1
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Emmerich HJ, Schneider L, Essen LO. Structural and Functional Analysis of a Prokaryotic (6-4) Photolyase from the Aquatic Pathogen Vibrio Cholerae †. Photochem Photobiol 2023; 99:1248-1257. [PMID: 36692077 DOI: 10.1111/php.13783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 01/19/2023] [Indexed: 01/25/2023]
Abstract
Photolyases are flavoproteins, which are able to repair UV-induced DNA lesions in a light-dependent manner. According to their substrate, they can be distinguished as CPD- and (6-4) photolyases. While CPD-photolyases repair the predominantly occurring cyclobutane pyrimidine dimer lesion, (6-4) photolyases catalyze the repair of the less prominent (6-4) photoproduct. The subgroup of prokaryotic (6-4) photolyases/FeS-BCP is one of the most ancient types of flavoproteins in the ubiquitously occurring photolyase & cryptochrome superfamily (PCSf). In contrast to canonical photolyases, prokaryotic (6-4) photolyases possess a few particular characteristics, including a lumazine derivative as antenna chromophore besides the catalytically essential flavin adenine dinucleotide as well as an elongated linker region between the N-terminal α/β-domain and the C-terminal all-α-helical domain. Furthermore, they can harbor an additional short subdomain, located at the C-terminus, with a binding site for a [4Fe-4S] cluster. So far, two crystal structures of prokaryotic (6-4) photolyases have been reported. Within this study, we present the high-resolution structure of the prokaryotic (6-4) photolyase from Vibrio cholerae and its spectroscopic characterization in terms of in vitro photoreduction and DNA-repair activity.
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Affiliation(s)
- Hans-Joachim Emmerich
- Unit for Structural Biochemistry, Department of Chemistry, Philipps University Marburg, Marburg, Germany
| | - Leonie Schneider
- Unit for Structural Biochemistry, Department of Chemistry, Philipps University Marburg, Marburg, Germany
| | - Lars-Oliver Essen
- Unit for Structural Biochemistry, Department of Chemistry, Philipps University Marburg, Marburg, Germany
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2
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Ren Z, Kang W, Gunawardana S, Bowatte K, Thoulass K, Kaeser G, Krauß N, Lamparter T, Yang X. Dynamic interplays between three redox cofactors in a DNA photolyase revealed by spectral decomposition. CELL REPORTS. PHYSICAL SCIENCE 2023; 4:101297. [PMID: 37064408 PMCID: PMC10104447 DOI: 10.1016/j.xcrp.2023.101297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
DNA repair catalyzed by photolyases is accomplished by a light-dependent electron transfer event from a fully reduced flavin adenine dinucleotide to a DNA lesion site. Prokaryotic DNA photolyase, PhrB, possesses a ribolumazine cofactor and a four-iron-four-sulfur cluster in addition to the catalytic flavin, but their functional roles are poorly understood. Here, we employ time-resolved absorption spectroscopy to probe light-induced responses in both solution and single crystals of PhrB. We jointly analyze a large collection of light-induced difference spectra from the wild-type and mutant PhrB obtained under different light and redox conditions. By applying singular value decomposition to 159 time series, we dissect light-induced spectral changes and examine the dynamic interplay between three cofactors. Our findings suggest that these cofactors form an interdependent redox network to coordinate light-induced redox responses. We propose that the ribolumazine cofactor serves as a photoprotective pigment under intense light or prolonged illumination, while the iron-sulfur cluster acts as a transient electron cache to maintain balance between two otherwise independent photoreactions of the flavin and ribolumazine.
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Affiliation(s)
- Zhong Ren
- Department of Chemistry, University of Illinois Chicago, Chicago, IL, USA
- Lead contact
| | - Weijia Kang
- Department of Chemistry, University of Illinois Chicago, Chicago, IL, USA
| | - Semini Gunawardana
- Department of Chemistry, University of Illinois Chicago, Chicago, IL, USA
| | - Kalinga Bowatte
- Department of Chemistry, University of Illinois Chicago, Chicago, IL, USA
| | - Katharina Thoulass
- Botanical Institute, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Gero Kaeser
- Botanical Institute, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Norbert Krauß
- Botanical Institute, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Tilman Lamparter
- Botanical Institute, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Xiaojing Yang
- Department of Chemistry, University of Illinois Chicago, Chicago, IL, USA
- Department of Ophthalmology and Vision Sciences, University of Illinois Chicago, Chicago, IL, USA
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3
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Wang Z, Li Z, Lei Y, Liu Y, Feng Y, Chen D, Ma S, Xiao Z, Hu M, Deng J, Wang Y, Zhang Q, Huang Y, Yang Y. Recombinant Photolyase-Thymine Alleviated UVB-Induced Photodamage in Mice by Repairing CPD Photoproducts and Ameliorating Oxidative Stress. Antioxidants (Basel) 2022; 11:antiox11122312. [PMID: 36552521 PMCID: PMC9774824 DOI: 10.3390/antiox11122312] [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] [Received: 10/19/2022] [Revised: 11/15/2022] [Accepted: 11/19/2022] [Indexed: 11/24/2022] Open
Abstract
Cyclobutane pyrimidine dimers (CPDs) are the main mutagenic DNA photoproducts caused by ultraviolet B (UVB) radiation and represent the major cause of photoaging and skin carcinogenesis. CPD photolyase can efficiently and rapidly repair CPD products. Therefore, they are candidates for the prevention of photodamage. However, these photolyases are not present in placental mammals. In this study, we produced a recombinant photolyase-thymine (rPHO) from Thermus thermophilus (T. thermophilus). The rPHO displayed CPD photorepair activity. It prevented UVB-induced DNA damage by repairing CPD photoproducts to pyrimidine monomers. Furthermore, it inhibited UVB-induced ROS production, lipid peroxidation, inflammatory responses, and apoptosis. UVB-induced wrinkle formation, epidermal hyperplasia, and collagen degradation in mice skin was significantly inhibited when the photolyase was applied topically to the skin. These results demonstrated that rPHO has promising protective effects against UVB-induced photodamage and may contribute to the development of anti-UVB skin photodamage drugs and cosmetic products.
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Affiliation(s)
- Zhaoyang Wang
- Department of Cell Biology, Jinan University, Guangzhou 510632, China
| | - Ziyi Li
- TYRAN Cosmetics Innovation Research Institute, Jinan University, Guangzhou 511447, China
| | - Yaling Lei
- Department of Cell Biology, Jinan University, Guangzhou 510632, China
| | - Yuan Liu
- Department of Cell Biology, Jinan University, Guangzhou 510632, China
| | - Yuqing Feng
- Department of Pharmacology, Jinan University, Guangzhou 510632, China
| | - Derong Chen
- Department of Cell Biology, Jinan University, Guangzhou 510632, China
| | - Siying Ma
- Department of Cell Biology, Jinan University, Guangzhou 510632, China
| | - Ziyan Xiao
- Department of Cell Biology, Jinan University, Guangzhou 510632, China
| | - Meirong Hu
- Department of Cell Biology, Jinan University, Guangzhou 510632, China
| | - Jingxian Deng
- Department of Pharmacology, Jinan University, Guangzhou 510632, China
| | - Yuxin Wang
- Department of Cell Biology, Jinan University, Guangzhou 510632, China
| | - Qihao Zhang
- Department of Cell Biology, Jinan University, Guangzhou 510632, China
- Guangdong Province Key Laboratory of Bioengineering Medicine, Guangzhou 510632, China
| | - Yadong Huang
- Department of Cell Biology, Jinan University, Guangzhou 510632, China
- TYRAN Cosmetics Innovation Research Institute, Jinan University, Guangzhou 511447, China
- Guangdong Province Key Laboratory of Bioengineering Medicine, Guangzhou 510632, China
- Correspondence: (Y.H.); (Y.Y.)
| | - Yan Yang
- Department of Cell Biology, Jinan University, Guangzhou 510632, China
- TYRAN Cosmetics Innovation Research Institute, Jinan University, Guangzhou 511447, China
- Guangdong Province Key Laboratory of Bioengineering Medicine, Guangzhou 510632, China
- Correspondence: (Y.H.); (Y.Y.)
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4
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Emmerich HJ, Saft M, Schneider L, Kock D, Batschauer A, Essen LO. A topologically distinct class of photolyases specific for UV lesions within single-stranded DNA. Nucleic Acids Res 2021; 48:12845-12857. [PMID: 33270891 PMCID: PMC7736829 DOI: 10.1093/nar/gkaa1147] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 11/07/2020] [Accepted: 11/09/2020] [Indexed: 11/30/2022] Open
Abstract
Photolyases are ubiquitously occurring flavoproteins for catalyzing photo repair of UV-induced DNA damages. All photolyases described so far have a bilobal architecture with a C-terminal domain comprising flavin adenine dinucleotide (FAD) as catalytic cofactor and an N-terminal domain capable of harboring an additional antenna chromophore. Using sequence-similarity network analysis we discovered a novel subgroup of the photolyase/cryptochrome superfamily (PCSf), the NewPHLs. NewPHL occur in bacteria and have an inverted topology with an N-terminal catalytic domain and a C-terminal domain for sealing the FAD binding site from solvent access. By characterizing two NewPHL we show a photochemistry characteristic of other PCSf members as well as light-dependent repair of CPD lesions. Given their common specificity towards single-stranded DNA many bacterial species use NewPHL as a substitute for DASH-type photolyases. Given their simplified architecture and function we suggest that NewPHL are close to the evolutionary origin of the PCSf.
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Affiliation(s)
- Hans-Joachim Emmerich
- Unit for Structural Biochemistry, Department of Chemistry, Philipps University Marburg, Hans-Meerwein Straße 4, 35032 Marburg, Germany
| | - Martin Saft
- Unit for Structural Biochemistry, Department of Chemistry, Philipps University Marburg, Hans-Meerwein Straße 4, 35032 Marburg, Germany
| | - Leonie Schneider
- Unit for Structural Biochemistry, Department of Chemistry, Philipps University Marburg, Hans-Meerwein Straße 4, 35032 Marburg, Germany
| | - Dennis Kock
- Department of Biology, Philipps University Marburg, Karl-von-Frisch-Straße 8, 35032 Marburg, Germany
| | - Alfred Batschauer
- Department of Biology, Philipps University Marburg, Karl-von-Frisch-Straße 8, 35032 Marburg, Germany
| | - Lars-Oliver Essen
- Unit for Structural Biochemistry, Department of Chemistry, Philipps University Marburg, Hans-Meerwein Straße 4, 35032 Marburg, Germany.,Center of Synthetic Microbiology, Philipps University Marburg, Hans-Meerwein Straße 4, 35032 Marburg, Germany
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5
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Terai Y, Sato R, Matsumura R, Iwai S, Yamamoto J. Enhanced DNA repair by DNA photolyase bearing an artificial light-harvesting chromophore. Nucleic Acids Res 2020; 48:10076-10086. [PMID: 32901252 PMCID: PMC7544235 DOI: 10.1093/nar/gkaa719] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 08/14/2020] [Accepted: 08/24/2020] [Indexed: 12/03/2022] Open
Abstract
Photolyases are flavoenzymes responsible for the repair of carcinogenic DNA damage caused by ultraviolet radiation. They harbor the catalytic cofactor flavin adenine dinucleotide (FAD). The light-driven electron transfer from the excited state of the fully-reduced form of FAD to the DNA lesions causes rearrangement of the covalent bonds, leading to the restoration of intact nucleobases. In addition to the catalytic chromophore, some photolyases bear a secondary chromophore with better light absorption capability than FAD, acting as a light-harvesting chromophore that harvests photons in sunlight efficiently and transfers light energy to the catalytic center, as observed in natural photoreceptor proteins. Inspired by nature, we covalently and site-specifically attached a synthetic chromophore to the surface of photolyase using oligonucleotides containing a modified nucleoside and a cyclobutane-type DNA lesion, and successfully enhanced its enzymatic activity in the light-driven DNA repair. Peptide mapping in combination with theoretical calculations identified the amino acid residue that binds to the chromophore, working as an artificial light-harvesting chromophore. Our results broaden the strategies for protein engineering and provide a guideline for tuning of the light perception abilities and enzymatic activity of the photoreceptor proteins.
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Affiliation(s)
- Yuma Terai
- Division of Chemistry, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan
| | - Ryuma Sato
- Center for Biosystems Dynamics Research, RIKEN, 6-2-3 Furuedai, Suita, Osaka 565-0874, Japan
| | - Risa Matsumura
- Division of Chemistry, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan
| | - Shigenori Iwai
- Division of Chemistry, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan
| | - Junpei Yamamoto
- Division of Chemistry, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan
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6
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Jahnke T, Hergenhahn U, Winter B, Dörner R, Frühling U, Demekhin PV, Gokhberg K, Cederbaum LS, Ehresmann A, Knie A, Dreuw A. Interatomic and Intermolecular Coulombic Decay. Chem Rev 2020; 120:11295-11369. [PMID: 33035051 PMCID: PMC7596762 DOI: 10.1021/acs.chemrev.0c00106] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Indexed: 12/11/2022]
Abstract
Interatomic or intermolecular Coulombic decay (ICD) is a nonlocal electronic decay mechanism occurring in weakly bound matter. In an ICD process, energy released by electronic relaxation of an excited atom or molecule leads to ionization of a neighboring one via Coulombic electron interactions. ICD has been predicted theoretically in the mid nineties of the last century, and its existence has been confirmed experimentally approximately ten years later. Since then, a number of fundamental and applied aspects have been studied in this quickly growing field of research. This review provides an introduction to ICD and draws the connection to related energy transfer and ionization processes. The theoretical approaches for the description of ICD as well as the experimental techniques developed and employed for its investigation are described. The existing body of literature on experimental and theoretical studies of ICD processes in different atomic and molecular systems is reviewed.
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Affiliation(s)
- Till Jahnke
- Institut
für Kernphysik, Goethe Universität, Max-von-Laue-Str. 1, 60438 Frankfurt, Germany
| | - Uwe Hergenhahn
- Fritz-Haber-Institut
der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany
- Max
Planck Institute for Plasma Physics, Wendelsteinstr. 1, 17491 Greifswald, Germany
- Leibniz
Institute of Surface Engineering (IOM), 04318 Leipzig, Germany
| | - Bernd Winter
- Fritz-Haber-Institut
der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany
| | - Reinhard Dörner
- Institut
für Kernphysik, Goethe Universität, Max-von-Laue-Str. 1, 60438 Frankfurt, Germany
| | - Ulrike Frühling
- Institut
für Experimentalphysik and Center for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Philipp V. Demekhin
- Institut
für Physik und CINSaT, Universität
Kassel, Heinrich-Plett-Str. 40, 34132 Kassel, Germany
| | - Kirill Gokhberg
- Physical-Chemistry
Institute, Ruprecht-Karls University, Im Neuenheimer Feld 229, 69120 Heidelberg, Germany
| | - Lorenz S. Cederbaum
- Physical-Chemistry
Institute, Ruprecht-Karls University, Im Neuenheimer Feld 229, 69120 Heidelberg, Germany
| | - Arno Ehresmann
- Institut
für Physik und CINSaT, Universität
Kassel, Heinrich-Plett-Str. 40, 34132 Kassel, Germany
| | - André Knie
- Institut
für Physik und CINSaT, Universität
Kassel, Heinrich-Plett-Str. 40, 34132 Kassel, Germany
| | - Andreas Dreuw
- Interdisciplinary
Center for Scientific Computing, Ruprecht-Karls
University, Im Neuenheimer
Feld 205, 69120 Heidelberg, Germany
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7
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A (6-4)-photolyase from the Antarctic bacterium Sphingomonas sp. UV9: recombinant production and in silico features. Extremophiles 2020; 24:887-896. [PMID: 32960344 DOI: 10.1007/s00792-020-01202-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 09/07/2020] [Indexed: 10/23/2022]
Abstract
Photolyases are proteins that enzymatically repair the UV-induced DNA damage by a protein-DNA electron transfer mechanism. They repair either cyclobutane pyrimidine dimers or pyrimidine (6-4) pyrimidone photoproducts or just (6-4)-photoproducts. In this work, we report the production and partial characterization of a recombinant (6-4)-photolyase (SphPhrB97) from a bacterial psychrotolerant Antarctic isolate identified as Sphingomonas sp. strain UV9. The spectrum analysis and the in silico study of SphPhrB97 suggest that this enzyme has similar features as compared to the (6-4)-photolyase from Agrobacterium tumefaciens (4DJA; PhrB), including the presence of three cofactors: FAD, DMRL (6,7-dimethyl-8-(1'-D-ribityl) lumazine), and an Fe-S cluster. The homology model of SphPhrB97 predicts that the DNA-binding pocket (area and volume) is larger as compared to (6-4)-photolyases from mesophilic microbes. Based on sequence comparison and on the homology model, we propose an electron transfer pathway towards the FAD cofactor involving the residues Trp342, Trp390, Tyr40, Tyr391, and Tyr399. The phylogenetic tree performed using curated and well-characterized prokaryotic (6-4)-photolyases suggests that SphPhrB97 may have an ancient evolutionary origin. The results suggest that SphPhrB97 is a cold-adapted enzyme, ready to cope with the UV irradiation stress found in a hostile environment, such as Antarctica.
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8
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Pathak R, Ergon Å, Stensvand A, Gislerød HR, Solhaug KA, Cadle-Davidson L, Suthaparan A. Functional Characterization of Pseudoidium neolycopersici Photolyase Reveals Mechanisms Behind the Efficacy of Nighttime UV on Powdery Mildew Suppression. Front Microbiol 2020; 11:1091. [PMID: 32547521 PMCID: PMC7272715 DOI: 10.3389/fmicb.2020.01091] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Accepted: 04/30/2020] [Indexed: 12/13/2022] Open
Abstract
Powdery mildews can be controlled by brief exposure to ultraviolet (UV) radiation with devastating effect on their developmental stages including conidia germination. The treatment effect can be impaired by subsequent exposure to UV-A/blue light. UV-A/blue light-activated photolyase may be responsible for this and therefore we tested the function of three cryptochrome/photolyase family (CPF)-like genes (OINE01015670_T110144, OINE01000912_T103440, and OINE01005061_T102555) identified in the obligate biotrophic fungus Pseudoidium neolycopersici, the cause of tomato powdery mildew. A photolyase-deficient mutant of Escherichia coli transformed with coding sequence of OINE01000912_T103440 and exposed to brief (UV)-C treatment (peak emission at 254 nm) showed photoreactivation and cell survival when exposed to subsequent blue light, indicating complementation of photolyase activity. In contrast, the same photolyase-deficient E. coli transformed with the coding sequences of other two CPF-like genes did not survive this treatment, even though their expression were confirmed at protein level. This confirmed that OINE01000912_T103440 is a gene encoding photolyase, here named PnPHR1, with functionality similar to the native photolyase in E. coli, and classified as a class I cyclobutane pyrimidine dimer (CPD) photolyase. Modeling of the 634-amino acid sequence of PnPHR1 suggested that it is capable of binding flavin adenine dinucleotide (FAD) and methenyltetrahydrofolate (MTHF). However, spectroscopic data of the protein produced in an E. coli expression system could only reveal the presence of a reduced form of FAD, i.e., FADH- as an intrinsic chromophore. Within the tested wavelength range of 365-525 nm, the survival of photolyase-deficient mutant E. coli transformed with PnPHR1 showed a broad action spectrum from 365 to 454 nm. This was very similar to the previously characterized action spectrum for survival of P. neolycopersici conidia that had been treated with UV-C. Quantitative RT-PCR revealed that the expression of PnPHR1 in P. neolycopersici conidia was induced by UV-C, and peak expression occurred 4 h after brief UV-C treatment. The expression of PnPHR1 was repressed when incubated in red light after the UV-C treatment, but not when incubated in UV-A/blue light. The results may explain why the disease-reducing effect of short wavelength UV is impaired by exposure to UV-A and blue light.
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Affiliation(s)
- Ranjana Pathak
- Department of Plant Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
| | - Åshild Ergon
- Department of Plant Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
| | - Arne Stensvand
- Department of Plant Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway.,Division of Biotechnology and Plant Health, Norwegian Institute of Bioeconomy Research, Ås, Norway
| | - Hans Ragnar Gislerød
- Department of Plant Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
| | - Knut Asbjørn Solhaug
- Faculty of Environmental Sciences and Natural Resource Management, Norwegian University of Life Sciences, Ås, Norway
| | - Lance Cadle-Davidson
- Grape Genetics Research Unit, Agricultural Research Service, United States Department of Agriculture, Geneva, NY, United States
| | - Aruppillai Suthaparan
- Department of Plant Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
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9
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Vechtomova YL, Telegina TA, Kritsky MS. Evolution of Proteins of the DNA Photolyase/Cryptochrome Family. BIOCHEMISTRY (MOSCOW) 2020; 85:S131-S153. [DOI: 10.1134/s0006297920140072] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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10
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Franz S, Ignatz E, Wenzel S, Zielosko H, Putu E, Maestre-Reyna M, Tsai MD, Yamamoto J, Mittag M, Essen LO. Structure of the bifunctional cryptochrome aCRY from Chlamydomonas reinhardtii. Nucleic Acids Res 2019; 46:8010-8022. [PMID: 30032195 PMCID: PMC6125616 DOI: 10.1093/nar/gky621] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 07/17/2018] [Indexed: 02/06/2023] Open
Abstract
Photolyases and cryptochromes form an almost ubiquitous family of blue light photoreceptors involved in the repair and maintenance of DNA integrity or regulatory control. We found that one cryptochrome from the green alga Chlamydomonas reinhardtii (CraCRY) is capable of both, control of transcript levels and the sexual cycle of the alga in a positive (germination) and negative manner (mating ability), as well as catalyzing the repair of UV-DNA lesions. Its 1.6 Å crystal structure shows besides the FAD chromophore an aromatic tetrad that is indispensable in animal-like type I cryptochromes for light-driven change of their signaling-active redox state and formation of a stable radical pair. Given CraCRY’s catalytic activity as (6-4) photolyase in vivo and in vitro, we present the first co-crystal structure of a cryptochrome with duplex DNA comprising a (6-4) pyrimidine–pyrimidone lesion. This 2.9 Å structure reveals a distinct conformation for the catalytic histidine His1, H357, that challenges previous models of a single-photon driven (6-4) photolyase mechanism.
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Affiliation(s)
- Sophie Franz
- Unit for Structural Biochemistry, Department of Chemistry, Philipps University Marburg, Hans-Meerwein Straße 4, 35032 Marburg, Germany
| | - Elisabeth Ignatz
- Unit for Structural Biochemistry, Department of Chemistry, Philipps University Marburg, Hans-Meerwein Straße 4, 35032 Marburg, Germany
| | - Sandra Wenzel
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich Schiller University, Am Planetarium 1, 07743 Jena, Germany
| | - Hannah Zielosko
- Unit for Structural Biochemistry, Department of Chemistry, Philipps University Marburg, Hans-Meerwein Straße 4, 35032 Marburg, Germany
| | | | - Manuel Maestre-Reyna
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Rd. Sec. 2, Taipei 115, Taiwan
| | - Ming-Daw Tsai
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Rd. Sec. 2, Taipei 115, Taiwan
| | - Junpei Yamamoto
- Division of Chemistry, Graduate School of Engineering Science, Osaka University, 1–3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan
| | - Maria Mittag
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich Schiller University, Am Planetarium 1, 07743 Jena, Germany
| | - Lars-Oliver Essen
- Unit for Structural Biochemistry, Department of Chemistry, Philipps University Marburg, Hans-Meerwein Straße 4, 35032 Marburg, Germany
- LOEWE Center of Synthetic Microbiology, Philipps University Marburg, Hans-Meerwein Straße 4, 35032 Marburg, Germany
- To whom correspondence should be addressed. Tel: +49 6421/28 22032; Fax: +49 6421/28 22012;
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11
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A highly efficient and cost-effective recombinant production of a bacterial photolyase from the Antarctic isolate Hymenobacter sp. UV11. Extremophiles 2018; 23:49-57. [DOI: 10.1007/s00792-018-1059-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 09/24/2018] [Indexed: 01/12/2023]
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12
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Ignatz E, Geisselbrecht Y, Kiontke S, Essen LO. Nicotinamide Adenine Dinucleotides Arrest Photoreduction of Class II DNA Photolyases in FADH ˙ State. Photochem Photobiol 2017; 94:81-87. [PMID: 28858395 DOI: 10.1111/php.12834] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 08/17/2017] [Indexed: 12/24/2022]
Abstract
All light-sensitive members of the photolyase/cryptochrome family rely on FAD as catalytic cofactor. Its activity is regulated by photoreduction, a light-triggered electron transfer process from a conserved tryptophan triad to the flavin. The stability of the reduced flavin depends on available external electron donors and oxygen. In this study, we show for the class II photolyase of Methanosarcina mazei, MmCPDII, that it utilizes physiologically relevant redox cofactors NADH and NADPH for the formation of the semiquinoid FAD in a light-dependent reaction. Using redox-inert variants MmCPDII/W388F and MmCPDII/W360F, we demonstrate that photoreduction by NADH and NADPH requires the class II-specific tryptophan cascade of MmCPDII. Finally, we confirmed that mutations in the tryptophan cascade can be introduced without any substantial structural disturbances by analyzing crystal structures of MmCPDII/W388F, MmCPDII/W360F and MmCPDII/Y345F.
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Affiliation(s)
- Elisabeth Ignatz
- Department of Chemistry, LOEWE Center for Synthetic Microbiology, Philipps University, Marburg, Germany
| | - Yann Geisselbrecht
- Department of Chemistry, LOEWE Center for Synthetic Microbiology, Philipps University, Marburg, Germany
| | - Stephan Kiontke
- Department of Chemistry, LOEWE Center for Synthetic Microbiology, Philipps University, Marburg, Germany.,Department of Biology/Chemistry, Division of Structural Biology, University of Osnabrück, Osnabrück, Germany
| | - Lars-Oliver Essen
- Department of Chemistry, LOEWE Center for Synthetic Microbiology, Philipps University, Marburg, Germany
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13
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Essen LO, Franz S, Banerjee A. Structural and evolutionary aspects of algal blue light receptors of the cryptochrome and aureochrome type. JOURNAL OF PLANT PHYSIOLOGY 2017; 217:27-37. [PMID: 28756992 DOI: 10.1016/j.jplph.2017.07.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2017] [Revised: 07/05/2017] [Accepted: 07/05/2017] [Indexed: 06/07/2023]
Abstract
Blue-light reception plays a pivotal role for algae to adapt to changing environmental conditions. In this review we summarize the current structural and mechanistic knowledge about flavin-dependent algal photoreceptors. We especially focus on the cryptochrome and aureochrome type photoreceptors in the context of their evolutionary divergence. Despite similar photochemical characteristics to orthologous photoreceptors from higher plants and animals the algal blue-light photoreceptors have developed a set of unique structural and mechanistic features that are summarized below.
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Affiliation(s)
- Lars-Oliver Essen
- Department of Biochemistry, Philipps-University, 35043 Marburg, Germany; LOEWE Center for Synthetic Microbiology, Philipps-University, 35043 Marburg, Germany.
| | - Sophie Franz
- Department of Biochemistry, Philipps-University, 35043 Marburg, Germany
| | - Ankan Banerjee
- Department of Biochemistry, Philipps-University, 35043 Marburg, Germany
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14
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Yamamoto J, Shimizu K, Kanda T, Hosokawa Y, Iwai S, Plaza P, Müller P. Loss of Fourth Electron-Transferring Tryptophan in Animal (6–4) Photolyase Impairs DNA Repair Activity in Bacterial Cells. Biochemistry 2017; 56:5356-5364. [DOI: 10.1021/acs.biochem.7b00366] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Junpei Yamamoto
- Graduate
School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan
| | - Kohei Shimizu
- Graduate
School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan
| | - Takahiro Kanda
- Graduate
School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan
| | - Yuhei Hosokawa
- Graduate
School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan
| | - Shigenori Iwai
- Graduate
School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan
| | - Pascal Plaza
- PASTEUR,
Département de chimie, École normale supérieure, UPMC Univ. Paris 06, CNRS, PSL Research University, 75005 Paris, France
- Sorbonne Universités, UPMC Univ. Paris 06, École normale supérieure, CNRS, PASTEUR, 75005 Paris, France
| | - Pavel Müller
- Institute
for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette cedex, France
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15
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Characterization of a cold-adapted DNA photolyase from C. psychrerythraea 34H. Extremophiles 2017; 21:919-932. [PMID: 28726126 DOI: 10.1007/s00792-017-0953-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 07/09/2017] [Indexed: 10/19/2022]
Abstract
The phrB gene encoding a putative cold-adapted DNA photolyase was cloned from the bacterial genomic DNA of Colwellia psychrerythraea 34H, a psychrophilic bacterium. Recombinant DNA photolyase, rCpPL, was overexpressed and purified from three different vectors. rCpPL binds its DNA substrate by flipping a cyclobutane pyrimidine dimer (CPD) into its active site and repairs CPD-containing DNA in vitro. rCpPL contains one catalytic flavin adenine dinucleotide (FAD) cofactor, but displays promiscuity in cofactor binding, in which either a flavin mononucleotide (FMN) or a methenyltetrahydrofolate (MTHF) molecule is bound as an antenna molecule and found in sub-stoichiometric amounts. The UV/Vis spectrum of oxidized rCpPL shows that the FADOX absorption maximum is the most red-shifted reported for a PL, suggesting a unique cavity electrostatic environment. Modest FAD vibronic structure suggests that the binding pocket is more flexible than warmer PLs, corroborating the hypothesis that psychrophilic proteins must be highly flexible to function at low temperatures. Fluorescence excitation data show that the freshly purified flavin cofactor is in its fully reduced state (FADH¯). A homology analysis of PL protein structures spanning 70 °C in growth temperature supports the data that the structure of CpPL is quite different from its warmer cousins.
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16
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Fungal cryptochrome with DNA repair activity reveals an early stage in cryptochrome evolution. Proc Natl Acad Sci U S A 2015; 112:15130-5. [PMID: 26578805 DOI: 10.1073/pnas.1514637112] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
DASH (Drosophila, Arabidopsis, Synechocystis, Human)-type cryptochromes (cry-DASH) belong to a family of flavoproteins acting as repair enzymes for UV-B-induced DNA lesions (photolyases) or as UV-A/blue light photoreceptors (cryptochromes). They are present in plants, bacteria, various vertebrates, and fungi and were originally considered as sensory photoreceptors because of their incapability to repair cyclobutane pyrimidine dimer (CPD) lesions in duplex DNA. However, cry-DASH can repair CPDs in single-stranded DNA, but their role in DNA repair in vivo remains to be clarified. The genome of the fungus Phycomyces blakesleeanus contains a single gene for a protein of the cryptochrome/photolyase family (CPF) encoding a cry-DASH, cryA, despite its ability to photoreactivate. Here, we show that cryA expression is induced by blue light in a Mad complex-dependent manner. Moreover, we demonstrate that CryA is capable of binding flavin (FAD) and methenyltetrahydrofolate (MTHF), fully complements the Escherichia coli photolyase mutant and repairs in vitro CPD lesions in single-stranded and double-stranded DNA with the same efficiency. These results support a role for Phycomyces cry-DASH as a photolyase and suggest a similar role for cry-DASH in mucoromycotina fungi.
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17
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Nohr D, Rodriguez R, Weber S, Schleicher E. How can EPR spectroscopy help to unravel molecular mechanisms of flavin-dependent photoreceptors? Front Mol Biosci 2015; 2:49. [PMID: 26389123 PMCID: PMC4555020 DOI: 10.3389/fmolb.2015.00049] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Accepted: 08/10/2015] [Indexed: 11/25/2022] Open
Abstract
Electron paramagnetic resonance (EPR) spectroscopy is a well-established spectroscopic method for the examination of paramagnetic molecules. Proteins can contain paramagnetic moieties in form of stable cofactors, transiently formed intermediates, or spin labels artificially introduced to cysteine sites. The focus of this review is to evaluate potential scopes of application of EPR to the emerging field of optogenetics. The main objective for EPR spectroscopy in this context is to unravel the complex mechanisms of light-active proteins, from their primary photoreaction to downstream signal transduction. An overview of recent results from the family of flavin-containing, blue-light dependent photoreceptors is given. In detail, mechanistic similarities and differences are condensed from the three classes of flavoproteins, the cryptochromes, LOV (Light-oxygen-voltage), and BLUF (blue-light using FAD) domains. Additionally, a concept that includes spin-labeled proteins and examination using modern pulsed EPR is introduced, which allows for a precise mapping of light-induced conformational changes.
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Affiliation(s)
- Daniel Nohr
- Department of Physical Chemistry, Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg Freiburg, Germany
| | - Ryan Rodriguez
- Department of Physical Chemistry, Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg Freiburg, Germany
| | - Stefan Weber
- Department of Physical Chemistry, Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg Freiburg, Germany
| | - Erik Schleicher
- Department of Physical Chemistry, Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg Freiburg, Germany
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18
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Scheerer P, Zhang F, Kalms J, von Stetten D, Krauß N, Oberpichler I, Lamparter T. The class III cyclobutane pyrimidine dimer photolyase structure reveals a new antenna chromophore binding site and alternative photoreduction pathways. J Biol Chem 2015; 290:11504-14. [PMID: 25784552 DOI: 10.1074/jbc.m115.637868] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Indexed: 11/06/2022] Open
Abstract
Photolyases are proteins with an FAD chromophore that repair UV-induced pyrimidine dimers on the DNA in a light-dependent manner. The cyclobutane pyrimidine dimer class III photolyases are structurally unknown but closely related to plant cryptochromes, which serve as blue-light photoreceptors. Here we present the crystal structure of a class III photolyase termed photolyase-related protein A (PhrA) of Agrobacterium tumefaciens at 1.67-Å resolution. PhrA contains 5,10-methenyltetrahydrofolate (MTHF) as an antenna chromophore with a unique binding site and mode. Two Trp residues play pivotal roles for stabilizing MTHF by a double π-stacking sandwich. Plant cryptochrome I forms a pocket at the same site that could accommodate MTHF or a similar molecule. The PhrA structure and mutant studies showed that electrons flow during FAD photoreduction proceeds via two Trp triads. The structural studies on PhrA give a clearer picture on the evolutionary transition from photolyase to photoreceptor.
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Affiliation(s)
- Patrick Scheerer
- From the Charité, University Medicine Berlin, Institute of Medical Physics and Biophysics (CC2), AG Protein X-ray Crystallography and Signal Transduction, Charitéplatz 1, D-10117 Berlin, Germany,
| | - Fan Zhang
- the Karlsruhe Institute of Technology (KIT), Botanical Institute, Kaiserstr. 2, D-76131 Karlsruhe, Germany
| | - Jacqueline Kalms
- From the Charité, University Medicine Berlin, Institute of Medical Physics and Biophysics (CC2), AG Protein X-ray Crystallography and Signal Transduction, Charitéplatz 1, D-10117 Berlin, Germany
| | - David von Stetten
- the Structural Biology Group, European Synchroton Radiation Facility, CS 40220, F-38043 Grenoble Cedex 9, France, and
| | - Norbert Krauß
- the Queen Mary University of London, School of Biological and Chemical Sciences, Mile End Road, London E1 4NS, United Kingdom
| | - Inga Oberpichler
- the Karlsruhe Institute of Technology (KIT), Botanical Institute, Kaiserstr. 2, D-76131 Karlsruhe, Germany,
| | - Tilman Lamparter
- the Karlsruhe Institute of Technology (KIT), Botanical Institute, Kaiserstr. 2, D-76131 Karlsruhe, Germany,
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19
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Kiontke S, Gnau P, Haselsberger R, Batschauer A, Essen LO. Structural and evolutionary aspects of antenna chromophore usage by class II photolyases. J Biol Chem 2014; 289:19659-69. [PMID: 24849603 DOI: 10.1074/jbc.m113.542431] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Light-harvesting and resonance energy transfer to the catalytic FAD cofactor are key roles for the antenna chromophores of light-driven DNA photolyases, which remove UV-induced DNA lesions. So far, five chemically diverse chromophores have been described for several photolyases and related cryptochromes, but no correlation between phylogeny and used antenna has been found. Despite a common protein topology, structural analysis of the distantly related class II photolyase from the archaeon Methanosarcina mazei (MmCPDII) as well as plantal orthologues indicated several differences in terms of DNA and FAD binding and electron transfer pathways. For MmCPDII we identify 8-hydroxydeazaflavin (8-HDF) as cognate antenna by in vitro and in vivo reconstitution, whereas the higher plant class II photolyase from Arabidopsis thaliana fails to bind any of the known chromophores. According to the 1.9 Å structure of the MmCPDII·8-HDF complex, its antenna binding site differs from other members of the photolyase-cryptochrome superfamily by an antenna loop that changes its conformation by 12 Å upon 8-HDF binding. Additionally, so-called N- and C-motifs contribute as conserved elements to the binding of deprotonated 8-HDF and allow predicting 8-HDF binding for most of the class II photolyases in the whole phylome. The 8-HDF antenna is used throughout the viridiplantae ranging from green microalgae to bryophyta and pteridophyta, i.e. mosses and ferns, but interestingly not in higher plants. Overall, we suggest that 8-hydroxydeazaflavin is a crucial factor for the survival of most higher eukaryotes which depend on class II photolyases to struggle with the genotoxic effects of solar UV exposure.
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Affiliation(s)
- Stephan Kiontke
- From the Biomedical Research Centre/FB15, Unit for Structural Biochemistry, Philipps-University, Hans-Meerwein-Strasse, D-35032 Marburg, Germany
| | - Petra Gnau
- From the Biomedical Research Centre/FB15, Unit for Structural Biochemistry, Philipps-University, Hans-Meerwein-Strasse, D-35032 Marburg, Germany
| | - Reinhard Haselsberger
- the School of Physical and Mathematical Sciences, Division of Physics and Applied Physics, Nanyang Technological University, SPMS-PAP-03-11, 21 Nanyang Link, Singapore 637371, and
| | - Alfred Batschauer
- the Faculty of Biology, Department of Plant Physiology and Photobiology, Philipps-University, Karl-von-Frisch-Strasse 8, D-35032 Marburg, Germany
| | - Lars-Oliver Essen
- From the Biomedical Research Centre/FB15, Unit for Structural Biochemistry, Philipps-University, Hans-Meerwein-Strasse, D-35032 Marburg, Germany,
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20
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Kianianmomeni A, Hallmann A. Algal photoreceptors: in vivo functions and potential applications. PLANTA 2014; 239:1-26. [PMID: 24081482 DOI: 10.1007/s00425-013-1962-5] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2013] [Accepted: 09/09/2013] [Indexed: 06/02/2023]
Abstract
Many algae, particularly microalgae, possess a sophisticated light-sensing system including photoreceptors and light-modulated signaling pathways to sense environmental information and secure the survival in a rapidly changing environment. Over the last couple of years, the multifaceted world of algal photobiology has enriched our understanding of the light absorption mechanisms and in vivo function of photoreceptors. Moreover, specific light-sensitive modules have already paved the way for the development of optogenetic tools to generate light switches for precise and spatial control of signaling pathways in individual cells and even in complex biological systems.
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Affiliation(s)
- Arash Kianianmomeni
- Department of Cellular and Developmental Biology of Plants, University of Bielefeld, Universitätsstr. 25, 33615, Bielefeld, Germany,
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21
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Crystal structure of a prokaryotic (6-4) photolyase with an Fe-S cluster and a 6,7-dimethyl-8-ribityllumazine antenna chromophore. Proc Natl Acad Sci U S A 2013; 110:7217-22. [PMID: 23589886 DOI: 10.1073/pnas.1302377110] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The (6-4) photolyases use blue light to reverse UV-induced (6-4) photoproducts in DNA. This (6-4) photorepair was thought to be restricted to eukaryotes. Here we report a prokaryotic (6-4) photolyase, PhrB from Agrobacterium tumefaciens, and propose that (6-4) photolyases are broadly distributed in prokaryotes. The crystal structure of photolyase related protein B (PhrB) at 1.45 Å resolution suggests a DNA binding mode different from that of the eukaryotic counterparts. A His-His-X-X-Arg motif is located within the proposed DNA lesion contact site of PhrB. This motif is structurally conserved in eukaryotic (6-4) photolyases for which the second His is essential for the (6-4) photolyase function. The PhrB structure contains 6,7-dimethyl-8-ribityllumazine as an antenna chromophore and a [4Fe-4S] cluster bound to the catalytic domain. A significant part of the Fe-S fold strikingly resembles that of the large subunit of eukaryotic and archaeal primases, suggesting that the PhrB-like photolyases branched at the base of the evolution of the cryptochrome/photolyase family. Our study presents a unique prokaryotic (6-4) photolyase and proposes that the prokaryotic (6-4) photolyases are the ancestors of the cryptochrome/photolyase family.
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22
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Harbach PHP, Schneider M, Faraji S, Dreuw A. Intermolecular Coulombic Decay in Biology: The Initial Electron Detachment from FADH(-) in DNA Photolyases. J Phys Chem Lett 2013; 4:943-949. [PMID: 26291360 DOI: 10.1021/jz400104h] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Intermolecular coulombic decay (ICD) is an efficient mechanism of low-energy electron generation in condensed phases and is discussed as their potential source in living cells, tissues, and materials. The first example of ICD as an operating mechanism in real biological systems, that is, in the DNA repair enzymes photolyases, is presented. Photolyase function involves light-induced electron detachment from a reduced flavin adenine dinucleotide (FADH(-)), followed by its transfer to the DNA-lesion triggering repair of covalently bound nucleobase dimers. Modern quantum chemical methods are employed to demonstrate that the transferred electron is efficiently generated via a resonant ICD process between the antenna pigment and the FADH(-) cofactors.
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Affiliation(s)
- Philipp H P Harbach
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 368, 69120 Heidelberg, Germany
| | - Matthias Schneider
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 368, 69120 Heidelberg, Germany
| | - Shirin Faraji
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 368, 69120 Heidelberg, Germany
| | - Andreas Dreuw
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 368, 69120 Heidelberg, Germany
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23
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Kritsky MS, Telegina TA, Vechtomova YL, Buglak AA. Why flavins are not competitors of chlorophyll in the evolution of biological converters of solar energy. Int J Mol Sci 2012; 14:575-93. [PMID: 23271372 PMCID: PMC3565283 DOI: 10.3390/ijms14010575] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2012] [Revised: 12/10/2012] [Accepted: 12/13/2012] [Indexed: 12/17/2022] Open
Abstract
Excited flavin molecules can photocatalyze reactions, leading to the accumulation of free energy in the products, and the data accumulated through biochemical experiments and by modeling prebiological processes suggest that flavins were available in the earliest stages of evolution. Furthermore, model experiments have shown that abiogenic flavin conjugated with a polyamino acid matrix, a pigment that photocatalyzes the phosphorylation of ADP to form ATP, could have been present in the prebiotic environment. Indeed, excited flavin molecules play key roles in many photoenzymes and regulatory photoreceptors, and the substantial structural differences between photoreceptor families indicate that evolution has repeatedly used flavins as chromophores for photoreceptor proteins. Some of these photoreceptors are equipped with a light-harvesting antenna, which transfers excitation energy to chemically reactive flavins in the reaction center. The sum of the available data suggests that evolution could have led to the formation of a flavin-based biological converter to convert light energy into energy in the form of ATP.
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Affiliation(s)
- Mikhail S. Kritsky
- A.N. Bach Institute of Biochemistry, Russian Academy of Sciences, House 33, Building 2, Leninsky Prospekt, Moscow 119071, Russia; E-Mails: (T.A.T.); (Y.L.V.); (A.A.B.)
| | - Taisiya A. Telegina
- A.N. Bach Institute of Biochemistry, Russian Academy of Sciences, House 33, Building 2, Leninsky Prospekt, Moscow 119071, Russia; E-Mails: (T.A.T.); (Y.L.V.); (A.A.B.)
| | - Yulia L. Vechtomova
- A.N. Bach Institute of Biochemistry, Russian Academy of Sciences, House 33, Building 2, Leninsky Prospekt, Moscow 119071, Russia; E-Mails: (T.A.T.); (Y.L.V.); (A.A.B.)
| | - Andrey A. Buglak
- A.N. Bach Institute of Biochemistry, Russian Academy of Sciences, House 33, Building 2, Leninsky Prospekt, Moscow 119071, Russia; E-Mails: (T.A.T.); (Y.L.V.); (A.A.B.)
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24
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Albarracín VH, Pathak GP, Douki T, Cadet J, Borsarelli CD, Gärtner W, Farias ME. Extremophilic Acinetobacter strains from high-altitude lakes in Argentinean Puna: remarkable UV-B resistance and efficient DNA damage repair. ORIGINS LIFE EVOL B 2012; 42:201-21. [PMID: 22644565 DOI: 10.1007/s11084-012-9276-3] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2011] [Accepted: 12/12/2011] [Indexed: 10/27/2022]
Abstract
High-Altitude Andean Lakes (HAAL) of the South American Andes are almost unexplored ecosystems of shallow lakes. The HAAL are recognized by a remarkably high UV exposure, strong changes in temperature and salinity, and a high content of toxic elements, especially arsenic. Being exposed to remarkably extreme conditions, they have been classified as model systems for the study of life on other planets. Particularly, Acinetobacter strains isolated from the HAAL were studied for their survival competence under strong UV-B irradiation. Clinical isolates, Acinetobacter baumannii and Acinetobacter johnsonii, served as reference material. Whereas the reference strains rapidly lost viability under UV-B irradiation, most HAAL-derived strains readily survived this exposure and showed less change in cell number after the treatment. Controls for DNA repair activity, comparing dark repair (DR) or photo repair (PR), gave evidence for the involvement of photolyases in the DNA repair. Comparative measurements by HPLC-mass spectrometry detected the number of photoproducts: bipyrimidine dimers under both PR and DR treatments were more efficiently repaired in the HAAL strains (up to 85 % PR and 38 % DR) than in the controls (31 % PR and zero DR ability). Analysis of cosmid-cloned total genomic DNA from the most effective DNA-photorepair strain (Ver3) yielded a gene (HQ443199) encoding a protein with clear photolyase signatures belonging to class I CPD-photolyases. Despite the relatively low sequence similarity of 41 % between the enzymes from Ver3 and from E. coli (PDB 1DNPA), a model-building approach revealed a high structural homology to the CPD-photolyase of E. coli.
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Affiliation(s)
- Virginia Helena Albarracín
- Planta Piloto de Procesos Industriales y Microbiológicos (PROIMI), CCT, CONICET, Av. Belgrano y Pasaje Caseros, 4000, S. M. de Tucumán, Argentina
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25
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Geisselbrecht Y, Frühwirth S, Schroeder C, Pierik AJ, Klug G, Essen LO. CryB from Rhodobacter sphaeroides: a unique class of cryptochromes with new cofactors. EMBO Rep 2012; 13:223-9. [PMID: 22290493 DOI: 10.1038/embor.2012.2] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2011] [Revised: 12/21/2011] [Accepted: 12/22/2011] [Indexed: 11/09/2022] Open
Abstract
Cryptochromes and photolyases are structurally related but have different biological functions in signalling and DNA repair. Proteobacteria and cyanobacteria harbour a new class of cryptochromes, called CryPro. We have solved the 2.7 Å structure of one of its members, cryptochrome B from Rhodobacter sphaeroides, which is a regulator of photosynthesis gene expression. The structure reveals that, in addition to the photolyase-like fold, CryB contains two cofactors only conserved in the CryPro subfamily: 6,7-dimethyl-8-ribityl-lumazine in the antenna-binding domain and a [4Fe-4S] cluster within the catalytic domain. The latter closely resembles the iron-sulphur cluster harbouring the large primase subunit PriL, indicating that PriL is evolutionarily related to the CryPro class of cryptochromes.
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Affiliation(s)
- Yann Geisselbrecht
- Department of Chemistry-Institute of Biochemistry, Philipps-University, Marburg, Germany
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26
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Selby CP, Sancar A. The second chromophore in Drosophila photolyase/cryptochrome family photoreceptors. Biochemistry 2011; 51:167-71. [PMID: 22175817 DOI: 10.1021/bi201536w] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The photolyase/cryptochrome family of proteins are FAD-containing flavoproteins which carry out blue-light-dependent functions including DNA repair, plant growth and development, and regulation of the circadian clock. In addition to FAD, many members of the family contain a second chromophore which functions as a photo-antenna, harvesting light and transferring the excitation energy to FAD and thus increasing the efficiency of the system. The second chromophore is methenyltetrahydrofolate (MTHF) in most photolyases characterized to date and FAD, FMN, or 5-deazariboflavin in others. To date, no second chromophore has been identified in cryptochromes. Drosophila contains three members of the cryptochrome/photolyase family: cyclobutane pyrimidine dimer (CPD) photolyase, (6-4) photoproduct photolyase, and cryptochrome. We developed an expression system capable of incorporating all known second chromophores into the cognate cryptochrome/photolyase family members. Using this system, we demonstrate that Drosophila CPD photolyase and (6-4) photolyase employ 5-deazariboflavin as their second chromophore, but Drosophila cryptochrome, which is evolutionarily closer to (6-4) photolyase than the CPD photolyase, lacks a second chromophore.
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Affiliation(s)
- Christopher P Selby
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599-7260, United States
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27
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Biskup T, Hitomi K, Getzoff ED, Krapf S, Koslowski T, Schleicher E, Weber S. Identifikation unerwarteter Elektronentransferpfade im Cryptochrom durch zeitaufgelöste Elektronenspinresonanz-Spektroskopie. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201104321] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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28
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Biskup T, Hitomi K, Getzoff ED, Krapf S, Koslowski T, Schleicher E, Weber S. Unexpected electron transfer in cryptochrome identified by time-resolved EPR spectroscopy. Angew Chem Int Ed Engl 2011; 50:12647-51. [PMID: 22086606 DOI: 10.1002/anie.201104321] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2011] [Indexed: 11/05/2022]
Abstract
Subtle differences in the local sequence and conformation of amino acids can result in diversity and specificity in electron transfer (ET) in proteins, despite structural conservation of the redox partners. For individual ET steps, distance is not necessarily the decisive parameter; orientation and solvent accessibility of the ET partners, and thus the stabilization of the charge-separated states, contribute substantially.
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Affiliation(s)
- Till Biskup
- Fachberich Physik, Freie Universität Berlin, Germany
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Chaves I, Pokorny R, Byrdin M, Hoang N, Ritz T, Brettel K, Essen LO, van der Horst GTJ, Batschauer A, Ahmad M. The cryptochromes: blue light photoreceptors in plants and animals. ANNUAL REVIEW OF PLANT BIOLOGY 2011; 62:335-64. [PMID: 21526969 DOI: 10.1146/annurev-arplant-042110-103759] [Citation(s) in RCA: 558] [Impact Index Per Article: 42.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Cryptochromes are flavoprotein photoreceptors first identified in Arabidopsis thaliana, where they play key roles in growth and development. Subsequently identified in prokaryotes, archaea, and many eukaryotes, cryptochromes function in the animal circadian clock and are proposed as magnetoreceptors in migratory birds. Cryptochromes are closely structurally related to photolyases, evolutionarily ancient flavoproteins that catalyze light-dependent DNA repair. Here, we review the structural, photochemical, and molecular properties of cry-DASH, plant, and animal cryptochromes in relation to biological signaling mechanisms and uncover common features that may contribute to better understanding the function of cryptochromes in diverse systems including in man.
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Affiliation(s)
- Inês Chaves
- Department of Genetics, Erasmus University Medical Center, 3000 CA Rotterdam, The Netherlands.
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Morita R, Nakane S, Shimada A, Inoue M, Iino H, Wakamatsu T, Fukui K, Nakagawa N, Masui R, Kuramitsu S. Molecular mechanisms of the whole DNA repair system: a comparison of bacterial and eukaryotic systems. J Nucleic Acids 2010; 2010:179594. [PMID: 20981145 PMCID: PMC2957137 DOI: 10.4061/2010/179594] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2010] [Accepted: 07/27/2010] [Indexed: 11/20/2022] Open
Abstract
DNA is subjected to many endogenous and exogenous damages. All organisms have developed a complex network of DNA repair mechanisms. A variety of different DNA repair pathways have been reported: direct reversal, base excision repair, nucleotide excision repair, mismatch repair, and recombination repair pathways. Recent studies of the fundamental mechanisms for DNA repair processes have revealed a complexity beyond that initially expected, with inter- and intrapathway complementation as well as functional interactions between proteins involved in repair pathways. In this paper we give a broad overview of the whole DNA repair system and focus on the molecular basis of the repair machineries, particularly in Thermus thermophilus HB8.
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Affiliation(s)
- Rihito Morita
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
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31
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Liedvogel M, Mouritsen H. Cryptochromes--a potential magnetoreceptor: what do we know and what do we want to know? J R Soc Interface 2010; 7 Suppl 2:S147-62. [PMID: 19906675 PMCID: PMC2844001 DOI: 10.1098/rsif.2009.0411.focus] [Citation(s) in RCA: 139] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2009] [Accepted: 10/22/2009] [Indexed: 01/14/2023] Open
Abstract
Cryptochromes have been suggested to be the primary magnetoreceptor molecules underlying light-dependent magnetic compass detection in migratory birds. Here we review and evaluate (i) what is known about these candidate magnetoreceptor molecules, (ii) what characteristics cryptochrome molecules must fulfil to possibly underlie light-dependent, radical pair based magnetoreception, (iii) what evidence supports the involvement of cryptochromes in magnetoreception, and (iv) what needs to be addressed in future research. The review focuses primarily on our knowledge of cryptochromes in the context of magnetoreception.
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Affiliation(s)
- Miriam Liedvogel
- AG Neurosensorik (Animal Navigation), Institut für Biologie und Umweltwissenschaften, University of Oldenburg, 26111 Oldenburg, Germany.
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32
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Schleicher E, Wenzel R, Ahmad M, Batschauer A, Essen LO, Hitomi K, Getzoff ED, Bittl R, Weber S, Okafuji A. The Electronic State of Flavoproteins: Investigations with Proton Electron-Nuclear Double Resonance. APPLIED MAGNETIC RESONANCE 2010; 37:339-352. [PMID: 26089595 PMCID: PMC4469238 DOI: 10.1007/s00723-009-0101-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Electron-nuclear double resonance (ENDOR) spectroscopy provides useful information on hyperfine interactions between nuclear magnetic moments and the magnetic moment of an unpaired electron spin. Because the hyperfine coupling constant reacts quite sensitively to polarity changes in the direct vicinity of the nucleus under consideration, ENDOR spectroscopy can be favorably used for the detection of subtle protein-cofactor interactions. A number of pulsed ENDOR studies on flavoproteins have been published during the past few years; most of them were designed to characterize the flavin cofactor by means of its protonation state, or to detect individual protein-cofactor interactions. The aim of this study is to compare the pulsed ENDOR spectra from different flavoproteins in terms of variations of characteristic proton hyperfine values. The general concept is to observe limits of possible influences on the cofactor's electronic state by surrounding amino acids. Furthermore, we compare ENDOR data obtained from in vivo experiments with in vitro data to emphasize the potential of the method for gaining molecular information in complex media.
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Affiliation(s)
- Erik Schleicher
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Albertstr.21, 79104 Freiburg, Germany
| | - Ringo Wenzel
- Institut für Experimentalphysik, Fachbereich Physik, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | | | - Alfred Batschauer
- Fachbereich Biologie, Philipps-Universität Marburg, Marburg, Germany
| | | | - Kenichi Hitomi
- Department of Molecular Biology, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Elizabeth D Getzoff
- Department of Molecular Biology, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Robert Bittl
- Institut für Experimentalphysik, Fachbereich Physik, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Stefan Weber
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Albertstr.21, 79104 Freiburg, Germany
| | - Asako Okafuji
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Albertstr.21, 79104 Freiburg, Germany
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Hendrischk AK, Frühwirth SW, Moldt J, Pokorny R, Metz S, Kaiser G, Jäger A, Batschauer A, Klug G. A cryptochrome-like protein is involved in the regulation of photosynthesis genes in Rhodobacter sphaeroides. Mol Microbiol 2009; 74:990-1003. [PMID: 19878455 DOI: 10.1111/j.1365-2958.2009.06912.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Blue light receptors belonging to the cryptochrome/photolyase family are found in all kingdoms of life. The functions of photolyases in repair of UV-damaged DNA as well as of cryptochromes in the light-dependent regulation of photomorphogenetic processes and in the circadian clock in plants and animals are well analysed. In prokaryotes, the only role of members of this protein family that could be demonstrated is DNA repair. Recently, we identified a gene for a cryptochrome-like protein (CryB) in the alpha-proteobacterium Rhodobacter sphaeroides. The protein lacks the typical C-terminal extension of cryptochromes, and is not related to the Cry DASH family. Here we demonstrate that CryB binds flavin adenine dinucleotide that can be photoreduced by blue light. CryB binds single-stranded DNA with very high affinity (K(d) approximately 10(-8) M) but double-stranded DNA and single-stranded RNA with far lower affinity (K(d) approximately 10(-6) M). Despite of that, no in vitro repair activity for pyrimidine dimers in single-stranded DNA could be detected. However, we show that CryB clearly affects the expression of genes for pigment-binding proteins and consequently the amount of photosynthetic complexes in R. sphaeroides. Thus, for the first time a role of a bacterial cryptochrome in gene regulation together with a biological function is demonstrated.
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Affiliation(s)
- Anne-Kathrin Hendrischk
- Institut für Mikrobiologie und Molekularbiologie, Justus-Liebig-Universität Giessen, Heinrich-Buff-Ring 26-32, D-35392 Giessen, Germany
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Kaiser G, Kleiner O, Beisswenger C, Batschauer A. Increased DNA repair in Arabidopsis plants overexpressing CPD photolyase. PLANTA 2009; 230:505-515. [PMID: 19521716 DOI: 10.1007/s00425-009-0962-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2009] [Accepted: 05/25/2009] [Indexed: 05/27/2023]
Abstract
Ultraviolet-B (UV-B, 280-320 nm) radiation may have severe negative effects on plants including damage to their genetic information. UV protection and DNA-repair mechanisms have evolved to either avoid or repair such damage. Since autotrophic plants are dependent on sunlight for their energy supply, an increase in the amount of UV-B reaching the earth's surface may affect the integrity of their genetic information if DNA damage is not repaired efficiently and rapidly. Here we show that overexpression of cyclobutane pyrimidine dimer (CPD) photolyase (EC 4.1.99.3) in Arabidopsis thaliana (L.), which catalyses the reversion of the major UV-B photoproduct in DNA (CPDs), strongly enhances the repair of CPDs and results in a moderate increase of biomass production under elevated UV-B.
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Affiliation(s)
- Gebhard Kaiser
- FB Biologie, Pflanzenphysiologie, Philipps-Universität Marburg, Karl-von-Frisch-Str. 8, 35032, Marburg, Germany
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Kodali G, Siddiqui SU, Stanley RJ. Charge redistribution in oxidized and semiquinone E. coli DNA photolyase upon photoexcitation: stark spectroscopy reveals a rationale for the position of Trp382. J Am Chem Soc 2009; 131:4795-807. [PMID: 19292445 DOI: 10.1021/ja809214r] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The electronic structure of the two lowest excited electronic states of FAD and FADH(*) in folate-depleted E. coli DNA photolyase (PL(OX) and PL(SQ), respectively) was measured using absorption Stark spectroscopy. The experimental analysis was supported by TDDFT calculations of both the charge redistribution and the difference dipole moments for the transitions of both oxidation states using lumiflavin as a model. The difference dipole moments and polarizabilities for PL(OX) are similar to those obtained in our previous work for flavins in simple solvents and in an FMN-containing flavoprotein. No such comparison can be made for PL(SQ), as we believe this to be the first experimental report of the direction and magnitude of excited-state charge redistribution in any flavosemiquinone. The picture that emerges from these studies is discussed in the context of electron transfer in photolyase, particularly for the semiquinone photoreduction process, which involves nearby tryptophan residues as electron donors. The direction of charge displacement derived from an analysis of the Stark spectra rationalizes the positioning of the critical Trp382 residue relative to the flavin for efficient vectorial electron transfer leading to photoreduction. The ramifications of vectorial charge redistribution are discussed in the context of the wider class of flavoprotein blue light photoreceptors.
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Affiliation(s)
- Goutham Kodali
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, USA
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36
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Müller M, Carell T. Structural biology of DNA photolyases and cryptochromes. Curr Opin Struct Biol 2009; 19:277-85. [PMID: 19487120 DOI: 10.1016/j.sbi.2009.05.003] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2009] [Revised: 04/28/2009] [Accepted: 05/08/2009] [Indexed: 10/20/2022]
Abstract
Photolyases repair cytotoxic and mutagenic UV-induced photolesions in DNA by using an amazing light-dependent repair mechanism. It involves light absorption, electron transfer from an excited reduced and deprotonated FADH(-) to the flipped-out photolesion, followed by the fragmentation of the photolesions. Cryptochromes are highly related proteins that no longer repair damaged DNA, but function as photoreceptors. They feature strikingly similar protein architectures to photolyases and contain an FAD cofactor as well. However, cryptochromes possess an additional signal-transmitting domain, attached either to the N-termini or C-termini. Recently, the field of photorepair and blue-light photoperception has experienced significant progress particularly in structural biology, which is summarized in this review. Today, crystal structures of many family members are known and most recently even complexes of photolyases and DASH-type cryptochrome bound to their DNA substrates became available providing insight into the critical electron and energy transfer reactions that enable genome repair.
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Affiliation(s)
- Markus Müller
- Center for Integrated Protein Science CiPS(M) at the Department of Chemistry and Biochemistry, Ludwig-Maximilians University Munich, Butenandtstr. 5-13, D-81377 Munich, Germany
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37
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Functional motifs in the (6-4) photolyase crystal structure make a comparative framework for DNA repair photolyases and clock cryptochromes. Proc Natl Acad Sci U S A 2009; 106:6962-7. [PMID: 19359474 DOI: 10.1073/pnas.0809180106] [Citation(s) in RCA: 99] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Homologous flavoproteins from the photolyase (PHR)/cryptochrome (CRY) family use the FAD cofactor in PHRs to catalyze DNA repair and in CRYs to tune the circadian clock and control development. To help address how PHR/CRY members achieve these diverse functions, we determined the crystallographic structure of Arabidopsis thaliana (6-4) PHR (UVR3), which is strikingly (>65%) similar in sequence to human circadian clock CRYs. The structure reveals a substrate-binding cavity specific for the UV-induced DNA lesion, (6-4) photoproduct, and cofactor binding sites different from those of bacterial PHRs and consistent with distinct mechanisms for activities and regulation. Mutational analyses were combined with this prototypic structure for the (6-4) PHR/clock CRY cluster to identify structural and functional motifs: phosphate-binding and Pro-Lys-Leu protrusion motifs constricting access to the substrate-binding cavity above FAD, sulfur loop near the external end of the Trp electron-transfer pathway, and previously undefined C-terminal helix. Our results provide a detailed, unified framework for investigations of (6-4) PHRs and the mammalian CRYs. Conservation of key residues and motifs controlling FAD access and activities suggests that regulation of FAD redox properties and radical stability is essential not only for (6-4) photoproduct DNA repair, but also for circadian clock-regulating CRY functions. The structural and functional results reported here elucidate archetypal relationships within this flavoprotein family and suggest how PHRs and CRYs use local residue and cofactor tuning, rather than larger structural modifications, to achieve their diverse functions encompassing DNA repair, plant growth and development, and circadian clock regulation.
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38
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Recognition and repair of UV lesions in loop structures of duplex DNA by DASH-type cryptochrome. Proc Natl Acad Sci U S A 2008; 105:21023-7. [PMID: 19074258 DOI: 10.1073/pnas.0805830106] [Citation(s) in RCA: 136] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
DNA photolyases and cryptochromes (cry) form a family of flavoproteins that use light energy in the blue/UV-A region for the repair of UV-induced DNA lesions or for signaling, respectively. Very recently, it was shown that members of the DASH cryptochrome subclade repair specifically cyclobutane pyrimidine dimers (CPDs) in UV-damaged single-stranded DNA. Here, we report the crystal structure of Arabidopsis cryptochrome 3 with an in-situ-repaired CPD substrate in single-stranded DNA. The structure shows a binding mode similar to that of conventional DNA photolyases. Furthermore, CPD lesions in double-stranded DNA are bound and repaired with similar efficiency as in single-stranded DNA if the CPD lesion is present in a loop structure. Together, these data reveal that DASH cryptochromes catalyze light-driven DNA repair like conventional photolyases but lack an efficient flipping mechanism for interaction with CPD lesions within duplex DNA.
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39
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Boussicault F, Robert M. Electron Transfer in DNA and in DNA-Related Biological Processes. Electrochemical Insights. Chem Rev 2008; 108:2622-45. [DOI: 10.1021/cr0680787] [Citation(s) in RCA: 125] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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40
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Active DNA photolyase encoded by a baculovirus from the insect Chrysodeixis chalcites. DNA Repair (Amst) 2008; 7:1309-18. [PMID: 18547877 DOI: 10.1016/j.dnarep.2008.04.013] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2008] [Revised: 04/21/2008] [Accepted: 04/21/2008] [Indexed: 10/22/2022]
Abstract
The genome of Chrysodeixis chalcites nucleopolyhedrovirus (ChchNPV) contains two open reading frames, Cc-phr1 and Cc-phr2, which encode putative class II CPD-DNA photolyases. CPD-photolyases repair UV-induced pyrimidine cyclobutane dimers using visible light as an energy source. Expression of Cc-phr2 provided photolyase deficient Escherichia coli cells with photoreactivating activity indicating that Cc-phr2 encodes an active photolyase. In contrast, Cc-phr1 did not rescue the photolyase deficiency. Cc-phr2 was overexpressed in E. coli and the resulting photolyase was purified till apparent homogeneity. Spectral measurements indicated the presence of FAD, but a second chromophore appeared to be absent. Recombinant Cc-phr2 photolyase was found to bind specifically F0 (8-hydroxy-7,8-didemethyl-5-deazariboflavin), which is an antenna chromophore present in various photolyases.. After reconstitution, FAD and F0 were present in approximately equimolar amounts. In reconstituted photolyase the F0 chromophore is functionally active as judged from the increase in the in vitro repair activity. This study demonstrates for the first time that a functional photolyase is encoded by an insect virus, which may have implications for the design of a new generation of baculoviruses with improved performance in insect pest control.
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41
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Cochrane JC, Strobel SA. Riboswitch effectors as protein enzyme cofactors. RNA (NEW YORK, N.Y.) 2008; 14:993-1002. [PMID: 18430893 PMCID: PMC2390802 DOI: 10.1261/rna.908408] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
The recently identified glmS ribozyme revealed that RNA enzymes, like protein enzymes, are capable of using small molecules as catalytic cofactors to promote chemical reactions. Flavin mononucleotide (FMN), S-adenosyl methionine (SAM), adenosyl cobalamin (AdoCbl), and thiamine pyrophosphate (TPP) are known ligands for RNA riboswitches in the control of gene expression, but are also catalytically powerful and ubiquitous cofactors in protein enzymes. If RNA, instead of just binding these molecules, could harness the chemical potential of the cofactor, it would significantly expand the enzymatic repertoire of ribozymes. Here we review the chemistry of AdoCbl, SAM, FMN, and TPP in protein enzymology and speculate on how these cofactors might have been used by ribozymes in the prebiotic RNA World or may still find application in modern biology.
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Affiliation(s)
- Jesse C Cochrane
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
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42
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Klar T, Pokorny R, Moldt J, Batschauer A, Essen LO. Cryptochrome 3 from Arabidopsis thaliana: structural and functional analysis of its complex with a folate light antenna. J Mol Biol 2006; 366:954-64. [PMID: 17188299 DOI: 10.1016/j.jmb.2006.11.066] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2006] [Revised: 12/02/2006] [Indexed: 11/19/2022]
Abstract
Cryptochromes are almost ubiquitous blue-light receptors and act in several species as central components of the circadian clock. Despite being evolutionary and structurally related with DNA photolyases, a class of light-driven DNA-repair enzymes, and having similar cofactor compositions, cryptochromes lack DNA-repair activity. Cryptochrome 3 from the plant Arabidopsis thaliana belongs to the DASH-type subfamily. Its crystal structure determined at 1.9 Angstroms resolution shows cryptochrome 3 in a dimeric state with the antenna cofactor 5,10-methenyltetrahydrofolate (MTHF) bound in a distance of 15.2 Angstroms to the U-shaped FAD chromophore. Spectroscopic studies on a mutant where a residue crucial for MTHF-binding, E149, was replaced by site-directed mutagenesis demonstrate that MTHF acts in cryptochrome 3 as a functional antenna for the photoreduction of FAD.
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Affiliation(s)
- Tobias Klar
- Philipps-Universität Marburg, Department of Chemistry, Hans-Meerwein-Strasse, D-35032 Marburg, Germany
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