1
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Liu Y, Lu R, Li M, Cheng D, Wang F, Ouyang X, Zhang Y, Zhang Q, Li J, Peng S. Dual-enzyme decorated semiconducting polymer nanoagents for second near-infrared photoactivatable ferroptosis-immunotherapy. MATERIALS HORIZONS 2024; 11:2406-2419. [PMID: 38440840 DOI: 10.1039/d3mh01844j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/06/2024]
Abstract
Enzymes provide a class of potential options to treat cancer, while the precise regulation of enzyme activities for effective and safe therapeutic actions has been poorly reported. Dual-enzyme decorated semiconducting polymer nanoagents for second near-infrared (NIR-II) photoactivatable ferroptosis-immunotherapy are reported in this study. Such nanoagents (termed SPHGA) consist of hemoglobin (Hb)-based semiconducting polymer (SP@Hb), adenosine deaminase (ADA) and glucose oxidase (GOx) with loadings in a thermal-responsive nanoparticle shell. NIR-II photoactivation of SPHGA results in the generation of heat to trigger on-demand releases of two enzymes (ADA and GOx) via destroying the thermal-responsive nanoparticle shells. In the tumor microenvironment, GOx oxidizes glucose to form hydrogen peroxide (H2O2), which promotes the Fenton reaction of iron in SP@Hb, resulting in an enhanced ferroptosis effect and immunogenic cell death (ICD). In addition, ADA degrades high-level adenosine to reverse the immunosuppressive microenvironment, thus amplifying antitumor immune responses. Via NIR-II photoactivatable ferroptosis-immunotherapy, SPHGA shows an improved effect to absolutely remove bilateral tumors and effectively suppress tumor metastases in subcutaneous 4T1 breast cancer models. This study presents a dual-enzyme-based nanoagent with controllable therapeutic actions for effective and precise cancer therapy.
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Affiliation(s)
- Yue Liu
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, Shanghai Engineering Research Center of Nano-Biomaterials and Regenerative Medicine, College of Biological Science and Medical Engineering, Donghua University, Shanghai 201620, China.
| | - Renjie Lu
- Department of Orthopedics, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200233, China
| | - Meng Li
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, Shanghai Engineering Research Center of Nano-Biomaterials and Regenerative Medicine, College of Biological Science and Medical Engineering, Donghua University, Shanghai 201620, China.
| | - Danling Cheng
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, Shanghai Engineering Research Center of Nano-Biomaterials and Regenerative Medicine, College of Biological Science and Medical Engineering, Donghua University, Shanghai 201620, China.
| | - Fengshuo Wang
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, Shanghai Engineering Research Center of Nano-Biomaterials and Regenerative Medicine, College of Biological Science and Medical Engineering, Donghua University, Shanghai 201620, China.
| | - Xumei Ouyang
- Zhuhai Institute of Translational Medicine, Zhuhai Precision Medical Center, Zhuhai People's Hospital (Zhuhai Hospital affiliated with Jinan University), Zhuhai, Guangdong 519000, China.
| | - Yitian Zhang
- Zhuhai Institute of Translational Medicine, Zhuhai Precision Medical Center, Zhuhai People's Hospital (Zhuhai Hospital affiliated with Jinan University), Zhuhai, Guangdong 519000, China.
| | - Qin Zhang
- Institute of Translational Medicine, Shanghai University, Shanghai 200444, China.
| | - Jingchao Li
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, Shanghai Engineering Research Center of Nano-Biomaterials and Regenerative Medicine, College of Biological Science and Medical Engineering, Donghua University, Shanghai 201620, China.
| | - Shaojun Peng
- Zhuhai Institute of Translational Medicine, Zhuhai Precision Medical Center, Zhuhai People's Hospital (Zhuhai Hospital affiliated with Jinan University), Zhuhai, Guangdong 519000, China.
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2
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Chretien A, Nagel MF, Botha S, de Wijn R, Brings L, Dörner K, Han H, Koliyadu JCP, Letrun R, Round A, Sato T, Schmidt C, Secareanu RC, von Stetten D, Vakili M, Wrona A, Bean R, Mancuso A, Schulz J, Pearson AR, Kottke T, Lorenzen K, Schubert R. Light-induced Trp in/Met out Switching During BLUF Domain Activation in ATP-bound Photoactivatable Adenylate Cyclase OaPAC. J Mol Biol 2024; 436:168439. [PMID: 38185322 DOI: 10.1016/j.jmb.2024.168439] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 11/28/2023] [Accepted: 01/03/2024] [Indexed: 01/09/2024]
Abstract
The understanding of signal transduction mechanisms in photoreceptor proteins is essential for elucidating how living organisms respond to light as environmental stimuli. In this study, we investigated the ATP binding, photoactivation and signal transduction process in the photoactivatable adenylate cyclase from Oscillatoria acuminata (OaPAC) upon blue light excitation. Structural models with ATP bound in the active site of native OaPAC at cryogenic as well as room temperature are presented. ATP is found in one conformation at cryogenic- and in two conformations at ambient-temperature, and is bound in an energetically unfavorable conformation for the conversion to cAMP. However, FTIR spectroscopic experiments confirm that this conformation is the native binding mode in dark state OaPAC and that transition to a productive conformation for ATP turnover only occurs after light activation. A combination of time-resolved crystallography experiments at synchrotron and X-ray Free Electron Lasers sheds light on the early events around the Flavin Adenine Dinucleotide (FAD) chromophore in the light-sensitive BLUF domain of OaPAC. Early changes involve the highly conserved amino acids Tyr6, Gln48 and Met92. Crucially, the Gln48 side chain performs a 180° rotation during activation, leading to the stabilization of the FAD chromophore. Cryo-trapping experiments allowed us to investigate a late light-activated state of the reaction and revealed significant conformational changes in the BLUF domain around the FAD chromophore. In particular, a Trpin/Metout transition upon illumination is observed for the first time in the BLUF domain and its role in signal transmission via α-helix 3 and 4 in the linker region between sensor and effector domain is discussed.
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Affiliation(s)
- Anaïs Chretien
- European XFEL GmbH, Schenefeld, Germany; Department of Chemistry, Universität Hamburg, Hamburg, Germany
| | - Marius F Nagel
- Department of Chemistry and Medical School OWL, Bielefeld University, Bielefeld, Germany
| | - Sabine Botha
- Department of Physics, Arizona State University, Tempe, AZ 85287-1504, USA; Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287-5001, USA
| | | | | | | | | | | | | | | | | | | | | | - David von Stetten
- European Molecular Biology Laboratory, Hamburg Unit, Hamburg, Germany
| | | | | | | | | | | | - Arwen R Pearson
- Institute for Nanostructure and Solid-State Physics, Universität Hamburg, Hamburg, Germany
| | - Tilman Kottke
- Department of Chemistry and Medical School OWL, Bielefeld University, Bielefeld, Germany
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3
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Ujfalusi-Pozsonyi K, Bódis E, Nyitrai M, Kengyel A, Telek E, Pécsi I, Fekete Z, Varnyuné Kis-Bicskei N, Mas C, Moussaoui D, Pernot P, Tully MD, Weik M, Schirò G, Kapetanaki SM, Lukács A. ATP-dependent conformational dynamics in a photoactivated adenylate cyclase revealed by fluorescence spectroscopy and small-angle X-ray scattering. Commun Biol 2024; 7:147. [PMID: 38307988 PMCID: PMC10837130 DOI: 10.1038/s42003-024-05842-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Accepted: 01/22/2024] [Indexed: 02/04/2024] Open
Abstract
Structural insights into the photoactivated adenylate cyclases can be used to develop new ways of controlling cellular cyclic adenosine monophosphate (cAMP) levels for optogenetic and other applications. In this work, we use an integrative approach that combines biophysical and structural biology methods to provide insight on the interaction of adenosine triphosphate (ATP) with the dark-adapted state of the photoactivated adenylate cyclase from the cyanobacterium Oscillatoria acuminata (OaPAC). A moderate affinity of the nucleotide for the enzyme was calculated and the thermodynamic parameters of the interaction have been obtained. Stopped-flow fluorescence spectroscopy and small-angle solution scattering have revealed significant conformational changes in the enzyme, presumably in the adenylate cyclase (AC) domain during the allosteric mechanism of ATP binding to OaPAC with small and large-scale movements observed to the best of our knowledge for the first time in the enzyme in solution upon ATP binding. These results are in line with previously reported drastic conformational changes taking place in several class III AC domains upon nucleotide binding.
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Affiliation(s)
- K Ujfalusi-Pozsonyi
- Department of Biophysics, Medical School, University of Pécs, 7624, Pécs, Hungary
| | - E Bódis
- Department of Biophysics, Medical School, University of Pécs, 7624, Pécs, Hungary
| | - M Nyitrai
- Department of Biophysics, Medical School, University of Pécs, 7624, Pécs, Hungary
| | - A Kengyel
- Department of Biophysics, Medical School, University of Pécs, 7624, Pécs, Hungary
| | - E Telek
- Department of Biophysics, Medical School, University of Pécs, 7624, Pécs, Hungary
| | - I Pécsi
- Department of Biophysics, Medical School, University of Pécs, 7624, Pécs, Hungary
| | - Z Fekete
- Department of Biophysics, Medical School, University of Pécs, 7624, Pécs, Hungary
| | | | - C Mas
- Univ. Grenoble Alpes, CNRS, CEA, EMBL, ISBG, F-38000, Grenoble, France
| | - D Moussaoui
- European Synchrotron Radiation Facility (ESRF), Grenoble, France
| | - P Pernot
- European Synchrotron Radiation Facility (ESRF), Grenoble, France
| | - M D Tully
- European Synchrotron Radiation Facility (ESRF), Grenoble, France
| | - M Weik
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - G Schirò
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - S M Kapetanaki
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, Grenoble, France.
- Department of Biophysics, Medical School, University of Pécs, 7624, Pécs, Hungary.
| | - A Lukács
- Department of Biophysics, Medical School, University of Pécs, 7624, Pécs, Hungary.
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4
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Nakasone Y, Murakami H, Tokonami S, Oda T, Terazima M. Time-resolved study on signaling pathway of photoactivated adenylate cyclase and its nonlinear optical response. J Biol Chem 2023; 299:105285. [PMID: 37742920 PMCID: PMC10634658 DOI: 10.1016/j.jbc.2023.105285] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 09/06/2023] [Accepted: 09/18/2023] [Indexed: 09/26/2023] Open
Abstract
Photoactivated adenylate cyclases (PACs) are multidomain BLUF proteins that regulate the cellular levels of cAMP in a light-dependent manner. The signaling route and dynamics of PAC from Oscillatoria acuminata (OaPAC), which consists of a light sensor BLUF domain, an adenylate cyclase domain, and a connector helix (α3-helix), were studied by detecting conformational changes in the protein moiety. Although circular dichroism and small-angle X-ray scattering measurements did not show significant changes upon light illumination, the transient grating method successfully detected light-induced changes in the diffusion coefficient (diffusion-sensitive conformational change (DSCC)) of full-length OaPAC and the BLUF domain with the α3-helix. DSCC of full-length OaPAC was observed only when both protomers in a dimer were photoconverted. This light intensity dependence suggests that OaPAC is a cyclase with a nonlinear light intensity response. The enzymatic activity indeed nonlinearly depends on light intensity, that is, OaPAC is activated under strong light conditions. It was also found that both DSCC and enzymatic activity were suppressed by a mutation in the W90 residue, indicating the importance of the highly conserved Trp in many BLUF domains for the function. Based on these findings, a reaction scheme was proposed together with the reaction dynamics.
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Affiliation(s)
- Yusuke Nakasone
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Hiroto Murakami
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Shunrou Tokonami
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Takashi Oda
- Department of Life Science and Research Center for Life Science, College of Science, Rikkyo University, Tokyo, Japan
| | - Masahide Terazima
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto, Japan.
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5
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Tokonami S, Nakasone Y, Terazima M. Effects of N- and C-terminal regions on oligomeric formation of blue light sensor protein SyPixD. Protein Sci 2023; 32:e4658. [PMID: 37184370 PMCID: PMC10211260 DOI: 10.1002/pro.4658] [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: 04/06/2023] [Revised: 05/08/2023] [Accepted: 05/10/2023] [Indexed: 05/16/2023]
Abstract
A sensor of blue-light using flavin adenine dinucleotide (BLUF) is a typical blue light photoreceptor domain that is found in many photosensor proteins in bacteria and some eukaryotic algae. SyPixD in Synechocystis is one of the well-studied BLUF proteins. In the dark state, it forms a decamer and, upon photoexcitation, a dissociation reaction takes place to yield dimers. Such change in the intermolecular interactions of the protomers is important for the biological function. The effect of the N- and C-terminal sequences on the stability of SyPixD oligomeric states and photoreactions of SyPixD were studied to understand how the oligomeric form is maintained with weak interaction. It was found that a few residues that frequently persist at the N-terminus after removing a tag for purification are sensitive to the stability of the decamer structure. Even two or three residues at the N-terminus considerably reduces decamer stability, whereas four or more residues completely prevent decamer formation. Unexpectedly, truncating C-terminal sequences, which locate far from any protomer interface and of which structure is undetermined in crystal structure, also destabilizes the decamer structure. This destabilization is also apparent from the dissociation reaction dynamics detected by the transient grating and transient absorption measurements. The dissociation reaction is faster and the yield increases when the C-terminus does not contain seven amino acid residues. Photoexcitation induces a conformational change in the C-terminus of the decamer but not the dimer.
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Affiliation(s)
- Shunrou Tokonami
- Department of Chemistry, Graduate School of ScienceKyoto UniversityKyotoJapan
| | - Yusuke Nakasone
- Department of Chemistry, Graduate School of ScienceKyoto UniversityKyotoJapan
| | - Masahide Terazima
- Department of Chemistry, Graduate School of ScienceKyoto UniversityKyotoJapan
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6
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Reza-González FA, Villatoro E, Reza MM, Jara-Cortés J, García-Ortega H, Blanco-Acuña EF, López-Cortés JG, Esturau-Escofet N, Aguirre-Soto A, Peon J. Two-photon isomerization properties of donor-acceptor Stenhouse adducts. Chem Sci 2023; 14:5783-5794. [PMID: 37265740 PMCID: PMC10231324 DOI: 10.1039/d3sc01223a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 04/21/2023] [Indexed: 06/03/2023] Open
Abstract
Donor-acceptor Stenhouse adducts (DASAs) are important photo-responsive molecules that undergo electrocyclic reactions after light absorption. From these properties, DASAs have received extensive attention as photo-switches with negative photochromism. Meanwhile, several photochemical applications require isomerization events to take place in highly localized volumes at variable depths. Such focused photoreactions can be achieved if the electronic excitation is induced through a non-linear optical process. In this contribution we describe DASAs substituted with extended donor groups which provide them with significant two-photon absorption properties. We characterized the photo-induced transformation of these DASAs from the open polymethinic form to their cyclopentenic isomer with the use of 800 nm femtosecond pulses. These studies verified that the biphotonic excitation produces equivalent photoreactions as linear absorbance. We also determined these DASAs' two-photon absorption cross sections from measurements of their photoconverted yield after biphotonic excitation. As we show, specific donor sections provide these systems with important biphotonic cross-sections as high as 615 GM units. Such properties make these DASAs among the most non-linearly active photo-switchable molecules. Calculations at the TDDFT level with the optimally tuned range-separated functional OT-CAM-B3LYP, together with quadratic response methods indicate that the non-linear photochemical properties in these molecules involve higher lying electronic states above the first excited singlet. This result is consistent with the observed relation between their two-photon chemistry and the onset of their short wavelength absorption features around 400 nm. This is the first report of the non-linear photochemistry of DASAs. The two-photon isomerization properties of DASAs extend their applications to 3D-photocontrol, non-linear lithography, variable depth birefringence, and localized drug delivery schemes.
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Affiliation(s)
| | - Emmanuel Villatoro
- Instituto de Química, Universidad Nacional Autónoma de México Ciudad de México Mexico
| | - Mariana M Reza
- Instituto de Química, Universidad Nacional Autónoma de México Ciudad de México Mexico
| | - Jesús Jara-Cortés
- Unidad Académica de Ciencias Básicas e Ingenierías, Universidad Autónoma de Nayarit Tepic 63155 Mexico
| | - Héctor García-Ortega
- Facultad de Química, Universidad Nacional Autónoma de México Ciudad de México Mexico
| | - Edgard F Blanco-Acuña
- Facultad de Química, Universidad Nacional Autónoma de México Ciudad de México Mexico
| | - José G López-Cortés
- Instituto de Química, Universidad Nacional Autónoma de México Ciudad de México Mexico
| | - Nuria Esturau-Escofet
- Instituto de Química, Universidad Nacional Autónoma de México Ciudad de México Mexico
| | - Alan Aguirre-Soto
- School of Engineering and Sciences, Tecnologico de Monterrey Monterey Nuevo Leon Mexico
| | - Jorge Peon
- Instituto de Química, Universidad Nacional Autónoma de México Ciudad de México Mexico
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7
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Blue Light Sensing BlsA-Mediated Modulation of Meropenem Resistance and Biofilm Formation in Acinetobacter baumannii. mSystems 2023; 8:e0089722. [PMID: 36622157 PMCID: PMC9948694 DOI: 10.1128/msystems.00897-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
The presence or absence of BlsA, a protein with a blue light-sensing flavin domain in the genomes of Acinetobacter species has aroused curiosity about its roles in the regulation of bacterial lifestyle under light. Genomic and transcriptomic analyses revealed the loss of BlsA in several multidrug-resistant (MDR) A. baumannii strains as well as the light-mediated induction of blsA, along with a possible BlsA-interacting partner BipA. Their direct in vivo interactions were verified using a bacterial two-hybrid system. The results demonstrated that the C-terminal region of BipA could bind to the C-terminal residues of BlsA under blue light at 23°C but not at 37°C. Genetic manipulations of blsA and bipA revealed that the coexistence of BlsA and BipA was required to induce the light-dependent expression of ompA in A. baumannii ATCC 17978 at 23°C. The same phenomenon occurred in the BlsA-deficient MDR strain in our functional complementation assay; however, the underlying molecular mechanism remains poorly understood. BlsA-modulated amounts of OmpA, the most abundant porin, in the outer membrane affected the membrane integrity and permeability of small molecules. Dark conditions or the deletion of ompA made the membrane more permeable to lipophilic ethidium bromide (EtBr) but not to meropenem. Interestingly, light illumination and low temperature conditions made the cells more sensitive to meropenem; however, this bactericidal effect was not noted in the blsA mutant or in the BlsA-deficient MDR strains. Light-mediated cell death and the reduction of biofilm formation at 23°C were abolished in the blsA mutant strain, suggesting multifaceted roles of BlsA in A. baumannii strains. IMPORTANCE Little is known about the functional roles of BlsA and its interacting partners in Acinetobacter species. Intriguingly, no BlsA homolog was found in several clinical isolates, suggesting that BlsA was not required inside the host because of the lack of blue light and the warm temperature conditions. As many chromophore-harboring proteins interact with various partners to control light-dependent cellular behaviors, the maintenance of blsA in the genomes of many Acinetobacter species during their evolution may be beneficial when fluctuations occur in two important environmental factors: light and temperature. Our study is the first to report the novel protein partner of BlsA, namely, BipA, and its contribution to multiple phenotypic changes, including meropenem resistance and biofilm formation. Rapid physiological acclimation to changing light or temperature conditions may be possible in the presence of the light-sensing BlsA protein, which may have more interacting partners than expected.
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8
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Ohlendorf R, Möglich A. Light-regulated gene expression in Bacteria: Fundamentals, advances, and perspectives. Front Bioeng Biotechnol 2022; 10:1029403. [PMID: 36312534 PMCID: PMC9614035 DOI: 10.3389/fbioe.2022.1029403] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Accepted: 09/29/2022] [Indexed: 11/13/2022] Open
Abstract
Numerous photoreceptors and genetic circuits emerged over the past two decades and now enable the light-dependent i.e., optogenetic, regulation of gene expression in bacteria. Prompted by light cues in the near-ultraviolet to near-infrared region of the electromagnetic spectrum, gene expression can be up- or downregulated stringently, reversibly, non-invasively, and with precision in space and time. Here, we survey the underlying principles, available options, and prominent examples of optogenetically regulated gene expression in bacteria. While transcription initiation and elongation remain most important for optogenetic intervention, other processes e.g., translation and downstream events, were also rendered light-dependent. The optogenetic control of bacterial expression predominantly employs but three fundamental strategies: light-sensitive two-component systems, oligomerization reactions, and second-messenger signaling. Certain optogenetic circuits moved beyond the proof-of-principle and stood the test of practice. They enable unprecedented applications in three major areas. First, light-dependent expression underpins novel concepts and strategies for enhanced yields in microbial production processes. Second, light-responsive bacteria can be optogenetically stimulated while residing within the bodies of animals, thus prompting the secretion of compounds that grant health benefits to the animal host. Third, optogenetics allows the generation of precisely structured, novel biomaterials. These applications jointly testify to the maturity of the optogenetic approach and serve as blueprints bound to inspire and template innovative use cases of light-regulated gene expression in bacteria. Researchers pursuing these lines can choose from an ever-growing, versatile, and efficient toolkit of optogenetic circuits.
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Affiliation(s)
- Robert Ohlendorf
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Andreas Möglich
- Department of Biochemistry, University of Bayreuth, Bayreuth, Germany
- Bayreuth Center for Biochemistry and Molecular Biology, Universität Bayreuth, Bayreuth, Germany
- North-Bavarian NMR Center, Universität Bayreuth, Bayreuth, Germany
- *Correspondence: Andreas Möglich,
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9
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Tolentino Collado J, Iuliano JN, Pirisi K, Jewlikar S, Adamczyk K, Greetham GM, Towrie M, Tame JRH, Meech SR, Tonge PJ, Lukacs A. Unraveling the Photoactivation Mechanism of a Light-Activated Adenylyl Cyclase Using Ultrafast Spectroscopy Coupled with Unnatural Amino Acid Mutagenesis. ACS Chem Biol 2022; 17:2643-2654. [PMID: 36038143 PMCID: PMC9486806 DOI: 10.1021/acschembio.2c00575] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The hydrogen bonding network that surrounds the flavin in blue light using flavin adenine dinucleotide (BLUF) photoreceptors plays a crucial role in sensing and communicating the changes in the electronic structure of the flavin to the protein matrix upon light absorption. Using time-resolved infrared spectroscopy (TRIR) and unnatural amino acid incorporation, we investigated the photoactivation mechanism and the role of the conserved tyrosine (Y6) in the forward reaction of the photoactivated adenylyl cyclase from Oscillatoria acuminata (OaPAC). Our work elucidates the direct connection between BLUF photoactivation and the structural and functional implications on the partner protein for the first time. The TRIR results demonstrate the formation of the neutral flavin radical as an intermediate species on the photoactivation pathway which decays to form the signaling state. Using fluorotyrosine analogues to modulate the physical properties of Y6, the TRIR data reveal that a change in the pKa and/or reduction potential of Y6 has a profound effect on the forward reaction, consistent with a mechanism involving proton transfer or proton-coupled electron transfer from Y6 to the electronically excited FAD. Decreasing the pKa from 9.9 to <7.2 and/or increasing the reduction potential by 200 mV of Y6 prevents proton transfer to the flavin and halts the photocycle at FAD•-. The lack of protonation of the anionic flavin radical can be directly linked to photoactivation of the adenylyl cyclase (AC) domain. While the 3F-Y6 and 2,3-F2Y6 variants undergo the complete photocycle and catalyze the conversion of ATP into cAMP, enzyme activity is abolished in the 3,5-F2Y6 and 2,3,5-F3Y6 variants where the photocycle is halted at FAD•-. Our results thus show that proton transfer plays an essential role in initiating the structural reorganization of the AC domain that results in AC activity.
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Affiliation(s)
| | - James N. Iuliano
- Department
of Chemistry, Stony Brook University, New York, New York 11794, United States
| | - Katalin Pirisi
- Department
of Biophysics, Medical School, University
of Pecs, Szigeti Street 12, Pecs 7624, Hungary
| | - Samruddhi Jewlikar
- Department
of Chemistry, Stony Brook University, New York, New York 11794, United States
| | - Katrin Adamczyk
- School
of Chemistry, University of East Anglia, Norwich NR4 7TJ, U.K.
| | - Gregory M. Greetham
- Central
Laser Facility, Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot OX11 0QX, U.K.
| | - Michael Towrie
- Central
Laser Facility, Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot OX11 0QX, U.K.
| | - Jeremy R. H. Tame
- Drug
Design Laboratory, Graduate School of Medical Life Science, Yokohama City University, Tsurumi, Yokohama 230-0045, Japan
| | - Stephen R. Meech
- School
of Chemistry, University of East Anglia, Norwich NR4 7TJ, U.K.,
| | - Peter J. Tonge
- Department
of Chemistry, Stony Brook University, New York, New York 11794, United States,
| | - Andras Lukacs
- Department
of Biophysics, Medical School, University
of Pecs, Szigeti Street 12, Pecs 7624, Hungary,
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10
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Mehta V, Khanppnavar B, Schuster D, Kantarci I, Vercellino I, Kosturanova A, Iype T, Stefanic S, Picotti P, Korkhov VM. Structure of Mycobacterium tuberculosis Cya, an evolutionary ancestor of the mammalian membrane adenylyl cyclases. eLife 2022; 11:77032. [PMID: 35980026 PMCID: PMC9433096 DOI: 10.7554/elife.77032] [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] [Received: 01/13/2022] [Accepted: 08/17/2022] [Indexed: 11/13/2022] Open
Abstract
Mycobacterium tuberculosis adenylyl cyclase (AC) Rv1625c / Cya is an evolutionary ancestor of the mammalian membrane ACs and a model system for studies of their structure and function. Although the vital role of ACs in cellular signaling is well established, the function of their transmembrane (TM) regions remains unknown. Here we describe the cryo-EM structure of Cya bound to a stabilizing nanobody at 3.6 Å resolution. The TM helices 1-5 form a structurally conserved domain that facilitates the assembly of the helical and catalytic domains. The TM region contains discrete pockets accessible from the extracellular and cytosolic side of the membrane. Neutralization of the negatively charged extracellular pocket Ex1 destabilizes the cytosolic helical domain and reduces the catalytic activity of the enzyme. The TM domain acts as a functional component of Cya, guiding the assembly of the catalytic domain and providing the means for direct regulation of catalytic activity in response to extracellular ligands.
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Affiliation(s)
- Ved Mehta
- Laboratory of Biomolecular Research, Paul Scherrer Institute, Villigen, Switzerland
| | - Basavraj Khanppnavar
- Laboratory of Biomolecular Research, Paul Scherrer Institute, Villigen, Switzerland
| | - Dina Schuster
- Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
| | - Ilayda Kantarci
- Laboratory of Biomolecular Research, Paul Scherrer Institute, Villigen, Switzerland
| | - Irene Vercellino
- Laboratory of Biomolecular Research, Paul Scherrer Institute, Villigen, Switzerland
| | - Angela Kosturanova
- Laboratory of Biomolecular Research, Paul Scherrer Institute, Villigen, Switzerland
| | - Tarun Iype
- Laboratory of Biomolecular Research, Paul Scherrer Institute, Villigen, Switzerland
| | - Sasa Stefanic
- Institute of Parasitology, University of Zurich, Zurich, Switzerland
| | - Paola Picotti
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Volodymyr M Korkhov
- Laboratory of Biomolecular Research, Paul Scherrer Institute, Villigen, Switzerland
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11
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The nature of proton-coupled electron transfer in a blue light using flavin domain. Proc Natl Acad Sci U S A 2022; 119:e2203996119. [PMID: 35737837 PMCID: PMC9245699 DOI: 10.1073/pnas.2203996119] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Proton-coupled electron transfer (PCET) is key to the activation of the blue light using flavin (BLUF) domain photoreceptors. Here, to elucidate the photocycle of the central FMN-Gln-Tyr motif in the BLUF domain of OaPAC, we eliminated the intrinsic interfering W90 in the mutant design. We integrated the stretched exponential function into the target analysis to account for the dynamic heterogeneity arising from the active-site solvation relaxation and the flexible H-bonding network as shown in the molecular dynamics simulation results, facilitating a simplified expression of the kinetics model. We find that, in both the functional wild-type (WT) and the nonfunctional Q48E and Q48A, forward PCET happens in the range of 105 ps to 344 ps, with a kinetic isotope effect (KIE) measured to be ∼1.8 to 2.4, suggesting that the nature of the forward PCET is concerted. Remarkably, only WT proceeds with an ultrafast reverse PCET process (31 ps, KIE = 4.0), characterized by an inverted kinetics of the intermediate FMNH˙. Our results reveal that the reverse PCET is driven by proton transfer via an intervening imidic Gln.
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12
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Tokonami S, Onose M, Nakasone Y, Terazima M. Slow Conformational Changes of Blue Light Sensor BLUF Proteins in Milliseconds. J Am Chem Soc 2022; 144:4080-4090. [PMID: 35196858 DOI: 10.1021/jacs.1c13121] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Blue light sensor using flavin (BLUF) proteins consist of flavin-binding BLUF domains and functional domains. Upon blue light excitation, the hydrogen bond network around the flavin chromophore changes, and the absorption spectrum in the visible region exhibits a red shift. Ultimately, the light information received in the BLUF domain is transmitted to the functional region. It has been believed that this red shift is complete within nanoseconds. In this study, slow reaction kinetics were discovered in milliseconds (τ1- and τ2-phase) for all the BLUF proteins examined (AppA, OaPAC, BlrP1, YcgF, PapB, SyPixD, and TePixD). Despite extensive reports on BLUF, this is the first clear observation of the BLUF protein absorption change with the duration in the millisecond time region. From the measurements of some domain-deleted mutants of OaPAC and two chimeric mutants of PixD proteins, it was found that the slower dynamics (τ2-phase) are strongly affected by the size and nature of the C-terminal region adjacent to the BLUF domain. Hence, this millisecond reaction is a significant indicator of conformational changes in the C-terminal region, which is essential for the biological functions. On the other hand, the τ1-phase commonly exists in all BLUF proteins, including any mutants. The origin of the slow dynamics was studied using site-specific mutants. These results clearly show the importance of Trp in the BLUF domain. Based on this, a reaction scheme for the BLUF reaction is proposed.
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Affiliation(s)
- Shunrou Tokonami
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Morihiko Onose
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Yusuke Nakasone
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Masahide Terazima
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
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13
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Abstract
Light activated proteins are at the heart of photobiology and optogenetics, so there is wide interest in understanding the mechanisms coupling optical excitation to protein function. In addition, such light activated proteins provide unique insights into the real-time dynamics of protein function. Using pump-probe spectroscopy, the function of a photoactive protein can be initiated by a sub-100 fs pulse of light, allowing subsequent protein dynamics to be probed from femtoseconds to milliseconds and beyond. Among the most interesting photoactive proteins are the blue light using flavin (BLUF) domain proteins, which regulate the response to light of a wide range of bacterial and some euglenoid processes. The photosensing mechanism of BLUF domains has long been a subject of debate. In contrast to other photoactive proteins, the electronic and nuclear structure of the chromophore (flavin) is the same in dark- and light-adapted states. Thus, the driving force for photoactivity is unclear.To address this question requires real-time observation of both chromophore excited state processes and their effect on the structure and dynamics of the surrounding protein matrix. In this Account we describe how time-resolved infrared (IR) experiments, coupled with chemical biology, provide important new insights into the signaling mechanism of BLUF domains. IR measurements are sensitive to changes in both chromophore electronic structure and protein hydrogen bonding interactions. These contributions are resolved by isotope labeling of the chromophore and protein separately. Further, a degree of control over BLUF photochemistry is achieved through mutagenesis, while unnatural amino acid substitution allows us to both fine-tune the photochemistry and time resolve protein dynamics with spatial resolution.Ultrafast studies of BLUF domains reveal non-single-exponential relaxation of the flavin excited state. That relaxation leads within one nanosecond to the original flavin ground state bound in a modified hydrogen-bonding network, as seen in transient and steady-state IR spectroscopy. The change in H-bond configuration arises from formation of an unusual enol (imine) form of a critical glutamine residue. The dynamics observed, complemented by quantum mechanical calculations, suggest a unique sequential electron then double proton transfer reaction as the driving force, followed by rapid reorganization in the binding site and charge recombination. Importantly, studies of several BLUF domains reveal an unexpected diversity in their dynamics, although the underlying structure appears highly conserved. It is suggested that this diversity reflects structural dynamics in the ground state at standard temperature, leading to a distribution of structures and photochemical outcomes. Time resolved IR measurements were extended to the millisecond regime for one BLUF domain, revealing signaling state formation on the microsecond time scale. The mechanism involves reorganization of a β-sheet connected to the chromophore binding pocket via a tryptophan residue. The potential of site-specific labeling amino acids with IR labels as a tool for probing protein structural dynamics was demonstrated.In summary, time-resolved IR studies of BLUF domains (along with related studies at visible wavelengths and quantum and molecular dynamics calculations) have resolved the photoactivation mechanism and real-time dynamics of signaling state formation. These measurements provide new insights into protein structural dynamics and will be important in optimizing the potential of BLUF domains in optobiology.
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Affiliation(s)
- Andras Lukacs
- Department of Biophysics, Medical School, University of Pécs, Szigeti str 12, 7624 Pécs, Hungary
| | - Peter J. Tonge
- Department of Chemistry, Stony Brook University, 100 Nicolls Road, Stony Brook, New York 11794-3400, United States
| | - Stephen R. Meech
- School of Chemistry, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, U.K
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14
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Fujisawa T, Masuda S, Takeuchi S, Tahara T. Femtosecond Time-Resolved Absorption Study of Signaling State of a BLUF Protein PixD from the Cyanobacterium Synechocystis: Hydrogen-Bond Rearrangement Completes during Forward Proton-Coupled Electron Transfer. J Phys Chem B 2021; 125:12154-12165. [PMID: 34726926 DOI: 10.1021/acs.jpcb.1c05957] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Femtosecond time-resolved absorption measurements were carried out for the dark and signaling states of a BLUF (Blue Light Using FAD) protein, PixD, from the cyanobacterium Synechocystis. When the dark state was excited, FAD semiquinone radical (FADH•) was produced from the S1 state, and FADH• led to the signaling state. On the other hand, photoexcitation of the signaling state generated FADH• and FAD anion radical (FAD•-), and they decayed back to the original signaling state. In both cases, FADH• was formed and decayed with a proton-coupled electron transfer (PCET) via the hydrogen-bond network that involves FAD, Gln50, and Tyr8, and hence the kinetics of FADH• directly reflects the hydrogen-bond structure in the FAD-binding sites. It was found that the formation rate of FADH• was significantly different between the dark and signaling states, whereas the decay rate was the same. This indicates that the hydrogen-bond network of FAD-Gln50-Tyr8 in the dark and signaling states is initially different but it becomes indistinguishable after FADH• is formed, implying that the FAD-Gln50-Tyr8 hydrogen-bond network is rearranged during the PCET to generate FADH•. The present results best agree with the model in which the Gln tautomerizes without rotation in the signaling-state formation.
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Affiliation(s)
- Tomotsumi Fujisawa
- Molecular Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako 351-0198, Japan
| | - Shinji Masuda
- Department of Life Science and Technology, Tokyo Institute of Technology, Yokohama 226-8501, Japan
| | - Satoshi Takeuchi
- Molecular Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako 351-0198, Japan.,Ultrafast Spectroscopy Research Team, RIKEN Center for Advanced Photonics (RAP), RIKEN, 2-1 Hirosawa, Wako 351-0198, Japan
| | - Tahei Tahara
- Molecular Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako 351-0198, Japan.,Ultrafast Spectroscopy Research Team, RIKEN Center for Advanced Photonics (RAP), RIKEN, 2-1 Hirosawa, Wako 351-0198, Japan
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15
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Fischer P, Mukherjee S, Schiewer E, Broser M, Bartl F, Hegemann P. The inner mechanics of rhodopsin guanylyl cyclase during cGMP-formation revealed by real-time FTIR spectroscopy. eLife 2021; 10:e71384. [PMID: 34665128 PMCID: PMC8575461 DOI: 10.7554/elife.71384] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 10/18/2021] [Indexed: 01/01/2023] Open
Abstract
Enzymerhodopsins represent a recently discovered class of rhodopsins which includes histidine kinase rhodopsin, rhodopsin phosphodiesterases, and rhodopsin guanylyl cyclases (RGCs). The regulatory influence of the rhodopsin domain on the enzyme activity is only partially understood and holds the key for a deeper understanding of intra-molecular signaling pathways. Here, we present a UV-Vis and FTIR study about the light-induced dynamics of a RGC from the fungus Catenaria anguillulae, which provides insights into the catalytic process. After the spectroscopic characterization of the late rhodopsin photoproducts, we analyzed truncated variants and revealed the involvement of the cytosolic N-terminus in the structural rearrangements upon photo-activation of the protein. We tracked the catalytic reaction of RGC and the free GC domain independently by UV-light induced release of GTP from the photolabile NPE-GTP substrate. Our results show substrate binding to the dark-adapted RGC and GC alike and reveal differences between the constructs attributable to the regulatory influence of the rhodopsin on the conformation of the binding pocket. By monitoring the phosphate rearrangement during cGMP and pyrophosphate formation in light-activated RGC, we were able to confirm the M state as the active state of the protein. The described setup and experimental design enable real-time monitoring of substrate turnover in light-activated enzymes on a molecular scale, thus opening the pathway to a deeper understanding of enzyme activity and protein-protein interactions.
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Affiliation(s)
- Paul Fischer
- Institute for Biology, Experimental Biophysics, Humboldt-Universität zu BerlinBerlinGermany
| | - Shatanik Mukherjee
- Institute of Biology, Biophysical Chemistry, Humboldt University of BerlinBerlinGermany
| | - Enrico Schiewer
- Institute for Biology, Experimental Biophysics, Humboldt-Universität zu BerlinBerlinGermany
| | - Matthias Broser
- Institute for Biology, Experimental Biophysics, Humboldt-Universität zu BerlinBerlinGermany
| | - Franz Bartl
- Institute of Biology, Biophysical Chemistry, Humboldt University of BerlinBerlinGermany
| | - Peter Hegemann
- Institute for Biology, Experimental Biophysics, Humboldt-Universität zu BerlinBerlinGermany
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16
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Photoreaction of photoactivated adenylate cyclase from cyanobacterium Microcoleus chthonoplastes. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY. B, BIOLOGY 2021; 221:112252. [PMID: 34265548 DOI: 10.1016/j.jphotobiol.2021.112252] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 05/19/2021] [Accepted: 06/28/2021] [Indexed: 11/21/2022]
Abstract
The photochemical reaction of photoactivated adenylate cyclase from cyanobacterium Microcoleus chthonoplastes PCC 7420 (mPAC), which consists of a Per-Arnt-Sim (PAS), a light‑oxygene-voltage (LOV), and an adenylate cyclase (AC) domain, was investigated mainly using the time-resolved transient grating method. An absorption spectral change associated with an adduct formation between its chromophore (flavin mononucleotide) and a cysteine residue was observed with a time constant of 0.66 μs. After this reaction, a significant diffusion coefficient (D)-change was observed with a time constant of 38 ms. The determined D-value was concentration-dependent indicating a rapid equilibrium between the dimer and tetramer. Combining the results of size exclusion chromatography and CD spectroscopy, we concluded that the photoinduced D-change was mainly attributed to the equilibrium shift from the dimer rich to the tetramer rich states upon light exposure. Since the reaction rate does not depend on concentration, the rate determining step of the tetramer formation is not the collision of proteins by diffusion, but a conformation change. The roles of the PAS and AC domains as well as the N- and C-terminal flanking helices of the LOV domain (A'α- and Jα-helices) were investigated using various truncated mutants. The PAS domain was found to be a strong dimerization site and is related to efficient signal transduction. It was found that simultaneous existence of the A'α- and Jα-helices in mPAC is important for the light-induced conformation change to lead the conformation change which induces the tetramer formation. The results suggest that the angle changes of the coiled-coil structures in the A'α and Jα-helices are essential for this conformation change. The reaction scheme of mPAC is proposed.
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17
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Seong J, Lin MZ. Optobiochemistry: Genetically Encoded Control of Protein Activity by Light. Annu Rev Biochem 2021; 90:475-501. [PMID: 33781076 DOI: 10.1146/annurev-biochem-072420-112431] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Optobiochemical control of protein activities allows the investigation of protein functions in living cells with high spatiotemporal resolution. Over the last two decades, numerous natural photosensory domains have been characterized and synthetic domains engineered and assembled into photoregulatory systems to control protein function with light. Here, we review the field of optobiochemistry, categorizing photosensory domains by chromophore, describing photoregulatory systems by mechanism of action, and discussing protein classes frequently investigated using optical methods. We also present examples of how spatial or temporal control of proteins in living cells has provided new insights not possible with traditional biochemical or cell biological techniques.
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Affiliation(s)
- Jihye Seong
- Brain Science Institute, Korea Institute of Science and Technology (KIST), Seoul 02792, South Korea;
| | - Michael Z Lin
- Department of Neurobiology, Stanford University, Stanford, California 94305, USA; .,Department of Bioengineering, Stanford University, Stanford, California 94305, USA.,Department of Chemical and Systems Biology, Stanford University, Stanford, California 94305, USA
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18
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Khrenova MG, Kulakova AM, Nemukhin AV. Light-Induced Change of Arginine Conformation Modulates the Rate of Adenosine Triphosphate to Cyclic Adenosine Monophosphate Conversion in the Optogenetic System Containing Photoactivated Adenylyl Cyclase. J Chem Inf Model 2021; 61:1215-1225. [PMID: 33677973 DOI: 10.1021/acs.jcim.0c01308] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
We report the first computational characterization of an optogenetic system composed of two photosensing BLUF (blue light sensor using flavin adenine dinucleotide) domains and two catalytic adenylyl cyclase (AC) domains. Conversion of adenosine triphosphate (ATP) to the reaction products, cyclic adenosine monophosphate (cAMP) and pyrophosphate (PPi), catalyzed by ACs initiated by excitation in photosensing domains has emerged in the focus of modern optogenetic applications because of the request in photoregulated enzymes that modulate cellular concentrations of signaling messengers. The photoactivated AC from the soil bacterium Beggiatoa sp. (bPAC) is an important model showing a considerable increase in the ATP to cAMP conversion rate in the catalytic domain after the illumination of the BLUF domain. The 1 μs classical molecular dynamics simulations reveal that the activation of the BLUF domain leading to tautomerization of Gln49 in the chromophore-binding pocket results in switching of the position of the side chain of Arg278 in the active site of AC. Allosteric signal transmission pathways between Gln49 from BLUF and Arg278 from AC were revealed by the dynamical network analysis. The Gibbs energy profiles of the ATP → cAMP + PPi reaction computed using QM(DFT(ωB97X-D3/6-31G**))/MM(CHARMM) molecular dynamics simulations for both Arg278 conformations in AC clarify the reaction mechanism. In the light-activated system, the corresponding arginine conformation stabilizes the pentacoordinated phosphorus of the α-phosphate group in the transition state, thus lowering the activation energy. Simulations of the bPAC system with the Tyr7Phe replacement in the BLUF demonstrate occurrence of both arginine conformations in an equal ratio, explaining the experimentally observed intermediate catalytic activity of the bPAC-Y7F variant as compared with the dark and light states of the wild-type bPAC.
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Affiliation(s)
- Maria G Khrenova
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russian Federation.,Bach Institute of Biochemistry, Federal Research Centre "Fundamentals of Biotechnology", Russian Academy of Sciences, Moscow 119071 Russian Federation
| | - Anna M Kulakova
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russian Federation
| | - Alexander V Nemukhin
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russian Federation.,Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow 119334, Russian Federation
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19
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Photoreaction Mechanisms of Flavoprotein Photoreceptors and Their Applications. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1293:189-206. [PMID: 33398814 DOI: 10.1007/978-981-15-8763-4_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
Abstract
Three classes of flavoprotein photoreceptors, cryptochromes (CRYs), light-oxygen-voltage (LOV)-domain proteins, and blue light using FAD (BLUF)-domain proteins, have been identified that control various physiological processes in multiple organisms. Accordingly, signaling activities of photoreceptors have been intensively studied and the related mechanisms have been exploited in numerous optogenetic tools. Herein, we summarize the current understanding of photoactivation mechanisms of the flavoprotein photoreceptors and review their applications.
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20
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Photoactivated Adenylyl Cyclases: Fundamental Properties and Applications. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021. [PMID: 33398810 DOI: 10.1007/978-981-15-8763-4_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/14/2023]
Abstract
Photoactivated adenylyl cyclase (PAC) was first discovered to be a sensor for photoavoidance in the flagellate Euglena gracilis. PAC is a flavoprotein that catalyzes the production of cAMP upon illumination with blue light, which enables us to optogenetically manipulate intracellular cAMP levels in various biological systems. Recent progress in genome sequencing has revealed several related proteins in bacteria and ameboflagellates. Among them, the PACs from sulfur bacterium Beggiatoa sp. and cyanobacterium Oscillatoria acuminata have been well characterized, including their crystalline structure. Although there have not been many reported optogenetic applications of PACs so far, they have the potential to be used in various fields within bioscience.
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21
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Chitrakar I, Iuliano JN, He Y, Woroniecka HA, Collado JT, Wint J, Walker SG, Tonge PJ, French JB. Structural Basis for the Regulation of Biofilm Formation and Iron Uptake in A. baumannii by the Blue-Light-Using Photoreceptor, BlsA. ACS Infect Dis 2020; 6:2592-2603. [PMID: 32926768 PMCID: PMC10035076 DOI: 10.1021/acsinfecdis.0c00156] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The opportunistic human pathogen, A. baumannii, senses and responds to light using the blue light sensing A (BlsA) photoreceptor protein. BlsA is a blue-light-using flavin adenine dinucleotide (BLUF) protein that is known to regulate a wide variety of cellular functions through interactions with different binding partners. Using immunoprecipitation of tagged BlsA in A. baumannii lysates, we observed a number of proteins that interact with BlsA, including several transcription factors. In addition to a known binding partner, the iron uptake regulator Fur, we identified the biofilm response regulator BfmR as a putative BlsA-binding partner. Using microscale thermophoresis, we determined that both BfmR and Fur bind to BlsA with nanomolar binding constants. To better understand how BlsA interacts with and regulates these transcription factors, we solved the X-ray crystal structures of BlsA in both a ground (dark) state and a photoactivated light state. Comparison of the light- and dark-state structures revealed that, upon photoactivation, the two α-helices comprising the variable domain of BlsA undergo a distinct conformational change. The flavin-binding site, however, remains largely unchanged from dark to light. These structures, along with docking studies of BlsA and Fur, reveal key mechanistic details about how BlsA propagates the photoactivation signal between protein domains and on to its binding partner. Taken together, our structural and biophysical data provide important insights into how BlsA controls signal transduction in A. baumannii and provides a likely mechanism for blue-light-dependent modulation of biofilm formation and iron uptake.
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Affiliation(s)
- Iva Chitrakar
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY, USA, 11790
- Biochemistry and Structural Biology Program, Stony Brook University, Stony Brook, NY, USA, 11790
| | - James N. Iuliano
- Department of Chemistry, Stony Brook University, Stony Brook, NY, USA, 11790
| | - YongLe He
- Department of Chemistry, Stony Brook University, Stony Brook, NY, USA, 11790
| | | | | | - Jinelle Wint
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY, USA, 11790
| | - Stephen G. Walker
- Department of Oral Biology and Pathology, Stony Brook University, Stony Brook, NY, USA, 11790
| | - Peter J. Tonge
- Biochemistry and Structural Biology Program, Stony Brook University, Stony Brook, NY, USA, 11790
- Department of Chemistry, Stony Brook University, Stony Brook, NY, USA, 11790
| | - Jarrod B. French
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY, USA, 11790
- Biochemistry and Structural Biology Program, Stony Brook University, Stony Brook, NY, USA, 11790
- Department of Chemistry, Stony Brook University, Stony Brook, NY, USA, 11790
- The Hormel Institute, University of Minnesota, Austin, MN, 55912
- To whom correspondence should be addressed: Jarrod B. French: ; (507)437-9637
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22
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Khannpnavar B, Mehta V, Qi C, Korkhov V. Structure and function of adenylyl cyclases, key enzymes in cellular signaling. Curr Opin Struct Biol 2020; 63:34-41. [PMID: 32334344 DOI: 10.1016/j.sbi.2020.03.003] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Revised: 03/01/2020] [Accepted: 03/06/2020] [Indexed: 12/19/2022]
Abstract
The adenylyl cyclases (ACs) catalyze the production of the ubiquitous second messenger, cAMP, which in turns acts on a number of effectors and thus regulates a plethora of cellular functions. As the key enzymes in the highly evolutionarily conserved cAMP pathway, the ACs control the physiology of the cells, tissues, organs and organisms in health and disease. A comprehensive understanding of the specific role of the ACs in these processes of life requires a deep mechanistic understanding of structure and mechanisms of action of these enzymes. Here we highlight the exciting recent reports on the biochemistry and structure and higher order organization of the ACs and their signaling complexes. These studies have provided the glimpses into the principles of the AC-mediated homeostatic control of cellular physiology.
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Affiliation(s)
- Basavraj Khannpnavar
- Institute of Biochemistry, ETH Zurich, Switzerland; Laboratory of Biomolecular Research, Paul Scherrer Institute, Villigen 5232, Switzerland
| | - Ved Mehta
- Laboratory of Biomolecular Research, Paul Scherrer Institute, Villigen 5232, Switzerland
| | - Chao Qi
- Institute of Biochemistry, ETH Zurich, Switzerland; Laboratory of Biomolecular Research, Paul Scherrer Institute, Villigen 5232, Switzerland
| | - Volodymyr Korkhov
- Institute of Biochemistry, ETH Zurich, Switzerland; Laboratory of Biomolecular Research, Paul Scherrer Institute, Villigen 5232, Switzerland.
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23
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Karadi K, Kapetanaki SM, Raics K, Pecsi I, Kapronczai R, Fekete Z, Iuliano JN, Collado JT, Gil AA, Orban J, Nyitrai M, Greetham GM, Vos MH, Tonge PJ, Meech SR, Lukacs A. Functional dynamics of a single tryptophan residue in a BLUF protein revealed by fluorescence spectroscopy. Sci Rep 2020; 10:2061. [PMID: 32029866 PMCID: PMC7005313 DOI: 10.1038/s41598-020-59073-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 01/23/2020] [Indexed: 11/17/2022] Open
Abstract
Blue Light Using Flavin (BLUF) domains are increasingly being adopted for use in optogenetic constructs. Despite this, much remains to be resolved on the mechanism of their activation. The advent of unnatural amino acid mutagenesis opens up a new toolbox for the study of protein structural dynamics. The tryptophan analogue, 7-aza-Trp (7AW) was incorporated in the BLUF domain of the Activation of Photopigment and pucA (AppA) photoreceptor in order to investigate the functional dynamics of the crucial W104 residue during photoactivation of the protein. The 7-aza modification to Trp makes selective excitation possible using 310 nm excitation and 380 nm emission, separating the signals of interest from other Trp and Tyr residues. We used Förster energy transfer (FRET) between 7AW and the flavin to estimate the distance between Trp and flavin in both the light- and dark-adapted states in solution. Nanosecond fluorescence anisotropy decay and picosecond fluorescence lifetime measurements for the flavin revealed a rather dynamic picture for the tryptophan residue. In the dark-adapted state, the major population of W104 is pointing away from the flavin and can move freely, in contrast to previous results reported in the literature. Upon blue-light excitation, the dominant tryptophan population is reorganized, moves closer to the flavin occupying a rigidly bound state participating in the hydrogen-bond network around the flavin molecule.
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Affiliation(s)
- Kristof Karadi
- Department of Biophysics, Medical School, University of Pécs, 7624, Pécs, Hungary.,Szentagothai Research Center, University of Pécs, 7624, Pécs, Hungary
| | - Sofia M Kapetanaki
- Department of Biophysics, Medical School, University of Pécs, 7624, Pécs, Hungary.,Szentagothai Research Center, University of Pécs, 7624, Pécs, Hungary
| | - Katalin Raics
- Department of Biophysics, Medical School, University of Pécs, 7624, Pécs, Hungary
| | - Ildiko Pecsi
- Department of Biophysics, Medical School, University of Pécs, 7624, Pécs, Hungary
| | - Robert Kapronczai
- Department of Biophysics, Medical School, University of Pécs, 7624, Pécs, Hungary
| | - Zsuzsanna Fekete
- Department of Biophysics, Medical School, University of Pécs, 7624, Pécs, Hungary
| | - James N Iuliano
- Department of Chemistry, Stony Brook University, Stony Brook, NY, 11794-3400, USA
| | | | - Agnieszka A Gil
- Department of Chemistry, Stony Brook University, Stony Brook, NY, 11794-3400, USA
| | - Jozsef Orban
- Department of Biophysics, Medical School, University of Pécs, 7624, Pécs, Hungary
| | - Miklos Nyitrai
- Department of Biophysics, Medical School, University of Pécs, 7624, Pécs, Hungary.,Szentagothai Research Center, University of Pécs, 7624, Pécs, Hungary
| | - Greg M Greetham
- Central Laser Facility, Harwell Science and Innovation Campus, Didcot, Oxfordshire, UK
| | - Marten H Vos
- LOB, CNRS, INSERM, Ecole Polytechnique, Institut Polytechnique de Paris, 91128, Palaiseau, Cedex, France
| | - Peter J Tonge
- Department of Chemistry, Stony Brook University, Stony Brook, NY, 11794-3400, USA
| | - Stephen R Meech
- School of Chemistry, University of East Anglia, Norwich, NR4 7TJ, UK
| | - Andras Lukacs
- Department of Biophysics, Medical School, University of Pécs, 7624, Pécs, Hungary. .,Szentagothai Research Center, University of Pécs, 7624, Pécs, Hungary.
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24
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Hirano M, Takebe M, Ishido T, Ide T, Matsunaga S. The C-terminal region affects the activity of photoactivated adenylyl cyclase from Oscillatoria acuminata. Sci Rep 2019; 9:20262. [PMID: 31889099 PMCID: PMC6937261 DOI: 10.1038/s41598-019-56721-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 12/13/2019] [Indexed: 11/09/2022] Open
Abstract
Photoactivated adenylyl cyclase (PAC) is a unique protein that, upon blue light exposure, catalyzes cAMP production. The crystal structures of two PACs, from Oscillatoria acuminata (OaPAC) and Beggiatoa sp. (bPAC), have been solved, and they show a high degree of similarity. However, the photoactivity of OaPAC is much lower than that of bPAC, and the regulatory mechanism of PAC photoactivity, which induces the difference in activity between OaPAC and bPAC, has not yet been clarified. Here, we investigated the role of the C-terminal region in OaPAC, the length of which is the only notable difference from bPAC. We found that the photoactivity of OaPAC was inversely proportional to the C-terminal length. However, the deletion of more than nine amino acids did not further increase the activity, indicating that the nine amino acids at the C-terminal critically affect the photoactivity. Besides, absorption spectral features of light-sensing domains (BLUF domains) of the C-terminal deletion mutants showed similar light-dependent spectral shifts as in WT, indicating that the C-terminal region influences the activity without interacting with the BLUF domain. The study characterizes new PAC mutants with modified photoactivities, which could be useful as optogenetics tools.
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Affiliation(s)
- Minako Hirano
- Bio Photonics Laboratory, The Graduate School for the Creation of New Photonics Industries, 1955-1 Kurematsu Nishi-ku, Hamamatsu, Shizuoka, 431-1202, Japan.
| | - Masumi Takebe
- Central Research Laboratory, Hamamatsu Photonics K.K., 5000 Hirakuchi Hamakita-ku, Hamamatsu, Shizuoka, 434-8601, Japan
| | - Tomoya Ishido
- Graduate School of Interdisciplinary Science and Engineering in Health Systems, Okayama University, 3-1-1 Tsushima-naka, Kita-ku, Okayama-shi, Okayama, 700-8530, Japan
| | - Toru Ide
- Graduate School of Interdisciplinary Science and Engineering in Health Systems, Okayama University, 3-1-1 Tsushima-naka, Kita-ku, Okayama-shi, Okayama, 700-8530, Japan
| | - Shigeru Matsunaga
- Central Research Laboratory, Hamamatsu Photonics K.K., 5000 Hirakuchi Hamakita-ku, Hamamatsu, Shizuoka, 434-8601, Japan.
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25
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Pezza A, Tuttobene M, Abatedaga I, Valle L, Borsarelli CD, Mussi MA. Through the eyes of a pathogen: light perception and signal transduction in Acinetobacter baumannii. Photochem Photobiol Sci 2019; 18:2363-2373. [PMID: 31290528 DOI: 10.1039/c9pp00261h] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Sunlight is a ubiquitous environmental stimulus for the great majority of living organisms on Earth; therefore it is logical to expect the development of "seeing mechanisms" which lead them to successfully adapt to particular ecological niches. Although these mechanisms were recognized in photosynthetic organisms, it was not until recent years that the scientific community found out about light perception in chemotrophic ones. In this review we summarize the current knowledge about the mechanism of light sensing through the blue light receptor BlsA in Acinetobacter baumannii. We highlight its function as a global regulator that pleiotropically modulates a large number of physiological processes, many of which are linked to the ability of this opportunist pathogen to persist in adverse intrahospital environments. Moreover, we describe with some specific examples the molecular basis of how this photoregulator senses blue light and translates this physical signal by modulating gene expression of target regulons. Finally, we discuss the possible course of these investigations needed to dissect this complex regulatory network, which ultimately will help us better understand the A. baumannii physiology.
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Affiliation(s)
- Alejandro Pezza
- Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET), 2000, Rosario, Argentina
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26
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Hall CR, Tolentino Collado J, Iuliano JN, Gil AA, Adamczyk K, Lukacs A, Greetham GM, Sazanovich I, Tonge PJ, Meech SR. Site-Specific Protein Dynamics Probed by Ultrafast Infrared Spectroscopy of a Noncanonical Amino Acid. J Phys Chem B 2019; 123:9592-9597. [DOI: 10.1021/acs.jpcb.9b09425] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | | | - James N. Iuliano
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400, United States
| | - Agnieszka A. Gil
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400, United States
| | - Katrin Adamczyk
- School of Chemistry, University of East Anglia, Norwich NR4 7TJ, U.K
| | - Andras Lukacs
- Department of Biophysics, Medical School, University of Pecs, Szigeti ut 12, 7624 Pecs, Hungary
| | - Gregory M. Greetham
- Central Laser Facility, Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, Oxon OX11 0QX, U.K
| | - Igor Sazanovich
- Central Laser Facility, Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, Oxon OX11 0QX, U.K
| | - Peter J. Tonge
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400, United States
| | - Stephen R. Meech
- School of Chemistry, University of East Anglia, Norwich NR4 7TJ, U.K
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27
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Mukherjee S, Hegemann P, Broser M. Enzymerhodopsins: novel photoregulated catalysts for optogenetics. Curr Opin Struct Biol 2019; 57:118-126. [PMID: 30954887 DOI: 10.1016/j.sbi.2019.02.003] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 02/03/2019] [Accepted: 02/06/2019] [Indexed: 12/22/2022]
Abstract
Enzymerhodopsins are a recently discovered class of natural rhodopsin-based photoreceptors with light-regulated enzyme activity. Currently, three different types of these fusion proteins with an N-terminal type-1 rhodopsin and a C-terminal enzyme domain have been identified, but their physiological relevance is mostly unknown. Among these, histidine kinase rhodopsins (HKR) are photo-regulated two-component-like signaling systems that trigger a phosphorylation cascade, whereas rhodopsin phosphodiesterase (RhoPDE) or rhodopsin guanylyl cyclase (RhGC) show either light-activated hydrolysis or production of cyclic nucleotides. RhGC, the best characterized enzymerhodopsin, is involved in the phototaxis of fungal zoospores and allows for optically controlled production of cyclic nucleotides in different cell-types. These photoreceptors have great optogenetic potential and possess several advantages over the hitherto existing tools to manipulate cyclic-nucleotide dynamics in living cells.
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Affiliation(s)
- Shatanik Mukherjee
- Institute for Biology, Experimental Biophysics, Humboldt-Universität zu Berlin, Germany.
| | - Peter Hegemann
- Institute for Biology, Experimental Biophysics, Humboldt-Universität zu Berlin, Germany
| | - Matthias Broser
- Institute for Biology, Experimental Biophysics, Humboldt-Universität zu Berlin, Germany.
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28
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Nakasone Y, Kikukawa K, Masuda S, Terazima M. Time-Resolved Study of Interprotein Signaling Process of a Blue Light Sensor PapB–PapA Complex. J Phys Chem B 2019; 123:3210-3218. [DOI: 10.1021/acs.jpcb.9b00196] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Yusuke Nakasone
- Department of Chemistry, Graduate School of Science, Kyoto University, Oiwake, Kitashirakawa,
Sakyo-ku, Kyoto 606-8502, Japan
| | - Koutaro Kikukawa
- Department of Chemistry, Graduate School of Science, Kyoto University, Oiwake, Kitashirakawa,
Sakyo-ku, Kyoto 606-8502, Japan
| | - Shinji Masuda
- Center for Biological Resources and Informatics, Tokyo Institute of Technology, Yokohama 226-5801, Japan
| | - Masahide Terazima
- Department of Chemistry, Graduate School of Science, Kyoto University, Oiwake, Kitashirakawa,
Sakyo-ku, Kyoto 606-8502, Japan
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29
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Grigorenko BL, Khrenova MG, Nemukhin AV. Amide-imide tautomerization in the glutamine side chain in enzymatic and photochemical reactions in proteins. Phys Chem Chem Phys 2018; 20:23827-23836. [PMID: 30202846 DOI: 10.1039/c8cp04817g] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Amide-imide tautomerization presents a pervasive class of chemical transformations in organic chemistry of natural compounds. In this Perspective, we describe two distinctively different protein systems, in which the amide-imide tautomerization in the glutamine side chain takes place in enzymatic or photochemical reactions. First, hydrolysis of guanosine triphosphate (GTP) catalyzed by the Ras-GAP protein complex suggests the occurrence of the imide tautomer of glutamine in reaction intermediates. Second, photoexcitation of flavin-binding protein domains (BLUFs) initiates a chain of reactions in the chromophore-binding pocket, including amide-imide tautomerization of glutamine. Mechanisms of these reactions at the atomic level have been revealed in quantum mechanics/molecular mechanics (QM/MM) simulations. To reinforce conclusions on the critical role of amide-imide tautomerization of glutamine in these reactions we describe results of new quantum chemistry and QM/MM calculations for relevant molecular model systems. We reexamine results of the recent IR spectroscopy studies of BLUF domains, which provide experimental evidences of Gln tautomerization in proteins. We also propose to validate the glutamine-assisted mechanism of enzymatic GTP hydrolysis by using IR spectroscopy in a proper range of wavenumbers.
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Affiliation(s)
- Bella L Grigorenko
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1/3, 119991 Moscow, Russian Federation.
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30
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Iwata T, Nagai T, Ito S, Osoegawa S, Iseki M, Watanabe M, Unno M, Kitagawa S, Kandori H. Hydrogen Bonding Environments in the Photocycle Process around the Flavin Chromophore of the AppA-BLUF domain. J Am Chem Soc 2018; 140:11982-11991. [DOI: 10.1021/jacs.8b05123] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Tatsuya Iwata
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
- Department of Pharmaceutical Sciences, Toho University, Funabashi, Chiba 274-8510, Japan
| | - Takashi Nagai
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Shota Ito
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Shinsuke Osoegawa
- Department of Chemistry and Applied Chemistry, Graduate School of Science and Engineering, Saga University, Saga 840-8502, Japan
| | - Mineo Iseki
- Department of Pharmaceutical Sciences, Toho University, Funabashi, Chiba 274-8510, Japan
| | - Masakatsu Watanabe
- The Graduate School for the Creation of New Photonics Industries, Nishi-ku, Hamamatsu 431-1202, Japan
| | - Masashi Unno
- Department of Chemistry and Applied Chemistry, Graduate School of Science and Engineering, Saga University, Saga 840-8502, Japan
| | - Shinya Kitagawa
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Hideki Kandori
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
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31
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Abstract
Sensory photoreceptors underpin light-dependent adaptations of organismal physiology, development, and behavior in nature. Adapted for optogenetics, sensory photoreceptors become genetically encoded actuators and reporters to enable the noninvasive, spatiotemporally accurate and reversible control by light of cellular processes. Rooted in a mechanistic understanding of natural photoreceptors, artificial photoreceptors with customized light-gated function have been engineered that greatly expand the scope of optogenetics beyond the original application of light-controlled ion flow. As we survey presently, UV/blue-light-sensitive photoreceptors have particularly allowed optogenetics to transcend its initial neuroscience applications by unlocking numerous additional cellular processes and parameters for optogenetic intervention, including gene expression, DNA recombination, subcellular localization, cytoskeleton dynamics, intracellular protein stability, signal transduction cascades, apoptosis, and enzyme activity. The engineering of novel photoreceptors benefits from powerful and reusable design strategies, most importantly light-dependent protein association and (un)folding reactions. Additionally, modified versions of these same sensory photoreceptors serve as fluorescent proteins and generators of singlet oxygen, thereby further enriching the optogenetic toolkit. The available and upcoming UV/blue-light-sensitive actuators and reporters enable the detailed and quantitative interrogation of cellular signal networks and processes in increasingly more precise and illuminating manners.
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Affiliation(s)
- Aba Losi
- Department of Mathematical, Physical and Computer Sciences , University of Parma , Parco Area delle Scienze 7/A-43124 Parma , Italy
| | - Kevin H Gardner
- Structural Biology Initiative, CUNY Advanced Science Research Center , New York , New York 10031 , United States.,Department of Chemistry and Biochemistry, City College of New York , New York , New York 10031 , United States.,Ph.D. Programs in Biochemistry, Chemistry, and Biology , The Graduate Center of the City University of New York , New York , New York 10016 , United States
| | - Andreas Möglich
- Lehrstuhl für Biochemie , Universität Bayreuth , 95447 Bayreuth , Germany.,Research Center for Bio-Macromolecules , Universität Bayreuth , 95447 Bayreuth , Germany.,Bayreuth Center for Biochemistry & Molecular Biology , Universität Bayreuth , 95447 Bayreuth , Germany
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32
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Scheib U, Broser M, Constantin OM, Yang S, Gao S, Mukherjee S, Stehfest K, Nagel G, Gee CE, Hegemann P. Rhodopsin-cyclases for photocontrol of cGMP/cAMP and 2.3 Å structure of the adenylyl cyclase domain. Nat Commun 2018; 9:2046. [PMID: 29799525 PMCID: PMC5967339 DOI: 10.1038/s41467-018-04428-w] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 04/26/2018] [Indexed: 12/17/2022] Open
Abstract
The cyclic nucleotides cAMP and cGMP are important second messengers that orchestrate fundamental cellular responses. Here, we present the characterization of the rhodopsin-guanylyl cyclase from Catenaria anguillulae (CaRhGC), which produces cGMP in response to green light with a light to dark activity ratio >1000. After light excitation the putative signaling state forms with τ = 31 ms and decays with τ = 570 ms. Mutations (up to 6) within the nucleotide binding site generate rhodopsin-adenylyl cyclases (CaRhACs) of which the double mutated YFP-CaRhAC (E497K/C566D) is the most suitable for rapid cAMP production in neurons. Furthermore, the crystal structure of the ligand-bound AC domain (2.25 Å) reveals detailed information about the nucleotide binding mode within this recently discovered class of enzyme rhodopsin. Both YFP-CaRhGC and YFP-CaRhAC are favorable optogenetic tools for non-invasive, cell-selective, and spatio-temporally precise modulation of cAMP/cGMP with light. Cyclic AMP and cGMP orchestrate a variety of cellular responses. Here, authors characterize the cGMP producing rhodopsin-guanylyl cyclase from C. anguillulae and derived adenylyl cyclase by a biochemical and structural approach which demonstrates the usability of these cyclases for optogenetic applications.
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Affiliation(s)
- Ulrike Scheib
- Institute for Biology, Experimental Biophysics, Humboldt-Universität zu Berlin, 10115, Berlin, Germany
| | - Matthias Broser
- Institute for Biology, Experimental Biophysics, Humboldt-Universität zu Berlin, 10115, Berlin, Germany
| | - Oana M Constantin
- Institute for Synaptic Physiology, Center for Molecular Neurobiology Hamburg, University Medical Center Hamburg-Eppendorf, 20251, Hamburg, Germany
| | - Shang Yang
- Department of Biology, Institute for Molecular Plant Physiology and Biophysics, Biocenter, Julius-Maximilians-University of Würzburg, Julius-von-Sachs-Platz 2, 97082, Würzburg, Germany
| | - Shiqiang Gao
- Department of Biology, Institute for Molecular Plant Physiology and Biophysics, Biocenter, Julius-Maximilians-University of Würzburg, Julius-von-Sachs-Platz 2, 97082, Würzburg, Germany
| | - Shatanik Mukherjee
- Institute for Biology, Experimental Biophysics, Humboldt-Universität zu Berlin, 10115, Berlin, Germany
| | - Katja Stehfest
- Institute for Biology, Experimental Biophysics, Humboldt-Universität zu Berlin, 10115, Berlin, Germany
| | - Georg Nagel
- Department of Biology, Institute for Molecular Plant Physiology and Biophysics, Biocenter, Julius-Maximilians-University of Würzburg, Julius-von-Sachs-Platz 2, 97082, Würzburg, Germany
| | - Christine E Gee
- Institute for Synaptic Physiology, Center for Molecular Neurobiology Hamburg, University Medical Center Hamburg-Eppendorf, 20251, Hamburg, Germany.
| | - Peter Hegemann
- Institute for Biology, Experimental Biophysics, Humboldt-Universität zu Berlin, 10115, Berlin, Germany.
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33
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Blain-Hartung M, Rockwell NC, Moreno MV, Martin SS, Gan F, Bryant DA, Lagarias JC. Cyanobacteriochrome-based photoswitchable adenylyl cyclases (cPACs) for broad spectrum light regulation of cAMP levels in cells. J Biol Chem 2018; 293:8473-8483. [PMID: 29632072 DOI: 10.1074/jbc.ra118.002258] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 04/02/2018] [Indexed: 12/18/2022] Open
Abstract
Class III adenylyl cyclases generate the ubiquitous second messenger cAMP from ATP often in response to environmental or cellular cues. During evolution, soluble adenylyl cyclase catalytic domains have been repeatedly juxtaposed with signal-input domains to place cAMP synthesis under the control of a wide variety of these environmental and endogenous signals. Adenylyl cyclases with light-sensing domains have proliferated in photosynthetic species depending on light as an energy source, yet are also widespread in nonphotosynthetic species. Among such naturally occurring light sensors, several flavin-based photoactivated adenylyl cyclases (PACs) have been adopted as optogenetic tools to manipulate cellular processes with blue light. In this report, we report the discovery of a cyanobacteriochrome-based photoswitchable adenylyl cyclase (cPAC) from the cyanobacterium Microcoleus sp. PCC 7113. Unlike flavin-dependent PACs, which must thermally decay to be deactivated, cPAC exhibits a bistable photocycle whose adenylyl cyclase could be reversibly activated and inactivated by blue and green light, respectively. Through domain exchange experiments, we also document the ability to extend the wavelength-sensing specificity of cPAC into the near IR. In summary, our work has uncovered a cyanobacteriochrome-based adenylyl cyclase that holds great potential for the design of bistable photoswitchable adenylyl cyclases to fine-tune cAMP-regulated processes in cells, tissues, and whole organisms with light across the visible spectrum and into the near IR.
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Affiliation(s)
- Matthew Blain-Hartung
- From the Department of Molecular and Cellular Biology, University of California, Davis, California 95616
| | - Nathan C Rockwell
- From the Department of Molecular and Cellular Biology, University of California, Davis, California 95616
| | - Marcus V Moreno
- From the Department of Molecular and Cellular Biology, University of California, Davis, California 95616
| | - Shelley S Martin
- From the Department of Molecular and Cellular Biology, University of California, Davis, California 95616
| | - Fei Gan
- the Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, and
| | - Donald A Bryant
- the Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, and.,the Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717
| | - J Clark Lagarias
- From the Department of Molecular and Cellular Biology, University of California, Davis, California 95616,
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