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Derunets AS, Selimzyanova AI, Rykov SV, Kuznetsov AE, Berezina OV. Strategies to enhance stress tolerance in lactic acid bacteria across diverse stress conditions. World J Microbiol Biotechnol 2024; 40:126. [PMID: 38446232 DOI: 10.1007/s11274-024-03905-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 01/21/2024] [Indexed: 03/07/2024]
Abstract
Lactic acid bacteria (LAB) hold significant importance in diverse fields, including food technology, industrial biotechnology, and medicine. As basic components of starter cultures, probiotics, immunomodulators, and live vaccines, LAB cells resist a variety of stressors, including temperature fluctuations, osmotic and pH shocks, exposure to oxidants and ultraviolet radiation, substrate deprivation, mechanical damage, and more. To stay alive in these adversities, LAB employ a wide range of stress response strategies supported by various mechanisms, for example rearrangement of metabolism, expression of specialized biomolecules (e.g., chaperones and antioxidants), exopolysaccharide synthesis, and complex repair and regulatory systems. LAB can coordinate responses to various stressors using global regulators. In this review, we summarize current knowledge about stress response strategies used by LAB and consider mechanisms of response to specific stressful factors, supported by illustrative examples. In addition, we discuss technical approaches to increase the stress resistance of LAB, including pre-adaptation, genetic modification of strains, and adjustment of cultivation conditions. A critical analysis of the recent findings in this field augments comprehension of stress tolerance mechanisms in LAB, paving the way for prospective research directions with implications in fundamental and practical areas.
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Affiliation(s)
- A S Derunets
- National Research Center Kurchatov Institute, Moscow, Russia.
| | | | - S V Rykov
- National Research Center Kurchatov Institute, Moscow, Russia
| | - A E Kuznetsov
- D. Mendeleev University of Chemical Technology of Russia, Moscow, Russia
| | - O V Berezina
- National Research Center Kurchatov Institute, Moscow, Russia
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2
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Rousseau BJG, Migliore A, Stanley RJ, Beratan DN. Adenine Fine-Tunes DNA Photolyase's Repair Mechanism. J Phys Chem B 2023; 127:2941-2954. [PMID: 36947863 DOI: 10.1021/acs.jpcb.3c00566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/24/2023]
Abstract
The comparative study of DNA repair by mesophilic and extremophilic photolyases helps us understand the evolution of these enzymes and their role in preserving life on our changing planet. The mechanism of repair of cyclobutane pyrimidine dimer lesions in DNA by electron transfer from the flavin adenine dinucleotide cofactor is the subject of intense interest. The role of adenine in mediating this process remains unresolved. Using microsecond molecular dynamics simulations, we find that adenine mediates the electron transfer in both mesophile and extremophile DNA photolyases through a similar mechanism. In fact, in all photolyases studied, the molecular conformations with the largest electronic couplings between the enzyme cofactor and DNA show the presence of adenine in 10-20% of the strongest-coupling tunneling pathways between the atoms of the electron donor and acceptor. Our theoretical analysis finds that adenine serves the critical role of fine-tuning rather than maximizing the donor-acceptor coupling within the range appropriate for the repair function.
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Affiliation(s)
- Benjamin J G Rousseau
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520, United States
| | - Agostino Migliore
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
- Department of Chemical Sciences, University of Padova, Via Marzolo 1, 35131 Padova, Italy
| | - Robert J Stanley
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - David N Beratan
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
- Department of Physics, Duke University, Durham, North Carolina 27708, United States
- Department of Biochemistry, Duke University, Durham, North Carolina 27710, United States
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3
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Transcriptomics Analysis of Primordium Formation in Pleurotus eryngii. Genes (Basel) 2021; 12:genes12121863. [PMID: 34946812 PMCID: PMC8700867 DOI: 10.3390/genes12121863] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 11/20/2021] [Accepted: 11/22/2021] [Indexed: 01/17/2023] Open
Abstract
Primordium formation is an important stage preceding the growth and development of the Pleurotus eryngii fruiting body. However, the molecular mechanisms underlying primordium formation remain unclear. In the present study, comparative transcriptomics was performed between mature mycelia and primordium to analyze the transcriptional properties during primordium formation in P. eryngii. A total of 19,655 differentially expressed genes (10,718 upregulated genes and 8937 downregulated genes) were identified. These differentially expressed genes were involved in cell wall degradation, carbohydrate hydrolysis, light perception, and cAMP signal transduction. These results aid further understanding of the transcriptional changes and the molecular processes underlying primordium formation and differentiation, which may lay the foundation for improving the cultivation and quality control of P. eryngii.
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Grinter R, Greening C. Cofactor F420: an expanded view of its distribution, biosynthesis and roles in bacteria and archaea. FEMS Microbiol Rev 2021; 45:fuab021. [PMID: 33851978 PMCID: PMC8498797 DOI: 10.1093/femsre/fuab021] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 04/11/2021] [Indexed: 12/11/2022] Open
Abstract
Many bacteria and archaea produce the redox cofactor F420. F420 is structurally similar to the cofactors FAD and FMN but is catalytically more similar to NAD and NADP. These properties allow F420 to catalyze challenging redox reactions, including key steps in methanogenesis, antibiotic biosynthesis and xenobiotic biodegradation. In the last 5 years, there has been much progress in understanding its distribution, biosynthesis, role and applications. Whereas F420 was previously thought to be confined to Actinobacteria and Euryarchaeota, new evidence indicates it is synthesized across the bacterial and archaeal domains, as a result of extensive horizontal and vertical biosynthetic gene transfer. F420 was thought to be synthesized through one biosynthetic pathway; however, recent advances have revealed variants of this pathway and have resolved their key biosynthetic steps. In parallel, new F420-dependent biosynthetic and metabolic processes have been discovered. These advances have enabled the heterologous production of F420 and identified enantioselective F420H2-dependent reductases for biocatalysis. New research has also helped resolve how microorganisms use F420 to influence human and environmental health, providing opportunities for tuberculosis treatment and methane mitigation. A total of 50 years since its discovery, multiple paradigms associated with F420 have shifted, and new F420-dependent organisms and processes continue to be discovered.
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Affiliation(s)
- Rhys Grinter
- Department of Microbiology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Chris Greening
- Department of Microbiology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
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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] [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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Fadanni J, Acocella A, Zerbetto F. White and Colored Noises as Driving Forces of Electron Transfer: The Photolyase Repair Mechanism as a Test Case. J Phys Chem Lett 2019; 10:4511-4516. [PMID: 31343886 DOI: 10.1021/acs.jpclett.9b01763] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
We introduce a model to investigate electron transfer where the explicit temporal propagation of the electronic wave function is modified by white and colored noises. Atomic energies are perturbed randomly to determine an electron transfer where the periodic electronic oscillations are greatly smothered and the transfer rates can reach up to the experimental time scale. Application to the photolyase enzyme that repairs the DNA lesions shows that the optimal conditions to reproduce the experimental lifetime are equivalent to a red or Brownian noise acting every 80 fs, that is, of ∼400 cm-1. Two-state model calculations show that the results of the quantum dynamics are robust and intrinsic to the use of noise in the simulations.
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Affiliation(s)
- Jacopo Fadanni
- Dipartimento di Chimica "G. Ciamician" , Università di Bologna , V. F. Selmi 2 , 40126 Bologna , Italy
| | - Angela Acocella
- Dipartimento di Chimica "G. Ciamician" , Università di Bologna , V. F. Selmi 2 , 40126 Bologna , Italy
| | - Francesco Zerbetto
- Dipartimento di Chimica "G. Ciamician" , Università di Bologna , V. F. Selmi 2 , 40126 Bologna , Italy
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7
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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] [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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8
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Sato R, Kitoh-Nishioka H, Ando K, Yamato T. Electron Transfer Pathways of Cyclobutane Pyrimidine Dimer Photolyase Revisited. J Phys Chem B 2018; 122:6912-6921. [PMID: 29890068 DOI: 10.1021/acs.jpcb.8b04333] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The photoinduced electron transfer (ET) reaction of cyclobutane pyrimidine dimer (CPD) photolyase plays an essential role in its DNA repair reaction, and the molecular mechanism of the ET reaction has attracted a large number of experimental and theoretical studies. We investigated the quantum mechanical nature of their ET reactions, characterized by multiple ET pathways of the CPD photolyase derived from Anacystis nidulans. Using the generalized Mulliken-Hush (GMH) method and the bridge green function (GF) methods, we estimated the electronic coupling matrix element, TDA, to be 36 ± 30 cm-1 from the donor (FADH-) to the acceptor (CPD). The estimated ET time was 386 ps, in good agreement with the experimental value (250 ps) in the literature. Furthermore, we performed the molecular dynamics (MD) simulations and ab initio molecular orbital (MO) calculations, and explored the electron tunneling pathway. We examined 20 different structures during the MD trajectory and quantitatively evaluated the electron tunneling currents for each of them. As a result, we demonstrated that the ET route via Asn349 was the dominant pathway among the five major routes via (Adenine/Asn349), (Adenine/Glu283), (Adenine/Glu283/Asn349/Met353), (Met353/Asn349), and (Asn349), indicating that Asn349 is an essential amino acid residue in the ET reaction.
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Affiliation(s)
- Ryuma Sato
- Department of Physics, Graduate School of Science , Nagoya University , Furo-cho, Chikusa-ku , Nagoya 464-8602 , Japan
| | - Hirotaka Kitoh-Nishioka
- Center for Computational Sciences , University of Tsukuba 1-1-1 Tennodai , Tsukuba , Ibaraki 305-8577 , Japan
| | - Koji Ando
- Department of Information and Sciences , Tokyo Woman's Christian University , 2-6-1 Zempukuji, Suginami-ku , Tokyo 167-8585 , Japan
| | - Takahisa Yamato
- Department of Physics, Graduate School of Science , Nagoya University , Furo-cho, Chikusa-ku , Nagoya 464-8602 , Japan.,Institute of Genetics and Molecular and Cellular Biology , University of Strasbourg , 1 rue Laurent Fries Parc d'Innovation 67404 Illkirch, Cedex, France
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Rousseau BJG, Shafei S, Migliore A, Stanley RJ, Beratan DN. Determinants of Photolyase's DNA Repair Mechanism in Mesophiles and Extremophiles. J Am Chem Soc 2018; 140:2853-2861. [PMID: 29401372 DOI: 10.1021/jacs.7b11926] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Light-driven DNA repair by extremophilic photolyases is of tremendous importance for understanding the early development of life on Earth. The mechanism for flavin adenine dinucleotide repair of DNA lesions is the subject of debate and has been studied mainly in mesophilic species. In particular, the role of adenine in the repair process is poorly understood. Using molecular docking, molecular dynamics simulations, electronic structure calculations, and electron tunneling pathways analysis, we examined adenine's role in DNA repair in four photolyases that thrive at different temperatures. Our results indicate that the contribution of adenine to the electronic coupling between the flavin and the cyclobutane pyrimidine dimer lesion to be repaired is significant in three (one mesophilic and two extremophilic) of the four enzymes studied. Our analysis suggests that thermophilic and hyperthermophilic photolyases have evolved structurally to preserve the functional position (and thus the catalytic function) of adenine at their high temperatures of operation. Water molecules can compete with adenine in establishing the strongest coupling pathway for the electron transfer repair process, but the adenine contribution remains substantial. The present study also reconciles prior seemingly contradictory conclusions on the role of adenine in mesophile electron transfer repair reactions, showing how adenine-mediated superexchange is conformationally gated.
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Affiliation(s)
| | | | | | - Robert J Stanley
- Department of Chemistry, Temple University , Philadelphia, Pennsylvania 19122, United States
| | - David N Beratan
- Department of Biochemistry, Duke University , Durham, North Carolina 27710, United States
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10
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Lee W, Kodali G, Stanley RJ, Matsika S. Coexistence of Different Electron-Transfer Mechanisms in the DNA Repair Process by Photolyase. Chemistry 2016; 22:11371-81. [PMID: 27362906 DOI: 10.1002/chem.201600656] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Revised: 05/18/2016] [Indexed: 11/07/2022]
Abstract
DNA photolyase has been the topic of extensive studies due to its important role of repairing photodamaged DNA, and its unique feature of using light as an energy source. A crucial step in the repair by DNA photolyase is the forward electron transfer from its cofactor (FADH(-) ) to the damaged DNA, and the detailed mechanism of this process has been controversial. In the present study, we examine the forward electron transfer in DNA photolyase by carrying out high-level ab initio calculations in combination with a quantum mechanical/molecular mechanical (QM/MM) approach, and by measuring fluorescence emission spectra at low temperature. On the basis of these computational and experimental results, we demonstrate that multiple decay pathways exist in DNA photolyase depending on the wavelength at excitation and the subsequent transition. This implies that the forward electron transfer in DNA photolyase occurs not only by superexchange mechanism but also by sequential electron transfer.
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Affiliation(s)
- Wook Lee
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania, 19122, USA.
| | - Goutham Kodali
- Teva Pharmaceuticals USA, Inc, 145 Brandywine Pkwy, West Chester, Pennsylvania, 19380, USA
| | - Robert J Stanley
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania, 19122, USA
| | - Spiridoula Matsika
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania, 19122, USA
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11
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Foulkes NS, Whitmore D, Vallone D, Bertolucci C. Studying the Evolution of the Vertebrate Circadian Clock: The Power of Fish as Comparative Models. ADVANCES IN GENETICS 2016; 95:1-30. [PMID: 27503352 DOI: 10.1016/bs.adgen.2016.05.002] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The utility of any model species cannot be judged solely in terms of the tools and approaches it provides for genetic analysis. A fundamental consideration is also how its biology has been shaped by the environment and the ecological niche which it occupies. By comparing different species occupying very different habitats we can learn how molecular and cellular mechanisms change during evolution in order to optimally adapt to their environment. Such knowledge is as important as understanding how these mechanisms work. This is illustrated by the use of fish models for studying the function and evolution of the circadian clock. In this review we outline our current understanding of how fish clocks sense and respond to light and explain how this differs fundamentally from the situation with mammalian clocks. In addition, we present results from comparative studies involving two species of blind cavefish, Astyanax mexicanus and Phreatichthys andruzzii. This work reveals the consequences of evolution in perpetual darkness for the circadian clock and its regulation by light as well as for other mechanisms such as DNA repair, sleep, and metabolism which directly or indirectly are affected by regular exposure to sunlight. Major differences in the cave habitats inhabited by these two cavefish species have a clear impact on shaping the molecular and cellular adaptations to life in complete darkness.
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Affiliation(s)
- N S Foulkes
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany; Centre for Organismal Studies, Ruprecht-Karls-Universität Heidelberg, Heidelberg, Germany
| | | | - D Vallone
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
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12
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Wijaya IMM, Domratcheva T, Iwata T, Getzoff ED, Kandori H. Single Hydrogen Bond Donation from Flavin N5 to Proximal Asparagine Ensures FAD Reduction in DNA Photolyase. J Am Chem Soc 2016; 138:4368-76. [PMID: 27002596 DOI: 10.1021/jacs.5b10533] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The spread of the absorbance of the stable FADH(•) radical (300-700 nm) allows CPD photolyase to highly efficiently form FADH(-), making it functional for DNA repair. In this study, FTIR spectroscopy detected a strong hydrogen bond, from FAD N5-H to the carbonyl group of the Asn378 side chain, that is modulated by the redox state of FAD. The observed characteristic frequency shifts were reproduced in quantum-mechanical models of the flavin binding site, which were then employed to elucidate redox tuning governed by Asn378. We demonstrate that enhanced hydrogen bonding of the Asn378 side chain with the FADH(•) radical increases thermodynamic stabilization of the radical state, and further ensures kinetic stabilization and accumulation of the fully reduced FADH(-) state.
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Affiliation(s)
| | - Tatiana Domratcheva
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research , Jahnstrasse 29, Heidelberg 69120, Germany
| | | | - Elizabeth D Getzoff
- Department of Integrative Structural and Computational Biology and The Skaggs Institute for Chemical Biology, The Scripps Research Institute , La Jolla, California 92037, United States
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13
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Wijaya IMM, Iwata T, Yamamoto J, Hitomi K, Iwai S, Getzoff ED, Kennis JTM, Mathes T, Kandori H. Flavin adenine dinucleotide chromophore charge controls the conformation of cyclobutane pyrimidine dimer photolyase α-helices. Biochemistry 2014; 53:5864-75. [PMID: 25152314 DOI: 10.1021/bi500638b] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Observations of light-receptive enzyme complexes are usually complicated by simultaneous overlapping signals from the chromophore, apoprotein, and substrate, so that only the initial, ultrafast, photon-chromophore reaction and the final, slow, protein conformational change provide separate, nonoverlapping signals. Each provides its own advantages, whereas sometimes the overlapping signals from the intervening time scales still cannot be fully deconvoluted. We overcome the problem by using a novel method to selectively isotope-label the apoprotein but not the flavin adenine dinucleotide (FAD) cofactor. This allowed the Fourier transform infrared (FTIR) signals to be separated from the apoprotein, FAD cofactor, and DNA substrate. Consequently, a comprehensive structure-function study by FTIR spectroscopy of the Escherichia coli cyclobutane pyrimidine dimer photolyase (CPD-PHR) DNA repair enzyme was possible. FTIR signals could be identified and assigned upon FAD photoactivation and DNA repair, which revealed protein dynamics for both processes beyond simple one-electron reduction and ejection, respectively. The FTIR data suggest that the synergistic cofactor-protein partnership in CPD-PHR linked to changes in the shape of FAD upon one-electron reduction may be coordinated with conformational changes in the apoprotein, allowing it to fit the DNA substrate. Activation of the CPD-PHR chromophore primes the apoprotein for subsequent DNA repair, suggesting that CPD-PHR is not simply an electron-ejecting structure. When FAD is activated, changes in its structure may trigger coordinated conformational changes in the apoprotein and thymine carbonyl of the substrate, highlighting the role of Glu275. In contrast, during DNA repair and release processes, primary conformational changes occur in the enzyme and DNA substrate, with little contribution from the FAD cofactor and surrounding amino acid residues.
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Affiliation(s)
- I M Mahaputra Wijaya
- Department of Frontier Materials and ‡OptoBio Technology Research Center, Nagoya Institute of Technology , Showa-ku, Nagoya 466-8555, Japan
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14
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Khokhlachev NS, Kalenov SV, Zanina OS, Tyupa DV, Baurina MM, Kuznetsov AY. The role of stress agents as operating factors in formation and functioning of granular aerobic activated sludge at model domestic wastewater treatment. Bioprocess Biosyst Eng 2014; 37:1771-9. [DOI: 10.1007/s00449-014-1149-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2013] [Accepted: 02/05/2014] [Indexed: 12/30/2022]
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15
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Kneuttinger AC, Kashiwazaki G, Prill S, Heil K, Müller M, Carell T. Formation and Direct Repair of UV-induced Dimeric DNA Pyrimidine Lesions. Photochem Photobiol 2013; 90:1-14. [PMID: 24354557 DOI: 10.1111/php.12197] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Accepted: 10/17/2013] [Indexed: 12/11/2022]
Abstract
Direct repair of UV-induced DNA lesions represents an elegant method for many organisms to deal with these highly mutagenic and cytotoxic compounds. Although the participating proteins are structurally well investigated, the exact repair mechanism of the photolyase enzymes remains a vivid subject of current research. In this review, we summarize and highlight the recent contributions to this exciting field.
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Affiliation(s)
- Andrea Christa Kneuttinger
- Center for Integrated Protein Sciences at the Department of Chemistry, Ludwig-Maximilians Universität München, Munich, Germany
| | - Gengo Kashiwazaki
- Center for Integrated Protein Sciences at the Department of Chemistry, Ludwig-Maximilians Universität München, Munich, Germany
| | - Stefan Prill
- Center for Integrated Protein Sciences at the Department of Chemistry, Ludwig-Maximilians Universität München, Munich, Germany
| | - Korbinian Heil
- Center for Integrated Protein Sciences at the Department of Chemistry, Ludwig-Maximilians Universität München, Munich, Germany
| | - Markus Müller
- Center for Integrated Protein Sciences at the Department of Chemistry, Ludwig-Maximilians Universität München, Munich, Germany
| | - Thomas Carell
- Center for Integrated Protein Sciences at the Department of Chemistry, Ludwig-Maximilians Universität München, Munich, Germany
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16
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Ruiz-González C, Simó R, Sommaruga R, Gasol JM. Away from darkness: a review on the effects of solar radiation on heterotrophic bacterioplankton activity. Front Microbiol 2013; 4:131. [PMID: 23734148 PMCID: PMC3661993 DOI: 10.3389/fmicb.2013.00131] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2013] [Accepted: 05/06/2013] [Indexed: 12/22/2022] Open
Abstract
Heterotrophic bacterioplankton are main consumers of dissolved organic matter (OM) in aquatic ecosystems, including the sunlit upper layers of the ocean and freshwater bodies. Their well-known sensitivity to ultraviolet radiation (UVR), together with some recently discovered mechanisms bacteria have evolved to benefit from photosynthetically available radiation (PAR), suggest that natural sunlight plays a relevant, yet difficult to predict role in modulating bacterial biogeochemical functions in aquatic ecosystems. Three decades of experimental work assessing the effects of sunlight on natural bacterial heterotrophic activity reveal responses ranging from high stimulation to total inhibition. In this review, we compile the existing studies on the topic and discuss the potential causes underlying these contrasting results, with special emphasis on the largely overlooked influences of the community composition and the previous light exposure conditions, as well as the different temporal and spatial scales at which exposure to solar radiation fluctuates. These intricate sunlight-bacteria interactions have implications for our understanding of carbon fluxes in aquatic systems, yet further research is necessary before we can accurately evaluate or predict the consequences of increasing surface UVR levels associated with global change.
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Affiliation(s)
- Clara Ruiz-González
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar, CSICBarcelona, Spain
- Département des Sciences Biologiques, Université du Québéc à MontréalMontréal, QC, Canada
| | - Rafel Simó
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar, CSICBarcelona, Spain
| | - Ruben Sommaruga
- Laboratory of Aquatic Photobiology and Plankton Ecology, Institute of Ecology, University of InnsbruckInnsbruck, Austria
| | - Josep M. Gasol
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar, CSICBarcelona, Spain
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17
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Gao S, Wang H, Zhang B, Lin Y. Surface-enhanced Raman scattering of uracil and uracil dimer on silver by density functional method. J Mol Struct 2013. [DOI: 10.1016/j.molstruc.2013.01.024] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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18
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Wijaya IMM, Zhang Y, Iwata T, Yamamoto J, Hitomi K, Iwai S, Getzoff ED, Kandori H. Detection of distinct α-helical rearrangements of cyclobutane pyrimidine dimer photolyase upon substrate binding by Fourier transform infrared spectroscopy. Biochemistry 2013; 52:1019-27. [PMID: 23331252 DOI: 10.1021/bi3016179] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Photolyases (PHRs) utilize near-ultraviolet (UV)-blue light to specifically repair the major photoproducts (PPs) of UV-induced damaged DNA. The cyclobutane pyrimidine dimer PHR (CPD-PHR) from Escherichia coli binds flavin adenine dinucleotide (FAD) as a cofactor and 5,10-methenyltetrahydrofolate as a light-harvesting pigment and specifically repairs CPD lesions. By comparison, a second photolyase known as (6-4) PHR, present in a range of higher organisms, uniquely repairs (6-4) PPs. To understand the repair mechanism and the substrate specificity that distinguish CPD-PHR from (6-4) PHR, we applied Fourier transform infrared (FTIR) spectroscopy to bacterial CPD-PHR in the presence or absence of a well-defined DNA substrate, as we have studied previously for vertebrate (6-4) PHR. PHRs show light-induced reduction of FAD, and photorepair by CPD-PHR involves the transfer of an electron from the photoexcited reduced FAD to the damaged DNA for cleaving the dimers to maintain the DNA's integrity. Here, we measured and analyzed difference FTIR spectra for the photoactivation and DNA photorepair processes of CPD-PHR. We identified light-dependent signals only in the presence of substrate. The signals, presumably arising from a protonated carboxylic acid or the DNA substrate, implicate conformational rearrangements of the protein and substrate during the repair process. Deuterium exchange FTIR measurements of CPD-PHR highlight potential differences in the photoactivation and photorepair mechanisms in comparison to those of (6-4) PHR. Although CPD-PHR and (6-4) PHR appear to exhibit similar overall structures, our studies indicate that distinct conformational rearrangements, especially in the α-helices, are initiated within these enzymes upon binding of their respective DNA substrates.
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Affiliation(s)
- I M Mahaputra Wijaya
- Department of Frontier Materials, Nagoya Institute of Technology, Nagoya 466-8555, Japan
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19
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Studer A, Cubillos VM, Lamare MD, Poulin R, Burritt DJ. Effects of ultraviolet radiation on an intertidal trematode parasite: an assessment of damage and protection. Int J Parasitol 2012; 42:453-61. [PMID: 22787586 DOI: 10.1016/j.ijpara.2012.02.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Trematode parasites are integral components of intertidal ecosystems which experience high levels of ultraviolet radiation. Although these parasites mostly live within hosts, their life cycle involves free-living larval transmission stages such as cercariae which are directly exposed to ambient conditions. UV has previously been shown to considerably reduce the survival of cercariae. Here, we investigated potential mechanisms of protection and damage related to UV in the intertidal trematode Maritrema novaezealandensis. Firstly, the presence of sunscreen compounds (i.e. mycosporine-like amino acids) was quantified in the parasite tissue producing cercariae within a snail host, as well as in the free-swimming cercariae themselves. Secondly, levels of oxidative stress in cercariae after exposure to UV were investigated (i.e.protein carbonyls, catalase and superoxide dismutase). Thirdly, the DNA damage (i.e. cyclobutane–pyrimidine dimers) was compared between cercariae exposed and not exposed to UV. Lastly, functional aspects(survival and infectivity) of cercariae were assessed, comparing cercariae under light conditions versus dark after exposure to UV. We confirmed the presence of my cosporine-like amino acids in cercariae-producing tissue from within snail hosts, but were unable to do so in cercariae directly. Results further suggested that exposure to UV induced high levels of oxidative stress in cercariae which was accompanied by a reduction in the levels of protective antioxidant enzymes present. We also identified higher levels of DNA damage in cercariae exposed to UV, compared with those not exposed. Moreover, no clear effect of light condition was found on survival and infectivity of cercariae after exposure to UV. We concluded that cercariae are highly susceptible to UV damage and that they have very little scope for protection against or repair of UV-induced damage.
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Affiliation(s)
- A Studer
- Department of Zoology, P.O. Box 56, Dunedin 9054, New Zealand.
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20
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Domratcheva T. Neutral Histidine and Photoinduced Electron Transfer in DNA Photolyases. J Am Chem Soc 2011; 133:18172-82. [DOI: 10.1021/ja203964d] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Tatiana Domratcheva
- Department of Biomolecular Mechanisms, Max-Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
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21
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Yasuda M, Nishinaka Y, Nakazono T, Hamasaki T, Nakamura N, Shiragami T, Pac C, Shima K. Photochemistry of Flavins in Micelles: Specific Effects of Anionic Surfactants on the Monomerization of Thymine Cyclobutane Dimers Photosensitized by Tetra-O-acyl Riboflavins*. Photochem Photobiol 2008. [DOI: 10.1111/j.1751-1097.1998.tb05186.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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22
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Weber S, Bittl R. Studies of Organic Protein Cofactors Using Electron Paramagnetic Resonance. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2007. [DOI: 10.1246/bcsj.80.2270] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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23
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Johnson AT, Wiest O. Structure and dynamics of poly(T) single-strand DNA: implications toward CPD formation. J Phys Chem B 2007; 111:14398-404. [PMID: 18052367 DOI: 10.1021/jp076371k] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The formation of cyclobutane pyrimidine dimers between adjacent thymines by UV radiation is thought to be the first event in a cascade leading to skin cancer. Recent studies showed that thymine dimers are fully formed within 1 ps of UV irradiation, suggesting that the conformation at the moment of excitation is the determining factor in whether a given base pair dimerizes. MD simulations on the 50 ns time scale are used to study the populations of reactive conformers that exist at any given time in T18 single-strand DNA. Trajectory analysis shows that only a small percentage of the conformations fulfill distance and dihedral requirements for thymine dimerization, in line with the experimentally observed quantum yield of 3%. Plots of the pairwise interactions in the structures predict hot spots of DNA damage where dimerization in the ssT18 is predicted to be most favored. The importance of hairpin formation by intra-strand base pairing for distinguishing reactive and unreactive base pairs is discussed in detail. The data presented thus explain the structural origin of the results from the ultrafast studies of thymine dimer formation.
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Affiliation(s)
- Andrew T Johnson
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556-5670, USA
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24
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Murakami M, Maeda K, Arai T. Dynamics of intramolecular electron transfer reaction of FAD studied by magnetic field effects on transient absorption spectra. J Phys Chem A 2007; 109:5793-800. [PMID: 16833913 DOI: 10.1021/jp0519722] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The kinetics of intermediates generated from intramolecular electron-transfer reaction by photo irradiation of the flavin adenine dinucleotide (FAD) molecule was studied by a magnetic field effect (MFE) on transient absorption (TA) spectra. Existence time of MFE and MFE action spectra have a strong dependence on the pH of solutions. The MFE action spectra have indicated the existence of interconversion between the radical pair and the cation form of the triplet excited state of flavin part. All rate constants of the triplet and the radical pair were determined by analysis of the MFE action spectra and decay kinetics of TA. The obtained values for the interconversion indicate that the formation of cation radical promotes the back electron-transfer reaction to the triplet excited state. Further, rate constants of spin relaxation and recombination have been studied by the time profiles of MFE at various pH. The drastic change of those two factors has been obtained and can be explained by SOC (spin-orbit coupling) induced back electron-transfer promoted by the formation of a stacking conformation at pH > 2.5.
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Affiliation(s)
- Masaaki Murakami
- Department of Chemistry, University of Tsukuba, 1-1-1 Tenno-dai, Tsukuba City, Ibaraki Pref, 305-8571, Japan
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25
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Wilson KE, Thompson JE, Huner NPA, Greenberg BM. Effects of Ultraviolet-A Exposure on Ultraviolet-B-induced Accumulation of Specific Flavonoids in Brassica napus¶. Photochem Photobiol 2007. [DOI: 10.1562/0031-8655(2001)0730678eouaeo2.0.co2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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26
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Huot Y, Jeffrey WH, Davis RF, Cullen JJ. Damage to DNA in Bacterioplankton: A Model of Damage by Ultraviolet Radiation and its Repair as Influenced by Vertical Mixing ¶. Photochem Photobiol 2007. [DOI: 10.1562/0031-8655(2000)0720062dtdiba2.0.co2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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27
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Green WB, McGuire PG, Miska KB, Kusewitt DF. Urokinase Activity in Corneal Fibroblasts may be Modulated by DNA Damage and Secreted Proteins¶. Photochem Photobiol 2007. [DOI: 10.1562/0031-8655(2001)0730318uaicfm2.0.co2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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28
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Ito T, Shinohara H, Nishimoto S. Conformational Effects on Photophysical Characteristics of C5-C5′-linked Dihydrothymine Dimers in Solution¶. Photochem Photobiol 2007. [DOI: 10.1562/0031-8655(2000)0720719ceopco2.0.co2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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29
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Lamare MD, Barker MF, Lesser MP, Marshall C. DNA photorepair in echinoid embryos: effects of temperature on repair rate in Antarctic and non-Antarctic species. ACTA ACUST UNITED AC 2007; 209:5017-28. [PMID: 17142690 DOI: 10.1242/jeb.02598] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
To determine if an Antarctic species repairs DNA at rates equivalent to warmer water equivalents, we examined repair of UV-damaged DNA in echinoid embryos and larvae. DNA repair by photoreactivation was compared in three species Sterechinus neumayeri (Antarctica), Evechinus chloroticus (New Zealand) and Diadema setosum (Tropical Australia) spanning a latitudinal gradient from polar (77.86 degrees S) to tropical (19.25 degrees S) environments. We compared rates of photoreactivation as a function of ambient and experimental temperature in all three species, and rates of photoreactivation as a function of embryonic developmental stage in Sterechinus. DNA damage was quantified from cyclobutane pyrimidine dimer (CPD) concentrations and rates of abnormal embryonic development. This study established that in the three species and in three developmental stages of Sterechinus, photoreactivation was the primary means of removing CPDs, was effective in repairing all CPDs in less than 24 h, and promoted significantly higher rates of normal development in UV-exposed embryos. CPD photorepair rate constant (k) in echinoid embryos ranged from 0.33 to 1.25 h(-1), equating to a time to 50% repair of between 0.6 and 2.1 h and time to 90%repair between 3.6 and 13.6 h. We observed that experimental temperature influenced photoreactivation rate. In Diadema plutei, the photoreactivation rate constant increased from k=0.58 h(-1) to 1.25 h(-1), with a Q(10)=2.15 between 22 degrees C and 32 degrees C. When compared among the three species across experimental temperatures (-1.9 to 32 degrees C), photoreactivation rates vary with a Q(10)=1.39. Photoreactivation rates were examined in three developmental stages of Sterechinus embryos, and while not significantly different, repair rates tended to be higher in the younger blastula and gastrula stages compared with later stage embryos. We concluded that photoreactivation is active in the Antarctic Sterechinus, but at a significantly slower (non-temperature compensated) rate. The low level of temperature compensation in photoreactivation may be one explanation for the relatively high sensitivity of Antarctic embryos to UV-R in comparison with non-Antarctic equivalents.
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Affiliation(s)
- Miles D Lamare
- Department of Marine Science, University of Otago, Dunedin, New Zealand.
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30
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Pirogova E, Vojisavljevic V, Fang Q, Cosic I. Computational analysis of DNA photolyases using digital signal processing methods. MOLECULAR SIMULATION 2006. [DOI: 10.1080/08927020601052997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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31
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Mu W, Han Q, Luo Z, Wang Y. Production of cis-syn thymine-thymine cyclobutane dimer oligonucleotide in the presence of acetone photosensitizer. Anal Biochem 2006; 353:117-23. [PMID: 16581009 DOI: 10.1016/j.ab.2006.03.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2006] [Revised: 02/18/2006] [Accepted: 03/03/2006] [Indexed: 11/17/2022]
Abstract
cis-syn Cyclobutane pyrimidine dimer (CPD) oligonucleotide was produced by UV irradiation in the presence of acetone photosensitizer. Acetone could enhance the productivity but evidently induced the photocleavage of oligonucleotide under a long time irradiation. A statistical approach of orthogonal design was applied to optimize the preparation condition for the production of the modified oligonucleotide. Optimal conditions for maximal cis-syn CPD oligonucleotide productivity were determined based on three factors: acetone concentration, initial oligonucleotide concentration, and irradiation time at several different levels. The optimal modified oligonucleotide that this optimization could produce was 32.7%. Through analysis of 20% polyacrylamide gel electrophoresis, it was found that modified oligonucleotide migrated slightly more slowly than the parent oligonucleotide. The photoreactivation of cis-syn thymine-thymine dimer oligonucleotide displayed the selectivity of the substrate specificity of DNA photolyase with high-performance liquid chromatography (HPLC) analysis.
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Affiliation(s)
- Wanmeng Mu
- School of Life Sciences, University of Science and Technology of China, Hefei
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32
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Wagenknecht HA. Electron transfer processes in DNA: mechanisms, biological relevance and applications in DNA analytics. Nat Prod Rep 2006; 23:973-1006. [PMID: 17119642 DOI: 10.1039/b504754b] [Citation(s) in RCA: 110] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In principle, DNA-mediated charge transfer processes can be categorized as oxidative hole transfer and reductive electron transfer. With respect to the routes of DNA damage most of the past research has been focused on the investigation of oxidative hole transfer or transport. On the other hand, the transport or transfer of excess electrons has a large potential for biomedical applications, mainly for DNA chip technology.
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Affiliation(s)
- Hans-Achim Wagenknecht
- University of Regensburg, Institute for Organic Chemistry, D-93040, Regensburg, Germany.
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33
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Schleicher E, Hessling B, Illarionova V, Bacher A, Weber S, Richter G, Gerwert K. Light-induced reactions of Escherichia coli DNA photolyase monitored by Fourier transform infrared spectroscopy. FEBS J 2005; 272:1855-66. [PMID: 15819881 DOI: 10.1111/j.1742-4658.2005.04617.x] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cyclobutane-type pyrimidine dimers generated by ultraviolet irradiation of DNA can be cleaved by DNA photolyase. The enzyme-catalysed reaction is believed to be initiated by the light-induced transfer of an electron from the anionic FADH- chromophore of the enzyme to the pyrimidine dimer. In this contribution, first infrared experiments using a novel E109A mutant of Escherichia coli DNA photolyase, which is catalytically active but unable to bind the second cofactor methenyltetrahydrofolate, are described. A stable blue-coloured form of the enzyme carrying a neutral FADH radical cofactor can be interpreted as an intermediate analogue of the light-driven DNA repair reaction and can be reduced to the enzymatically active FADH- form by red-light irradiation. Difference Fourier transform infrared (FT-IR) spectroscopy was used to monitor vibronic bands of the blue radical form and of the fully reduced FADH- form of the enzyme. Preliminary band assignments are based on experiments with 15N-labelled enzyme and on experiments with D2O as solvent. Difference FT-IR measurements were also used to observe the formation of thymidine dimers by ultraviolet irradiation and their repair by light-driven photolyase catalysis. This study provides the basis for future time-resolved FT-IR studies which are aimed at an elucidation of a detailed molecular picture of the light-driven DNA repair process.
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Affiliation(s)
- Erik Schleicher
- Lehrstuhl für Organische Chemie und Biochemie, Technische Universität München, Germany
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34
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Qiu X, Sundin GW, Wu L, Zhou J, Tiedje JM. Comparative analysis of differentially expressed genes in Shewanella oneidensis MR-1 following exposure to UVC, UVB, and UVA radiation. J Bacteriol 2005; 187:3556-64. [PMID: 15866945 PMCID: PMC1111996 DOI: 10.1128/jb.187.10.3556-3564.2005] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We previously reported that Shewanella oneidensis MR-1 is highly sensitive to UVC (254 nm), UVB (290 to 320 nm), and UVA (320 to 400 nm). Here we delineated the cellular response of MR-1 to UV radiation damage by analyzing the transcriptional profile during a 1-h recovering period after UVC, UVB, and UVA exposure at a dose that yields about a 20% survival rate. Although the SOS response was observed with all three treatments, the induction was more robust in response to short-wavelength UV radiation (UVB and UVC). Similarly, more prophage-related genes were induced by short-wavelength UV radiation. MR-1 showed an active detoxification mechanism in response to UVA, which included the induction of antioxidant enzymes and iron-sequestering proteins to scavenge reactive oxygen species. In addition, a great number of genes encoding multidrug and heavy metal efflux pumps were induced following UVA irradiation. Our data suggested that activation of prophages appears the major lethal factor in MR-1 following UVC or UVB irradiation, whereas oxidative damage contributes greatly to the high UVA sensitivity in MR-1.
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Affiliation(s)
- Xiaoyun Qiu
- Center for Microbial Ecology, Michigan State University, East Lansing, MI 48824, USA
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35
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Weber S. Light-driven enzymatic catalysis of DNA repair: a review of recent biophysical studies on photolyase. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2005; 1707:1-23. [PMID: 15721603 DOI: 10.1016/j.bbabio.2004.02.010] [Citation(s) in RCA: 254] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2003] [Accepted: 02/02/2004] [Indexed: 11/19/2022]
Abstract
More than 50 years ago, initial experiments on enzymatic photorepair of ultraviolet (UV)-damaged DNA were reported [Proc. Natl. Acad. Sci. U. S. A. 35 (1949) 73]. Soon after this discovery, it was recognized that one enzyme, photolyase, is able to repair UV-induced DNA lesions by effectively reversing their formation using blue light. The enzymatic process named DNA photoreactivation depends on a non-covalently bound cofactor, flavin adenine dinucleotide (FAD). Flavins are ubiquitous redox-active catalysts in one- and two-electron transfer reactions of numerous biological processes. However, in the case of photolyase, not only the ground-state redox properties of the FAD cofactor are exploited but also, and perhaps more importantly, its excited-state properties. In the catalytically active, fully reduced redox form, the FAD absorbs in the blue and near-UV ranges of visible light. Although there is no direct experimental evidence, it appears generally accepted that starting from the excited singlet state, the chromophore initiates a reductive cleavage of the two major DNA photodamages, cyclobutane pyrimidine dimers and (6-4) photoproducts, by short-distance electron transfer to the DNA lesion. Back electron transfer from the repaired DNA segment is believed to eventually restore the initial redox states of the cofactor and the DNA nucleobases, resulting in an overall reaction with net-zero exchanged electrons. Thus, the entire process represents a true catalytic cycle. Many biochemical and biophysical studies have been carried out to unravel the fundamentals of this unique mode of action. The work has culminated in the elucidation of the three-dimensional structure of the enzyme in 1995 that revealed remarkable details, such as the FAD-cofactor arrangement in an unusual U-shaped configuration. With the crystal structure of the enzyme at hand, research on photolyases did not come to an end but, for good reason, intensified: the geometrical structure of the enzyme alone is not sufficient to fully understand the enzyme's action on UV-damaged DNA. Much effort has therefore been invested to learn more about, for example, the geometry of the enzyme-substrate complex, and the mechanism and pathways of intra-enzyme and enzyme <-->DNA electron transfer. Many of the key results from biochemical and molecular biology characterizations of the enzyme or the enzyme-substrate complex have been summarized in a number of reviews. Complementary to these articles, this review focuses on recent biophysical studies of photoreactivation comprising work performed from the early 1990s until the present.
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Affiliation(s)
- Stefan Weber
- Institute of Experimental Physics, Free University Berlin, Arnimallee 14, 14195 Berlin, Germany.
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36
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Qiu X, Sundin GW, Chai B, Tiedje JM. Survival of Shewanella oneidensis MR-1 after UV radiation exposure. Appl Environ Microbiol 2005; 70:6435-43. [PMID: 15528503 PMCID: PMC525172 DOI: 10.1128/aem.70.11.6435-6443.2004] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We systematically investigated the physiological response as well as DNA damage repair and damage tolerance in Shewanella oneidensis MR-1 following UVC, UVB, UVA, and solar light exposure. MR-1 showed the highest UVC sensitivity among Shewanella strains examined, with D37 and D10 values of 5.6 and 16.5% of Escherichia coli K-12 values. Stationary cells did not show an increased UVA resistance compared to exponential-phase cells; instead, they were more sensitive at high UVA dose. UVA-irradiated MR-1 survived better on tryptic soy agar than Luria-Bertani plates regardless of the growth stage. A 20% survival rate of MR-1 was observed following doses of 3.3 J of UVC m(-2), 568 J of UVB m(-2), 25 kJ of UVA m(-2), and 558 J of solar UVB m(-2), respectively. Photoreactivation conferred an increased survival rate to MR-1 of as much as 177- to 365-fold, 11- to 23-fold, and 3- to 10-fold following UVC, UVB, and solar light irradiation, respectively. A significant UV mutability to rifampin resistance was detected in both UVC- and UVB-treated samples, with the mutation frequency in the range of 10(-5) to 10(-6). Unlike in E. coli, the expression levels of the nucleotide excision repair (NER) component genes uvrA, uvrB, and uvrD were not damage inducible in MR-1. Complementation of Pseudomonas aeruginosa UA11079 (uvrA deficient) with uvrA of MR-1 increased the UVC survival of this strain by more than 3 orders of magnitude. Loss of damage inducibility of the NER system appears to contribute to the high sensitivity of this bacterium to UVR as well as to other DNA-damaging agents.
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Affiliation(s)
- Xiaoyun Qiu
- Center for Microbial Ecology, Michigan State University, East Lansing, Michigan 48824, USA
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Carell T, Epple R, Gramlich V. Synthesis and structure of (carboxymethyl)-functionalized cyclobuta-fused uracil dimers. Helv Chim Acta 2004. [DOI: 10.1002/hlca.19970800718] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Saxena C, Sancar A, Zhong D. Femtosecond Dynamics of DNA Photolyase: Energy Transfer of Antenna Initiation and Electron Transfer of Cofactor Reduction. J Phys Chem B 2004. [DOI: 10.1021/jp048376c] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Chaitanya Saxena
- Departments of Physics, Chemistry, and Biochemistry, OSU Biophysics, Chemical Physics, and Biochemistry Programs, 174 West 18th Avenue, The Ohio State University, Columbus, Ohio 43210, and Department of Biochemistry and Biophysics, Mary Ellen Johns Building, CB 7260, University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599
| | - Aziz Sancar
- Departments of Physics, Chemistry, and Biochemistry, OSU Biophysics, Chemical Physics, and Biochemistry Programs, 174 West 18th Avenue, The Ohio State University, Columbus, Ohio 43210, and Department of Biochemistry and Biophysics, Mary Ellen Johns Building, CB 7260, University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599
| | - Dongping Zhong
- Departments of Physics, Chemistry, and Biochemistry, OSU Biophysics, Chemical Physics, and Biochemistry Programs, 174 West 18th Avenue, The Ohio State University, Columbus, Ohio 43210, and Department of Biochemistry and Biophysics, Mary Ellen Johns Building, CB 7260, University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599
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39
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Qu ZW, Zhu H, Zhang RB, Zhang XD, Ai XC, Zhang XK, Zhang QY. Cycloreversion of Formylcyclobutane Radical Anion: Two-Step Rotating Mechanism. J Phys Chem A 2004. [DOI: 10.1021/jp031307y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Zheng-wang Qu
- State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Center for Molecular Science, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100080, P.R. China, and Max-Planck-Institut für Strömungsforschung, Göttingen D-37073, Germany
| | - Hui Zhu
- State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Center for Molecular Science, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100080, P.R. China, and Max-Planck-Institut für Strömungsforschung, Göttingen D-37073, Germany
| | - Ru-bo Zhang
- State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Center for Molecular Science, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100080, P.R. China, and Max-Planck-Institut für Strömungsforschung, Göttingen D-37073, Germany
| | - Xiao-dong Zhang
- State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Center for Molecular Science, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100080, P.R. China, and Max-Planck-Institut für Strömungsforschung, Göttingen D-37073, Germany
| | - Xi-cheng Ai
- State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Center for Molecular Science, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100080, P.R. China, and Max-Planck-Institut für Strömungsforschung, Göttingen D-37073, Germany
| | - Xing-kang Zhang
- State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Center for Molecular Science, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100080, P.R. China, and Max-Planck-Institut für Strömungsforschung, Göttingen D-37073, Germany
| | - Qi-yuan Zhang
- State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Center for Molecular Science, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100080, P.R. China, and Max-Planck-Institut für Strömungsforschung, Göttingen D-37073, Germany
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40
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Volcov F, Goldman C. The efficiency of photolyase and indole complexes to repair DNA containing dimers of pyrimidine: A theoretical analysis of the electron transfer reactions. J Chem Phys 2004; 120:3381-6. [PMID: 15268493 DOI: 10.1063/1.1640612] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We analyze the effects of competing reactions to the efficiency of enzymatic splitting of pyrimidine dimers formed in DNA by the incidence of ultraviolet radiation. This is accomplished with the aid of a formula that expresses the efficiency of the repair in terms of parameters that regulate the reaction rates for primary and for back long-range electron transfers taking place in the process. Comparison of experimental data with estimations on account of this formula supports early conjectures in the literature that attribute the relative high performance of the enzymatic complexes of photolyase to its ability to suppress the back reaction.
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Affiliation(s)
- Flavia Volcov
- Instituto de Fisica, Universidade de Sao Paulo, CP 66318, 05315-970, Sao Paulo, Brazil
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41
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Cintolesi F, Ritz T, Kay C, Timmel C, Hore P. Anisotropic recombination of an immobilized photoinduced radical pair in a 50-μT magnetic field: a model avian photomagnetoreceptor. Chem Phys 2003. [DOI: 10.1016/s0301-0104(03)00320-3] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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42
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Wang YC, Lee PJ, Shih CM, Chen HY, Lee CC, Chang YY, Hsu YT, Liang YJ, Wang LY, Han WH, Wang YC. Damage formation and repair efficiency in the p53 gene of cell lines and blood lymphocytes assayed by multiplex long quantitative polymerase chain reaction. Anal Biochem 2003; 319:206-15. [PMID: 12871714 DOI: 10.1016/s0003-2697(03)00330-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
We examined ultraviolet (UV) irradiation and cisplatin treatment damage formation and repair efficiency in the p53 tumor suppressor gene of various cultured cell lines and lymphocytes using a nonradioactive multiplex long quantitative polymerase chain reaction (QPCR) assay, which amplified a 7-kb fragment of the target gene and a 500-bp fragment of the template control to successfully increase the sensitivity and reliability of the assay. The multiplex long QPCR detected a lesion frequency of 0.63 lesions/10kb/10J/m(2) in the p53 gene of fibroblast cells. In addition, the multiplex long QPCR assay detected pronounced differences in the repair of UV damage in the p53 gene among repair-proficient CRL-1475 cells and repair-deficient XP-A and XP-C cells. The multiplex long QPCR assay was also evaluated as a sensitive assay for the detection of DNA damage induced by cisplatin. The data indicated that the lesion frequency in the p53 gene was 1.27-1.75 times higher in the H23 cisplatin-sensitive cell than in the H1435 cisplatin-resistant cell at the IC(70) dose. After 8-h and 24-h repair periods, only 13 and 75% of cisplatin-induced damage had been removed in the H23 cells, whereas these values were 92 and 100% in the H1435 cells. In addition, our data indicate that multiplex long QPCR is a sensitive method for validly estimating repair in freshly isolated lymphocytes. The results suggest that the current protocol of the multiplex long QPCR method can be used to assess the damage formation and repair efficiency of various agents at biologically relevant doses and to allow a more precise determination of gene-specific repair in disease susceptibility and drug resistance in epidemiological studies.
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Affiliation(s)
- Yu-Chieh Wang
- Department of Biology, National Taiwan Normal University, Taipei, Taiwan, ROC.
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43
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Sancar A. Structure and function of DNA photolyase and cryptochrome blue-light photoreceptors. Chem Rev 2003; 103:2203-37. [PMID: 12797829 DOI: 10.1021/cr0204348] [Citation(s) in RCA: 932] [Impact Index Per Article: 44.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Aziz Sancar
- Department of Biochemistry and Biophysics, Mary Ellen Jones Building, CB 7260, University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599, USA.
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Qu ZW, Zhu H, Zhang XK, Zhang QY. Density functional investigation on electron-transfer catalysis of cycloreversion of cyclobutane: radical anion mechanism. J Comput Chem 2003; 24:340-4. [PMID: 12548725 DOI: 10.1002/jcc.10177] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The mechanism of cycloreversion of cyclobutane radical anion (c-C(4)H(8) (-)) has been investigated at the UB3LYP/6-31++G(d,p) level, and compared with those of neutral c-C(4)H(8) and c-C(4)H(8) (+) radical cation. Although both c-C(4)H(8) (-) and C(2)H(4) are shown to be Rydberg states unstable with respect to electron ejection, the activation barrier for the "rotating" cycloreversion of c-C(4)H(8) (-) (37.3 kcal/mol) is lower by about 25.2 kcal/mol than that of c-C(4)H(8), and even the intervention of tetramethylene radical anion intermediate may reduce the activation barrier for the cycloreversion of c-C(4)H(8) by about 8.4 kcal/mol, mainly due to stronger electron-deficiency of intermediate biradical species than close-shell cyclobutanes. For the cycloreversion for c-C(4)H(8) (-), side isomerization reaction may be efficiently prevented by the low kinetic stability of tetramethylene radical anion intermediate towards dissociation, just different from the radical cation case. Our theoretical results have suggested the possibility of electron-attachment catalysis of the cycloreversion of some electron-deficient substituted cyclobutanes.
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Affiliation(s)
- Zheng-Wang Qu
- State Key Laboratory for Structural Chemistry of Unstable & Stable Species, Center for Molecular Science, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100080, People's Republic of China.
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45
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You YH, Lee DH, Yoon JH, Nakajima S, Yasui A, Pfeifer GP. Cyclobutane pyrimidine dimers are responsible for the vast majority of mutations induced by UVB irradiation in mammalian cells. J Biol Chem 2001; 276:44688-94. [PMID: 11572873 DOI: 10.1074/jbc.m107696200] [Citation(s) in RCA: 211] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The most prevalent DNA lesions induced by UVB are the cyclobutane pyrimidine dimers (CPDs) and the pyrimidine (6-4) pyrimidone photoproducts ((6-4)PPs). It has been a long standing controversy as to which of these photoproduct is responsible for mutations in mammalian cells. Here we have introduced photoproduct-specific DNA photolyases into a mouse cell line carrying the transgenic mutation reporter genes lacI and cII. Exposure of the photolyase-expressing cell lines to photoreactivating light resulted in almost complete repair of either CPDs or (6-4)PPs within less than 3 h. The mutations produced by the remaining, nonrepaired photoproducts were scored. The mutant frequency in the cII gene after photoreactivation by CPD photolyase was reduced from 127 x 10(-5) to 34 x 10(-5) (background, 8-10 x 10(-5)). Photoreactivation with (6-4) photolyase did not lower the mutant frequency appreciably. In the lacI gene the mutant frequency after photoreactivation repair of CPDs was reduced from 148 x 10(-5) to 28 x 10(-5) (background, 6-10 x 10(-5)). Mutation spectra obtained with and without photoreactivation by CPD photolyase indicated that the remaining mutations were derived from background mutations, unrepaired CPDs, and other DNA photopoducts including perhaps a small contribution from (6-4)PPs. We conclude that CPDs are responsible for at least 80% of the UVB-induced mutations in this mammalian cell model.
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Affiliation(s)
- Y H You
- Department of Biology, Beckman Research Institute of the City of Hope, Duarte, California 91010, USA
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Schmitz M, Tavan P, Nonella M. Vibrational analysis of carbonyl modes in different stages of light-induced cyclopyrimidine dimer repair reactions. Chem Phys Lett 2001. [DOI: 10.1016/s0009-2614(01)01221-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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48
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Weber S, Richter G, Schleicher E, Bacher A, Möbius K, Kay CW. Substrate binding to DNA photolyase studied by electron paramagnetic resonance spectroscopy. Biophys J 2001; 81:1195-204. [PMID: 11463661 PMCID: PMC1301589 DOI: 10.1016/s0006-3495(01)75777-3] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Structural changes in Escherichia coli DNA photolyase induced by binding of a (cis,syn)-cyclobutane pyrimidine dimer (CPD) are studied by continuous-wave electron paramagnetic resonance and electron-nuclear double resonance spectroscopies, using the flavin adenine dinucleotide (FAD) cofactor in its neutral radical form as a naturally occurring electron spin probe. The electron paramagnetic resonance/electron-nuclear double resonance spectral changes are consistent with a large distance (> or =0.6 nm) between the CPD lesion and the 7,8-dimethyl isoalloxazine ring of FAD, as was predicted by recent model calculations on photolyase enzyme-substrate complexes. Small shifts of the isotropic proton hyperfine coupling constants within the FAD's isoalloxazine moiety can be understood in terms of the cofactor binding site becoming more nonpolar because of the displacement of water molecules upon CPD docking to the enzyme. Molecular orbital calculations of hyperfine couplings using density functional theory, in conjunction with an isodensity polarized continuum model, are presented to rationalize these shifts in terms of the changed polarity of the medium surrounding the FAD cofactor.
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Affiliation(s)
- S Weber
- Institute of Experimental Physics, Free University Berlin, 14195 Berlin, Germany.
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49
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Medvedev D, Stuchebrukhov AA. DNA repair mechanism by photolyase: electron transfer path from the photolyase catalytic cofactor FADH(-) to DNA thymine dimer. J Theor Biol 2001; 210:237-48. [PMID: 11371177 DOI: 10.1006/jtbi.2001.2291] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Photolyase is an enzyme that catalyses photorepair of thymine dimers in UV damaged DNA by electron transfer reaction. The structure of the photolyase/DNA complex is unknown at present. Using crystal structure coordinates of the substrate-free enzyme from E. coli, we have recently built a computer molecular model of a thymine dimer docked to photolyase catalytic site and studied molecular dynamics of the system. In this paper, we present analysis of the electronic coupling and electron transfer pathway between the catalytic cofactor FADH(-) and the pyrimidine dimer by the method of interatomic tunneling currents. Electronic structure is treated in the extended Hückel approximation. The root mean square transfer matrix element is about 6 cm(-1), which is consistent with the experimentally determined rate of transfer. We find that electron transfer mechanism responsible for the repair utilizes an unusual folded conformation of FADH(-) in photolyases, in which the isoalloxazine ring of the flavin and the adenine are in close proximity, and the peculiar features of the docked orientation of the dimer. The tunneling currents show explicitly that despite of the close proximity between the donor and acceptor complexes, the electron transfer mechanism between the flavin and the thymine bases is not direct, but indirect, with the adenine acting as an intermediate. These calculations confirm the previously made conclusion based on an indirect evidence for such mechanism.
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Affiliation(s)
- D Medvedev
- Department of Chemistry, University of California, Davis, CA 95616, USA
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50
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Wilson KE, Thompson JE, Huner NP, Greenberg BM. Effects of ultraviolet-A exposure on ultraviolet-B-induced accumulation of specific flavonoids in Brassica napus. Photochem Photobiol 2001; 73:678-84. [PMID: 11421075 DOI: 10.1562/0031-8655(2001)073<0678:eouaeo>2.0.co;2] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Many plant species are able to acclimate to changes in ultraviolet-B radiation (UVB) (290-320 nm) exposure. Due to the wide range of targets of UVB, plants have evolved diverse repair and protection mechanisms. These include increased biosynthesis of UVB screening compounds, elevated antioxidant activity and increased rates of DNA repair. We have shown previously that Brassica napus L. cv Topas plants can acclimate quite effectively to environmentally relevant increases in UVB through the accumulation of specific flavonoids in the leaf epidermis. However, B. napus was found to lose other flavonoids when plants are exposed to ultraviolet-A radiation (UVA) (320-400 nm) and/or UVB (Wilson et al. [1998] Photochem. Photobiol. 67, 547-553). In this study we demonstrate that the levels of all the extractable flavonoids in the leaves of B. napus plants are decreased in a dose-dependent manner in response to UVA exposure. Additionally, the accumulation of the extractable flavonoids was examined following a shift from photosynthetically active radiation (PAR) + UVA to PAR + UVB to assess if preexposure to UVA affected UVB-induced flavonoid accumulation. UVA preexposures were found to impede UVB-induced accumulation of some flavonoids. This down regulation was particularly evident for quercetin-3-O-sophoroside and quercetin-3-O-sophoroside-7-O-glucoside, which is interesting because quercetins have been demonstrated to be induced by UVB and correlated with UVB tolerance in some plant species. The photobiological nature of these UVA-mediated effects on flavonoid accumulation implies complex interactions between UVA and UVB responses.
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Affiliation(s)
- K E Wilson
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada N2L 3G1
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