1
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Bao Y, Fang W. A recombinant fungal photolyase autonomously enters human cell nuclei to fix UV-induced DNA lesions. Biotechnol Lett 2024; 46:459-467. [PMID: 38523200 DOI: 10.1007/s10529-024-03474-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 01/24/2024] [Accepted: 02/10/2024] [Indexed: 03/26/2024]
Abstract
Solar ultraviolet radiations induced DNA damages in human skin cells with cyclobutane pyrimidine dimers (CPD) and (6-4) photoproducts (6-4PPs) as the most frequent lesions. CPDs are repaired much slower than 6-4PPs by the nucleotide excision repair pathway, which are thus the major lesions that interfere with key cellular processes and give rise to gene mutations, possibly resulting in skin cancer. In prokaryotes and multicellular eukaryotes other than placental mammals, CPDs can be rapidly repaired by CPD photolyases in one simple enzymatic reaction using the energy of blue light. In this study, we aim to construct recombinant CPD photolyases that can autonomously enter human cell nuclei to fix UV-induced CPDs. A fly cell penetration peptide and a viral nucleus localization signal peptide were recombined with a fungal CPD photolyase to construct a recombinant protein. This engineered CPD photolyase autonomously crosses cytoplasm and nuclear membrane of human cell nuclei, which then efficiently photo-repairs UV-induced CPD lesions in the genomic DNA. This further protects the cells by increasing SOD activity, and decreasing cellular ROSs, malondialdehyde and apoptosis.
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Affiliation(s)
- Yuting Bao
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Institute of Microbiology, College of Life Science, Zhejiang University, Hangzhou, China
| | - Weiguo Fang
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Institute of Microbiology, College of Life Science, Zhejiang University, Hangzhou, China.
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2
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Otake M, Teranishi M, Komatsu C, Hara M, Yoshiyama KO, Hidema J. Poaceae plants transfer cyclobutane pyrimidine dimer photolyase to chloroplasts for ultraviolet-B resistance. Plant Physiol 2024; 195:326-342. [PMID: 38345835 PMCID: PMC11060685 DOI: 10.1093/plphys/kiae060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 01/07/2024] [Indexed: 05/02/2024]
Abstract
Photoreactivation enzyme that repairs cyclobutane pyrimidine dimer (CPD) induced by ultraviolet-B radiation, commonly called CPD photolyase (PHR) is essential for plants living under sunlight. Rice (Oryza sativa) PHR (OsPHR) is a unique triple-targeting protein. The signal sequences required for its translocation to the nucleus or mitochondria are located in the C-terminal region but have yet to be identified for chloroplasts. Here, we identified sequences located in the N-terminal region, including the serine-phosphorylation site at position 7 of OsPHR, and found that OsPHR is transported/localized to chloroplasts via a vesicle transport system under the control of serine-phosphorylation. However, the sequence identified in this study is only conserved in some Poaceae species, and in many other plants, PHR is not localized to the chloroplasts. Therefore, we reasoned that Poaceae species need the ability to repair CPD in the chloroplast genome to survive under sunlight and have uniquely acquired this mechanism for PHR chloroplast translocation.
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Affiliation(s)
- Momo Otake
- Graduate School of Life Sciences, Tohoku University, Sendai 980-8577, Japan
| | - Mika Teranishi
- Graduate School of Life Sciences, Tohoku University, Sendai 980-8577, Japan
| | - Chiharu Komatsu
- Graduate School of Life Sciences, Tohoku University, Sendai 980-8577, Japan
| | - Mamoru Hara
- Graduate School of Life Sciences, Tohoku University, Sendai 980-8577, Japan
| | | | - Jun Hidema
- Graduate School of Life Sciences, Tohoku University, Sendai 980-8577, Japan
- Division for the Establishment of Frontier Sciences of the Organization for Advanced Studies, Tohoku University, Sendai, Miyagi 980-8577, Japan
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3
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Cellini A, Shankar MK, Nimmrich A, Hunt LA, Monrroy L, Mutisya J, Furrer A, Beale EV, Carrillo M, Malla TN, Maj P, Vrhovac L, Dworkowski F, Cirelli C, Johnson PJM, Ozerov D, Stojković EA, Hammarström L, Bacellar C, Standfuss J, Maj M, Schmidt M, Weinert T, Ihalainen JA, Wahlgren WY, Westenhoff S. Directed ultrafast conformational changes accompany electron transfer in a photolyase as resolved by serial crystallography. Nat Chem 2024; 16:624-632. [PMID: 38225270 PMCID: PMC10997514 DOI: 10.1038/s41557-023-01413-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 11/28/2023] [Indexed: 01/17/2024]
Abstract
Charge-transfer reactions in proteins are important for life, such as in photolyases which repair DNA, but the role of structural dynamics remains unclear. Here, using femtosecond X-ray crystallography, we report the structural changes that take place while electrons transfer along a chain of four conserved tryptophans in the Drosophila melanogaster (6-4) photolyase. At femto- and picosecond delays, photoreduction of the flavin by the first tryptophan causes directed structural responses at a key asparagine, at a conserved salt bridge, and by rearrangements of nearby water molecules. We detect charge-induced structural changes close to the second tryptophan from 1 ps to 20 ps, identifying a nearby methionine as an active participant in the redox chain, and from 20 ps around the fourth tryptophan. The photolyase undergoes highly directed and carefully timed adaptations of its structure. This questions the validity of the linear solvent response approximation in Marcus theory and indicates that evolution has optimized fast protein fluctuations for optimal charge transfer.
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Affiliation(s)
- Andrea Cellini
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Madan Kumar Shankar
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden
| | - Amke Nimmrich
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
- Department of Chemistry, University of Washington, Seattle, WA, USA
| | - Leigh Anna Hunt
- Department of Chemistry - Ångström Laboratory, Uppsala University, Uppsala, Sweden
| | - Leonardo Monrroy
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden
| | - Jennifer Mutisya
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden
| | | | | | | | - Tek Narsingh Malla
- Physics Department, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Piotr Maj
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden
| | - Lidija Vrhovac
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden
| | | | | | | | | | - Emina A Stojković
- Department of Biology, Northeastern Illinois University, Chicago, IL, USA
| | - Leif Hammarström
- Department of Chemistry - Ångström Laboratory, Uppsala University, Uppsala, Sweden
| | | | | | - Michał Maj
- Department of Chemistry - Ångström Laboratory, Uppsala University, Uppsala, Sweden
| | - Marius Schmidt
- Physics Department, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | | | - Janne A Ihalainen
- Department of Biological and Environmental Sciences, Nanoscience Center, University of Jyvaskyla, Jyvaskyla, Finland
| | - Weixiao Yuan Wahlgren
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
- Department of Chemistry and Molecular Biology and the Swedish NMR Centre, University of Gothenburg, Gothenburg, Sweden
| | - Sebastian Westenhoff
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden.
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden.
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4
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Peng H, Zhang YL, Ying SH, Feng MG. Rad2, Rad14 and Rad26 recover Metarhizium robertsii from solar UV damage through photoreactivation in vivo. Microbiol Res 2024; 280:127589. [PMID: 38154444 DOI: 10.1016/j.micres.2023.127589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Revised: 12/14/2023] [Accepted: 12/18/2023] [Indexed: 12/30/2023]
Abstract
Rad2, Rad14 and Rad26 recover ultraviolet (UV) damage by nucleotide excision repair (NER) in budding yeast but their functions in filamentous fungi have not been elucidated. Here, we report mechanistically different anti-UV effects of nucleus-specific Rad2, Rad14 and Rad26 orthologs in Metarhizium robertsii, an insect-pathogenic fungus. The null mutants of rad2, rad14 and rad26 showed a decrease of ∼90% in conidial resistance to UVB irradiation. When conidia were impaired at a UVB dose of 0.15 J/cm2, they were photoreactivated (germinated) by only 6-13% through a 5-h light plus 19-h dark incubation, whereas 100%, 80% and 70% of the wild-type conidia were photoreactivated at 0.15, 0.3 and 0.4 J/cm2, respectively. The dose-dependent photoreactivation rates were far greater than the corresponding 24-h dark reactivation rates and were largely enhanced by the overexpression (OE) of rad2, rad14 or rad26 in the wild-type strain. The OE strains exhibited markedly greater activities in photoreactivation of conidia inactivated at 0.5-0.7 J/cm2 than did the wild-type strain. Confirmed interactions of Rad2, Rad14 and Rad26 with photolyase regulators and/or Rad1 or Rad10 suggest that each of these proteins could have evolved into a component of the photolyase regulator-cored protein complex to mediate photoreactivation. The interactions inhibited in the null mutants resulted in transcriptional abolishment or repression of those factors involved in the complex. In conclusion, the anti-UV effects of Rad2, Rad14 and Rad26 depend primarily on DNA photorepair-dependent photoreactivation in M. robertsii and mechanistically differ from those of yeast orthologs depending on NER.
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Affiliation(s)
- Han Peng
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China; Clinical Research Institute, Zhejiang Provincial People's Hospital, Hangzhou, Zhejiang, China
| | - Yi-Lu Zhang
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Sheng-Hua Ying
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Ming-Guang Feng
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China.
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5
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de Lima PPDABM, Fiorotti J, Paulino PG, Corval ARDC, Mesquita E, Corrêa TA, Lopes ADSC, Oliveira RJVD, Santos HA, Bittencourt VREP, Angelo IDC, Golo PS. Metarhizium pingshaense photolyase expression and virulence to Rhipicephalus microplus after UV-B exposure. J Basic Microbiol 2024; 64:94-105. [PMID: 37696778 DOI: 10.1002/jobm.202300346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 08/18/2023] [Accepted: 08/28/2023] [Indexed: 09/13/2023]
Abstract
The current study examined the impact of ultraviolet (UV)-B radiation in Metarhizium pingshaense blastospores' photolyase expression and their virulence against Rhipicephalus microplus. Blastospores were exposed to UV under laboratory and field conditions. Ticks were treated topically with fungal suspension and exposed to UV-B in the laboratory for three consecutive days. The expression of cyclobutane pyrimidine dimmers (CPDs)-photolyase gene maphr1-2 in blastospores after UV exposure followed by white light exposure was accessed after 0, 8, 12, 24, 36, and 48 h. Average relative germination of blastospores 24 h after in vitro UV exposure was 8.4% lower than 48 h. Despite this, the relative germination of blastospores exposed to UV in the field 18 h (95.7 ± 0.3%) and 28 h (97.3 ± 0.8%) after exposure were not different (p > 0.05). Ticks treated with fungus and not exposed to UV exhibited 0% survival 10 days after the treatment, while fungus-treated ticks exposed to UV exhibited 50 ± 11.2% survival. Expression levels of maphr1-2 8, 12, and 24 h after UV-B exposure were not different from time zero. Maphr1-2 expression peak in M. pingshaense blastospores occurred 36 h after UV-B exposure, in the proposed conditions and times analyzed, suggesting repair mechanisms other than CPD-mediated-photoreactivation might be leading blastospores' germination from 0 to 24 h.
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Affiliation(s)
- Pamella Pryscila de A B M de Lima
- Programa de Pós-Graduação em Ciências Veterinárias, Instituto de Veterinária, Universidade Federal Rural do Rio de Janeiro (UFRRJ), Seropédica, Rio de Janeiro, Brazil
| | - Jessica Fiorotti
- Programa de Pós-Graduação em Ciências Veterinárias, Instituto de Veterinária, Universidade Federal Rural do Rio de Janeiro (UFRRJ), Seropédica, Rio de Janeiro, Brazil
- Departamento de Bioquímica e Imunologia, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo (USP), Ribeirão Preto SP, Brazil
| | - Patrícia G Paulino
- Programa de Pós-Graduação em Ciências Veterinárias, Instituto de Veterinária, Universidade Federal Rural do Rio de Janeiro (UFRRJ), Seropédica, Rio de Janeiro, Brazil
| | - Amanda R da C Corval
- Programa de Pós-Graduação em Ciências Veterinárias, Instituto de Veterinária, Universidade Federal Rural do Rio de Janeiro (UFRRJ), Seropédica, Rio de Janeiro, Brazil
| | - Emily Mesquita
- Programa de Pós-Graduação em Ciências Veterinárias, Instituto de Veterinária, Universidade Federal Rural do Rio de Janeiro (UFRRJ), Seropédica, Rio de Janeiro, Brazil
| | - Thaís A Corrêa
- Programa de Pós-Graduação em Ciências Veterinárias, Instituto de Veterinária, Universidade Federal Rural do Rio de Janeiro (UFRRJ), Seropédica, Rio de Janeiro, Brazil
| | - Adriani da S C Lopes
- Programa de Pós-Graduação em Ciências Veterinárias, Instituto de Veterinária, Universidade Federal Rural do Rio de Janeiro (UFRRJ), Seropédica, Rio de Janeiro, Brazil
| | - Rafael José V de Oliveira
- Laboratório de Bioprocessos, Centro de Tecnologias Estratégicas do Nordeste (CETENE), Recife, Pernambuco, Brazil
| | - Huarrisson A Santos
- Departamento de Epidemiologia e Saúde Pública, Instituto de Veterinária, UFRRJ, Seropédica, Rio de Janeiro, Brazil
| | - Vânia R E P Bittencourt
- Departamento de Parasitologia Animal, Instituto de Veterinária, UFRRJ, Seropédica, Rio de Janeiro, Brazil
| | - Isabele da C Angelo
- Departamento de Epidemiologia e Saúde Pública, Instituto de Veterinária, UFRRJ, Seropédica, Rio de Janeiro, Brazil
| | - Patrícia S Golo
- Departamento de Parasitologia Animal, Instituto de Veterinária, UFRRJ, Seropédica, Rio de Janeiro, Brazil
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6
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Torres-Obreque K, Gonçalves FG, Ferraro RB, Fuentes-León F, Menck CFM, Costa-Silva TA, Monteiro G, Perego P, Rangel-Yagui CDO. Recombinant production of a highly efficient photolyase from Thermus thermophilus. Biotechnol J 2024; 19:e2300325. [PMID: 38385504 DOI: 10.1002/biot.202300325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 12/09/2023] [Accepted: 12/14/2023] [Indexed: 02/23/2024]
Abstract
Ultraviolet (UV) radiation from sunlight can damage DNA, inducing mutagenesis and eventually leading to skin cancer. Topical sunscreens are used to avoid the effect of UV irradiation, but the topical application of DNA repair enzymes, such as photolyase, can provide active photoprotection by DNA recovery. Here we produced a recombinant Thermus thermophilus photolyase expressed in Escherichia coli, evaluated the kinetic parameters of bacterial growth and the kinetics and stability of the enzyme. The maximum biomass (𝑋𝑚𝑎𝑥 ) of 2.0 g L-1 was reached after 5 h of cultivation, corresponding to 𝑃X = 0.4 g L-1 h. The µ𝑚𝑎𝑥 corresponded to 1.0 h-1 . Photolyase was purified by affinity chromatography and high amounts of pure enzyme were obtained (3.25 mg L-1 of cultivation). Two different methods demonstrated the enzyme activity on DNA samples and very low enzyme concentrations, such as 15 µg mL-1 , already resulted in 90% of CPD photodamage removal. We also determined photolyase kM of 9.5 nM, confirming the potential of the enzyme at very low concentrations, and demonstrated conservation of enzyme activity after freezing (-20°C) and lyophilization. Therefore, we demonstrate T. thermophilus photolyase capacity of CPD damage repair and its potential as an active ingredient to be incorporated in dermatological products.
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Affiliation(s)
- Karin Torres-Obreque
- Department of Biochemical and Pharmaceutical Technology, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
- Department of Civil, Chemical and Environmental Engineering, University of Genoa, Genova, Italy
| | - Felipe Gobbi Gonçalves
- Department of Biochemical and Pharmaceutical Technology, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Rafael Bertelli Ferraro
- Department of Biochemical and Pharmaceutical Technology, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Fabiana Fuentes-León
- Department of Civil, Chemical and Environmental Engineering, University of Genoa, Genova, Italy
| | | | - Tales Alexandre Costa-Silva
- Department of Biochemical and Pharmaceutical Technology, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Gisele Monteiro
- Department of Biochemical and Pharmaceutical Technology, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Patrizia Perego
- Department of Civil, Chemical and Environmental Engineering, University of Genoa, Genova, Italy
| | - Carlota de Oliveira Rangel-Yagui
- Department of Biochemical and Pharmaceutical Technology, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
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7
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Christou NE, Apostolopoulou V, Melo DVM, Ruppert M, Fadini A, Henkel A, Sprenger J, Oberthuer D, Günther S, Pateras A, Rahmani Mashhour A, Yefanov OM, Galchenkova M, Reinke PYA, Kremling V, Scheer TES, Lange ER, Middendorf P, Schubert R, De Zitter E, Lumbao-Conradson K, Herrmann J, Rahighi S, Kunavar A, Beale EV, Beale JH, Cirelli C, Johnson PJM, Dworkowski F, Ozerov D, Bertrand Q, Wranik M, Bacellar C, Bajt S, Wakatsuki S, Sellberg JA, Huse N, Turk D, Chapman HN, Lane TJ. Time-resolved crystallography captures light-driven DNA repair. Science 2023; 382:1015-1020. [PMID: 38033070 DOI: 10.1126/science.adj4270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 10/05/2023] [Indexed: 12/02/2023]
Abstract
Photolyase is an enzyme that uses light to catalyze DNA repair. To capture the reaction intermediates involved in the enzyme's catalytic cycle, we conducted a time-resolved crystallography experiment. We found that photolyase traps the excited state of the active cofactor, flavin adenine dinucleotide (FAD), in a highly bent geometry. This excited state performs electron transfer to damaged DNA, inducing repair. We show that the repair reaction, which involves the lysis of two covalent bonds, occurs through a single-bond intermediate. The transformation of the substrate into product crowds the active site and disrupts hydrogen bonds with the enzyme, resulting in stepwise product release, with the 3' thymine ejected first, followed by the 5' base.
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Affiliation(s)
- Nina-Eleni Christou
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Virginia Apostolopoulou
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Diogo V M Melo
- European XFEL GmbH, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Matthias Ruppert
- Institute for Nanostructure and Solid-State Physics, CFEL Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Alisia Fadini
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London SW7 2AZ, UK
| | - Alessandra Henkel
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Janina Sprenger
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Dominik Oberthuer
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Sebastian Günther
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Anastasios Pateras
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Aida Rahmani Mashhour
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Oleksandr M Yefanov
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Marina Galchenkova
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Patrick Y A Reinke
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Viviane Kremling
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - T Emilie S Scheer
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Esther R Lange
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Philipp Middendorf
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Robin Schubert
- European XFEL GmbH, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Elke De Zitter
- Université Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, 38000 Grenoble, France
| | - Koya Lumbao-Conradson
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Rd, Menlo Park, CA 94025, USA
| | - Jonathan Herrmann
- Department of Structural Biology, Stanford University, 318 Campus Drive West, Stanford, CA 94305-5151, USA
| | - Simin Rahighi
- Department of Structural Biology, Stanford University, 318 Campus Drive West, Stanford, CA 94305-5151, USA
| | - Ajda Kunavar
- Laboratory for Fluid Dynamics and Thermodynamics, Faculty of Mechanical Engineering, University of Ljubljana, Aškerčeva 6, 1000 Ljubljana, Slovenia
| | - Emma V Beale
- Paul Scherrer Institute, CH-5232 Villigen PSI, Switzerland
| | - John H Beale
- Paul Scherrer Institute, CH-5232 Villigen PSI, Switzerland
| | | | | | | | - Dmitry Ozerov
- Paul Scherrer Institute, CH-5232 Villigen PSI, Switzerland
| | | | | | | | - Saša Bajt
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Soichi Wakatsuki
- Department of Structural Biology, Stanford University, 318 Campus Drive West, Stanford, CA 94305-5151, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, 2575 Sand Hill Rd, Menlo Park, CA 94025, USA
| | - Jonas A Sellberg
- Biomedical and X-ray Physics, Department of Applied Physics, AlbaNova University Center, KTH Royal Institute of Technology, S-106 91 Stockholm, Sweden
| | - Nils Huse
- The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761 Hamburg, Germany
- Institute for Nanostructure and Solid-State Physics, CFEL Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Dušan Turk
- Department of Biochemistry and Molecular and Structural Biology, Jožef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
- Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins, Jamova 39, 1000 Ljubljana, Slovenia
| | - Henry N Chapman
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761 Hamburg, Germany
- Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Thomas J Lane
- Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761 Hamburg, Germany
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8
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Zhao X, Liu W, Aiwaili P, Zhang H, Xu Y, Gu Z, Gao J, Hong B. PHOTOLYASE/BLUE LIGHT RECEPTOR2 regulates chrysanthemum flowering by compensating for gibberellin perception. Plant Physiol 2023; 193:2848-2864. [PMID: 37723123 PMCID: PMC10663108 DOI: 10.1093/plphys/kiad503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 08/10/2023] [Accepted: 08/27/2023] [Indexed: 09/20/2023]
Abstract
The gibberellins (GAs) receptor GA INSENSITIVE DWARF1 (GID1) plays a central role in GA signal perception and transduction. The typical photoperiodic plant chrysanthemum (Chrysanthemum morifolium) only flowers when grown in short-day photoperiods. In addition, chrysanthemum flowering is also controlled by the aging pathway, but whether and how GAs participate in photoperiod- and age-dependent regulation of flowering remain unknown. Here, we demonstrate that photoperiod affects CmGID1B expression in response to GAs and developmental age. Moreover, we identified PHOTOLYASE/BLUE LIGHT RECEPTOR2, an atypical photocleavage synthase, as a CRYPTOCHROME-INTERACTING bHLH1 interactor with which it forms a complex in response to short days to activate CmGID1B transcription. Knocking down CmGID1B raised endogenous bioactive GA contents and GA signal perception, in turn modulating the expression of the aging-related genes MicroRNA156 and SQUAMOSA PROMOTER BINDING PROTEIN-LIKE3. We propose that exposure to short days accelerates the juvenile-to-adult transition by increasing endogenous GA contents and response to GAs, leading to entry into floral transformation.
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Affiliation(s)
- Xin Zhao
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, China Agricultural University, Beijing 100193, China
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Wenwen Liu
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, China Agricultural University, Beijing 100193, China
| | - Palinuer Aiwaili
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, China Agricultural University, Beijing 100193, China
| | - Han Zhang
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, China Agricultural University, Beijing 100193, China
| | - Yanjie Xu
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, China Agricultural University, Beijing 100193, China
| | - Zhaoyu Gu
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, China Agricultural University, Beijing 100193, China
| | - Junping Gao
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, China Agricultural University, Beijing 100193, China
| | - Bo Hong
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, China Agricultural University, Beijing 100193, China
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9
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Hosokawa Y, Morita H, Nakamura M, Yamamoto J. A deazariboflavin chromophore kinetically stabilizes reduced FAD state in a bifunctional cryptochrome. Sci Rep 2023; 13:16682. [PMID: 37794070 PMCID: PMC10551024 DOI: 10.1038/s41598-023-43930-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 09/30/2023] [Indexed: 10/06/2023] Open
Abstract
An animal-like cryptochrome derived from Chlamydomonas reinhardtii (CraCRY) is a bifunctional flavoenzyme harboring flavin adenine dinucleotide (FAD) as a photoreceptive/catalytic center and functions both in the regulation of gene transcription and the repair of UV-induced DNA lesions in a light-dependent manner, using different FAD redox states. To address how CraCRY stabilizes the physiologically relevant redox state of FAD, we investigated the thermodynamic and kinetic stability of the two-electron reduced anionic FAD state (FADH-) in CraCRY and related (6-4) photolyases. The thermodynamic stability of FADH- remained almost the same compared to that of all tested proteins. However, the kinetic stability of FADH- varied remarkably depending on the local structure of the secondary pocket, where an auxiliary chromophore, 8-hydroxy-7,8-didemethyl-5-deazariboflavin (8-HDF), can be accommodated. The observed effect of 8-HDF uptake on the enhancement of the kinetic stability of FADH- suggests an essential role of 8-HDF in the bifunctionality of CraCRY.
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Affiliation(s)
- Yuhei Hosokawa
- Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka, 560-8531, Japan
| | - Hiroyoshi Morita
- Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka, 560-8531, Japan
| | - Mai Nakamura
- Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka, 560-8531, Japan
| | - Junpei Yamamoto
- Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka, 560-8531, Japan.
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10
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Zhang YL, Peng H, Zhang K, Ying SH, Feng MG. Divergent roles of Rad4 and Rad23 homologs in Metarhizium robertsii's resistance to solar ultraviolet damage. Appl Environ Microbiol 2023; 89:e0099423. [PMID: 37655890 PMCID: PMC10537586 DOI: 10.1128/aem.00994-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 07/13/2023] [Indexed: 09/02/2023] Open
Abstract
The anti-ultraviolet (UV) role of a Rad4-Rad23-Rad33 complex in budding yeast relies on nucleotide excision repair (NER), which is mechanistically distinct from photorepair of DNA lesions generated under solar UV irradiation but remains poorly known in filamentous fungi. Here, two nucleus-specific Rad4 paralogs (Rad4A and Rad4B) and nucleocytoplasmic shuttling Rad23 ortholog are functionally characterized by multiple analyses of their null mutants in Metarhizium robertsii, an entomopathogenic fungus lacking Rad33. Rad4A was proven to interact with Rad23 and contribute significantly more to conidial UVB resistance (90%) than Rad23 (65%). Despite no other biological function, Rad4A exhibited a very high activity in photoreactivation of UVB-impaired/inactivated conidia by 5-h light exposure due to its interaction with Rad10, an anti-UV protein clarified previously to have acquired a similar photoreactivation activity through its interaction with a photolyase in M. robertsii. The NER activity of Rad4A or Rad23 was revealed by lower reactivation rates of moderately impaired conidia after 24-h dark incubation but hardly observable at the end of 12-h dark incubation, suggesting an infeasibility of its NER activity in the field where nighttime is too short. Aside from a remarkable contribution to conidial UVB resistance, Rad23 had pleiotropic effect in radial growth, aerial conidiation, antioxidant response, and cell wall integrity but no photoreactivation activity. However, Rad4B proved redundant in function. The high photoreactivation activity of Rad4A unveils its essentiality for M. robertsii's fitness to solar UV irradiation and is distinct from the yeast homolog's anti-UV role depending on NER. IMPORTANCE Resilience of solar ultraviolet (UV)-impaired cells is crucial for the application of fungal insecticides based on formulated conidia. Anti-UV roles of Rad4, Rad23, and Rad33 rely upon nucleotide excision repair (NER) of DNA lesions in budding yeast. Among two Rad4 paralogs and Rad23 ortholog characterized in Metarhizium robertsii lacking Rad33, Rad4A contributes to conidial UVB resistance more than Rad23, which interacts with Rad4A rather than functionally redundant Rad4B. Rad4A acquires a high activity in photoreactivation of conidia severely impaired or inactivated by UVB irradiation through its interaction with Rad10, another anti-UV protein previously proven to interact with a photorepair-required photolyase. The NER activity of either Rad4A or Rad23 is seemingly extant but unfeasible under field conditions. Rad23 has pleiotropic effect in the asexual cycle in vitro but no photoreactivation activity. Therefore, the strong anti-UV role of Rad4A depends on photoreactivation, unveiling a scenario distinct from the yeast homolog's NER-reliant anti-UV role.
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Affiliation(s)
- Yi-Lu Zhang
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Han Peng
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Ke Zhang
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Sheng-Hua Ying
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Ming-Guang Feng
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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12
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Rademacher A, Erdel F, Weinmann R, Rippe K. Assessing the Phase Separation Propensity of Proteins in Living Cells Through Optodroplet Formation. Methods Mol Biol 2023; 2563:395-411. [PMID: 36227485 DOI: 10.1007/978-1-0716-2663-4_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Phase separation is emerging as a key mechanism to describe the formation of membraneless organelles in the cell. It depends on the multivalent (self-) interaction properties of the macromolecules involved and can be observed in aqueous solutions under controlled conditions in vitro with purified components. However, to experimentally demonstrate that this process indeed occurs in the complex environment of living cells remains difficult. Here, we describe an assay based on light-induced association of proteins into complexes termed optodroplets that are in the hundred nm to μm size range. The formation and dissociation of these optodroplets can be followed over time in living cells by fluorescence microscopy to evaluate the propensity of proteins to demix and to form phase-separated subcompartments. The optodroplet assay is based on the fusion of a protein of interest with the photolyase homology region (PHR) protein domain from Arabidopsis thaliana, which can undergo reversible homo-oligomerization upon illumination with blue light. Using this approach, candidate proteins and their interaction-deficient or interaction-enhanced variants can be compared to each other or to reference proteins with known phase separation features. By quantifying the resulting microscopy images, the propensity of a given protein construct to assemble into a phase-separated subcompartment can be assessed.
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Affiliation(s)
- Anne Rademacher
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) and Bioquant, Heidelberg, Germany
| | - Fabian Erdel
- MCD, Centre de Biologie Intégrative (CBI), University of Toulouse, CNRS, Toulouse, France
| | - Robin Weinmann
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) and Bioquant, Heidelberg, Germany
| | - Karsten Rippe
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) and Bioquant, Heidelberg, Germany.
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13
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Shim JG, Cho SG, Kim SH, Chuon K, Meas S, Choi A, Jung KH. Heliorhodopsin Helps Photolyase to Enhance the DNA Repair Capacity. Microbiol Spectr 2022; 10:e0221522. [PMID: 36219103 PMCID: PMC9769723 DOI: 10.1128/spectrum.02215-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 09/24/2022] [Indexed: 01/06/2023] Open
Abstract
Light quality is a significant factor for living organisms that have photosensory systems, such as rhodopsin, a seven alpha-helical transmembrane protein with the retinal chromophore. Here, we report, for the first time, the function of new rhodopsin, which is an inverted 7-transmembrane protein, isolated from Trichococcus flocculiformis. T. flocculiformis heliorhodopsin (TfHeR) works as a regulatory helper rhodopsin that binds with class 2 cyclobutane pyrimidine dimer (CPDII) photolyase to broaden the spectrum and upregulate DNA repair activity. We have confirmed their interaction through isothermal titration calorimetry (dissociation constant of 21.7 μM) and identified the charged residues for the interaction. Based on in vivo and in vitro experiments, we showed that the binding of heliorhodopsin with photolyase improved photolyase activity by about 3-fold to repair UV-caused DNA damage. Also, the DNA repair activity of TfHeR/T. flocculiformis photolyase (TfPHR) was observed in the presence of green light. Our results suggested that heliorhodopsin directly controls the activity of photolyase and coevolves to broaden the activity spectrum by protein-protein interaction. IMPORTANCE This study reports a function for Heliorhodopsin working as a regulatory helper rhodopsin that with CPDII photolyase to broaden the spectrum and upregulating the DNA repair activity. Our results suggested that heliorhodopsin directly controls photolyase activity and coevolves to broaden the DNA repair capacity by protein-protein interaction.
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Affiliation(s)
- Jin-gon Shim
- Department of Life Science, Sogang University, Seoul, South Korea
| | - Shin-Gyu Cho
- Department of Life Science, Sogang University, Seoul, South Korea
- Research Institute for Basic Science, Sogang University, Seoul, South Korea
| | - Se-Hwan Kim
- Department of Life Science, Sogang University, Seoul, South Korea
| | - Kimleng Chuon
- Department of Life Science, Sogang University, Seoul, South Korea
| | - Seanghun Meas
- Department of Life Science, Sogang University, Seoul, South Korea
| | - Ahreum Choi
- Research Center for Endangered Species, National Institute of Ecology, Yeongyang-gun, Gyeongsangbuk-do, South Korea
| | - Kwang-Hwan Jung
- Department of Life Science, Sogang University, Seoul, South Korea
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14
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Qu C, Li N, Liu T, He Y, Miao J. Preparation of CPD Photolyase Nanoliposomes Derived from Antarctic Microalgae and Their Effect on UVB-Induced Skin Damage in Mice. Int J Mol Sci 2022; 23:ijms232315148. [PMID: 36499473 PMCID: PMC9738781 DOI: 10.3390/ijms232315148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 11/24/2022] [Accepted: 11/25/2022] [Indexed: 12/03/2022] Open
Abstract
UVB radiation is known to trigger the block of DNA replication and transcription by forming cyclobutane pyrimidine dimer (CPD), which results in severe skin damage. CPD photolyase, a kind of DNA repair enzyme, can efficiently repair CPDs that are absent in humans and mice. Although exogenous CPD photolyases have beneficial effects on skin diseases, the mechanisms of CPD photolyases on the skin remain unknown. Here, this study prepared CPD photolyase nanoliposomes (CPDNL) from Antarctic Chlamydomonas sp. ICE-L, which thrives in harsh, high-UVB conditions, and evaluated their protective mechanisms against UVB-induced damage in mice. CPDNL were optimized using response surface methodology, characterized by a mean particle size of 105.5 nm, with an encapsulation efficiency of 63.3%. Topical application of CPDNL prevented UVB-induced erythema, epidermal thickness, and wrinkles in mice. CPDNL mitigated UVB-induced DNA damage by significantly decreasing the CPD concentration. CPDNL exhibited antioxidant properties as they reduced the production of reactive oxygen species (ROS) and malondialdehyde. Through activation of the NF-κB pathway, CPDNL reduced the expression of pro-inflammatory cytokines including IL-6, TNF-α, and COX-2. Furthermore, CPDNL suppressed the MAPK signaling activation by downregulating the mRNA and protein expression of ERK, JNK, and p38 as well as AP-1. The MMP-1 and MMP-2 expressions were also remarkably decreased, which inhibited the collagen degradation. Therefore, we concluded that CPDNL exerted DNA repair, antioxidant, anti-inflammation, and anti-wrinkle properties as well as collagen protection via regulation of the NF-κB/MAPK/MMP signaling pathways in UVB-induced mice, demonstrating that Antarctic CPD photolyases have the potential for skincare products against UVB and photoaging.
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Affiliation(s)
- Changfeng Qu
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao 266061, China
- Laboratory for Marine Drugs and Bioproducts, Qingdao Pilot National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Marine Natural Products Research and Development Laboratory, Qingdao Key Laboratory, Qingdao 266061, China
| | - Nianxu Li
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao 266061, China
| | - Tianlong Liu
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao 266061, China
| | - Yingying He
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao 266061, China
| | - Jinlai Miao
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao 266061, China
- Laboratory for Marine Drugs and Bioproducts, Qingdao Pilot National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Marine Natural Products Research and Development Laboratory, Qingdao Key Laboratory, Qingdao 266061, China
- Correspondence: ; Tel.: +86-532-88967430
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15
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Acosta S, Canclini L, Marizcurrena JJ, Castro-Sowinski S, Hernández P. Photo-repair effect of a bacterial Antarctic CPD-photolyase on UVC-induced DNA lesions in human keratinocytes. Environ Toxicol Pharmacol 2022; 96:104001. [PMID: 36273708 DOI: 10.1016/j.etap.2022.104001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 09/30/2022] [Accepted: 10/18/2022] [Indexed: 06/16/2023]
Abstract
Exposure to ultraviolet radiation from sunlight induces oxidative DNA lesions and bipyrimidine photoproducts that can lead to photo-aging and skin carcinogenesis. CPD-photolyases are flavoproteins that repair cyclobutane pyrimidine dimers using blue light as an energy source. In the present work, we evaluated the photo-repair effect of the recombinant CPD-photolyase PhrAHym from the Antarctic bacterium Hymenobacter sp. UV11 on DNA lesions in human keratinocytes induced by UVC light. By performing immunochemistry assays we observed that PhrAHym repairs in a highly efficient way the CPD-photoproducts and reduces the γH2AX formation. Since this enzyme is non-cytotoxic and repairs UVC-induced DNA lesions in human keratinocytes, we propose that PhrAHym could be used as a biotherapeutic agent against UV-induced skin cancer, photoaging, and related diseases.
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Affiliation(s)
- Silvina Acosta
- Departamento de Genética, Instituto de Investigaciones Biológicas Clemente Estable, Avenida Italia 3318, Montevideo 11600, Uruguay
| | - Lucía Canclini
- Departamento de Genética, Instituto de Investigaciones Biológicas Clemente Estable, Avenida Italia 3318, Montevideo 11600, Uruguay
| | - Juan José Marizcurrena
- Sección Bioquímica, Facultad de Ciencias, Universidad de la República, Iguá 4225, Montevideo 11400, Uruguay
| | - Susana Castro-Sowinski
- Sección Bioquímica, Facultad de Ciencias, Universidad de la República, Iguá 4225, Montevideo 11400, Uruguay; Laboratorio de Microbiología Molecular, Instituto de Investigaciones Biológicas Clemente Estable, Avenida Italia 3318, Montevideo 11600, Uruguay
| | - Paola Hernández
- Departamento de Genética, Instituto de Investigaciones Biológicas Clemente Estable, Avenida Italia 3318, Montevideo 11600, Uruguay.
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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: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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Deppisch P, Helfrich-Förster C, Senthilan PR. The Gain and Loss of Cryptochrome/Photolyase Family Members during Evolution. Genes (Basel) 2022; 13:genes13091613. [PMID: 36140781 PMCID: PMC9498864 DOI: 10.3390/genes13091613] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 09/02/2022] [Accepted: 09/05/2022] [Indexed: 11/20/2022] Open
Abstract
The cryptochrome/photolyase (CRY/PL) family represents an ancient group of proteins fulfilling two fundamental functions. While photolyases repair UV-induced DNA damages, cryptochromes mainly influence the circadian clock. In this study, we took advantage of the large number of already sequenced and annotated genes available in databases and systematically searched for the protein sequences of CRY/PL family members in all taxonomic groups primarily focusing on metazoans and limiting the number of species per taxonomic order to five. Using BLASTP searches and subsequent phylogenetic tree and motif analyses, we identified five distinct photolyases (CPDI, CPDII, CPDIII, 6-4 photolyase, and the plant photolyase PPL) and six cryptochrome subfamilies (DASH-CRY, mammalian-type MCRY, Drosophila-type DCRY, cnidarian-specific ACRY, plant-specific PCRY, and the putative magnetoreceptor CRY4. Manually assigning the CRY/PL subfamilies to the species studied, we have noted that over evolutionary history, an initial increase of various CRY/PL subfamilies was followed by a decrease and specialization. Thus, in more primitive organisms (e.g., bacteria, archaea, simple eukaryotes, and in basal metazoans), we find relatively few CRY/PL members. As species become more evolved (e.g., cnidarians, mollusks, echinoderms, etc.), the CRY/PL repertoire also increases, whereas it appears to decrease again in more recent organisms (humans, fruit flies, etc.). Moreover, our study indicates that all cryptochromes, although largely active in the circadian clock, arose independently from different photolyases, explaining their different modes of action.
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Cellini A, Shankar MK, Wahlgren WY, Nimmrich A, Furrer A, James D, Wranik M, Aumonier S, Beale EV, Dworkowski F, Standfuss J, Weinert T, Westenhoff S. Structural basis of the radical pair state in photolyases and cryptochromes. Chem Commun (Camb) 2022; 58:4889-4892. [PMID: 35352724 PMCID: PMC9008703 DOI: 10.1039/d2cc00376g] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We present the structure of a photoactivated animal (6-4) photolyase in its radical pair state, captured by serial crystallography. We observe how a conserved asparigine moves towards the semiquinone FAD chromophore and stabilizes it by hydrogen bonding. Several amino acids around the final tryptophan radical rearrange, opening it up to the solvent. The structure explains how the protein environment stabilizes the radical pair state, which is crucial for function of (6-4) photolyases and cryptochromes. The structural response of the drosophila (6-4) photolyase to photoinduced electron transfer along a chain of tryptophans is revealed using a serial crystallographic snapshot of the protein in its radical pair state.![]()
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Affiliation(s)
- Andrea Cellini
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden.
| | - Madan Kumar Shankar
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden.
| | - Weixiao Yuan Wahlgren
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden.
| | - Amke Nimmrich
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden.
| | - Antonia Furrer
- Division of Biology and Chemistry-Laboratory for Biomolecular Research, Paul Scherrer Institut, 5232 Villigen, Switzerland
| | - Daniel James
- Division of Biology and Chemistry-Laboratory for Biomolecular Research, Paul Scherrer Institut, 5232 Villigen, Switzerland
| | - Maximilian Wranik
- Division of Biology and Chemistry-Laboratory for Biomolecular Research, Paul Scherrer Institut, 5232 Villigen, Switzerland
| | - Sylvain Aumonier
- Photon Science Division - Laboratory for Macromolecules and Bioimaging (LSB), Paul Scherrer Institut, 5232 Villigen, Switzerland
| | - Emma V Beale
- Photon Science Division - Laboratory for Synchrotron Radiation and Femtochemistry (LSF), Paul Scherrer Institut, 5232 Villigen, Switzerland
| | - Florian Dworkowski
- Photon Science Division - Laboratory for Macromolecules and Bioimaging (LSB), Paul Scherrer Institut, 5232 Villigen, Switzerland
| | - Jörg Standfuss
- Division of Biology and Chemistry-Laboratory for Biomolecular Research, Paul Scherrer Institut, 5232 Villigen, Switzerland
| | - Tobias Weinert
- Division of Biology and Chemistry-Laboratory for Biomolecular Research, Paul Scherrer Institut, 5232 Villigen, Switzerland
| | - Sebastian Westenhoff
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden.
- Department of Chemistry-BMC, University of Uppsala, Husargatan 3, 75237 Uppsala, Sweden
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19
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Wang H, Liu H, Yu Q, Fan F, Liu S, Feng G, Zhang P. A CPD photolyase gene PnPHR1 from Antarctic moss Pohlia nutans is involved in the resistance to UV-B radiation and salinity stress. Plant Physiol Biochem 2021; 167:235-244. [PMID: 34385002 DOI: 10.1016/j.plaphy.2021.08.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 07/05/2021] [Accepted: 08/05/2021] [Indexed: 05/24/2023]
Abstract
In Antarctic continent, the organisms are exposed to high ultraviolet (UV) radiation because of damaged stratospheric ozone. UV causes DNA lesions due to the accumulation of photoproducts. Photolyase can repair UV-damaged DNA in a light-dependent process by electron transfer mechanism. Here, we isolated a CPD photolyase gene PnPHR1 from Antarctic moss Pohlia nutans, which encodes a protein of theoretical molecular weight of 69.1 KDa. The expression level of PnPHR1 was increased by UV-B irradiation. Enzyme activity assay in vitro showed that PnPHR1 exhibited photoreactivation activity, which can repair CPD photoproducts in a light-dependent manner. The complementation assay of repair-deficient E. coli strain SY2 demonstrated that PnPHR1 gene enhanced the survival rate of SY2 strain after UV-B radiation. Additionally, overexpression of PnPHR1 enhanced the Arabidopsis resistance to UV-B radiation and salinity stress, which also conferred plant tolerance to oxidative stress by decreasing ROS production and increasing ROS clearance. Our work shows that PnPHR1 encodes an active CPD photolyase, which may participate in the adaptation of P. nutans to polar environments.
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Affiliation(s)
- Huijuan Wang
- National Glycoengineering Research Center and School of Life Science, Shandong University, Qingdao, 266237, China
| | - Hongwei Liu
- National Glycoengineering Research Center and School of Life Science, Shandong University, Qingdao, 266237, China; Medical Administration Department, Shinan District Health Bureau, Qingdao, 266073, China
| | - Qian Yu
- National Glycoengineering Research Center and School of Life Science, Shandong University, Qingdao, 266237, China
| | - Fenghua Fan
- National Glycoengineering Research Center and School of Life Science, Shandong University, Qingdao, 266237, China
| | - Shenghao Liu
- Marine Ecology Research Center, First Institute of Oceanography, Natural Resources Ministry, Qingdao, 266061, China
| | - Guihua Feng
- National Glycoengineering Research Center and School of Life Science, Shandong University, Qingdao, 266237, China
| | - Pengying Zhang
- National Glycoengineering Research Center and School of Life Science, Shandong University, Qingdao, 266237, China.
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20
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Cellini A, Yuan Wahlgren W, Henry L, Pandey S, Ghosh S, Castillon L, Claesson E, Takala H, Kübel J, Nimmrich A, Kuznetsova V, Nango E, Iwata S, Owada S, Stojković EA, Schmidt M, Ihalainen JA, Westenhoff S. The three-dimensional structure of Drosophila melanogaster (6-4) photolyase at room temperature. Acta Crystallogr D Struct Biol 2021; 77:1001-1009. [PMID: 34342273 PMCID: PMC8329860 DOI: 10.1107/s2059798321005830] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 06/06/2021] [Indexed: 11/10/2022] Open
Abstract
(6-4) photolyases are flavoproteins that belong to the photolyase/cryptochrome family. Their function is to repair DNA lesions using visible light. Here, crystal structures of Drosophila melanogaster (6-4) photolyase [Dm(6-4)photolyase] at room and cryogenic temperatures are reported. The room-temperature structure was solved to 2.27 Å resolution and was obtained by serial femtosecond crystallography (SFX) using an X-ray free-electron laser. The crystallization and preparation conditions are also reported. The cryogenic structure was solved to 1.79 Å resolution using conventional X-ray crystallography. The structures agree with each other, indicating that the structural information obtained from crystallography at cryogenic temperature also applies at room temperature. Furthermore, UV-Vis absorption spectroscopy confirms that Dm(6-4)photolyase is photoactive in the crystals, giving a green light to time-resolved SFX studies on the protein, which can reveal the structural mechanism of the photoactivated protein in DNA repair.
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Affiliation(s)
- Andrea Cellini
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 405 30 Gothenburg, Sweden
| | - Weixiao Yuan Wahlgren
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 405 30 Gothenburg, Sweden
| | - Léocadie Henry
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 405 30 Gothenburg, Sweden
| | - Suraj Pandey
- Physics Department, University of Wisconsin-Milwaukee, 3135 North Maryland Avenue, Milwaukee, WI 53211, USA
| | - Swagatha Ghosh
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 405 30 Gothenburg, Sweden
| | - Leticia Castillon
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 405 30 Gothenburg, Sweden
| | - Elin Claesson
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 405 30 Gothenburg, Sweden
| | - Heikki Takala
- Department of Biological and Environmental Science, Nanoscience Center, University of Jyvaskyla, 40014 Jyvaskyla, Finland
- Department of Anatomy, Faculty of Medicine, University of Helsinki, Box 63, 00014 Helsinki, Finland
| | - Joachim Kübel
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 405 30 Gothenburg, Sweden
| | - Amke Nimmrich
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 405 30 Gothenburg, Sweden
| | - Valentyna Kuznetsova
- Department of Biological and Environmental Science, Nanoscience Center, University of Jyvaskyla, 40014 Jyvaskyla, Finland
| | - Eriko Nango
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577, Japan
| | - So Iwata
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Shigeki Owada
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Emina A. Stojković
- Department of Biology, Northeastern Illinois University, 5500 North St Louis Avenue, Chicago, IL 60625, USA
| | - Marius Schmidt
- Physics Department, University of Wisconsin-Milwaukee, 3135 North Maryland Avenue, Milwaukee, WI 53211, USA
| | - Janne A. Ihalainen
- Department of Biological and Environmental Science, Nanoscience Center, University of Jyvaskyla, 40014 Jyvaskyla, Finland
| | - Sebastian Westenhoff
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 405 30 Gothenburg, Sweden
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21
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Pehlivanoglu B, Aysal A, Demir Kececi S, Ekmekci S, Erdogdu IH, Ertunc O, Gundogdu B, Kelten Talu C, Sahin Y, Toper MH. A Nobel-Winning Scientist: Aziz Sancar and the Impact of his Work on the Molecular Pathology of Neoplastic Diseases. Turk Patoloji Derg 2021; 37:93-105. [PMID: 33973640 PMCID: PMC10512686 DOI: 10.5146/tjpath.2020.01504] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 08/14/2020] [Indexed: 11/18/2022] Open
Abstract
Aziz Sancar, Nobel Prize winning Turkish scientist, made several discoveries which had a major impact on molecular sciences, particularly disciplines that focus on carcinogenesis and cancer treatment, including molecular pathology. Cloning the photolyase gene, which was the initial step of his work on DNA repair mechanisms, discovery of the "Maxicell" method, explanation of the mechanism of nucleotide excision repair and transcription-coupled repair, discovery of "molecular matchmakers", and mapping human excision repair genes at single nucleotide resolution constitute his major research topics. Moreover, Sancar discovered the cryptochromes, the clock genes in humans, in 1998, and this discovery led to substantial progress in the understanding of the circadian clock and the introduction of the concept of "chrono-chemoterapy" for more effective therapy in cancer patients. This review focuses on Aziz Sancar's scientific studies and their reflections on molecular pathology of neoplastic diseases. While providing a new perspective for researchers working in the field of pathology and molecular pathology, this review is also an evidence of how basic sciences and clinical sciences complete each other.
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Affiliation(s)
- Burcin Pehlivanoglu
- Department of Molecular Pathology, Dokuz Eylul University, Graduate School of Health Sciences, Izmir, Turkey
| | - Anil Aysal
- Department of Molecular Pathology, Dokuz Eylul University, Graduate School of Health Sciences, Izmir, Turkey
| | - Sibel Demir Kececi
- Department of Molecular Pathology, Dokuz Eylul University, Graduate School of Health Sciences, Izmir, Turkey
| | - Sumeyye Ekmekci
- Department of Molecular Pathology, Dokuz Eylul University, Graduate School of Health Sciences, Izmir, Turkey
| | - Ibrahim Halil Erdogdu
- Department of Molecular Pathology, Dokuz Eylul University, Graduate School of Health Sciences, Izmir, Turkey
| | - Onur Ertunc
- Department of Molecular Pathology, Dokuz Eylul University, Graduate School of Health Sciences, Izmir, Turkey
| | - Betul Gundogdu
- Department of Molecular Pathology, Dokuz Eylul University, Graduate School of Health Sciences, Izmir, Turkey
| | - Canan Kelten Talu
- Department of Molecular Pathology, Dokuz Eylul University, Graduate School of Health Sciences, Izmir, Turkey
| | - Yasemin Sahin
- Department of Molecular Pathology, Dokuz Eylul University, Graduate School of Health Sciences, Izmir, Turkey
| | - Muhammed Hasan Toper
- Department of Molecular Pathology, Dokuz Eylul University, Graduate School of Health Sciences, Izmir, Turkey
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22
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Banaś AK, Zgłobicki P, Kowalska E, Bażant A, Dziga D, Strzałka W. All You Need Is Light. Photorepair of UV-Induced Pyrimidine Dimers. Genes (Basel) 2020; 11:E1304. [PMID: 33158066 PMCID: PMC7694213 DOI: 10.3390/genes11111304] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 10/27/2020] [Accepted: 10/27/2020] [Indexed: 12/18/2022] Open
Abstract
Although solar light is indispensable for the functioning of plants, this environmental factor may also cause damage to living cells. Apart from the visible range, including wavelengths used in photosynthesis, the ultraviolet (UV) light present in solar irradiation reaches the Earth's surface. The high energy of UV causes damage to many cellular components, with DNA as one of the targets. Putting together the puzzle-like elements responsible for the repair of UV-induced DNA damage is of special importance in understanding how plants ensure the stability of their genomes between generations. In this review, we have presented the information on DNA damage produced under UV with a special focus on the pyrimidine dimers formed between the neighboring pyrimidines in a DNA strand. These dimers are highly mutagenic and cytotoxic, thus their repair is essential for the maintenance of suitable genetic information. In prokaryotic and eukaryotic cells, with the exception of placental mammals, this is achieved by means of highly efficient photorepair, dependent on blue/UVA light, which is performed by specialized enzymes known as photolyases. Photolyase properties, as well as their structure, specificity and action mechanism, have been briefly discussed in this paper. Additionally, the main gaps in our knowledge on the functioning of light repair in plant organelles, its regulation and its interaction between different DNA repair systems in plants have been highlighted.
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Affiliation(s)
- Agnieszka Katarzyna Banaś
- Department of Plant Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland; (A.K.B.); (P.Z.); (E.K.); (A.B.)
| | - Piotr Zgłobicki
- Department of Plant Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland; (A.K.B.); (P.Z.); (E.K.); (A.B.)
| | - Ewa Kowalska
- Department of Plant Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland; (A.K.B.); (P.Z.); (E.K.); (A.B.)
| | - Aneta Bażant
- Department of Plant Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland; (A.K.B.); (P.Z.); (E.K.); (A.B.)
| | - Dariusz Dziga
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland;
| | - Wojciech Strzałka
- Department of Plant Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland; (A.K.B.); (P.Z.); (E.K.); (A.B.)
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23
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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24
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Ma H, Holub D, Gillet N, Kaeser G, Thoulass K, Elstner M, Krauß N, Lamparter T. Two aspartate residues close to the lesion binding site of Agrobacterium (6-4) photolyase are required for Mg 2+ stimulation of DNA repair. FEBS J 2019; 286:1765-1779. [PMID: 30706696 DOI: 10.1111/febs.14770] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 12/05/2018] [Accepted: 01/28/2019] [Indexed: 12/25/2022]
Abstract
Prokaryotic (6-4) photolyases branch at the base of the evolution of cryptochromes and photolyases. Prototypical members contain an iron-sulphur cluster which was lost in the evolution of the other groups. In the Agrobacterium (6-4) photolyase PhrB, the repair of DNA lesions containing UV-induced (6-4) pyrimidine dimers is stimulated by Mg2+ . We propose that Mg2+ is required for efficient lesion binding and for charge stabilization after electron transfer from the FADH- chromophore to the DNA lesion. Furthermore, two highly conserved Asp residues close to the DNA-binding site are essential for the effect of Mg2+ . Simulations show that two Mg2+ bind to the region around these residues. On the other hand, DNA repair by eukaryotic (6-4) photolyases is not increased by Mg2+ . In these photolyases, structurally overlapping regions contain no Asp but positively charged Lys or Arg. During the evolution of photolyases, the role of Mg2+ in charge stabilization and enhancement of DNA binding was therefore taken over by a postiviely charged amino acid. Besides PhrB, another prokaryotic (6-4) photolyase from the marine cyanobacterium Prochlorococcus marinus, PromaPL, which contains no iron-sulphur cluster, was also investigated. This photolyase is stimulated by Mg2+ as well. The evolutionary loss of the iron-sulphur cluster due to limiting iron concentrations can occur in a marine environment as a result of iron deprivation. However, the evolutionary replacement of Mg2+ by a positively charged amino acid is unlikely to occur in a marine environment because the concentration of divalent cations in seawater is always sufficient. We therefore assume that this transition could have occurred in a freshwater environment.
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Affiliation(s)
- Hongju Ma
- Botanical Institute, Karlsruhe Institute of Technology, Germany
| | - Daniel Holub
- Department for Theoretical Chemical Biology, Institute for Physical Chemistry, Karlsruhe Institute for Technology, Germany
| | - Natacha Gillet
- Department for Theoretical Chemical Biology, Institute for Physical Chemistry, Karlsruhe Institute for Technology, Germany
| | - Gero Kaeser
- Botanical Institute, Karlsruhe Institute of Technology, Germany
| | | | - Marcus Elstner
- Department for Theoretical Chemical Biology, Institute for Physical Chemistry, Karlsruhe Institute for Technology, Germany
| | - Norbert Krauß
- Botanical Institute, Karlsruhe Institute of Technology, Germany
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25
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Abstract
Short-range electron-transfer (ET) reactions in biological systems are usually ultrafast, having transfer rates comparable to or even faster than corresponding environmental fluctuations, and often display nonexponential behaviors. To understand these nonequilibrium ET dynamics, we carried out detailed theoretical analyses based on the Sumi-Marcus model. It is shown that the ET dynamics is largely determined by the relative time scales of the ET reaction and its surrounding motions. Significantly, different environmental fluctuations can produce a variety of apparent ET dynamics even with the same driving force, Δ Go, and reorganization energy, λ. We applied our analyses to an ultrafast ET process in DNA repair by (6-4) photolyase and directly obtained the inner and outer reorganization energies (λi and λo) as well as the free energy Δ Go of various mutants, providing mechanical insight into ultrafast short-range ET reactions in proteins.
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Affiliation(s)
- Yangyi Lu
- Department of Physics, Department of Chemistry and Biochemistry, Programs of Biophysics, Chemical Physics, and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Dongping Zhong
- Department of Physics, Department of Chemistry and Biochemistry, Programs of Biophysics, Chemical Physics, and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
- Center for Ultrafast Science and Technology, School of Chemistry and Chemical Engineering, School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai 200240, China
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26
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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. J Plant Physiol 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] [What about the content of this article? (0)] [Affiliation(s)] [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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27
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König S, Juhas M, Jäger S, Kottke T, Büchel C. The cryptochrome-photolyase protein family in diatoms. J Plant Physiol 2017; 217:15-19. [PMID: 28720252 DOI: 10.1016/j.jplph.2017.06.015] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 06/28/2017] [Accepted: 06/29/2017] [Indexed: 06/07/2023]
Abstract
The cryptochrome - photolyase family (CPF) consists of homologous flavoproteins having completely different functions involving DNA repair, circadian rhythm and/or photoreception. From the original photolyases, working either as (6-4) or cyclobutane pyrimidine dimer photolyases, the animal- and plant-type cryptochromes, respectively, evolved and also the more intermediate DASH cryptochromes. Whereas animal cryptochromes work mostly in clock-related functions, plant cryptochromes are also directly involved in developmental processes such as hypocotyl elongation or flower induction. In diatoms, all types of cryptochromes and photolyases were predicted from genome sequences. However, up to now only two proteins have been characterised in more detail, CPF1 and CryP. CPF1 is related to animal-type cryptochromes, but works as a (6-4) photolyase in addition to having photoreceptor functions. It was shown to interact with the CLOCK:Bmal1 heterodimer in a heterologous system, and thus is probably involved in clock-related processes. Moreover, CPF1 directly influences transcription. The latter was also true for CryP, which is a cryptochrome distantly related to plant-type cryptochromes. In addition, CryP influences light-harvesting protein accumulation. For all diatom cryptochromes, down-stream signalling has to proceed via interaction partners different from the classical proteins involved in cryptochrome signalling in higher plants, because these candidates are missing in diatoms.
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Affiliation(s)
- Sarah König
- Institute of Molecular Biosciences, Goethe University Frankfurt, 60438 Frankfurt, Germany
| | - Matthias Juhas
- Institute of Molecular Biosciences, Goethe University Frankfurt, 60438 Frankfurt, Germany
| | - Stefanie Jäger
- Institute of Molecular Biosciences, Goethe University Frankfurt, 60438 Frankfurt, Germany
| | - Tilman Kottke
- Physical and Biophysical Chemistry, Bielefeld University, 33615 Bielefeld, Germany
| | - Claudia Büchel
- Institute of Molecular Biosciences, Goethe University Frankfurt, 60438 Frankfurt, Germany.
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Cohrs KC, Schumacher J. The Two Cryptochrome/Photolyase Family Proteins Fulfill Distinct Roles in DNA Photorepair and Regulation of Conidiation in the Gray Mold Fungus Botrytis cinerea. Appl Environ Microbiol 2017; 83:e00812-17. [PMID: 28667107 PMCID: PMC5561282 DOI: 10.1128/aem.00812-17] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 06/24/2017] [Indexed: 12/13/2022] Open
Abstract
The plant-pathogenic leotiomycete Botrytis cinerea is known for the strict regulation of its asexual differentiation programs by environmental light conditions. Sclerotia are formed in constant darkness; black/near-UV (NUV) light induces conidiation; and blue light represses both differentiation programs. Sensing of black/NUV light is attributed to proteins of the cryptochrome/photolyase family (CPF). To elucidate the molecular basis of the photoinduction of conidiation, we functionally characterized the two CPF proteins encoded in the genome of B. cinerea as putative positive-acting components. B. cinerea CRY1 (BcCRY1), a cyclobutane pyrimidine dimer (CPD) photolyase, acts as the major enzyme of light-driven DNA repair (photoreactivation) and has no obvious role in signaling. In contrast, BcCRY2, belonging to the cry-DASH proteins, is dispensable for photorepair but performs regulatory functions by repressing conidiation in white and especially black/NUV light. The transcription of bccry1 and bccry2 is induced by light in a White Collar complex (WCC)-dependent manner, but neither light nor the WCC is essential for the repression of conidiation through BcCRY2 when bccry2 is constitutively expressed. Further, BcCRY2 affects the transcript levels of both WCC-induced and WCC-repressed genes, suggesting a signaling function downstream of the WCC. Since both CPF proteins are dispensable for photoinduction by black/NUV light, the origin of this effect remains elusive and may be connected to a yet unknown UV-light-responsive system.IMPORTANCEBotrytis cinerea is an economically important plant pathogen that causes gray mold diseases in a wide variety of plant species, including high-value crops and ornamental flowers. The spread of disease in the field relies on the formation of conidia, a process that is regulated by different light qualities. While this feature has been known for a long time, we are just starting to understand the underlying molecular mechanisms. Conidiation in B. cinerea is induced by black/near-UV light, whose sensing is attributed to the action of cryptochrome/photolyase family (CPF) proteins. Here we report on the distinct functions of two CPF proteins in the photoresponse of B. cinerea While BcCRY1 acts as the major photolyase in photoprotection, BcCRY2 acts as a cryptochrome with a signaling function in regulating photomorphogenesis (repression of conidiation).
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Affiliation(s)
- Kim C Cohrs
- Institut für Biologie und Biotechnologie der Pflanzen (IBBP), Westfälische Wilhelms-Universität (WWU), Münster, Germany
| | - Julia Schumacher
- Institut für Biologie und Biotechnologie der Pflanzen (IBBP), Westfälische Wilhelms-Universität (WWU), Münster, Germany
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29
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Murata Y, Osakabe M. Photo-enzymatic repair of UVB-induced DNA damage in the two-spotted spider mite Tetranychus urticae. Exp Appl Acarol 2017; 71:15-34. [PMID: 27873138 DOI: 10.1007/s10493-016-0100-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 11/10/2016] [Indexed: 06/06/2023]
Abstract
Ambient ultraviolet-B (UVB) radiation induces lethal effects in the two-spotted spider mite Tetranychus urticae, whereas photoreactivation by irradiation with ultraviolet-A and visible light (VIS) plays an important role to increase survival of mites irradiated by UVB. The physiological mechanisms and ecological significance of photoreactivation in terrestrial arthropods have not been shown clearly. We verified the biological impact and accumulation of DNA lesions by UVB irradiation and the repair of them by photoreactivation in T. urticae larvae. Survival of UVB-irradiated larvae decreased with increasing UVB dose, but recovered remarkably with VIS exposure after UVB irradiation (photoreactivation). The DNA lesions, cyclobutane pyrimidine dimers (CPDs) and 6-4 pyrimidine-pyrimidine photoproducts (6-4PPs) linearly increased with the UVB dose. The CPDs were repaired after exposure to VIS, whereas the frequency of 6-4PPs was unaffected by VIS; CPD photolyase genes, but not (6-4) photolyase genes, have been found in the T. urticae genome. Therefore, DNA damage and CPD photo enzymatic repair (PER) is significant for survival in this mite under ambient UVB radiation. Unexpectedly, gene expression of CPD photolyase was unaffected by irradiation with UVB and VIS. Instead, expression of xeroderma pigmentosum A (XPA) was increased by irradiation. XPA is a core factor in nucleotide excision repair (NER), which is a repair system unrelated to photo energy. The relationship between gene expression and enzymatic repair remains unclear. To elucidate the PER process in T. urticae, further study will be necessary on the gene expression patterns and molecular functions of CPD photolyase in PER and of XPA in NER.
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Affiliation(s)
- Yasumasa Murata
- Laboratory of Ecological Information, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan.
| | - Masahiro Osakabe
- Laboratory of Ecological Information, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan
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30
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Manova V, Georgieva R, Borisov B, Stoilov L. Efficient removal of cyclobutane pyrimidine dimers in barley: differential contribution of light-dependent and dark DNA repair pathways. Physiol Plant 2016; 158:236-253. [PMID: 27021252 DOI: 10.1111/ppl.12446] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Revised: 02/02/2016] [Accepted: 02/18/2016] [Indexed: 06/05/2023]
Abstract
Barley stress response to ultraviolet radiation (UV) has been intensively studied at both the physiological and morphological level. However, the ability of barley genome to repair UV-induced lesions at the DNA level is far less characterized. In this study, we have investigated the relative contribution of light-dependent and dark DNA repair pathways for the efficient elimination of cyclobutane pyrimidine dimers (CPDs) from the genomic DNA of barley leaf seedlings. The transcriptional activity of barley CPD photolyase gene in respect to the light-growth conditions and UV-C irradiation of the plants has also been analyzed. Our results show that CPDs induced in the primary barley leaf at frequencies potentially damaging DNA at the single-gene level are removed efficiently and exclusively by photorepair pathway, whereas dark repair is hardly detectable, even at higher CPD frequency. A decrease of initially induced CPDs under dark is observed but only after prolonged incubation, suggesting the activation of light-independent DNA damage repair and/or tolerance mechanisms. The green barley seedlings possess greater capacity for CPD photorepair than the etiolated ones, with efficiency of CPD removal dependent on the intensity and quality of recovering light. The higher repair rate of CPDs measured in the green leaves correlates with the higher transcriptional activity of barley CPD photolyase gene. Visible light and UV-C radiation affect differentially the expression of CPD photolyase gene particularly in the etiolated leaves. We propose that the CPD repair potential of barley young seedlings may influence their response to UV-stress.
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Affiliation(s)
- Vasilissa Manova
- Department of Molecular Genetics, Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, Sofia, 1113, Bulgaria.
| | - Ralitsa Georgieva
- Department of Molecular Genetics, Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, Sofia, 1113, Bulgaria
| | - Borislav Borisov
- Department of Molecular Genetics, Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, Sofia, 1113, Bulgaria
- National Bank for Industrial Microorganisms and Cell Cultures, Sofia, 1756, Bulgaria
| | - Lubomir Stoilov
- Department of Molecular Genetics, Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, Sofia, 1113, Bulgaria
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Faraji S, Zhong D, Dreuw A. Characterization of the Intermediate in and Identification of the Repair Mechanism of (6-4) Photolesions by Photolyases. Angew Chem Int Ed Engl 2016; 55:5175-8. [PMID: 26996356 PMCID: PMC4921128 DOI: 10.1002/anie.201511950] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2015] [Revised: 01/27/2016] [Indexed: 11/09/2022]
Abstract
Quantum mechanics/molecular mechanics calculations are employed to assign previously recorded experimental spectroscopic signatures of the intermediates occurring during the photo-induced repair of (6-4) photolesions by photolyases to specific molecular structures. Based on this close comparison of experiment and theory it is demonstrated that the acting repair mechanism involves proton transfer from the protonated His365 to the N3' nitrogen of the lesion, which proceeds simultaneously with intramolecular OH transfer along an oxetane-like transition state.
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Affiliation(s)
- Shirin Faraji
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls Heidelberg University, Im Neuenheimer Feld 368, 69120 Heidelberg, Germany
| | - Dongping Zhong
- Departments of Physics, Department of Chemistry and Biochemistry, and Programs of Biophysics, Chemical Physics and Biochemistry, The Ohio State University, Columbus Ohio 43210, USA,
| | - Andreas Dreuw
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls Heidelberg University, Im Neuenheimer Feld 368, 69120 Heidelberg, Germany,
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Li N, Teranishi M, Yamaguchi H, Matsushita T, Watahiki MK, Tsuge T, Li SS, Hidema J. UV-B-Induced CPD Photolyase Gene Expression is Regulated by UVR8-Dependent and -Independent Pathways in Arabidopsis. Plant Cell Physiol 2015; 56:2014-23. [PMID: 26272552 DOI: 10.1093/pcp/pcv121] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Accepted: 08/09/2015] [Indexed: 05/21/2023]
Abstract
Plants have evolved various mechanisms that protect against the harmful effects of UV-B radiation (280-315 nm) on growth and development. Cyclobutane pyrimidine dimer (CPD) photolyase, the repair enzyme for UV-B-induced CPDs, is essential for protecting cells from UV-B radiation. Expression of the CPD photolyase gene (PHR) is controlled by light with various wavelengths including UV-B, but the mechanisms of this regulation remain poorly understood. In this study, we investigated the regulation of PHR expression by light with various wavelengths, in particular low-fluence UV-B radiation (280 nm, 0.2 µmol m(-2) s(-1)), in Arabidopsis thaliana seedlings grown under light-dark cycles for 7 d and then adapted to the dark for 3 d. Low-fluence UV-B radiation induced CPDs but not reactive oxygen species. AtPHR expression was effectively induced by UV-B, UV-A (375 nm) and blue light. Expression induced by UV-A and blue light was predominantly regulated by the cryptochrome-dependent pathway, whereas phytochromes A and B played a minor but noticeable role. Expression induced by UV-B was predominantly regulated by the UVR8-dependent pathway. AtPHR expression was also mediated by a UVR8-independent pathway, which is correlated with CPD accumulation induced by UV-B radiation. These results indicate that Arabidopsis has evolved diverse mechanisms to regulate CPD photolyase expression by multiple photoreceptor signaling pathways, including UVR8-dependent and -independent pathways, as protection against harmful effects of UV-B radiation.
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Affiliation(s)
- Nan Li
- Graduate School of Life Sciences, Tohoku University, Sendai, 980-8577 Japan
| | - Mika Teranishi
- Graduate School of Life Sciences, Tohoku University, Sendai, 980-8577 Japan
| | - Hiroko Yamaguchi
- Graduate School of Life Sciences, Tohoku University, Sendai, 980-8577 Japan
| | - Tomonao Matsushita
- Faculty of Agriculture, Kyushu University, Fukuoka, 812-8581 Japan PRESTO, JST, Saitama, 332-0012 Japan
| | - Masaaki K Watahiki
- Division of Biological Sciences, Faculty of Science, Hokkaido University, Sapporo, 060-0810 Japan
| | - Tomohiko Tsuge
- Institute for Chemical Research, Kyoto University, Uji, 611-0011 Japan
| | - Shao-Shan Li
- Key Laboratory of Ecology and Environmental Science in Guangdong Higher Education, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Jun Hidema
- Graduate School of Life Sciences, Tohoku University, Sendai, 980-8577 Japan
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Abstract
BACKGROUND Photolyases and cryptochromes are evolutionarily related flavoproteins, which however perform distinct physiological functions. Photolyases (PHR) are evolutionarily ancient enzymes. They are activated by light and repair DNA damage caused by UV radiation. Although cryptochromes share structural similarity with DNA photolyases, they lack DNA repair activity. Cryptochrome (CRY) is one of the key elements of the circadian system in animals. In plants, CRY acts as a blue light receptor to entrain circadian rhythms, and mediates a variety of light responses, such as the regulation of flowering and seedling growth. RESULTS We performed a comprehensive evolutionary analysis of the CRY/PHR superfamily. The superfamily consists of 7 major subfamilies: CPD class I and CPD class II photolyases, (6-4) photolyases, CRY-DASH, plant PHR2, plant CRY and animal CRY. Although the whole superfamily evolved primarily under strong purifying selection (average ω = 0.0168), some subfamilies did experience strong episodic positive selection during their evolution. Photolyases were lost in higher animals that suggests natural selection apparently became weaker in the late stage of evolutionary history. The evolutionary time estimates suggested that plant and animal CRYs evolved in the Neoproterozoic Era (~1000-541 Mya), which might be a result of adaptation to the major climate and global light regime changes occurred in that period of the Earth's geological history.
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Affiliation(s)
- Qiming Mei
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, People’s Republic of China
| | - Volodymyr Dvornyk
- School of Biological Sciences, the University of Hong Kong, Pokfulam Rd., Hong Kong SAR, People’s Republic of China
- Department of Life Sciences, College of Science and General Studies, Alfaisal University, Riyadh, Kingdom of Saudi Arabia
- * E-mail:
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Boros G, Miko E, Muramatsu H, Weissman D, Emri E, van der Horst GTJ, Szegedi A, Horkay I, Emri G, Karikó K, Remenyik É. Identification of Cyclobutane Pyrimidine Dimer-Responsive Genes Using UVB-Irradiated Human Keratinocytes Transfected with In Vitro-Synthesized Photolyase mRNA. PLoS One 2015; 10:e0131141. [PMID: 26121660 PMCID: PMC4488231 DOI: 10.1371/journal.pone.0131141] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Accepted: 05/27/2015] [Indexed: 12/16/2022] Open
Abstract
Major biological effects of UVB are attributed to cyclobutane pyrimidine dimers (CPDs), the most common photolesions formed on DNA. To investigate the contribution of CPDs to UVB-induced changes of gene expression, a model system was established by transfecting keratinocytes with pseudouridine-modified mRNA (Ψ-mRNA) encoding CPD-photolyase. Microarray analyses of this model system demonstrated that more than 50% of the gene expression altered by UVB was mediated by CPD photolesions. Functional classification of the gene targets revealed strong effects of CPDs on the regulation of the cell cycle and transcriptional machineries. To confirm the microarray data, cell cycle-regulatory genes, CCNE1 and CDKN2B that were induced exclusively by CPDs were selected for further investigation. Following UVB irradiation, expression of these genes increased significantly at both mRNA and protein levels, but not in cells transfected with CPD-photolyase Ψ-mRNA and exposed to photoreactivating light. Treatment of cells with inhibitors of c-Jun N-terminal kinase (JNK) blocked the UVB-dependent upregulation of both genes suggesting a role for JNK in relaying the signal of UVB-induced CPDs into transcriptional responses. Thus, photolyase mRNA-based experimental platform demonstrates CPD-dependent and -independent events of UVB-induced cellular responses, and, as such, has the potential to identify novel molecular targets for treatment of UVB-mediated skin diseases.
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Affiliation(s)
- Gábor Boros
- Department of Dermatology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Edit Miko
- Department of Dermatology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Hiromi Muramatsu
- Department of Neurosurgery, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Drew Weissman
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Eszter Emri
- Department of Dermatology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | | | - Andrea Szegedi
- Department of Dermatology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
- Department of Dermatological Allergology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Irén Horkay
- Department of Dermatology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Gabriella Emri
- Department of Dermatology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
- * E-mail:
| | - Katalin Karikó
- Department of Neurosurgery, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Éva Remenyik
- Department of Dermatology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
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Abstract
Photolyases, a class of flavoproteins, use blue light to repair two types of ultraviolet-induced DNA damage, a cyclobutane pyrimidine dimer (CPD) and a pyrimidine-pyrimidone (6-4) photoproduct (6-4PP). In this perspective, we review the recent progress in the repair dynamics and mechanisms of both types of DNA restoration by photolyases. We first report the spectroscopic characterization of flavin in various redox states and the active-site solvation dynamics in photolyases. We then systematically summarize the detailed repair dynamics of damaged DNA by photolyases and a biomimetic system through resolving all elementary steps on ultrafast timescales, including multiple intermolecular electron- and proton-transfer reactions and bond-breaking and -making processes. We determined the unique electron tunneling pathways, identified the key functional residues and revealed the molecular origin of high repair efficiency, and thus elucidate the molecular mechanisms and repair photocycles at the most fundamental level. We finally conclude that the active sites of photolyases, unlike the aqueous solution for the biomimetic system, provide a unique electrostatic environment and local flexibility and thus a dedicated synergy for all elementary dynamics to maximize the repair efficiency. This repair photomachine is the first enzyme that the entire functional evolution is completely mapped out in real time.
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Affiliation(s)
- Zheyun Liu
- Department of Physics, Department of Chemistry and Biochemistry, and Programs of Biophysics, Chemical Physics, and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA.
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36
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Fortunato AE, Annunziata R, Jaubert M, Bouly JP, Falciatore A. Dealing with light: the widespread and multitasking cryptochrome/photolyase family in photosynthetic organisms. J Plant Physiol 2015; 172:42-54. [PMID: 25087009 DOI: 10.1016/j.jplph.2014.06.011] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Revised: 06/17/2014] [Accepted: 06/19/2014] [Indexed: 05/19/2023]
Abstract
Light is essential for the life of photosynthetic organisms as it is a source of energy and information from the environment. Light excess or limitation can be a cause of stress however. Photosynthetic organisms exhibit sophisticated mechanisms to adjust their physiology and growth to the local environmental light conditions. The cryptochrome/photolyase family (CPF) is composed of flavoproteins with similar structures that display a variety of light-dependent functions. This family encompasses photolyases, blue-light activated enzymes that repair ultraviolet-light induced DNA damage, and cryptochromes, known for their photoreceptor functions in terrestrial plants. For this review, we searched extensively for CPFs in the available genome databases to trace the distribution and evolution of this protein family in photosynthetic organisms. By merging molecular data with current knowledge from the functional characterization of CPFs from terrestrial and aquatic organisms, we discuss their roles in (i) photoperception, (ii) biological rhythm regulation and (iii) light-induced stress responses. We also explore their possible implication in light-related physiological acclimation and their distribution in phototrophs living in different environments. The outcome of this structure-function analysis reconstructs the complex scenarios in which CPFs have evolved, as highlighted by the novel functions and biochemical properties of the most recently described family members in algae.
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Affiliation(s)
- Antonio Emidio Fortunato
- Sorbonne Universités, UPMC Univ Paris 06, UMR 7238, Computational and Quantitative Biology, F-75006 Paris, France; CNRS, UMR 7238, Computational and Quantitative Biology, F-75006 Paris, France
| | - Rossella Annunziata
- Sorbonne Universités, UPMC Univ Paris 06, UMR 7238, Computational and Quantitative Biology, F-75006 Paris, France; CNRS, UMR 7238, Computational and Quantitative Biology, F-75006 Paris, France
| | - Marianne Jaubert
- Sorbonne Universités, UPMC Univ Paris 06, UMR 7238, Computational and Quantitative Biology, F-75006 Paris, France; CNRS, UMR 7238, Computational and Quantitative Biology, F-75006 Paris, France
| | - Jean-Pierre Bouly
- Sorbonne Universités, UPMC Univ Paris 06, UMR 7238, Computational and Quantitative Biology, F-75006 Paris, France; CNRS, UMR 7238, Computational and Quantitative Biology, F-75006 Paris, France.
| | - Angela Falciatore
- Sorbonne Universités, UPMC Univ Paris 06, UMR 7238, Computational and Quantitative Biology, F-75006 Paris, France; CNRS, UMR 7238, Computational and Quantitative Biology, F-75006 Paris, France.
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Takahashi S, Teranishi M, Izumi M, Takahashi M, Takahashi F, Hidema J. Transport of rice cyclobutane pyrimidine dimer photolyase into mitochondria relies on a targeting sequence located in its C-terminal internal region. Plant J 2014; 79:951-963. [PMID: 24947012 DOI: 10.1111/tpj.12598] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Revised: 06/03/2014] [Accepted: 06/16/2014] [Indexed: 05/29/2023]
Abstract
The cyclobutane pyrimidine dimer (CPD), which represents a major type of DNA damage induced by ultraviolet-B (UVB) radiation, is a principal cause of UVB-induced growth inhibition in plants. CPD photolyase is the primary enzyme for repairing CPDs and is crucial for determining the sensitivity of Oryza sativa (rice) to UVB radiation. CPD photolyase is widely distributed among species ranging from eubacteria to eukaryotes, and is classified into class I or II based on its primary structure. We previously demonstrated that rice CPD photolyase (OsPHR), which belongs to class II and is encoded by a single-copy gene, is a unique nuclear/mitochondrial/chloroplast triple-targeting protein; however, the location and nature of the organellar targeting information contained within OsPHR are unknown. Here, the nuclear and mitochondrial targeting signal sequences of OsPHR were identified by systematic deletion analysis. The nuclear and mitochondrial targeting sequences are harbored within residues 487-489 and 391-401 in the C-terminal region of OsPHR (506 amino acid residues), respectively. The mitochondrial targeting signal represents a distinct topogenic sequence that differs structurally and functionally from classical N-terminal pre-sequences, and this region, in addition to its role in localization to the mitochondria, is essential for the proper functioning of the CPD photolyase. Furthermore, the mitochondrial targeting sequence, which is characteristic of class-II CPD photolyases, was acquired before the divergence of class-II CPD photolyases in eukaryotes. These results indicate that rice plants have evolved a CPD photolyase that functions in mitochondria to protect cells from the harmful effects of UVB radiation.
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Affiliation(s)
- Sayaka Takahashi
- Department of Environmental Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, 980-8577, Japan
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Guzmán-Moreno J, Flores-Martínez A, Brieba LG, Herrera-Estrella A. The Trichoderma reesei Cry1 protein is a member of the cryptochrome/photolyase family with 6-4 photoproduct repair activity. PLoS One 2014; 9:e100625. [PMID: 24964051 PMCID: PMC4070973 DOI: 10.1371/journal.pone.0100625] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Accepted: 05/28/2014] [Indexed: 12/24/2022] Open
Abstract
DNA-photolyases use UV-visible light to repair DNA damage caused by UV radiation. The two major types of DNA damage are cyclobutane pyrimidine dimers (CPD) and 6–4 photoproducts (6-4PP), which are repaired under illumination by CPD and 6–4 photolyases, respectively. Cryptochromes are proteins related to DNA photolyases with strongly reduced or lost DNA repair activity, and have been shown to function as blue-light photoreceptors and to play important roles in circadian rhythms in plants and animals. Both photolyases and cryptochromes belong to the cryptochrome/photolyase family, and are widely distributed in all organisms. Here we describe the characterization of cry1, a member of the cryptochrome/photolyase protein family of the filamentous fungus Trichoderma reesei. We determined that cry1 transcript accumulates when the fungus is exposed to light, and that such accumulation depends on the photoreceptor Blr1 and is modulated by Envoy. Conidia of cry1 mutants show decreased photorepair capacity of DNA damage caused by UV light. In contrast, strains over-expressing Cry1 show increased repair, as compared to the parental strain even in the dark. These observations suggest that Cry1 may be stimulating other systems involved in DNA repair, such as the nucleotide excision repair system. We show that Cry1, heterologously expressed and purified from E. coli, is capable of binding to undamaged and 6-4PP damaged DNA. Photorepair assays in vitro clearly show that Cry1 repairs 6-4PP, but not CPD and Dewar DNA lesions.
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Affiliation(s)
- Jesús Guzmán-Moreno
- Departamento de Biología, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, México
| | - Alberto Flores-Martínez
- Departamento de Biología, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, México
| | - Luis G. Brieba
- Laboratorio Nacional de Genómica para la Biodiversidad, Cinvestav Irapuato, Irapuato, Guanajuato, México
| | - Alfredo Herrera-Estrella
- Laboratorio Nacional de Genómica para la Biodiversidad, Cinvestav Irapuato, Irapuato, Guanajuato, México
- * E-mail:
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39
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Affiliation(s)
- Agostino Migliore
- Department
of Chemistry, Department of Biochemistry, and Department of Physics, Duke University, Durham, North Carolina 27708, United States
| | - Nicholas F. Polizzi
- Department
of Chemistry, Department of Biochemistry, and Department of Physics, Duke University, Durham, North Carolina 27708, United States
| | - Michael
J. Therien
- Department
of Chemistry, Department of Biochemistry, and Department of Physics, Duke University, Durham, North Carolina 27708, United States
| | - David N. Beratan
- Department
of Chemistry, Department of Biochemistry, and Department of Physics, Duke University, Durham, North Carolina 27708, United States
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40
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Puviani M, Barcella A, Milani M. Efficacy of a photolyase-based device in the treatment of cancerization field in patients with actinic keratosis and non-melanoma skin cancer. GIORN ITAL DERMAT V 2013; 148:693-698. [PMID: 24442053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Eryfotona AK-NMSC (ISDIN Spain) is a film-forming medical device in cream or fluid formulation containing the DNA-repair enzyme photolyase and high-protection UV filters in liposomes (repairsomes) indicated in the treatment of cancerization field in patients with actinic keratosis (AK) or non-melanoma skin cancer (NMSC). Photolyase is an enzyme that recognizes and directly repairs UV-induced DNA damage. The most common UV-induced DNA damage is the formation of cyclobutane pyrimidine dimers (CPD). Clinical studies evaluating the histological and cellular effects of Eryfotona AK-NMSC have shown a potential benefit in the treatment of the cancerization field in AK patients. In particular the use of Eryfotona AK-NMSC improves the confocal microscopic appearance of skin at the cancerization field level. In addition, Eryfotona AK-NMSC improves the p53 gene expression at keratinocyte level. In this study we reported a series of 6 cases of patients with AK or NMSC lesions treated with Eryfotona AK-NMSC fluid, both as coadjuvant and as single treatment, applied twice daily in the affected area with photograph documentation. Clinical photographs of the skin lesions at baseline and after Eryfotona AK-NMSC treatment were taken in all cases using a high-definition digital camera. Six patients with multiple AK lesions of the scalp or face with or without NMSC were treated for a mean of 1-3 months with Eryfotona AK-NMSC fluid formulation. Image documentations before and after treatment of this clinical series show a great improvement in AK lesions count and of cancerization field. This clinical series supports the clinical efficacy of the use of photolyase and high-protection UV filters in the treatment of cancerization field and AK lesions in patients with actinic damage.
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MESH Headings
- Aged
- Anticarcinogenic Agents/administration & dosage
- Anticarcinogenic Agents/therapeutic use
- Carcinoma, Squamous Cell/drug therapy
- Carcinoma, Squamous Cell/enzymology
- Carcinoma, Squamous Cell/genetics
- Carcinoma, Squamous Cell/pathology
- Cell Transformation, Neoplastic/drug effects
- Deoxyribodipyrimidine Photo-Lyase/administration & dosage
- Deoxyribodipyrimidine Photo-Lyase/metabolism
- Deoxyribodipyrimidine Photo-Lyase/therapeutic use
- Ear/pathology
- Face/pathology
- Follow-Up Studies
- Genes, p53/drug effects
- Humans
- Keratinocytes/drug effects
- Keratinocytes/metabolism
- Keratosis, Actinic/drug therapy
- Keratosis, Actinic/enzymology
- Keratosis, Actinic/genetics
- Keratosis, Actinic/pathology
- Liposomes
- Male
- Middle Aged
- Scalp/drug effects
- Scalp/pathology
- Skin Neoplasms/drug therapy
- Skin Neoplasms/enzymology
- Skin Neoplasms/genetics
- Skin Neoplasms/pathology
- Sunscreening Agents/administration & dosage
- Sunscreening Agents/metabolism
- Sunscreening Agents/therapeutic use
- Time Factors
- Treatment Outcome
- Tumor Suppressor Protein p53/drug effects
- Tumor Suppressor Protein p53/metabolism
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Affiliation(s)
- M Puviani
- Struttura Semplice di Dermatologia e Dermatologia Chirurgica, Ospedale di Sassuolo , Sassuolo, Modena, Italy
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41
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Fraĭkin GI, Belenikina NS, Piniaskina EV, Rubin AB. [New photo-induced effects of reactivation and protection of yeast cells under lethal UVB radiation]. Izv Akad Nauk Ser Biol 2013:754-759. [PMID: 25518562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Brief exposure of yeasts to low-intensity monochromatic light (400-730 nm) has revealed the effects of photoreactivation and photoprotection of the cells inactivated by medium wave UVB radiation (290-320 nm). The red spectral region with a maximum at 680 nm has been found to be the most active in the initiation of photoreactivation and photoprotection. It has been noted that, according to the regularities investigated, these processes differ fundamentally from the known processes of enzymatic photoreactivation and photoprotection, which have a spectral response limited by, respectively, blue (< 450 nm) and near (< 380 nm) UV light. The data obtained make possible to consider the observed effects of photoreactivation and photoprotection as the manifestation of functioning of some light-dependent defense system capable of increasing the resistance of cells to UVB radiation.
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Boros G, Miko E, Muramatsu H, Weissman D, Emri E, Rózsa D, Nagy G, Juhász A, Juhász I, van der Horst G, Horkay I, Remenyik É, Karikó K, Emri G. Transfection of pseudouridine-modified mRNA encoding CPD-photolyase leads to repair of DNA damage in human keratinocytes: a new approach with future therapeutic potential. J Photochem Photobiol B 2013; 129:93-9. [PMID: 24211294 DOI: 10.1016/j.jphotobiol.2013.09.010] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Revised: 09/26/2013] [Accepted: 09/29/2013] [Indexed: 12/19/2022]
Abstract
UVB irradiation induces harmful photochemical reactions, including formation of Cyclobutane Pyrimidine Dimers (CPDs) in DNA. Accumulation of unrepaired CPD lesions causes inflammation, premature ageing and skin cancer. Photolyases are DNA repair enzymes that can rapidly restore DNA integrity in a light-dependent process called photoreactivation, but these enzymes are absent in humans. Here, we present a novel mRNA-based gene therapy method that directs synthesis of a marsupial, Potorous tridactylus, CPD-photolyase in cultured human keratinocytes. Pseudouridine was incorporated during in vitro transcription to make the mRNA non-immunogenic and highly translatable. Keratinocytes transfected with lipofectamine-complexed mRNA expressed photolyase in the nuclei for at least 2days. Exposing photolyase mRNA-transfected cells to UVB irradiation resulted in significantly less CPD in those cells that were also treated with photoreactivating light, which is required for photolyase activity. The functional photolyase also diminished other UVB-mediated effects, including induction of IL-6 and inhibition of cell proliferation. These results demonstrate that pseudouridine-containing photolyase mRNA is a powerful tool to repair UVB-induced DNA lesions. The pseudouridine-modified mRNA approach has a strong potential to discern cellular effects of CPD in UV-related cell biological studies. The mRNA-based transient expression of proteins offers a number of opportunities for future application in medicine.
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Affiliation(s)
- Gábor Boros
- Department of Dermatology, Medical and Health Science Center, University of Debrecen, Nagyerdei korut 98, 4032 Debrecen, Hungary.
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43
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Teranishi M, Nakamura K, Furukawa H, Hidema J. Identification of a phosphorylation site in cyclobutane pyrimidine dimer photolyase of rice. Plant Physiol Biochem 2013; 63:24-29. [PMID: 23220084 DOI: 10.1016/j.plaphy.2012.11.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Accepted: 11/12/2012] [Indexed: 05/29/2023]
Abstract
Cyclobutane pyrimidine dimer (CPD) photolyase monomerises ultraviolet (UV) radiation-induced CPDs present in DNA, using energy from UVA and visible light. In plants, CPD photolyase activity is a crucial factor for determining UVB sensitivity. We previously demonstrated that native rice CPD photolyase is phosphorylated. To determine the phosphorylation site(s), the phosphorylation status of CPD photolyase was analyzed in rice varieties that have amino acid alterations at the potential phosphorylation sites. In wild-rice species, CPD photolyase was phosphorylated. In Poaceae species, CPD photolyase was phosphorylated in wheat but not in maize. Mutant CPD photolyase proteins, in which these putative phosphorylated residues were replaced with alanine residues, were synthesized using an insect cell-free translation system. A slow-migrating band disappeared when the serine residue at position 7 was mutated. A phospho-specific antibody was generated to determine whether this residue is phosphorylated in CPD photolyase. Only the slow-migrating band of native rice CPD photolyase was detected using this antibody, indicating that the serine residue at position 7 is a phosphorylation site in native rice CPD photolyase.
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Affiliation(s)
- Mika Teranishi
- Department of Environmental Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai 980-8577, Japan.
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44
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Kizilel R, Demir E, Azizoglu S, Asımgi H, Kavakli IH, Kizilel S. Investigation of real-time photorepair activity on DNA via surface plasmon resonance. PLoS One 2012; 7:e44392. [PMID: 22952969 PMCID: PMC3430658 DOI: 10.1371/journal.pone.0044392] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2012] [Accepted: 08/06/2012] [Indexed: 11/18/2022] Open
Abstract
The cyclobutane pyrimidine dimer (CPD) and 6–4 lesion formations along with the specific breaks on strands are the most common type of DNA damage caused by Ultraviolet light (UV) irradiation. CPD photolyase I and II construct two subfamilies of flavoproteins, which have recognition and repair capabilities of CPD sites on both single stranded (ssDNA) and double stranded DNA (dsDNA) with the aid of blue light energy. The other types of flavoprotein family consist of cryptochromes (CRY) that act as photoreceptors in plants, or circadian rhythm regulators in animals. Recent findings showed that a specific type of Cryptochrome-Drosophila, Arabidopsis, Synechocystis, Human (CRY-DASH) has photorepair activity on ssDNA. In this work, real-time interactions between CRY-DASH and ss/dsDNA as well as the interactions between Vibrio cholerae photolyase (VcPHR) and ss/dsDNA were investigated using Surface Plasmon Resonance (SPR). The interactions were then characterized and compared in order to investigate the effect of different types of flavoprotein on UV damaged ss/dsDNA. SPR results confirm the specific binding of VcPHR and CRY-DASH with UV treated DNA. This study is the first instance to quantify the interactions of UV treated and untreated DNA with flavoproteins.
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Affiliation(s)
- Rıza Kizilel
- Chemical and Biological Engineering, Koc University, Sariyer, Istanbul, Turkey
- * E-mail: (SK); (IHK); (RK)
| | - Enis Demir
- Chemical and Biological Engineering, Koc University, Sariyer, Istanbul, Turkey
| | - Selimcan Azizoglu
- Chemical and Biological Engineering, Koc University, Sariyer, Istanbul, Turkey
| | - Hande Asımgi
- Chemical and Biological Engineering, Koc University, Sariyer, Istanbul, Turkey
- Material Science and Engineering, Koc University, Sariyer, Istanbul, Turkey
| | - Ibrahim Halil Kavakli
- Chemical and Biological Engineering, Koc University, Sariyer, Istanbul, Turkey
- Material Science and Engineering, Koc University, Sariyer, Istanbul, Turkey
- Molecular Biology and Genetics, Koc University, Sariyer, Istanbul, Turkey
- * E-mail: (SK); (IHK); (RK)
| | - Seda Kizilel
- Chemical and Biological Engineering, Koc University, Sariyer, Istanbul, Turkey
- Material Science and Engineering, Koc University, Sariyer, Istanbul, Turkey
- * E-mail: (SK); (IHK); (RK)
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45
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Asimgil H, Kavakli IH. Purification and characterization of five members of photolyase/cryptochrome family from Cyanidioschyzon merolae. Plant Sci 2012; 185-186:190-198. [PMID: 22325881 DOI: 10.1016/j.plantsci.2011.10.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2011] [Revised: 10/10/2011] [Accepted: 10/11/2011] [Indexed: 05/31/2023]
Abstract
The photolyase/cryptochrome family is a large family of flavoproteins that possess different functions and use blue light as an energy source. Photolyases repair UV-induced DNA damage, whereas cryptochromes regulate the growth and development of plants in a blue-light dependent manner. In this paper, we report the characterization of five genes the photolyase/cryptochrome family from the red algae Cyanidioschyzon merolae. Phylogenetic analysis indicated that one gene is close to the (6-4) photolyase, 3 to the cryptochrome-dash (CRY-DASH), and one gene is an independent clade. We investigated the diversity and similarity of the enzymes' biochemical and photochemical properties. Both biochemical and complementation assays indicated that one of the CRY-DASH genes (CmPHR6) is not involved in the repair of either ssDNA or dsDNA. In addition, we isolated the first known (6-4) photolyase from C. merolae, the most primitive photosynthetic organism, which will give evolutionary insights into this protein family.
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Affiliation(s)
- Hande Asimgil
- College of Engineering Chemical and Biological Engineering, Koç University, Rumeli Feneri Yolu, 34450 Sariyer, Istanbul, Turkey.
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46
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Oberpichler I, Pierik AJ, Wesslowski J, Pokorny R, Rosen R, Vugman M, Zhang F, Neubauer O, Ron EZ, Batschauer A, Lamparter T. A photolyase-like protein from Agrobacterium tumefaciens with an iron-sulfur cluster. PLoS One 2011; 6:e26775. [PMID: 22066008 PMCID: PMC3204975 DOI: 10.1371/journal.pone.0026775] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2011] [Accepted: 10/03/2011] [Indexed: 01/08/2023] Open
Abstract
Photolyases and cryptochromes are evolutionarily related flavoproteins with distinct functions. While photolyases can repair UV-induced DNA lesions in a light-dependent manner, cryptochromes regulate growth, development and the circadian clock in plants and animals. Here we report about two photolyase-related proteins, named PhrA and PhrB, found in the phytopathogen Agrobacterium tumefaciens. PhrA belongs to the class III cyclobutane pyrimidine dimer (CPD) photolyases, the sister class of plant cryptochromes, while PhrB belongs to a new class represented in at least 350 bacterial organisms. Both proteins contain flavin adenine dinucleotide (FAD) as a primary catalytic cofactor, which is photoreduceable by blue light. Spectral analysis of PhrA confirmed the presence of 5,10-methenyltetrahydrofolate (MTHF) as antenna cofactor. PhrB comprises also an additional chromophore, absorbing in the short wavelength region but its spectrum is distinct from known antenna cofactors in other photolyases. Homology modeling suggests that PhrB contains an Fe-S cluster as cofactor which was confirmed by elemental analysis and EPR spectroscopy. According to protein sequence alignments the classical tryptophan photoreduction pathway is present in PhrA but absent in PhrB. Although PhrB is clearly distinguished from other photolyases including PhrA it is, like PhrA, required for in vivo photoreactivation. Moreover, PhrA can repair UV-induced DNA lesions in vitro. Thus, A. tumefaciens contains two photolyase homologs of which PhrB represents the first member of the cryptochrome/photolyase family (CPF) that contains an iron-sulfur cluster.
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Affiliation(s)
- Inga Oberpichler
- Karlsruhe Institute of Technology, Botany I, Karlsruhe, Germany.
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47
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Fink M, Thompson JS, Thoma F. Contributions of histone H3 nucleosome core surface mutations to chromatin structures, silencing and DNA repair. PLoS One 2011; 6:e26210. [PMID: 22053185 PMCID: PMC3203891 DOI: 10.1371/journal.pone.0026210] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2011] [Accepted: 09/22/2011] [Indexed: 11/18/2022] Open
Abstract
Histone H3 mutations in residues that cluster in a discrete region on the nucleosome surface around lysine 79 of H3 affect H3-K79 methylation, impair transcriptional silencing in subtelomeric chromatin, and reveal distinct contributions of histone H3 to various DNA-damage response and repair pathways. These residues might act by recruitment of silencing and DNA-damage response factors. Alternatively, their location on the nucleosome surface suggests a possible involvement in nucleosome positioning, stability and nucleosome interactions. Here, we show that the yeast H3 mutants hht2-T80A, hht2-K79E, hht2-L70S, and hht2-E73D show normal nucleosome positioning and stability in minichromosomes. However, loss of silencing in a subtelomeric URA3 gene correlates with a shift of the promoter nucleosome, while nucleosome positions and stability in the coding region are maintained. Moreover, the H3 mutants show normal repair of UV lesions by photolyase and nucleotide excision repair in minichromosomes and slightly enhanced repair in the subtelomeric region. Thus, these results support a role of those residues in the recruitment of silencing proteins and argue against a general role in nucleosome organization.
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Affiliation(s)
- Michel Fink
- Department of Biology, Institute of Cell Biology, ETH Zurich, Zurich, Switzerland
| | - Jeffrey S. Thompson
- Department of Biology, Denison University, Granville, Ohio, United States of America
| | - Fritz Thoma
- Department of Biology, Institute of Cell Biology, ETH Zurich, Zurich, Switzerland
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48
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Chaves I, Nijman RM, Biernat MA, Bajek MI, Brand K, da Silva AC, Saito S, Yagita K, Eker APM, van der Horst GTJ. The Potorous CPD photolyase rescues a cryptochrome-deficient mammalian circadian clock. PLoS One 2011; 6:e23447. [PMID: 21858120 PMCID: PMC3156801 DOI: 10.1371/journal.pone.0023447] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2011] [Accepted: 07/17/2011] [Indexed: 11/21/2022] Open
Abstract
Despite the sequence and structural conservation between cryptochromes and photolyases, members of the cryptochrome/photolyase (flavo)protein family, their functions are divergent. Whereas photolyases are DNA repair enzymes that use visible light to lesion-specifically remove UV-induced DNA damage, cryptochromes act as photoreceptors and circadian clock proteins. To address the functional diversity of cryptochromes and photolyases, we investigated the effect of ectopically expressed Arabidopsis thaliana (6-4)PP photolyase and Potorous tridactylus CPD-photolyase (close and distant relatives of mammalian cryptochromes, respectively), on the performance of the mammalian cryptochromes in the mammalian circadian clock. Using photolyase transgenic mice, we show that Potorous CPD-photolyase affects the clock by shortening the period of behavioral rhythms. Furthermore, constitutively expressed CPD-photolyase is shown to reduce the amplitude of circadian oscillations in cultured cells and to inhibit CLOCK/BMAL1 driven transcription by interacting with CLOCK. Importantly, we show that Potorous CPD-photolyase can restore the molecular oscillator in the liver of (clock-deficient) Cry1/Cry2 double knockout mice. These data demonstrate that a photolyase can act as a true cryptochrome. These findings shed new light on the importance of the core structure of mammalian cryptochromes in relation to its function in the circadian clock and contribute to our further understanding of the evolution of the cryptochrome/photolyase protein family.
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Affiliation(s)
- Inês Chaves
- Department of Genetics, Center for Biomedical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Romana M. Nijman
- Department of Genetics, Center for Biomedical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | | | - Monika I. Bajek
- Department of Genetics, Center for Biomedical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Karl Brand
- Department of Genetics, Center for Biomedical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - António Carvalho da Silva
- Department of Genetics, Center for Biomedical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Shoko Saito
- Department of Genetics, Center for Biomedical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Kazuhiro Yagita
- Department of Neuroscience and Cell Biology, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - André P. M. Eker
- Department of Genetics, Center for Biomedical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
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Biernat MA, Ros VID, Vlak JM, van Oers MM. Baculovirus cyclobutane pyrimidine dimer photolyases show a close relationship with lepidopteran host homologues. Insect Mol Biol 2011; 20:457-464. [PMID: 21477200 DOI: 10.1111/j.1365-2583.2011.01076.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Cyclobutane pyrimidine dimer (CPD) photolyases repair ultraviolet (UV)-induced DNA damage using blue light. To get insight in the origin of baculovirus CPD photolyase (phr) genes, homologues in the lepidopteran insects Chrysodeixis chalcites, Spodoptera exigua and Trichoplusia ni were identified and characterized. Lepidopteran and baculovirus phr genes each form a monophyletic group, and together form a well-supported clade within the insect photolyases. This suggests that baculoviruses obtained their phr genes from an ancestral lepidopteran insect host. A likely evolutionary scenario is that a granulovirus, Spodoptera litura GV or a direct ancestor, obtained a phr gene. Subsequently, it was horizontally transferred from this granulovirus to several group II nucleopolyhedroviruses (NPVs), including those that infect noctuids of the Plusiinae subfamily.
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Affiliation(s)
- M A Biernat
- Laboratory of Virology, Wageningen University, Wageningen, The Netherlands
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50
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Takahashi M, Teranishi M, Ishida H, Kawasaki J, Takeuchi A, Yamaya T, Watanabe M, Makino A, Hidema J. Cyclobutane pyrimidine dimer (CPD) photolyase repairs ultraviolet-B-induced CPDs in rice chloroplast and mitochondrial DNA. Plant J 2011; 66:433-42. [PMID: 21251107 DOI: 10.1111/j.1365-313x.2011.04500.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Plants use sunlight as energy for photosynthesis; however, plant DNA is exposed to the harmful effects of ultraviolet-B (UV-B) radiation (280-320 nm) in the process. UV-B radiation damages nuclear, chloroplast and mitochondrial DNA by the formation of cyclobutane pyrimidine dimers (CPDs), which are the primary UV-B-induced DNA lesions, and are a principal cause of UV-B-induced growth inhibition in plants. Repair of CPDs is therefore essential for plant survival while exposed to UV-B-containing sunlight. Nuclear repair of the UV-B-induced CPDs involves the photoreversal of CPDs, photoreactivation, which is mediated by CPD photolyase that monomerizes the CPDs in DNA by using the energy of near-UV and visible light (300-500 nm). To date, the CPD repair processes in plant chloroplasts and mitochondria remain poorly understood. Here, we report the photoreactivation of CPDs in chloroplast and mitochondrial DNA in rice. Biochemical and subcellular localization analyses using rice strains with different levels of CPD photolyase activity and transgenic rice strains showed that full-length CPD photolyase is encoded by a single gene, not a splice variant, and is expressed and targeted not only to nuclei but also to chloroplasts and mitochondria. The results indicate that rice may have evolved a CPD photolyase that functions in chloroplasts, mitochondria and nuclei, and that contains DNA to protect cells from the harmful effects of UV-B radiation.
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Affiliation(s)
- Masaaki Takahashi
- Graduate School of Life Sciences, Tohoku University, Sendai 980-8577, Japan
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