1
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Ribeiro RS, Mencalha AL, de Souza da Fonseca A. Could violet-blue lights increase the bacteria resistance against ultraviolet radiation mediated by photolyases? Lasers Med Sci 2023; 38:253. [PMID: 37930459 DOI: 10.1007/s10103-023-03924-w] [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: 08/16/2023] [Accepted: 10/26/2023] [Indexed: 11/07/2023]
Abstract
Studies have demonstrated bacterial inactivation by radiations at wavelengths between 400 and 500 nm emitted by low-power light sources. The phototoxic activity of these radiations could occur by oxidative damage in DNA and membrane proteins/lipids. However, some cellular mechanisms can reverse these damages in DNA, allowing the maintenance of genetic stability. Photoreactivation is among such mechanisms able to repair DNA damages induced by ultraviolet radiation, ranging from ultraviolet A to blue radiations. In this review, studies on the effects of violet and blue lights emitted by low-power LEDs on bacteria were accessed by PubMed, and discussed the repair of ultraviolet-induced DNA damage by photoreactivation mechanisms. Data from such studies suggested bacterial inactivation after exposure to violet (405 nm) and blue (425-460 nm) radiations emitted from LEDs. However, other studies showed bacterial photoreactivation induced by radiations at 348-440 nm. This process occurs by photolyase enzymes, which absorb photons at wavelengths and repair DNA damage. Although authors have reported bacterial inactivation after exposure to violet and blue radiations emitted from LEDs, pre-exposure to such radiations at low fluences could activate the photolyases, increasing resistance to DNA damage induced by ultraviolet radiation.
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Affiliation(s)
- Rickson Souza Ribeiro
- Departamento de Biofísica e Biometria, Instituto de Biologia Roberto Alcantara Gomes, Universidade do Estado do Rio de Janeiro, Boulevard Vinte e Oito de Setembro, 87, Fundos, Vila Isabel, Rio de Janeiro, 20551030, Brazil
| | - Andre Luiz Mencalha
- Departamento de Biofísica e Biometria, Instituto de Biologia Roberto Alcantara Gomes, Universidade do Estado do Rio de Janeiro, Boulevard Vinte e Oito de Setembro, 87, Fundos, Vila Isabel, Rio de Janeiro, 20551030, Brazil
| | - Adenilson de Souza da Fonseca
- Departamento de Biofísica e Biometria, Instituto de Biologia Roberto Alcantara Gomes, Universidade do Estado do Rio de Janeiro, Boulevard Vinte e Oito de Setembro, 87, Fundos, Vila Isabel, Rio de Janeiro, 20551030, Brazil.
- Departamento de Ciências Fisiológicas, Instituto Biomédico, Universidade Federal do Estado do Rio de Janeiro, Rua Frei Caneca, 94, Rio de Janeiro, 20211040, Brazil.
- Centro de Ciências da Saúde, Centro Universitário Serra dos Órgãos, Avenida Alberto Torres, Teresópolis, Rio de Janeiro, 11125964004, Brazil.
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2
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Bangruwa N, Srivastava M, Mishra D. CISS-Based Label-Free Novel Electrochemical Impedimetric Detection of UVC-Induced DNA Damage. ACS OMEGA 2022; 7:37705-37713. [PMID: 36312421 PMCID: PMC9609074 DOI: 10.1021/acsomega.2c04659] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Accepted: 10/06/2022] [Indexed: 06/16/2023]
Abstract
In this work, we demonstrate chiral-induced spin selectivity (CISS)-based label-free electrochemical impedimetric detection of radiation-induced DNA damage using the electrons' spin as a novel tool of sensing. For this, self-assembled monolayers (SAMs) of short ds-DNA (of length 7.14 nm) are prepared on arrays of multilayer thin film devices comprising a gold overlay (500 μm diameter with 10 nm thickness) on a nickel thin film (100 nm) fabricated by the physical vapor deposition technique. Subsequently, the SAMs of ds-DNA are exposed to ultraviolet C (UVC) radiation for a prolonged period of 8 h to induce structural perturbations in DNA. The susceptibility of DNA to radiation-induced damage was probed by recording the spin-dependent electrochemical impedimetric spectra, wherein a continuous sinusoidal wave of the amplitude of 10 mV was superimposed on DC bias in the frequency range of 100-105 Hz, with simultaneous spin injection through the attached DNA. The inherent correlation between the charge-transfer resistance (R ct) and the spin selectivity of electrons through DNA was taken into account for the detection of DNA damage for the first time with a limit of detection achieved up to 10 picomolar concentrations of DNA. As the spin-polarized electrons directly probe the structural symmetry, it is robust against perturbation from electronic signals usually found in conventional electrochemical biosensors.
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Affiliation(s)
- Neeraj Bangruwa
- Department
of Physics and Astrophysics, University
of Delhi, New Delhi110007, India
| | - Manish Srivastava
- Department
of Chemical Engineering and Technology, Indian Institute of Technology, (BHU), Varanasi221005, India
| | - Debabrata Mishra
- Department
of Physics and Astrophysics, University
of Delhi, New Delhi110007, India
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3
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Ramírez-Gamboa D, Díaz-Zamorano AL, Meléndez-Sánchez ER, Reyes-Pardo H, Villaseñor-Zepeda KR, López-Arellanes ME, Sosa-Hernández JE, Coronado-Apodaca KG, Gámez-Méndez A, Afewerki S, Iqbal HMN, Parra-Saldivar R, Martínez-Ruiz M. Photolyase Production and Current Applications: A Review. Molecules 2022; 27:molecules27185998. [PMID: 36144740 PMCID: PMC9505440 DOI: 10.3390/molecules27185998] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 08/20/2022] [Accepted: 08/24/2022] [Indexed: 11/16/2022] Open
Abstract
The photolyase family consists of flavoproteins with enzyme activity able to repair ultraviolet light radiation damage by photoreactivation. DNA damage by the formation of a cyclobutane pyrimidine dimer (CPD) and a pyrimidine-pyrimidone (6-4) photoproduct can lead to multiple affections such as cellular apoptosis and mutagenesis that can evolve into skin cancer. The development of integrated applications to prevent the negative effects of prolonged sunlight exposure, usually during outdoor activities, is imperative. This study presents the functions, characteristics, and types of photolyases, their therapeutic and cosmetic applications, and additionally explores some photolyase-producing microorganisms and drug delivery systems.
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Affiliation(s)
- Diana Ramírez-Gamboa
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey 64849, Mexico
| | | | | | - Humberto Reyes-Pardo
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey 64849, Mexico
| | | | | | - Juan Eduardo Sosa-Hernández
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey 64849, Mexico
- Tecnologico de Monterrey, Institute of Advanced Materials for Sustainable Manufacturing, Monterrey 64849, Mexico
| | - Karina G. Coronado-Apodaca
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey 64849, Mexico
- Tecnologico de Monterrey, Institute of Advanced Materials for Sustainable Manufacturing, Monterrey 64849, Mexico
| | - Ana Gámez-Méndez
- Department of Basic Sciences, Universidad de Monterrey, Av. Ignacio Morones Prieto 4500 Pte, San Pedro Garza Garcia 66238, Mexico
| | - Samson Afewerki
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
- Division of Gastroenterology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Hafiz M. N. Iqbal
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey 64849, Mexico
- Tecnologico de Monterrey, Institute of Advanced Materials for Sustainable Manufacturing, Monterrey 64849, Mexico
| | - Roberto Parra-Saldivar
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey 64849, Mexico
- Tecnologico de Monterrey, Institute of Advanced Materials for Sustainable Manufacturing, Monterrey 64849, Mexico
- Correspondence: (R.P.-S.); (M.M.-R.)
| | - Manuel Martínez-Ruiz
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey 64849, Mexico
- Tecnologico de Monterrey, Institute of Advanced Materials for Sustainable Manufacturing, Monterrey 64849, Mexico
- Correspondence: (R.P.-S.); (M.M.-R.)
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4
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Schleicher E, Rein S, Illarionov B, Lehmann A, Al Said T, Kacprzak S, Bittl R, Bacher A, Fischer M, Weber S. Selective 13C labelling reveals the electronic structure of flavocoenzyme radicals. Sci Rep 2021; 11:18234. [PMID: 34521887 PMCID: PMC8440535 DOI: 10.1038/s41598-021-97588-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 08/24/2021] [Indexed: 02/08/2023] Open
Abstract
Flavocoenzymes are nearly ubiquitous cofactors that are involved in the catalysis and regulation of a wide range of biological processes including some light-induced ones, such as the photolyase-mediated DNA repair, magnetoreception of migratory birds, and the blue-light driven phototropism in plants. One of the factors that enable versatile flavin-coenzyme biochemistry and biophysics is the fine-tuning of the cofactor's frontier orbital by interactions with the protein environment. Probing the singly-occupied molecular orbital (SOMO) of the intermediate radical state of flavins is therefore a prerequisite for a thorough understanding of the diverse functions of the flavoprotein family. This may be ultimately achieved by unravelling the hyperfine structure of a flavin by electron paramagnetic resonance. In this contribution we present a rigorous approach to obtaining a hyperfine map of the flavin's chromophoric 7,8-dimethyl isoalloxazine unit at an as yet unprecedented level of resolution and accuracy. We combine powerful high-microwave-frequency/high-magnetic-field electron-nuclear double resonance (ENDOR) with 13C isotopologue editing as well as spectral simulations and density functional theory calculations to measure and analyse 13C hyperfine couplings of the flavin cofactor in DNA photolyase. Our data will provide the basis for electronic structure considerations for a number of flavin radical intermediates occurring in blue-light photoreceptor proteins.
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Affiliation(s)
- Erik Schleicher
- grid.5963.9Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Albertstr. 21, 79104 Freiburg, Germany
| | - Stephan Rein
- grid.5963.9Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Albertstr. 21, 79104 Freiburg, Germany
| | - Boris Illarionov
- grid.9026.d0000 0001 2287 2617Institut für Lebensmittelchemie, Universität Hamburg, Grindelallee 117, 20146 Hamburg, Germany
| | - Ariane Lehmann
- grid.5963.9Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Albertstr. 21, 79104 Freiburg, Germany
| | - Tarek Al Said
- grid.5963.9Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Albertstr. 21, 79104 Freiburg, Germany
| | - Sylwia Kacprzak
- grid.5963.9Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Albertstr. 21, 79104 Freiburg, Germany ,grid.423218.ePresent Address: Bruker BioSpin GmbH, Silberstreifen 4, 76287 Rheinstetten, Germany
| | - Robert Bittl
- grid.14095.390000 0000 9116 4836Fachbereich Physik, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Adelbert Bacher
- grid.6936.a0000000123222966Department Chemie, Technische Universität München, Lichtenbergstr. 4, 85748 Garching, Germany
| | - Markus Fischer
- grid.9026.d0000 0001 2287 2617Institut für Lebensmittelchemie, Universität Hamburg, Grindelallee 117, 20146 Hamburg, Germany
| | - Stefan Weber
- grid.5963.9Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Albertstr. 21, 79104 Freiburg, Germany
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5
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Kandori H. Structure/Function Study of Photoreceptive Proteins by FTIR Spectroscopy. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2020. [DOI: 10.1246/bcsj.20200109] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Hideki Kandori
- Department of Life Science and Applied Chemistry & OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya, Aichi 466-8555, Japan
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6
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Soler-Arango J, Figoli C, Muraca G, Bosch A, Brelles-Mariño G. The Pseudomonas aeruginosa biofilm matrix and cells are drastically impacted by gas discharge plasma treatment: A comprehensive model explaining plasma-mediated biofilm eradication. PLoS One 2019; 14:e0216817. [PMID: 31233528 PMCID: PMC6590783 DOI: 10.1371/journal.pone.0216817] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 04/28/2019] [Indexed: 12/21/2022] Open
Abstract
Biofilms are microbial communities encased in a protective matrix composed of exopolymeric substances including exopolysaccharides, proteins, lipids, and extracellular DNA. Biofilms cause undesirable effects such as biofouling, equipment damage, prostheses colonization, and disease. Biofilms are also more resilient than free-living cells to regular decontamination methods and therefore, alternative methods are needed to eradicate them. The use of non-thermal atmospheric pressure plasmas is a good alternative as plasmas contain reactive species, free radicals, and UV photons well-known for their decontamination potential against free microorganisms. Pseudomonas aeruginosa biofilms colonize catheters, indwelling devices, and prostheses. Plasma effects on cell viability have been previously documented for P. aeruginosa biofilms. Nonetheless, the effect of plasma on the biofilm matrix has received less attention and there is little evidence regarding the changes the matrix undergoes. The aim of this work was to study the effect plasma exerts mostly on the P. aeruginosa biofilm matrix and to expand the existing knowledge about its effect on sessile cells in order to achieve a better understanding of the mechanism/s underlying plasma-mediated biofilm inactivation. We report a reduction in the amount of the biofilm matrix, the loss of its tridimensional structure, and morphological changes in sessile cells at long exposure times. We show chemical and structural changes on the biofilm matrix (mostly on carbohydrates and eDNA) and cells (mostly on proteins and lipids) that are more profound with longer plasma exposure times. We also demonstrate the presence of lipid oxidation products confirming cell membrane lipid peroxidation as plasma exposure time increases. To our knowledge this is the first report providing detailed evidence of the variety of chemical and structural changes that occur mostly on the biofilm matrix and sessile cells as a consequence of the plasma treatment. Based on our results, we propose a comprehensive model explaining plasma-mediated biofilm inactivation.
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Affiliation(s)
- Juliana Soler-Arango
- Biofilm Eradication Laboratory, Center for Research and Development of Industrial Fermentations, Consejo Nacional de Investigaciones Científicas y Técnicas (CINDEFI, CCT-LA PLATA-CONICET), Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
| | - Cecilia Figoli
- Bioespectroscopy Laboratory, Center for Research and Development of Industrial Fermentations, Consejo Nacional de Investigaciones Científicas y Técnicas (CINDEFI, CCT-LA PLATA-CONICET), Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
| | - Giuliana Muraca
- Biofilm Eradication Laboratory, Center for Research and Development of Industrial Fermentations, Consejo Nacional de Investigaciones Científicas y Técnicas (CINDEFI, CCT-LA PLATA-CONICET), Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
| | - Alejandra Bosch
- Bioespectroscopy Laboratory, Center for Research and Development of Industrial Fermentations, Consejo Nacional de Investigaciones Científicas y Técnicas (CINDEFI, CCT-LA PLATA-CONICET), Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
- * E-mail: (AB); (GBM)
| | - Graciela Brelles-Mariño
- Biofilm Eradication Laboratory, Center for Research and Development of Industrial Fermentations, Consejo Nacional de Investigaciones Científicas y Técnicas (CINDEFI, CCT-LA PLATA-CONICET), Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
- * E-mail: (AB); (GBM)
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7
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Portero LR, Alonso-Reyes DG, Zannier F, Vazquez MP, Farías ME, Gärtner W, Albarracín VH. Photolyases and Cryptochromes in UV-resistant Bacteria from High-altitude Andean Lakes. Photochem Photobiol 2019; 95:315-330. [DOI: 10.1111/php.13061] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 11/18/2018] [Indexed: 11/30/2022]
Affiliation(s)
- Luciano Raúl Portero
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas (LIMLA); Planta Piloto de Procesos Industriales y Microbiológicos (PROIMI); CCT; CONICET; Tucumán Argentina
- Centro de Investigaciones y Servicios de Microscopía Electrónica (CISME-CONICET-UNT); CCT, CONICET; Tucumán Argentina
| | - Daniel G. Alonso-Reyes
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas (LIMLA); Planta Piloto de Procesos Industriales y Microbiológicos (PROIMI); CCT; CONICET; Tucumán Argentina
- Centro de Investigaciones y Servicios de Microscopía Electrónica (CISME-CONICET-UNT); CCT, CONICET; Tucumán Argentina
| | - Federico Zannier
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas (LIMLA); Planta Piloto de Procesos Industriales y Microbiológicos (PROIMI); CCT; CONICET; Tucumán Argentina
- Centro de Investigaciones y Servicios de Microscopía Electrónica (CISME-CONICET-UNT); CCT, CONICET; Tucumán Argentina
| | - Martín P. Vazquez
- Instituto de Agrobiotecnología de Rosario (INDEAR); Predio CCT Rosario; Santa Fe Argentina
| | - María Eugenia Farías
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas (LIMLA); Planta Piloto de Procesos Industriales y Microbiológicos (PROIMI); CCT; CONICET; Tucumán Argentina
| | - Wolfgang Gärtner
- Institute for Analytical Chemistry; University of Leipzig; Leipzig Germany
| | - Virginia Helena Albarracín
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas (LIMLA); Planta Piloto de Procesos Industriales y Microbiológicos (PROIMI); CCT; CONICET; Tucumán Argentina
- Centro de Investigaciones y Servicios de Microscopía Electrónica (CISME-CONICET-UNT); CCT, CONICET; Tucumán Argentina
- Facultad de Ciencias Naturales; Instituto Miguel Lillo; Universidad Nacional de Tucumán; Tucumán Argentina
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8
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Characterization of antimicrobial activities of olive phenolics on yeasts using conventional methods and mid-infrared spectroscopy. Journal of Food Science and Technology 2018; 56:149-158. [PMID: 30728556 DOI: 10.1007/s13197-018-3468-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Revised: 09/19/2018] [Accepted: 10/18/2018] [Indexed: 10/28/2022]
Abstract
Olive fruit is very rich in terms of phenolic compounds. Antimicrobial activities of various phenolic compounds against bacteria and fungi are well established; however, their effects on yeasts have not been examined. Aim of this study was to investigate the antimicrobial effects induced by olive phenolic compounds, including tyrosol, hydroxytyrosol, oleuropein, luteolin and apigenin against two yeast species, Aureobasidium pullulans and Saccharomyces cerevisiae. For this purpose, yeasts were treated with various concentrations (12.5-1000 ppm) of phenolic compounds and reduction in yeast population was followed with optical density measurements with microplate reader, yeast colony forming units and mid-infrared spectroscopy. All phenolic compounds were effective on both yeasts, especially 200 ppm and higher concentrations have significant antimicrobial activity; however, effects of lower levels depend on the type of phenolic compound. According to mid-infrared spectral data, significant changes were observed in 1200-900 cm-1 range corresponding to carbohydrates of yeast structure as a result of exposure to all phenolic compounds except tyrosol. Spectra of tyrosol and luteolin treated yeasts also showed changes in 1750-1500 cm-1 related to amide section and 3600-3000 cm-1 fatty acid region. Since phenolic compounds from olives were effective against yeasts, they could be used in food applications where yeast growth showed problem. In addition, FTIR spectroscopy could be successfully used to monitor and characterize antimicrobial activity of phenolic compounds on yeasts as complementary to conventional microbiological methods.
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9
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Müller P, Ignatz E, Kiontke S, Brettel K, Essen LO. Sub-nanosecond tryptophan radical deprotonation mediated by a protein-bound water cluster in class II DNA photolyases. Chem Sci 2017; 9:1200-1212. [PMID: 29675165 PMCID: PMC5885780 DOI: 10.1039/c7sc03969g] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2017] [Accepted: 12/10/2017] [Indexed: 01/01/2023] Open
Abstract
Light activation of class II DNA photolyases is enhanced by a unique cluster of protein-bound water molecules.
Class II DNA photolyases are flavoenzymes occurring in both prokaryotes and eukaryotes including higher plants and animals. Despite considerable structural deviations from the well-studied class I DNA photolyases, they share the main biological function, namely light-driven repair of the most common UV-induced lesions in DNA, the cyclobutane pyrimidine dimers (CPDs). For DNA repair activity, photolyases require the fully reduced flavin adenine dinucleotide cofactor, FADH–, which can be obtained from oxidized or semi-reduced FAD by a process called photoactivation. Using transient absorption spectroscopy, we have examined the initial electron and proton transfer reactions leading to photoactivation of the class II DNA photolyase from Methanosarcina mazei. Upon photoexcitation, FAD is reduced via a distinct (class II-specific) chain of three tryptophans, giving rise to an FAD˙– TrpH˙+ radical pair. The distal Trp388H˙+ deprotonates to Trp388˙ in 350 ps, i.e., by three orders of magnitude faster than TrpH˙+ in aqueous solution or in any previously studied photolyase. We identified a class II-specific cluster of protein-bound water molecules ideally positioned to serve as the primary proton acceptor. The high rate of Trp388H˙+ deprotonation counters futile radical pair recombination and ensures efficient photoactivation.
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Affiliation(s)
- Pavel Müller
- Institute for Integrative Biology of the Cell (I2BC) , CEA , CNRS , Univ. Paris-Sud , Université Paris-Saclay , 91198 , Gif-sur-Yvette cedex , France .
| | - Elisabeth Ignatz
- Department of Chemistry , LOEWE Center for Synthetic Microbiology , Philipps University , 35032 Marburg , Germany .
| | - Stephan Kiontke
- Department of Chemistry , LOEWE Center for Synthetic Microbiology , Philipps University , 35032 Marburg , Germany .
| | - Klaus Brettel
- Institute for Integrative Biology of the Cell (I2BC) , CEA , CNRS , Univ. Paris-Sud , Université Paris-Saclay , 91198 , Gif-sur-Yvette cedex , France .
| | - Lars-Oliver Essen
- Department of Chemistry , LOEWE Center for Synthetic Microbiology , Philipps University , 35032 Marburg , Germany .
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10
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Zhang F, Ma H, Bowatte K, Kwiatkowski D, Mittmann E, Qasem H, Krauß N, Zeng X, Ren Z, Scheerer P, Yang X, Lamparter T. Crystal Structures of Bacterial (6-4) Photolyase Mutants with Impaired DNA Repair Activity. Photochem Photobiol 2017; 93:304-314. [DOI: 10.1111/php.12699] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 11/29/2016] [Indexed: 11/27/2022]
Affiliation(s)
- Fan Zhang
- Karlsruhe Institute of Technology; Botanical Institute; Karlsruhe Germany
- Institute of Materials; China Academy of Engineering Physics; Mianyang China
| | - Hongju Ma
- Karlsruhe Institute of Technology; Botanical Institute; Karlsruhe Germany
| | - Kalinga Bowatte
- Department of Chemistry; University of Illinois at Chicago; Chicago IL
| | - Dennis Kwiatkowski
- Charité - Universitätsmedizin Berlin; Institute of Medical Physics and Biophysics (CC2); Group Protein X-ray Crystallography and Signal Transduction; Berlin Germany
| | - Esther Mittmann
- Karlsruhe Institute of Technology; Botanical Institute; Karlsruhe Germany
| | - Heba Qasem
- Karlsruhe Institute of Technology; Botanical Institute; Karlsruhe Germany
| | - Norbert Krauß
- Karlsruhe Institute of Technology; Botanical Institute; Karlsruhe Germany
| | - Xiaoli Zeng
- Department of Chemistry; University of Illinois at Chicago; Chicago IL
| | - Zhong Ren
- Department of Chemistry; University of Illinois at Chicago; Chicago IL
| | - Patrick Scheerer
- Charité - Universitätsmedizin Berlin; Institute of Medical Physics and Biophysics (CC2); Group Protein X-ray Crystallography and Signal Transduction; Berlin Germany
| | - Xiaojing Yang
- Department of Chemistry; University of Illinois at Chicago; Chicago IL
| | - Tilman Lamparter
- Karlsruhe Institute of Technology; Botanical Institute; Karlsruhe Germany
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11
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Yamada D, Dokainish HM, Iwata T, Yamamoto J, Ishikawa T, Todo T, Iwai S, Getzoff ED, Kitao A, Kandori H. Functional Conversion of CPD and (6-4) Photolyases by Mutation. Biochemistry 2016; 55:4173-83. [PMID: 27431478 DOI: 10.1021/acs.biochem.6b00361] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Ultraviolet (UV) light from the sun damages DNA by forming a cyclobutane pyrimidine dimer (CPD) and pyrimidine(6-4)pyrimidone photoproducts [(6-4) PP]. Photolyase (PHR) enzymes utilize near-UV/blue light for DNA repair, which is initiated by light-induced electron transfer from the fully reduced flavin adenine dinucleotide chromophore. Despite similar structures and repair mechanisms, the functions of PHR are highly selective; CPD PHR repairs CPD, but not (6-4) PP, and vice versa. In this study, we attempted functional conversion between CPD and (6-4) PHRs. We found that a triple mutant of (6-4) PHR is able to repair the CPD photoproduct, though the repair efficiency is 1 order of magnitude lower than that of wild-type CPD PHR. Difference Fourier transform infrared spectra for repair demonstrate the lack of secondary structural alteration in the mutant, suggesting that the triple mutant gains substrate binding ability while it does not gain the optimized conformational changes from light-induced electron transfer to the release of the repaired DNA. Interestingly, the (6-4) photoproduct is not repaired by the reverse mutation of CPD PHR, and eight additional mutations (total of 11 mutations) introduced into CPD PHR are not sufficient. The observed asymmetric functional conversion is interpreted in terms of a more complex repair mechanism for (6-4) repair, which was supported by quantum chemical/molecular mechanical calculation. These results suggest that CPD PHR may represent an evolutionary origin for photolyase family proteins.
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Affiliation(s)
- Daichi Yamada
- Department of Frontier Materials, Nagoya Institute of Technology , Showa-ku, Nagoya 466-8555, Japan
| | - Hisham M Dokainish
- Institute of Molecular and Cellular Biosciences, The University of Tokyo , 1-1-1, Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Tatsuya Iwata
- Department of Frontier Materials, Nagoya Institute of Technology , Showa-ku, Nagoya 466-8555, Japan.,OptoBioTechnology Research Center, Nagoya Institute of Technology , Showa-ku, Nagoya 466-8555, Japan
| | - Junpei Yamamoto
- Graduate School of Engineering Science, Osaka University , Toyonaka, Osaka 560-8531, Japan
| | - Tomoko Ishikawa
- Department of Radiation Biology and Medical Genetics, Graduate School of Medicine, Osaka University , Osaka 565-0871, Japan
| | - Takeshi Todo
- Department of Radiation Biology and Medical Genetics, Graduate School of Medicine, Osaka University , Osaka 565-0871, Japan
| | - Shigenori Iwai
- Graduate School of Engineering Science, Osaka University , Toyonaka, Osaka 560-8531, Japan
| | - Elizabeth D Getzoff
- Department of Integrative Structural and Computational Biology and The Skaggs Institute for Chemical Biology, The Scripps Research Institute , La Jolla, California 92037, United States
| | - Akio Kitao
- Institute of Molecular and Cellular Biosciences, The University of Tokyo , 1-1-1, Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Hideki Kandori
- Department of Frontier Materials, Nagoya Institute of Technology , Showa-ku, Nagoya 466-8555, Japan.,OptoBioTechnology Research Center, Nagoya Institute of Technology , Showa-ku, Nagoya 466-8555, Japan
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12
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Faghihzadeh F, Anaya NM, Schifman LA, Oyanedel-Craver V. Fourier transform infrared spectroscopy to assess molecular-level changes in microorganisms exposed to nanoparticles. ACTA ACUST UNITED AC 2016. [DOI: 10.1007/s41204-016-0001-8] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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13
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Müller P, Brettel K, Grama L, Nyitrai M, Lukacs A. Photochemistry of Wild-Type and N378D Mutant E. coli DNA Photolyase with Oxidized FAD Cofactor Studied by Transient Absorption Spectroscopy. Chemphyschem 2016; 17:1329-40. [PMID: 26852903 DOI: 10.1002/cphc.201501077] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Indexed: 01/02/2023]
Abstract
DNA photolyases (PLs) and evolutionarily related cryptochrome (CRY) blue-light receptors form a widespread superfamily of flavoproteins involved in DNA photorepair and signaling functions. They share a flavin adenine dinucleotide (FAD) cofactor and an electron-transfer (ET) chain composed typically of three tryptophan residues that connect the flavin to the protein surface. Four redox states of FAD are relevant for the various functions of PLs and CRYs: fully reduced FADH(-) (required for DNA photorepair), fully oxidized FADox (blue-light-absorbing dark state of CRYs), and the two semireduced radical states FAD(.-) and FADH(.) formed in ET reactions. The PL of Escherichia coli (EcPL) has been studied for a long time and is often used as a reference system; however, EcPL containing FADox has so far not been investigated on all relevant timescales. Herein, a detailed transient absorption study of EcPL on timescales from nanoseconds to seconds after excitation of FADox is presented. Wild-type EcPL and its N378D mutant, in which the asparagine facing the N5 of the FAD isoalloxazine is replaced by aspartic acid, known to protonate FAD(.-) (formed by ET from the tryptophan chain) in plant CRYs in about 1.5 μs, are characterized. Surprisingly, the mutant protein does not show this protonation. Instead, FAD(.-) is converted in 3.3 μs into a state with spectral features that are different from both FADH(.) and FAD(.-) . Such a conversion does not occur in wild-type EcPL. The chemical nature and formation mechanism of the atypical FAD radical in N378D mutant EcPL are discussed.
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Affiliation(s)
- Pavel Müller
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France.
| | - Klaus Brettel
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France.
| | - Laszlo Grama
- Department of Biophysics, Medical School, University of Pecs, 12 str. Szigeti, 7624, Pecs, Hungary
| | - Miklos Nyitrai
- Department of Biophysics, Medical School, University of Pecs, 12 str. Szigeti, 7624, Pecs, Hungary
| | - Andras Lukacs
- Department of Biophysics, Medical School, University of Pecs, 12 str. Szigeti, 7624, Pecs, Hungary.
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14
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Yamada D, Iwata T, Yamamoto J, Hitomi K, Todo T, Iwai S, Getzoff ED, Kandori H. Structural role of two histidines in the (6-4) photolyase reaction. Biophys Physicobiol 2015; 12:139-44. [PMID: 27493863 PMCID: PMC4736838 DOI: 10.2142/biophysico.12.0_139] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Accepted: 11/16/2015] [Indexed: 12/01/2022] Open
Abstract
Photolyases (PHRs) are DNA repair enzymes that revert UV-induced photoproducts, either cyclobutane pyrimidine dimers (CPD) or (6-4) photoproducts (PPs), into normal bases to maintain genetic integrity. (6-4) PHR must catalyze not only covalent bond cleavage, but also hydroxyl or amino group transfer, yielding a more complex mechanism than that postulated for CPD PHR. Previous mutation analysis revealed the importance of two histidines in the active center, H354 and H358 for Xenopus (6-4) PHR, whose mutations significantly lowered the enzymatic activity. Based upon highly sensitive FTIR analysis of the repair function, here we report that both H354A and H358A mutants of Xenopus (6-4) PHR still maintain their repair activity, although the efficiency is much lower than that of the wild type. Similar difference FTIR spectra between the wild type and mutant proteins suggest a common mechanism of repair in which (6-4) PP binds to the active center of each mutant, and is released after repair, as occurs in the wild type. Similar FTIR spectra also suggest that a decrease in volume by the H-to-A mutation is possibly compensated by the addition of water molecule( s). Such a modified environment is sufficient for the repair function that is probably controlled by proton-coupled electron transfer between the enzyme and substrate. On the other hand, two histidines must work in a concerted manner in the active center of the wild-type enzyme, which significantly raises the repair efficiency.
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Affiliation(s)
- Daichi Yamada
- Department of Frontier Materials, Nagoya Institute of Technology, Nagoya, Aichi 466-8555, Japan
| | - Tatsuya Iwata
- Department of Frontier Materials, Nagoya Institute of Technology, Nagoya, Aichi 466-8555, Japan; OptoBioTechnology Research Center, Nagoya Institute of Technology, Nagoya, Aichi 466-8555, Japan
| | - Junpei Yamamoto
- Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Kenichi Hitomi
- Department of Integrative Structural and Computational Biology and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Takeshi Todo
- Department of Radiation Biology and Medical Genetics, Graduate School of Medicine, Osaka University, Osaka 565-0871, Japan
| | - Shigenori Iwai
- Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Elizabeth D Getzoff
- Department of Integrative Structural and Computational Biology and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Hideki Kandori
- Department of Frontier Materials, Nagoya Institute of Technology, Nagoya, Aichi 466-8555, Japan; OptoBioTechnology Research Center, Nagoya Institute of Technology, Nagoya, Aichi 466-8555, Japan
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15
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Paulus B, Bajzath C, Melin F, Heidinger L, Kromm V, Herkersdorf C, Benz U, Mann L, Stehle P, Hellwig P, Weber S, Schleicher E. Spectroscopic characterization of radicals and radical pairs in fruit fly cryptochrome - protonated and nonprotonated flavin radical-states. FEBS J 2015; 282:3175-89. [PMID: 25879256 DOI: 10.1111/febs.13299] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Revised: 03/21/2015] [Accepted: 04/14/2015] [Indexed: 01/05/2023]
Abstract
Drosophila melanogaster cryptochrome is one of the model proteins for animal blue-light photoreceptors. Using time-resolved and steady-state optical spectroscopy, we studied the mechanism of light-induced radical-pair formation and decay, and the photoreduction of the FAD cofactor. Exact kinetics on a microsecond to minutes timescale could be extracted for the wild-type protein using global analysis. The wild-type exhibits a fast photoreduction reaction from the oxidized FAD to the FAD(•-) state with a very positive midpoint potential of ~ +125 mV, although no further reduction could be observed. We could also demonstrate that the terminal tryptophan of the conserved triad, W342, is directly involved in electron transfer; however, photoreduction could not be completely inhibited in a W342F mutant. The investigation of another mutation close to the FAD cofactor, C416N, rather unexpectedly reveals accumulation of a protonated flavin radical on a timescale of several seconds. The obtained data are critically discussed with the ones obtained from another protein, Escherichia coli photolyase, and we conclude that the amino acid opposite N(5) of the isoalloxazine moiety of FAD is able to (de)stabilize the protonated FAD radical but not to significantly modulate the kinetics of any light-inducted reactions.
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Affiliation(s)
- Bernd Paulus
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Germany
| | - Csaba Bajzath
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Germany
| | - Frédéric Melin
- Laboratoire de Bioélectrochimie et Spectroscopie Université de Strasbourg, France
| | - Lorenz Heidinger
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Germany
| | - Viktoria Kromm
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Germany
| | | | - Ulrike Benz
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Germany
| | - Lisa Mann
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Germany
| | - Patricia Stehle
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Germany
| | - Petra Hellwig
- Laboratoire de Bioélectrochimie et Spectroscopie Université de Strasbourg, France
| | - Stefan Weber
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Germany
| | - Erik Schleicher
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Germany
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16
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Mahaputra Wijaya IM, Iwata T, Yamamoto J, Hitomi K, Iwai S, Getzoff ED, Kandori H. FTIR study of CPD photolyase with substrate in single strand DNA. Biophysics (Nagoya-shi) 2015; 11:39-45. [PMID: 27493513 PMCID: PMC4736783 DOI: 10.2142/biophysics.11.39] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 12/17/2014] [Indexed: 12/01/2022] Open
Abstract
Photolyases (PHRs) utilize near UV/blue light to specifically repair the major photoproducts (PPs) of UV-induced damaged DNA. The cyclobutane pyrimidine dimer (CPD)-PHR binds flavin adenine dinucleotide (FAD) as a cofactor and repairs CPD lesions in double-stranded DNA. To understand the activation and repair mechanism of CPD-PHR, we applied light-induced difference Fourier transform infrared (FTIR) spectroscopy to CPD-PHR, whose signals were identified by use of isotope-labeling. To further investigate the enzymatic function, here we study the activation and repair mechanism of CPD-PHR with the substrate in single strand DNA, and the obtained FTIR spectra are compared with those in double-stranded DNA, the natural substrate. The difference spectra of photoactivation, the fully-reduced (FADH−) minus semiquinone (FADH•) spectra, are almost identical in the presence of single strand and double-stranded DNA, except for slight spectral modification in the amide-I region. On the other hand, the difference spectra of photorepair were highly substrate dependent. Strong bands of the C=O stretch (1,720–1,690 cm−1) and phosphate vibrations (1,090–1,060 cm−1) of double-stranded DNA may have disappeared in the case of single strand DNA. However, an isotope-labeled enzyme study revealed that spectral features upon DNA repair are similar between both substrates, and the main reason for the apparent spectral difference originates from structural flexibility of DNA after repair.
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Affiliation(s)
- I M Mahaputra Wijaya
- Department of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Tatsuya Iwata
- Department of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan; OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Junpei Yamamoto
- Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Kenichi Hitomi
- Department of Integrative Structural and Computational Biology and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037
| | - Shigenori Iwai
- Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Elizabeth D Getzoff
- Department of Integrative Structural and Computational Biology and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037
| | - Hideki Kandori
- Department of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan; OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
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17
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Wijaya IMM, Iwata T, Yamamoto J, Hitomi K, Iwai S, Getzoff ED, Kennis JTM, Mathes T, Kandori H. Flavin adenine dinucleotide chromophore charge controls the conformation of cyclobutane pyrimidine dimer photolyase α-helices. Biochemistry 2014; 53:5864-75. [PMID: 25152314 DOI: 10.1021/bi500638b] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Observations of light-receptive enzyme complexes are usually complicated by simultaneous overlapping signals from the chromophore, apoprotein, and substrate, so that only the initial, ultrafast, photon-chromophore reaction and the final, slow, protein conformational change provide separate, nonoverlapping signals. Each provides its own advantages, whereas sometimes the overlapping signals from the intervening time scales still cannot be fully deconvoluted. We overcome the problem by using a novel method to selectively isotope-label the apoprotein but not the flavin adenine dinucleotide (FAD) cofactor. This allowed the Fourier transform infrared (FTIR) signals to be separated from the apoprotein, FAD cofactor, and DNA substrate. Consequently, a comprehensive structure-function study by FTIR spectroscopy of the Escherichia coli cyclobutane pyrimidine dimer photolyase (CPD-PHR) DNA repair enzyme was possible. FTIR signals could be identified and assigned upon FAD photoactivation and DNA repair, which revealed protein dynamics for both processes beyond simple one-electron reduction and ejection, respectively. The FTIR data suggest that the synergistic cofactor-protein partnership in CPD-PHR linked to changes in the shape of FAD upon one-electron reduction may be coordinated with conformational changes in the apoprotein, allowing it to fit the DNA substrate. Activation of the CPD-PHR chromophore primes the apoprotein for subsequent DNA repair, suggesting that CPD-PHR is not simply an electron-ejecting structure. When FAD is activated, changes in its structure may trigger coordinated conformational changes in the apoprotein and thymine carbonyl of the substrate, highlighting the role of Glu275. In contrast, during DNA repair and release processes, primary conformational changes occur in the enzyme and DNA substrate, with little contribution from the FAD cofactor and surrounding amino acid residues.
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Affiliation(s)
- I M Mahaputra Wijaya
- Department of Frontier Materials and ‡OptoBio Technology Research Center, Nagoya Institute of Technology , Showa-ku, Nagoya 466-8555, Japan
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18
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Liu Z, Tan C, Guo X, Li J, Wang L, Zhong D. Dynamic Determination of Active-Site Reactivity in Semiquinone Photolyase by the Cofactor Photoreduction. J Phys Chem Lett 2014; 5:820-825. [PMID: 24803991 PMCID: PMC3985926 DOI: 10.1021/jz500077s] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2014] [Accepted: 02/11/2014] [Indexed: 05/07/2023]
Abstract
Photolyase contains a flavin cofactor in a fully reduced form as its functional state to repair ultraviolet-damaged DNA upon blue light absorption. However, after purification, the cofactor exists in its oxidized or neutral semiquinone state. Such oxidization eliminates the repair function, but it can be reverted by photoreduction, a photoinduced process with a series of electron-transfer (ET) reactions. With femtosecond absorption spectroscopy and site-directed mutagenesis, we completely recharacterized such photoreduction dynamics in the semiquinone state. Comparing with all previous studies, we identified a new intramolecular ET pathway, determined stretched ET behaviors, refined all ET time scales, and finally evaluated the driving forces and reorganization energies for eight elementary ET reactions. Combined with the oxidized-state photoreduction dynamics, we elucidated the different active-site properties of the reduction ability and structural flexibility in the oxidized and semiquinone states, leading to the dramatically different ET dynamics and photoreduction efficiency in the two states.
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19
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Spexard M, Thöing C, Beel B, Mittag M, Kottke T. Response of the Sensory Animal-like Cryptochrome aCRY to Blue and Red Light As Revealed by Infrared Difference Spectroscopy. Biochemistry 2014; 53:1041-50. [DOI: 10.1021/bi401599z] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Meike Spexard
- Physical
and Biophysical Chemistry, Department of Chemistry, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
| | - Christian Thöing
- Physical
and Biophysical Chemistry, Department of Chemistry, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
| | - Benedikt Beel
- Institute
of General Botany and Plant Physiology, Friedrich Schiller University, Am Planetarium 1, 07743 Jena, Germany
| | - Maria Mittag
- Institute
of General Botany and Plant Physiology, Friedrich Schiller University, Am Planetarium 1, 07743 Jena, Germany
| | - Tilman Kottke
- Physical
and Biophysical Chemistry, Department of Chemistry, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
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20
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Abstract
Light-induced difference Fourier transform infrared (FTIR) spectroscopy is a powerful, sensitive, and informative method to study structure-function relationships in photoreceptive proteins. Strong absorption of water in the IR region is always problematic in this method, but if water content in the sample is controlled during measurements, this method can provide useful information on a single protein-bound water molecule. We established three kinds of sample preparations: hydrated film, redissolved sample, and concentrated solution. Hydrated films were used for the measurements of LOV and BLUF domains, where accurate difference FTIR spectra were obtained in the whole mid-IR region (4,000-800 cm(-1)). Vibrations of S-H stretch of cysteine, O-H stretch of water, and O-H stretch of tyrosine provide important information on hydrogen bonds in these proteins. Redissolved samples were used for the measurements of (6-4) photolyase, in which enzymatic turnover takes place. From the illumination time-dependence of excess amount of substrate, it is possible to isolate the signal originating from the binding of enzyme to substrate. If proteins are less tolerant to drying, as for example cryptochromes of the DASH type, concentrated solution is used. Detailed methodological aspects in light-induced difference FTIR spectroscopy are reviewed by mainly focusing on our results.
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Affiliation(s)
- Daichi Yamada
- Department of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya, 466-8555, Japan
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21
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Wijaya IMM, Zhang Y, Iwata T, Yamamoto J, Hitomi K, Iwai S, Getzoff ED, Kandori H. Detection of distinct α-helical rearrangements of cyclobutane pyrimidine dimer photolyase upon substrate binding by Fourier transform infrared spectroscopy. Biochemistry 2013; 52:1019-27. [PMID: 23331252 DOI: 10.1021/bi3016179] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Photolyases (PHRs) utilize near-ultraviolet (UV)-blue light to specifically repair the major photoproducts (PPs) of UV-induced damaged DNA. The cyclobutane pyrimidine dimer PHR (CPD-PHR) from Escherichia coli binds flavin adenine dinucleotide (FAD) as a cofactor and 5,10-methenyltetrahydrofolate as a light-harvesting pigment and specifically repairs CPD lesions. By comparison, a second photolyase known as (6-4) PHR, present in a range of higher organisms, uniquely repairs (6-4) PPs. To understand the repair mechanism and the substrate specificity that distinguish CPD-PHR from (6-4) PHR, we applied Fourier transform infrared (FTIR) spectroscopy to bacterial CPD-PHR in the presence or absence of a well-defined DNA substrate, as we have studied previously for vertebrate (6-4) PHR. PHRs show light-induced reduction of FAD, and photorepair by CPD-PHR involves the transfer of an electron from the photoexcited reduced FAD to the damaged DNA for cleaving the dimers to maintain the DNA's integrity. Here, we measured and analyzed difference FTIR spectra for the photoactivation and DNA photorepair processes of CPD-PHR. We identified light-dependent signals only in the presence of substrate. The signals, presumably arising from a protonated carboxylic acid or the DNA substrate, implicate conformational rearrangements of the protein and substrate during the repair process. Deuterium exchange FTIR measurements of CPD-PHR highlight potential differences in the photoactivation and photorepair mechanisms in comparison to those of (6-4) PHR. Although CPD-PHR and (6-4) PHR appear to exhibit similar overall structures, our studies indicate that distinct conformational rearrangements, especially in the α-helices, are initiated within these enzymes upon binding of their respective DNA substrates.
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Affiliation(s)
- I M Mahaputra Wijaya
- Department of Frontier Materials, Nagoya Institute of Technology, Nagoya 466-8555, Japan
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22
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Yamada D, Zhang Y, Iwata T, Hitomi K, Getzoff ED, Kandori H. Fourier-transform infrared study of the photoactivation process of Xenopus (6-4) photolyase. Biochemistry 2012; 51:5774-83. [PMID: 22747528 DOI: 10.1021/bi300530x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Photolyases (PHRs) are blue light-activated DNA repair enzymes that maintain genetic integrity by reverting UV-induced photoproducts into normal bases. The flavin adenine dinucleotide (FAD) chromophore of PHRs has four different redox states: oxidized (FAD(ox)), anion radical (FAD(•-)), neutral radical (FADH(•)), and fully reduced (FADH(-)). We combined difference Fourier-transform infrared (FTIR) spectroscopy with UV-visible spectroscopy to study the detailed photoactivation process of Xenopus (6-4) PHR. Two photons produce the enzymatically active, fully reduced PHR from oxidized FAD: FAD(ox) is converted to semiquinone via light-induced one-electron and one-proton transfers and then to FADH(-) by light-induced one-electron transfer. We successfully trapped FAD(•-) at 200 K, where electron transfer occurs but proton transfer does not. UV-visible spectroscopy following 450 nm illumination of FAD(ox) at 277 K defined the FADH(•)/FADH(-) mixture and allowed calculation of difference FTIR spectra among the four redox states. The absence of a characteristic C=O stretching vibration indicated that the proton donor is not a protonated carboxylic acid. Structural changes in Trp and Tyr are suggested by UV-visible and FTIR analysis of FAD(•-) at 200 K. Spectral analysis of amide I vibrations revealed structural perturbation of the protein's β-sheet during initial electron transfer (FAD(•-) formation), a transient increase in α-helicity during proton transfer (FADH(•) formation), and reversion to the initial amide I signal following subsequent electron transfer (FADH(-) formation). Consequently, in (6-4) PHR, unlike cryptochrome-DASH, formation of enzymatically active FADH(-) did not perturb α-helicity. Protein structural changes in the photoactivation of (6-4) PHR are discussed on the basis of these FTIR observations.
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Affiliation(s)
- Daichi Yamada
- Department of Frontier Materials, Nagoya Institute of Technology, Nagoya 466-8555, Japan
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23
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Magnetically sensitive light-induced reactions in cryptochrome are consistent with its proposed role as a magnetoreceptor. Proc Natl Acad Sci U S A 2012; 109:4774-9. [PMID: 22421133 DOI: 10.1073/pnas.1118959109] [Citation(s) in RCA: 228] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Among the biological phenomena that fall within the emerging field of "quantum biology" is the suggestion that magnetically sensitive chemical reactions are responsible for the magnetic compass of migratory birds. It has been proposed that transient radical pairs are formed by photo-induced electron transfer reactions in cryptochrome proteins and that their coherent spin dynamics are influenced by the geomagnetic field leading to changes in the quantum yield of the signaling state of the protein. Despite a variety of supporting evidence, it is still not clear whether cryptochromes have the properties required to respond to magnetic interactions orders of magnitude weaker than the thermal energy, k(B)T. Here we demonstrate that the kinetics and quantum yields of photo-induced flavin-tryptophan radical pairs in cryptochrome are indeed magnetically sensitive. The mechanistic origin of the magnetic field effect is clarified, its dependence on the strength of the magnetic field measured, and the rates of relevant spin-dependent, spin-independent, and spin-decoherence processes determined. We argue that cryptochrome is fit for purpose as a chemical magnetoreceptor.
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24
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Maeda K, Neil SRT, Henbest KB, Weber S, Schleicher E, Hore PJ, Mackenzie SR, Timmel CR. Following Radical Pair Reactions in Solution: A Step Change in Sensitivity Using Cavity Ring-Down Detection. J Am Chem Soc 2011; 133:17807-15. [DOI: 10.1021/ja206783t] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kiminori Maeda
- Department of Chemistry, University of Oxford, Inorganic Chemistry Laboratory, Oxford, OX1 3QR, U.K
- Centre for Advanced Electron Spin Resonance, University of Oxford, OX1 3QR, U.K
| | - Simon R. T. Neil
- Department of Chemistry, University of Oxford, Physical and Theoretical Chemistry Laboratory, Oxford, OX1 3QZ, U.K
| | - Kevin B. Henbest
- Department of Chemistry, University of Oxford, Inorganic Chemistry Laboratory, Oxford, OX1 3QR, U.K
- Centre for Advanced Electron Spin Resonance, University of Oxford, OX1 3QR, U.K
| | - Stefan Weber
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Albertstraße 21, 79104 Freiburg, Germany
| | - Erik Schleicher
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Albertstraße 21, 79104 Freiburg, Germany
| | - P. J. Hore
- Department of Chemistry, University of Oxford, Physical and Theoretical Chemistry Laboratory, Oxford, OX1 3QZ, U.K
| | - Stuart R. Mackenzie
- Department of Chemistry, University of Oxford, Physical and Theoretical Chemistry Laboratory, Oxford, OX1 3QZ, U.K
| | - Christiane R. Timmel
- Department of Chemistry, University of Oxford, Inorganic Chemistry Laboratory, Oxford, OX1 3QR, U.K
- Centre for Advanced Electron Spin Resonance, University of Oxford, OX1 3QR, U.K
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25
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El Khoury Y, Hellwig P. A combined far-infrared spectroscopic and electrochemical approach for the study of iron-sulfur proteins. Chemphyschem 2011; 12:2669-74. [PMID: 21887734 DOI: 10.1002/cphc.201100165] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2011] [Revised: 06/15/2011] [Indexed: 11/11/2022]
Abstract
Herein, we present the development of a far-infrared spectroscopic approach for studying metalloenzyme active sites in a redox-dependent manner. An electrochemical cell with 5 mm path and based on silicon windows was found to be appropriate for the measurement of aqueous solutions down to 200 cm(-1) . The cell was probed with the infrared redox signature of the metal-ligand vibrations of different iron-sulfur proteins. Each Fe-S cluster type was found to show a specific spectral signature. As a common feature, a downshift of the frequency of the Fe-S vibrations was seen upon reduction, in line with the increase of the Fe-S bond. This downshift was found to be fully reversible. Electrochemically induced FTIR difference spectroscopy in the far infrared is now possible, opening new perspectives on the understanding of metalloproteins in function of the redox state.
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Affiliation(s)
- Youssef El Khoury
- Institut de Chimie, UMR, Laboratoire de spectroscopie vibrationnelle et électrochimie des biomolécules Université de Strasbourg, France
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Zhang Y, Iwata T, Yamamoto J, Hitomi K, Iwai S, Todo T, Getzoff ED, Kandori H. FTIR study of light-dependent activation and DNA repair processes of (6-4) photolyase. Biochemistry 2011; 50:3591-8. [PMID: 21462921 DOI: 10.1021/bi1019397] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The UV component of sunlight threatens all life on the earth by damaging DNA. The photolyase (PHR) DNA repair proteins maintain genetic integrity by harnessing blue light to restore intact bases from the major UV-induced photoproducts, cyclobutane pyrimidine dimers (CPD), and (6-4) photoproducts ((6-4) PPs). The (6-4) PHR must catalyze not only covalent bond cleavage between two pyrmidine bases but also hydroxyl or amino group transfer from the 5'- to 3'-pyrimidine base, requiring a more complex mechanism than that postulated for CPD PHR. In this paper, we apply Fourier transform infrared (FTIR) spectroscopy to (6-4) PHR and report difference FTIR spectra that correspond to its photoactivation, substrate binding, and light-dependent DNA repair processes. The presence of DNA carrying a single (6-4) PP uniquely influences vibrations of the protein backbone and a protonated carboxylic acid, whereas photoactivation produces IR spectral changes for the FAD cofactor and the surrounding protein. Difference FTIR spectra for the light-dependent DNA damage repair reaction directly show significant DNA structural changes in the (6-4) lesion and the neighboring phosphate group. Time-dependent illumination of samples with different enzyme:substrate stoichiometries successfully distinguished signals characteristic of structural changes in the protein and the DNA resulting from binding and catalysis.
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Affiliation(s)
- Yu Zhang
- Department of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
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Alvarez-Ordóñez A, Mouwen DJM, López M, Prieto M. Fourier transform infrared spectroscopy as a tool to characterize molecular composition and stress response in foodborne pathogenic bacteria. J Microbiol Methods 2011; 84:369-78. [PMID: 21256893 DOI: 10.1016/j.mimet.2011.01.009] [Citation(s) in RCA: 98] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2010] [Accepted: 01/11/2011] [Indexed: 10/18/2022]
Abstract
Vibrational spectroscopy techniques have shown capacity to provide non-destructive, rapid, relevant information on microbial systematics, useful for classification and identification. Infrared spectroscopy enables the biochemical signatures from microbiological structures to be extracted and analyzed, in conjunction with advanced chemometrics. In addition, a number of recent studies have shown that Fourier Transform Infrared (FT-IR) spectroscopy can help understand the molecular basis of events such as the adaptive tolerance responses expressed by bacteria when exposed to stress conditions in the environment (e.g. those that cells confront in food and during food processing). The current review gives an overview of the published experimental techniques, data-processing algorithms and approaches used in FT-IR spectroscopy to assess the mechanisms of bacterial inactivation by food processing technologies and antimicrobial compounds, to monitor the spore and membrane properties of foodborne pathogens in changing environments, to detect stress-injured microorganisms in food-related environments, to assess dynamic changes in bacterial populations, and to study bacterial tolerance responses.
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Rastogi RP, Richa, Kumar A, Tyagi MB, Sinha RP. Molecular mechanisms of ultraviolet radiation-induced DNA damage and repair. J Nucleic Acids 2010; 2010:592980. [PMID: 21209706 PMCID: PMC3010660 DOI: 10.4061/2010/592980] [Citation(s) in RCA: 603] [Impact Index Per Article: 43.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2010] [Revised: 08/15/2010] [Accepted: 09/28/2010] [Indexed: 11/20/2022] Open
Abstract
DNA is one of the prime molecules, and its stability is of utmost importance for proper functioning and existence of all living systems. Genotoxic chemicals and radiations exert adverse effects on genome stability. Ultraviolet radiation (UVR) (mainly UV-B: 280-315 nm) is one of the powerful agents that can alter the normal state of life by inducing a variety of mutagenic and cytotoxic DNA lesions such as cyclobutane-pyrimidine dimers (CPDs), 6-4 photoproducts (6-4PPs), and their Dewar valence isomers as well as DNA strand breaks by interfering the genome integrity. To counteract these lesions, organisms have developed a number of highly conserved repair mechanisms such as photoreactivation, base excision repair (BER), nucleotide excision repair (NER), and mismatch repair (MMR). Additionally, double-strand break repair (by homologous recombination and nonhomologous end joining), SOS response, cell-cycle checkpoints, and programmed cell death (apoptosis) are also operative in various organisms with the expense of specific gene products. This review deals with UV-induced alterations in DNA and its maintenance by various repair mechanisms.
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Affiliation(s)
- Rajesh P Rastogi
- Laboratory of Photobiology and Molecular Microbiology, Centre of Advanced Study in Botany, Banaras Hindu University, Varanasi 221005, India
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Immeln D, Pokorny R, Herman E, Moldt J, Batschauer A, Kottke T. Photoreaction of plant and DASH cryptochromes probed by infrared spectroscopy: the neutral radical state of flavoproteins. J Phys Chem B 2010; 114:17155-61. [PMID: 21128641 DOI: 10.1021/jp1076388] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Flavoprotein radicals are important intermediates in many biochemical processes. In the blue light sensor plant cryptochrome, the radical state acts as a signaling state. An isolation and assignment of infrared bands of flavin radicals in the most relevant spectral region of carbonyl stretches is missing because of their overlap with absorption of water and the protein moiety. In this study, the neutral radical state of flavoproteins was investigated by Fourier transform infrared difference spectroscopy. The light-induced conversion of oxidized to neutral radical state was monitored in a plant cryptochrome and that of radical to fully reduced state in a DASH cryptochrome. A pure difference spectrum of flavin radical minus oxidized state was obtained from a point mutant of a phototropin LOV (light-, oxygen-, or voltage-sensitive) domain. The analysis of the spectra revealed a correlation between the frequencies of carbonyl vibrations of the flavin radical state and those of its visible absorption. Plant cryptochrome shows a very low frequency of the carbonyl stretch in the radical state. It is postulated that the downshift is caused by the charge of an adjacent aspartate, which donated its proton to flavin N(5). Contributions from the protein moiety to the spectra were isolated for DASH and plant cryptochromes. As a conclusion, the photosensitive domain of plant cryptochromes shows changes in secondary structure upon illumination, which might be related to signaling.
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Affiliation(s)
- Dominik Immeln
- Department of Chemistry, Biophysical Chemistry, Bielefeld University, Universitätsstrasse 25, 33615 Bielefeld, Germany
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Iwata T, Zhang Y, Hitomi K, Getzoff ED, Kandori H. Key dynamics of conserved asparagine in a cryptochrome/photolyase family protein by fourier transform infrared spectroscopy. Biochemistry 2010; 49:8882-91. [PMID: 20828134 DOI: 10.1021/bi1009979] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Cryptochromes (Crys) and photolyases (Phrs) are flavoproteins that contain an identical cofactor (flavin adenine dinucleotide, FAD) within the same protein architecture but whose physiological functions are entirely different. In this study, we investigated light-induced conformational changes of a cyanobacterium Cry/Phr-like protein (SCry-DASH) with UV-visible and Fourier transform infrared (FTIR) spectroscopy. We developed a system for measuring light-induced difference spectra under the concentrated conditions. In the presence of a reducing agent, SCry-DASH showed photoreduction to the reduced form, and we identified a signal unique for an anionic form in the process. Difference FTIR spectra enabled us to assign characteristic FTIR bands to the respective redox forms of FAD. An asparagine residue, which anchors the FAD embedded within the protein, is conserved not only in the cyanobacterial protein but also in Phrs and other Crys, including the mammalian clock-related Crys. By characterizing an asparagine-to-cysteine (N392C) mutant of SCry-DASH, which mimics an insect specific Cry, we identified structural changes of the carbonyl group of this conserved asparagine upon light irradiation. We also found that the N392C mutant is stabilized in the anionic form. We did not observe a signal from protonated carboxylic acid residues during the reduction process, suggesting that the carboxylic acid moiety would not be directly involved as a proton donor to FAD in the system. These results are in contrast to plant specific Crys represented by Arabidopsis thaliana Cry1 that carry Asp at the position. We discuss potential roles for this conserved asparagine position and functional diversity in the Cry/Phr frame.
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Affiliation(s)
- Tatsuya Iwata
- Department of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya, Japan
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31
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Light-induced activation of class II cyclobutane pyrimidine dimer photolyases. DNA Repair (Amst) 2010; 9:495-505. [PMID: 20227927 DOI: 10.1016/j.dnarep.2010.01.014] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2009] [Revised: 01/16/2010] [Accepted: 01/19/2010] [Indexed: 11/23/2022]
Abstract
Light-induced activation of class II cyclobutane pyrimidine dimer (CPD) photolyases of Arabidopsis thaliana and Oryza sativa has been examined by UV/Vis and pulsed Davies-type electron-nuclear double resonance (ENDOR) spectroscopy, and the results compared with structure-known class I enzymes, CPD photolyase and (6-4) photolyase. By ENDOR spectroscopy, the local environment of the flavin adenine dinucleotide (FAD) cofactor is probed by virtue of proton hyperfine couplings that report on the electron-spin density at the positions of magnetic nuclei. Despite the amino-acid sequence dissimilarity as compared to class I enzymes, the results indicate similar binding motifs for FAD in the class II photolyases. Furthermore, the photoreduction kinetics starting from the FAD cofactor in the fully oxidized redox state, FAD(ox), have been probed by UV/Vis spectroscopy. In Escherichia coli (class I) CPD photolyase, light-induced generation of FADH from FAD(ox), and subsequently FADH(-) from FADH, proceeds in a step-wise fashion via a chain of tryptophan residues. These tryptophans are well conserved among the sequences and within all known structures of class I photolyases, but completely lacking from the equivalent positions of class II photolyase sequences. Nevertheless, class II photolyases show photoreduction kinetics similar to those of the class I enzymes. We propose that a different, but also effective, electron-transfer cascade is conserved among the class II photolyases. The existence of such electron transfer pathways is supported by the observation that the catalytically active fully reduced flavin state obtained by photoreduction is maintained even under oxidative conditions in all three classes of enzymes studied in this contribution.
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Thiagarajan V, Villette S, Espagne A, Eker APM, Brettel K, Byrdin M. DNA Repair by Photolyase: A Novel Substrate with Low Background Absorption around 265 nm for Transient Absorption Studies in the UV. Biochemistry 2009; 49:297-303. [DOI: 10.1021/bi901562a] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Viruthachalam Thiagarajan
- CEA, iBiTecS, Service de Bioénergétique Biologie Structurale et Mécanismes, 91191 Gif-sur-Yvette, France
- CNRS, URA 2096, 91191 Gif-sur-Yvette, France
| | - Sandrine Villette
- CEA, iBiTecS, Service de Bioénergétique Biologie Structurale et Mécanismes, 91191 Gif-sur-Yvette, France
- CNRS, URA 2096, 91191 Gif-sur-Yvette, France
| | - Agathe Espagne
- CEA, iBiTecS, Service de Bioénergétique Biologie Structurale et Mécanismes, 91191 Gif-sur-Yvette, France
- CNRS, URA 2096, 91191 Gif-sur-Yvette, France
| | - Andre P. M. Eker
- Department of Cell Biology and Genetics, Medical Genetics Centre, Erasmus University Medical Centre, P.O. Box 2040, 3000 CA Rotterdam, The Netherlands
| | - Klaus Brettel
- CEA, iBiTecS, Service de Bioénergétique Biologie Structurale et Mécanismes, 91191 Gif-sur-Yvette, France
- CNRS, URA 2096, 91191 Gif-sur-Yvette, France
| | - Martin Byrdin
- CEA, iBiTecS, Service de Bioénergétique Biologie Structurale et Mécanismes, 91191 Gif-sur-Yvette, France
- CNRS, URA 2096, 91191 Gif-sur-Yvette, France
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Magnetic-field effect on the photoactivation reaction of Escherichia coli DNA photolyase. Proc Natl Acad Sci U S A 2008; 105:14395-9. [PMID: 18799743 DOI: 10.1073/pnas.0803620105] [Citation(s) in RCA: 112] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
One of the two principal hypotheses put forward to explain the primary magnetoreception event underlying the magnetic compass sense of migratory birds is based on a magnetically sensitive chemical reaction. It has been proposed that a spin-correlated radical pair is produced photochemically in a cryptochrome and that the rates and yields of the subsequent chemical reactions depend on the orientation of the protein in the Earth's magnetic field. The suitability of cryptochrome for this purpose has been argued, in part, by analogy with DNA photolyase, although no effects of applied magnetic fields have yet been reported for any member of the cryptochrome/photolyase family. Here, we demonstrate a magnetic-field effect on the photochemical yield of a flavin-tryptophan radical pair in Escherichia coli photolyase. This result provides a proof of principle that photolyases, and most likely by extension also cryptochromes, have the fundamental properties needed to form the basis of a magnetic compass.
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34
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Hoang N, Bouly JP, Ahmad M. Evidence of a light-sensing role for folate in Arabidopsis cryptochrome blue-light receptors. MOLECULAR PLANT 2008; 1:68-74. [PMID: 20031915 DOI: 10.1093/mp/ssm008] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Arabidopsis cryptochromes cry1 and cry2 are blue-light signalling molecules with significant structural similarity to photolyases--a class of blue-light-sensing DNA repair enzymes. Like photolyases, purified plant cryptochromes have been shown to bind both flavin and pterin chromophores. The flavin functions as a light sensor and undergoes reduction in response to blue light that initiates the signalling cascade. However, the role of the pterin in plant cryptochromes has until now been unknown. Here, we show that the action spectrum for light-dependent degradation of cry2 has a significant peak of activity at 380 nm, consistent with absorption by a pterin cofactor. We further show that cry1 protein expressed in living insect cells responds with greater sensitivity to 380 nm light than to 450 nm, consistent with a light-harvesting antenna pigment that transfers excitation energy to the oxidized flavin of cry1. The pterin biosynthesis inhibitor DHAP selectively reduces cryptochrome responsivity at 380 nm but not 450 nm blue light in these cell cultures, indicating that the antenna pigment is a folate cofactor similar to that of photolyases.
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Affiliation(s)
- Nathalie Hoang
- Université Paris VI, Casier 156, 4 Place Jussieu, 75005 Paris, France
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35
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Xu L, Zhang D, Mu W, van Berkel WJH, Luo Z. Reversible resolution of flavin and pterin cofactors of His-tagged Escherichia coli DNA photolyase. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2006; 1764:1454-61. [PMID: 16938496 DOI: 10.1016/j.bbapap.2006.06.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2006] [Revised: 06/05/2006] [Accepted: 06/13/2006] [Indexed: 11/23/2022]
Abstract
Escherichia coli photolyase catalyzes the repair of cyclobutane pyrimidine dimers (CPD) in DNA under near UV/blue-light irradiation. The enzyme contains flavin adenine dinucleotide (FAD) and methenyltetrahydrofolate (MTHF) as noncovalently bound light sensing cofactors. To study the apoprotein-chromophore interactions we developed a new procedure to prepare apo-photolyase. MTHF-free photolyase was obtained by binding the C-terminal His-tagged holoenzyme to a metal-affinity column at neutral pH and washing the column with deionized water. Under these conditions the flavin remains bound and the defolated enzyme can be released from the column with 0.5 M imidazole pH 7.2. The MTHF-free protein was still capable of DNA repair, showing 70% activity of native enzyme. Fluorescence polarization experiments confirmed that MTHF binding is weakened at low ionic strength. Apo-photolyase was obtained by treating the His-tagged holoenzyme with 0.5 M imidazole pH 10.0. The apo-photolyase thus obtained was highly reconstitutable and bound nearly stoichiometric amounts of FAD(ox). Photolyase reconstituted with FAD(ox) had about 34% activity of native enzyme, which increased to 83% when FAD(ox) was reduced to FADH(-). Reconstitution kinetics performed at 20 degrees C showed that apo-photolyase associates with FADH(-) much faster (k(obs) approximately 3,000 M(-1) s(-1)) than with FAD(ox) (k(obs)=16 [corrected] M(-1) s(-1)). The dissociation constant of the photolyase-FAD(ox) complex is about 2.3 microM and that of E-FADH(-) is not higher than 20 nM (pH 7.2).
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Affiliation(s)
- Lei Xu
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China.
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36
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Kottke T, Batschauer A, Ahmad M, Heberle J. Blue-light-induced changes in Arabidopsis cryptochrome 1 probed by FTIR difference spectroscopy. Biochemistry 2006; 45:2472-9. [PMID: 16489739 DOI: 10.1021/bi051964b] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Cryptochromes are blue-light photoreceptors that regulate a variety of responses in animals and plants, including circadian entrainment in Drosophila and photomorphogenesis in Arabidopsis. They comprise a photolyase homology region (PHR) of about 500 amino acids and a C-terminal extension of varying length. In the PHR domain, flavin adenine dinucleotide (FAD) is noncovalently bound. The presence of a second chromophore, such as methenyltetrahydrofolate, in animal and plant cryptochromes is still under debate. Arabidopsis cryptochrome 1 (CRY1) has been intensively studied with regard to function and interaction of the protein in vivo and in vitro. However, little is known about the pathway from light absorption to signal transduction on the molecular level. We investigated the full-length CRY1 protein by Fourier transform infrared (FTIR) and UV/vis difference spectroscopy. Starting from the fully oxidized state of the chromophore FAD, a neutral flavoprotein radical is formed upon illumination in the absence of any exogenous electron donor. A preliminary assignment of the chromophore bands is presented. The FTIR difference spectrum reveals only moderate changes in secondary structure of the apoprotein in response to the photoreduction of the chromophore. Deprotonation of an aspartic or glutamic acid, probably D396, accompanies radical formation, as is deduced from the negative band at 1734 cm(-)(1) in D(2)O. The main positive band at 1524 cm(-)(1) in the FTIR spectrum shows a strong shift to lower frequencies as compared to other flavoproteins. Together with the unusual blue-shift of the absorption in the visible range to 595 nm, this clearly distinguishes the radical form of CRY1 from those of structurally highly homologous DNA photolyases. As a consequence, the direct comparison of cryptochrome to photolyase in terms of photoreactivity and mechanism has to be made with caution.
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Affiliation(s)
- Tilman Kottke
- IBI-2, Structural Biology, Research Center Jülich, 52425 Jülich, Germany.
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Lamb DC, Kim Y, Yermalitskaya LV, Yermalitsky VN, Lepesheva GI, Kelly SL, Waterman MR, Podust LM. A second FMN binding site in yeast NADPH-cytochrome P450 reductase suggests a mechanism of electron transfer by diflavin reductases. Structure 2006; 14:51-61. [PMID: 16407065 DOI: 10.1016/j.str.2005.09.015] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2005] [Revised: 09/19/2005] [Accepted: 09/19/2005] [Indexed: 11/22/2022]
Abstract
NADPH-cytochrome P450 reductase transfers two reducing equivalents derived from a hydride ion of NADPH via FAD and FMN to the large family of microsomal cytochrome P450 monooxygenases in one-electron transfer steps. The mechanism of electron transfer by diflavin reductases remains elusive and controversial. Here, we determined the crystal structure of truncated yeast NADPH-cytochrome P450 reductase, which is functionally active toward its physiological substrate cytochrome P450, and discovered a second FMN binding site at the interface of the connecting and FMN binding domains. The two FMN binding sites have different accessibilities to the bulk solvent and different amino acid environments, suggesting stabilization of different electronic structures of the reduced flavin. Since only one FMN cofactor is required for function, a hypothetical mechanism of electron transfer is discussed that proposes shuttling of a single FMN between these two sites coupled with the transition between two semiquinone forms, neutral (blue) and anionic (red).
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Affiliation(s)
- David C Lamb
- Wolfson Laboratory of P450 Biodiversity, Swansea Medical School University of Wales Swansea, Swansea, Wales SA2 8PP, UK
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Abstract
Members of the photolyase/cryptochrome family of blue-light photoreceptors are monomeric proteins of 50-70 kDa that contain two noncovalently bound chromophores/cofactors: either folate or deazaflavin, which act as a photoantenna, and a two electron-reduced FAD, which acts as a catalytic cofactor. DNA photolyases bind their substrates with high affinity and specificity and subsequently use blue light as a cosubstrate for the in situ conversion of ultraviolet-induced cyclobutane pyrimidine dimers and (6-4) photoproducts to canonical bases, thereby restoring the integrity of DNA. The determinants for binding, as well as the mechanism of the photolysis reaction, have been studied extensively using highly purified enzyme. In contrast, neither the substrate nor the reaction catalyzed by the closely related cryptochromes has been identified. This chapter describes methods used to purify DNA photolyases from a variety of organisms using an Escherichia coli overexpression system, as well as the properties of the purified enzymes and some of the assays commonly used to study DNA binding and repair by these enzymes in vitro.
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Affiliation(s)
- Gwendolyn B Sancar
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, USA
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