thioether linkage between the C10 carbon of phycoviolobilin and the sidechain of Cys494 during the change in state from green-absorbing to blue-absorbing forms. Complex changes in the binding pocket propagate the signal to other domains for downstream signaling. Here, we report time-resolved circular dichroism experiments in addition to pump-probe absorption measurements for interpretation of the biophysical mechanism of the green-to-blue photoconversion process of this receptor.
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Affiliation(s)
- Jonathan A Clinger
- Department of Biosciences, Rice University, Houston, Texas 77005, United States
| | - Eefei Chen
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, United States
| | - David S Kliger
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, United States
| | - George N Phillips
- Department of Biosciences, Rice University, Houston, Texas 77005, United States.,Department of Chemistry, Rice University, Houston, Texas 77005, United States
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44
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Orädd F, Andersson M. Tracking Membrane Protein Dynamics in Real Time. J Membr Biol 2021; 254:51-64. [PMID: 33409541 PMCID: PMC7936944 DOI: 10.1007/s00232-020-00165-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 12/11/2020] [Indexed: 12/14/2022]
Abstract
Abstract Membrane proteins govern critical cellular processes and are central to human health and associated disease. Understanding of membrane protein function is obscured by the vast ranges of structural dynamics—both in the spatial and time regime—displayed in the protein and surrounding membrane. The membrane lipids have emerged as allosteric modulators of membrane protein function, which further adds to the complexity. In this review, we discuss several examples of membrane dependency. A particular focus is on how molecular dynamics (MD) simulation have aided to map membrane protein dynamics and how enhanced sampling methods can enable observing the otherwise inaccessible biological time scale. Also, time-resolved X-ray scattering in solution is highlighted as a powerful tool to track membrane protein dynamics, in particular when combined with MD simulation to identify transient intermediate states. Finally, we discuss future directions of how to further develop this promising approach to determine structural dynamics of both the protein and the surrounding lipids. Graphic Abstract ![]()
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Affiliation(s)
- Fredrik Orädd
- Department of Chemistry, Umeå University, Umeå, Sweden
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45
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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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46
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Stepanenko OV, Stepanenko OV, Turoverov KK, Kuznetsova IM. Probing the allostery in dimeric near-infrared biomarkers derived from the bacterial phytochromes: The impact of the T204A substitution on the inter-monomer interaction. Int J Biol Macromol 2020; 162:894-902. [PMID: 32569685 DOI: 10.1016/j.ijbiomac.2020.06.162] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 06/16/2020] [Accepted: 06/17/2020] [Indexed: 11/24/2022]
Abstract
In dimeric near-infrared (NIR) biomarkers engineered from bacterial phytochromes the covalent binding of BV to the cysteine residue in one monomer of a protein allosterically prevents the chromophore embedded into the pocket of the other monomer from the covalent binding to the cysteine residue. In this work, we analyzed the impact on inter-monomeric allosteric effects in dimeric NIR biomarkers of substitutions at position 204, one of the target residues of mutagenesis at the evolution of these proteins. The T204A substitution in iRFP713, developed on the basis of RpBphP2, and in its mutant variant iRFP713/C15S/V256C, in which the ligand covalent attachment site was changed, resulted in the rearrangement of the hydrogen bond network joining the chromophore with the adjacent amino acids and bound water molecules in its local environment. The change in the intramolecular contacts between the chromophore and its protein environment in iRFP713/C15S/V256C caused by the T204A substitution reduced the negative cooperativity of cofactor binding. We discuss the possible influence of cross-talk between monomers the functioning of full-length phytochromes.
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Affiliation(s)
- Olesya V Stepanenko
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 4, Tikhoretsky ave., St. Petersburg 194064, Russia
| | - Olga V Stepanenko
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 4, Tikhoretsky ave., St. Petersburg 194064, Russia
| | - Konstantin K Turoverov
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 4, Tikhoretsky ave., St. Petersburg 194064, Russia.
| | - Irina M Kuznetsova
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 4, Tikhoretsky ave., St. Petersburg 194064, Russia
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Isaksson L, Gustavsson E, Persson C, Brath U, Vrhovac L, Karlsson G, Orekhov V, Westenhoff S. Signaling Mechanism of Phytochromes in Solution. Structure 2020; 29:151-160.e3. [PMID: 32916102 DOI: 10.1016/j.str.2020.08.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 05/19/2020] [Accepted: 08/21/2020] [Indexed: 12/31/2022]
Abstract
Phytochrome proteins guide the red/far-red photoresponse of plants, fungi, and bacteria. Crystal structures suggest that the mechanism of signal transduction from the chromophore to the output domains involves refolding of the so-called PHY tongue. It is currently not clear how the two other notable structural features of the phytochrome superfamily, the so-called helical spine and a knot in the peptide chain, are involved in photoconversion. Here, we present solution NMR data of the complete photosensory core module from Deinococcus radiodurans. Photoswitching between the resting and the active states induces changes in amide chemical shifts, residual dipolar couplings, and relaxation dynamics. All observables indicate a photoinduced structural change in the knot region and lower part of the helical spine. This implies that a conformational signal is transduced from the chromophore to the helical spine through the PAS and GAF domains. The discovered pathway underpins functional studies of plant phytochromes and may explain photosensing by phytochromes under biological conditions.
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Affiliation(s)
- Linnéa Isaksson
- Department of Chemistry and Molecular Biology, University of Gothenburg, 41390 Gothenburg, Sweden
| | - Emil Gustavsson
- Department of Chemistry and Molecular Biology, University of Gothenburg, 41390 Gothenburg, Sweden; Swedish NMR Center, Department of Chemistry and Molecular Biology, University of Gothenburg, 41390 Gothenburg, Sweden
| | - Cecilia Persson
- Swedish NMR Center, Department of Chemistry and Molecular Biology, University of Gothenburg, 41390 Gothenburg, Sweden
| | - Ulrika Brath
- Swedish NMR Center, Department of Chemistry and Molecular Biology, University of Gothenburg, 41390 Gothenburg, Sweden
| | - Lidija Vrhovac
- Department of Chemistry and Molecular Biology, University of Gothenburg, 41390 Gothenburg, Sweden
| | - Göran Karlsson
- Swedish NMR Center, Department of Chemistry and Molecular Biology, University of Gothenburg, 41390 Gothenburg, Sweden
| | - Vladislav Orekhov
- Department of Chemistry and Molecular Biology, University of Gothenburg, 41390 Gothenburg, Sweden; Swedish NMR Center, Department of Chemistry and Molecular Biology, University of Gothenburg, 41390 Gothenburg, Sweden
| | - Sebastian Westenhoff
- Department of Chemistry and Molecular Biology, University of Gothenburg, 41390 Gothenburg, Sweden.
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Chen H, Li D, Cai Y, Wu LF, Song T. Bacteriophytochrome from Magnetospirillum magneticum affects phototactic behavior in response to light. FEMS Microbiol Lett 2020; 367:5895327. [PMID: 32821904 DOI: 10.1093/femsle/fnaa142] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Accepted: 08/19/2020] [Indexed: 01/03/2023] Open
Abstract
Phytochromes are a class of photoreceptors found in plants and in some fungi, cyanobacteria, and photoautotrophic and heterotrophic bacteria. Although phytochromes have been structurally characterized in some bacteria, their biological and ecological roles in magnetotactic bacteria remain unexplored. Here, we describe the biochemical characterization of recombinant bacteriophytochrome (BphP) from magnetotactic bacteria Magnetospirillum magneticum AMB-1 (MmBphP). The recombinant MmBphP displays all the characteristic features, including the property of binding to biliverdin (BV), of a genuine phytochrome. Site-directed mutagenesis identified that cysteine-14 is important for chromophore covalent binding and photoreversibility. Arginine-240 and histidine-246 play key roles in binding to BV. The N-terminal photosensory core domain of MmBphP lacking the C-terminus found in other phytochromes is sufficient to exhibit the characteristic red/far-red-light-induced fast photoreversibility of phytochromes. Moreover, our results showed MmBphP is involved in the phototactic response, suggesting its conservative role as a stress protectant. This finding provided us a better understanding of the physiological function of this group of photoreceptors and photoresponse of magnetotactic bacteria.
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Affiliation(s)
- Haitao Chen
- Beijing Key Laboratory of Biological Electromagnetism, Institute of Electrical Engineering, Chinese Academy of Sciences, Beijing 100190, China.,School of Electronic, Electrical and Communication Engineering, University of Chinese Academy of Sciences, Beijing 100049, China.,France-China International Laboratory of Evolution and Development of Magnetotactic Multicellular Organisms, Chinese Academy of Sciences, Beijing 100190, China
| | - Dandan Li
- National Institute of Biological Sciences, Beijing 102206, China
| | - Yao Cai
- Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing 100029, China
| | - Long-Fei Wu
- France-China International Laboratory of Evolution and Development of Magnetotactic Multicellular Organisms, CNRS, F-13402 Marseille, France.,LCB, Aix Marseille University, CNRS, F-13402 Marseille, France
| | - Tao Song
- Beijing Key Laboratory of Biological Electromagnetism, Institute of Electrical Engineering, Chinese Academy of Sciences, Beijing 100190, China.,School of Electronic, Electrical and Communication Engineering, University of Chinese Academy of Sciences, Beijing 100049, China.,France-China International Laboratory of Evolution and Development of Magnetotactic Multicellular Organisms, Chinese Academy of Sciences, Beijing 100190, China
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49
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Henry L, Berntsson O, Panman MR, Cellini A, Hughes AJ, Kosheleva I, Henning R, Westenhoff S. New Light on the Mechanism of Phototransduction in Phototropin. Biochemistry 2020; 59:3206-3215. [PMID: 32786255 DOI: 10.1021/acs.biochem.0c00324] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Phototropins are photoreceptor proteins that regulate blue light-dependent biological processes for efficient photosynthesis in plants and algae. The proteins consist of a photosensory domain that responds to the ambient light and an output module that triggers cellular responses. The photosensory domain of phototropin from Chlamydomonas reinhardtii contains two conserved LOV (light-oxygen-voltage) domains with flavin chromophores. Blue light triggers the formation of a covalent cysteine-flavin adduct and upregulates the phototropin kinase activity. Little is known about the structural mechanism that leads to kinase activation and how the two LOV domains contribute to this. Here, we investigate the role of the LOV1 domain from C. reinhardtii phototropin by characterizing the structural changes occurring after blue light illumination with nano- to millisecond time-resolved X-ray solution scattering. By structurally fitting the data with atomic models generated by molecular dynamics simulations, we find that adduct formation induces a rearrangement of the hydrogen bond network from the buried chromophore to the protein surface. In particular, the change in conformation and the associated hydrogen bonding of the conserved glutamine 120 induce a global movement of the β-sheet, ultimately driving a change in the electrostatic potential on the protein surface. On the basis of the change in the electrostatics, we propose a structural model of how LOV1 and LOV2 domains interact and regulate the full-length phototropin from C. reinhardtii. This provides a rationale for how LOV photosensor proteins function and contributes to the optimal design of optogenetic tools based on LOV domains.
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Affiliation(s)
- L Henry
- Department of Chemistry and Molecular Biology, University of Gothenburg, 40530 Gothenburg, Sweden
| | - O Berntsson
- Department of Chemistry and Molecular Biology, University of Gothenburg, 40530 Gothenburg, Sweden.,MAX IV Laboratory, Lund University, P.O. Box 118, 221 00 Lund, Sweden
| | - M R Panman
- Department of Chemistry and Molecular Biology, University of Gothenburg, 40530 Gothenburg, Sweden
| | - A Cellini
- Department of Chemistry and Molecular Biology, University of Gothenburg, 40530 Gothenburg, Sweden
| | - A J Hughes
- Department of Chemistry and Molecular Biology, University of Gothenburg, 40530 Gothenburg, Sweden
| | - I Kosheleva
- Center for Advanced Radiation Sources, The University of Chicago, Chicago, Illinois 60637, United States
| | - R Henning
- Center for Advanced Radiation Sources, The University of Chicago, Chicago, Illinois 60637, United States
| | - S Westenhoff
- Department of Chemistry and Molecular Biology, University of Gothenburg, 40530 Gothenburg, Sweden
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50
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Abstract
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Due
to the recent advances in X-ray free electron laser techniques,
bilin-containing cyanobacteriochrome photoreceptors have become prime
targets for the ever-expanding field of time-resolved structural biology.
However, to facilitate these challenging studies, it is essential
that the time scales of any structural changes during the photocycles
of cyanobacteriochromes be established. Here, we have used visible
and infrared transient absorption spectroscopy to probe the photocycle
of a model cyanobacteriochrome system, TePixJ. The kinetics span multiple
orders of magnitude from picoseconds to seconds. Localized changes
in the bilin binding pocket occur in picoseconds to nanoseconds, followed
by more large-scale changes in protein structure, including formation
and breakage of a second thioether linkage, in microseconds to milliseconds.
The characterization of the entire photocycle will provide a vital
frame of reference for future time-resolved structural studies of
this model photoreceptor.
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Affiliation(s)
- Samantha J O Hardman
- Manchester Institute of Biotechnology and Department of Chemistry, School of Natural Sciences, Faculty of Science and Engineering, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
| | - Derren J Heyes
- Manchester Institute of Biotechnology and Department of Chemistry, School of Natural Sciences, Faculty of Science and Engineering, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
| | - Igor V Sazanovich
- Central Laser Facility, Research Complex at Harwell, Science and Technology Facilities Council, Harwell Oxford, Didcot OX11 0QX, United Kingdom
| | - Nigel S Scrutton
- Manchester Institute of Biotechnology and Department of Chemistry, School of Natural Sciences, Faculty of Science and Engineering, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
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