1
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Hird C, Flanagan E, Franklin CE, Cramp RL. Cold-induced skin darkening does not protect amphibian larvae from UV-associated DNA damage. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART A, ECOLOGICAL AND INTEGRATIVE PHYSIOLOGY 2024; 341:272-281. [PMID: 38197718 DOI: 10.1002/jez.2780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 12/05/2023] [Accepted: 12/14/2023] [Indexed: 01/11/2024]
Abstract
Amphibian declines are sometimes correlated with increasing levels of ultraviolet radiation (UVR). While disease is often implicated in declines, environmental factors such as temperature and UVR play an important role in disease epidemiology. The mutagenic effects of UVR exposure on amphibians are worse at low temperatures. Amphibians from cold environments may be more susceptible to increasing UVR. However, larvae of some species demonstrate cold acclimation, reducing UV-induced DNA damage at low temperatures. Understanding of the mechanisms underpinning this response is lacking. We reared Limnodynastes peronii larvae in cool (15°C) or warm (25°C) waters before acutely exposing them to 1.5 h of high intensity (80 µW cm-2 ) UVBR. We measured the color of larvae and mRNA levels of a DNA repair enzyme. We reared larvae at 25°C in black or white containers to elicit a skin color response, and then measured DNA damage levels in the skin and remaining carcass following UVBR exposure. Cold-acclimated larvae were darker and displayed lower levels of DNA damage than warm-acclimated larvae. There was no difference in CPD-photolyase mRNA levels between cold- and warm-acclimated larvae. Skin darkening in larvae did not reduce their accumulation of DNA damage following UVR exposure. Our results showed that skin darkening does not explain cold-induced reductions in UV-associated DNA damage in L. peronii larvae. Beneficial cold-acclimation is more likely underpinned by increased CPD-photolyase abundance and/or increased photolyase activity at low temperatures.
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Affiliation(s)
- Coen Hird
- School of the Environment, The University of Queensland, Brisbane (Magandjin), Queensland, Australia
| | - Emer Flanagan
- School of Biological Sciences, The University of Edinburgh, Edinburgh, UK
| | - Craig E Franklin
- School of the Environment, The University of Queensland, Brisbane (Magandjin), Queensland, Australia
| | - Rebecca L Cramp
- School of the Environment, The University of Queensland, Brisbane (Magandjin), Queensland, Australia
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2
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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] [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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3
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Al-Sadek T, Yusuf N. Ultraviolet Radiation Biological and Medical Implications. Curr Issues Mol Biol 2024; 46:1924-1942. [PMID: 38534742 DOI: 10.3390/cimb46030126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 02/27/2024] [Accepted: 02/28/2024] [Indexed: 03/28/2024] Open
Abstract
Ultraviolet (UV) radiation plays a crucial role in the development of melanoma and non-melanoma skin cancers. The types of UV radiation are differentiated by wavelength: UVA (315 to 400 nm), UVB (280 to 320 nm), and UVC (100 to 280 nm). UV radiation can cause direct DNA damage in the forms of cyclobutane pyrimidine dimers (CPDs) and 6-4 photoproducts (6-4PPs). In addition, UV radiation can also cause DNA damage indirectly through photosensitization reactions caused by reactive oxygen species (ROS), which manifest as 8-hydroxy-2'-deoxyguanine (8-OHdG). Both direct and indirect DNA damage can lead to mutations in genes that promote the development of skin cancers. The development of melanoma is largely influenced by the signaling of the melanocortin one receptor (MC1R), which plays an essential role in the synthesis of melanin in the skin. UV-induced mutations in the BRAF and NRAS genes are also significant risk factors in melanoma development. UV radiation plays a significant role in basal cell carcinoma (BCC) development by causing mutations in the Hedgehog (Hh) pathway, which dysregulates cell proliferation and survival. UV radiation can also induce the development of squamous cell carcinoma via mutations in the TP53 gene and upregulation of MMPs in the stroma layer of the skin.
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Affiliation(s)
- Tarek Al-Sadek
- Department of Dermatology, UAB Heersink School of Medicine, Birmingham, AL 35294, USA
| | - Nabiha Yusuf
- Department of Dermatology, UAB Heersink School of Medicine, Birmingham, AL 35294, USA
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4
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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] [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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5
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Maestre-Reyna M, Wang PH, Nango E, Hosokawa Y, Saft M, Furrer A, Yang CH, Gusti Ngurah Putu EP, Wu WJ, Emmerich HJ, Caramello N, Franz-Badur S, Yang C, Engilberge S, Wranik M, Glover HL, Weinert T, Wu HY, Lee CC, Huang WC, Huang KF, Chang YK, Liao JH, Weng JH, Gad W, Chang CW, Pang AH, Yang KC, Lin WT, Chang YC, Gashi D, Beale E, Ozerov D, Nass K, Knopp G, Johnson PJM, Cirelli C, Milne C, Bacellar C, Sugahara M, Owada S, Joti Y, Yamashita A, Tanaka R, Tanaka T, Luo F, Tono K, Zarzycka W, Müller P, Alahmad MA, Bezold F, Fuchs V, Gnau P, Kiontke S, Korf L, Reithofer V, Rosner CJ, Seiler EM, Watad M, Werel L, Spadaccini R, Yamamoto J, Iwata S, Zhong D, Standfuss J, Royant A, Bessho Y, Essen LO, Tsai MD. Visualizing the DNA repair process by a photolyase at atomic resolution. Science 2023; 382:eadd7795. [PMID: 38033054 DOI: 10.1126/science.add7795] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 10/05/2023] [Indexed: 12/02/2023]
Abstract
Photolyases, a ubiquitous class of flavoproteins, use blue light to repair DNA photolesions. In this work, we determined the structural mechanism of the photolyase-catalyzed repair of a cyclobutane pyrimidine dimer (CPD) lesion using time-resolved serial femtosecond crystallography (TR-SFX). We obtained 18 snapshots that show time-dependent changes in four reaction loci. We used these results to create a movie that depicts the repair of CPD lesions in the picosecond-to-nanosecond range, followed by the recovery of the enzymatic moieties involved in catalysis, completing the formation of the fully reduced enzyme-product complex at 500 nanoseconds. Finally, back-flip intermediates of the thymine bases to reanneal the DNA were captured at 25 to 200 microseconds. Our data cover the complete molecular mechanism of a photolyase and, importantly, its chemistry and enzymatic catalysis at work across a wide timescale and at atomic resolution.
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Affiliation(s)
- Manuel Maestre-Reyna
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Rd. Sec. 2, Nankang, Taipei 115, Taiwan
- Department of Chemistry, National Taiwan University, 1, Roosevelt Rd. Sec. 4, Taipei 106, Taiwan
| | - Po-Hsun Wang
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Rd. Sec. 2, Nankang, Taipei 115, Taiwan
| | - Eriko Nango
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577, Japan
| | - Yuhei Hosokawa
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Rd. Sec. 2, Nankang, Taipei 115, Taiwan
- Department of Chemistry, National Taiwan University, 1, Roosevelt Rd. Sec. 4, Taipei 106, Taiwan
- Division of Chemistry, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan
| | - Martin Saft
- Department of Chemistry, Philipps University Marburg, Hans-Meerwein Strasse 4, Marburg 35032, Germany
| | - Antonia Furrer
- Paul Scherrer Institute, Forschungstrasse 111, 5232 Villigen PSI, Switzerland
| | - Cheng-Han Yang
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Rd. Sec. 2, Nankang, Taipei 115, Taiwan
| | | | - Wen-Jin Wu
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Rd. Sec. 2, Nankang, Taipei 115, Taiwan
| | - Hans-Joachim Emmerich
- Department of Chemistry, Philipps University Marburg, Hans-Meerwein Strasse 4, Marburg 35032, Germany
| | - Nicolas Caramello
- European Synchrotron Radiation Facility, 38043 Grenoble, France
- Hamburg Centre for Ultrafast Imaging, Universität Hamburg, 22761 Hamburg, Germany
| | - Sophie Franz-Badur
- Department of Chemistry, Philipps University Marburg, Hans-Meerwein Strasse 4, Marburg 35032, Germany
| | - Chao Yang
- Department of Physics, The Ohio State University, Columbus, OH 43210, USA
| | - Sylvain Engilberge
- European Synchrotron Radiation Facility, 38043 Grenoble, France
- Université Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), 38044 Grenoble, France
| | - Maximilian Wranik
- Paul Scherrer Institute, Forschungstrasse 111, 5232 Villigen PSI, Switzerland
| | | | - Tobias Weinert
- Paul Scherrer Institute, Forschungstrasse 111, 5232 Villigen PSI, Switzerland
| | - Hsiang-Yi Wu
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Rd. Sec. 2, Nankang, Taipei 115, Taiwan
| | - Cheng-Chung Lee
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Rd. Sec. 2, Nankang, Taipei 115, Taiwan
| | - Wei-Cheng Huang
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Rd. Sec. 2, Nankang, Taipei 115, Taiwan
| | - Kai-Fa Huang
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Rd. Sec. 2, Nankang, Taipei 115, Taiwan
| | - Yao-Kai Chang
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Rd. Sec. 2, Nankang, Taipei 115, Taiwan
| | - Jiahn-Haur Liao
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Rd. Sec. 2, Nankang, Taipei 115, Taiwan
| | - Jui-Hung Weng
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Rd. Sec. 2, Nankang, Taipei 115, Taiwan
| | - Wael Gad
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Rd. Sec. 2, Nankang, Taipei 115, Taiwan
| | - Chiung-Wen Chang
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Rd. Sec. 2, Nankang, Taipei 115, Taiwan
| | - Allan H Pang
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Rd. Sec. 2, Nankang, Taipei 115, Taiwan
| | - Kai-Chun Yang
- Department of Chemistry, National Taiwan University, 1, Roosevelt Rd. Sec. 4, Taipei 106, Taiwan
| | - Wei-Ting Lin
- Department of Chemistry, National Taiwan University, 1, Roosevelt Rd. Sec. 4, Taipei 106, Taiwan
| | - Yu-Chen Chang
- Department of Chemistry, National Taiwan University, 1, Roosevelt Rd. Sec. 4, Taipei 106, Taiwan
| | - Dardan Gashi
- Paul Scherrer Institute, Forschungstrasse 111, 5232 Villigen PSI, Switzerland
| | - Emma Beale
- Paul Scherrer Institute, Forschungstrasse 111, 5232 Villigen PSI, Switzerland
| | - Dmitry Ozerov
- Paul Scherrer Institute, Forschungstrasse 111, 5232 Villigen PSI, Switzerland
| | - Karol Nass
- Paul Scherrer Institute, Forschungstrasse 111, 5232 Villigen PSI, Switzerland
| | - Gregor Knopp
- Paul Scherrer Institute, Forschungstrasse 111, 5232 Villigen PSI, Switzerland
| | - Philip J M Johnson
- Paul Scherrer Institute, Forschungstrasse 111, 5232 Villigen PSI, Switzerland
| | - Claudio Cirelli
- Paul Scherrer Institute, Forschungstrasse 111, 5232 Villigen PSI, Switzerland
| | - Chris Milne
- Paul Scherrer Institute, Forschungstrasse 111, 5232 Villigen PSI, Switzerland
| | - Camila Bacellar
- Paul Scherrer Institute, Forschungstrasse 111, 5232 Villigen PSI, Switzerland
| | | | - Shigeki Owada
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5198, Japan
| | - Yasumasa Joti
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5198, Japan
| | - Ayumi Yamashita
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Rie Tanaka
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Tomoyuki Tanaka
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Fangjia Luo
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5198, Japan
| | - Kensuke Tono
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5198, Japan
| | - Wiktoria Zarzycka
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Pavel Müller
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Maisa Alkheder Alahmad
- Department of Chemistry, Philipps University Marburg, Hans-Meerwein Strasse 4, Marburg 35032, Germany
| | - Filipp Bezold
- Department of Chemistry, Philipps University Marburg, Hans-Meerwein Strasse 4, Marburg 35032, Germany
| | - Valerie Fuchs
- Department of Chemistry, Philipps University Marburg, Hans-Meerwein Strasse 4, Marburg 35032, Germany
| | - Petra Gnau
- Department of Chemistry, Philipps University Marburg, Hans-Meerwein Strasse 4, Marburg 35032, Germany
| | - Stephan Kiontke
- Department of Chemistry, Philipps University Marburg, Hans-Meerwein Strasse 4, Marburg 35032, Germany
| | - Lukas Korf
- Department of Chemistry, Philipps University Marburg, Hans-Meerwein Strasse 4, Marburg 35032, Germany
| | - Viktoria Reithofer
- Department of Chemistry, Philipps University Marburg, Hans-Meerwein Strasse 4, Marburg 35032, Germany
| | - Christian Joshua Rosner
- Department of Chemistry, Philipps University Marburg, Hans-Meerwein Strasse 4, Marburg 35032, Germany
| | - Elisa Marie Seiler
- Department of Chemistry, Philipps University Marburg, Hans-Meerwein Strasse 4, Marburg 35032, Germany
| | - Mohamed Watad
- Department of Chemistry, Philipps University Marburg, Hans-Meerwein Strasse 4, Marburg 35032, Germany
| | - Laura Werel
- Department of Chemistry, Philipps University Marburg, Hans-Meerwein Strasse 4, Marburg 35032, Germany
| | - Roberta Spadaccini
- Department of Chemistry, Philipps University Marburg, Hans-Meerwein Strasse 4, Marburg 35032, Germany
- Dipartimento di Scienze e tecnologie, Universita degli studi del Sannio, Benevento, Italy
| | - Junpei Yamamoto
- Division of Chemistry, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan
| | - So Iwata
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Dongping Zhong
- Department of Physics, The Ohio State University, Columbus, OH 43210, USA
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
- Center for Ultrafast Science and Technology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jörg Standfuss
- Paul Scherrer Institute, Forschungstrasse 111, 5232 Villigen PSI, Switzerland
| | - Antoine Royant
- European Synchrotron Radiation Facility, 38043 Grenoble, France
- Université Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), 38044 Grenoble, France
| | - Yoshitaka Bessho
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Rd. Sec. 2, Nankang, Taipei 115, Taiwan
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
| | - Lars-Oliver Essen
- Department of Chemistry, Philipps University Marburg, Hans-Meerwein Strasse 4, Marburg 35032, Germany
| | - Ming-Daw Tsai
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Rd. Sec. 2, Nankang, Taipei 115, Taiwan
- Institute of Biochemical Sciences, National Taiwan University, 1, Roosevelt Rd. Sec. 4, Taipei 106, Taiwan
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6
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Ribeiro RS, Mencalha AL, de Souza da Fonseca A. Could violet-blue lights increase the bacteria resistance against ultraviolet radiation mediated by photolyases? Lasers Med Sci 2023; 38:253. [PMID: 37930459 DOI: 10.1007/s10103-023-03924-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 10/26/2023] [Indexed: 11/07/2023]
Abstract
Studies have demonstrated bacterial inactivation by radiations at wavelengths between 400 and 500 nm emitted by low-power light sources. The phototoxic activity of these radiations could occur by oxidative damage in DNA and membrane proteins/lipids. However, some cellular mechanisms can reverse these damages in DNA, allowing the maintenance of genetic stability. Photoreactivation is among such mechanisms able to repair DNA damages induced by ultraviolet radiation, ranging from ultraviolet A to blue radiations. In this review, studies on the effects of violet and blue lights emitted by low-power LEDs on bacteria were accessed by PubMed, and discussed the repair of ultraviolet-induced DNA damage by photoreactivation mechanisms. Data from such studies suggested bacterial inactivation after exposure to violet (405 nm) and blue (425-460 nm) radiations emitted from LEDs. However, other studies showed bacterial photoreactivation induced by radiations at 348-440 nm. This process occurs by photolyase enzymes, which absorb photons at wavelengths and repair DNA damage. Although authors have reported bacterial inactivation after exposure to violet and blue radiations emitted from LEDs, pre-exposure to such radiations at low fluences could activate the photolyases, increasing resistance to DNA damage induced by ultraviolet radiation.
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Affiliation(s)
- Rickson Souza Ribeiro
- Departamento de Biofísica e Biometria, Instituto de Biologia Roberto Alcantara Gomes, Universidade do Estado do Rio de Janeiro, Boulevard Vinte e Oito de Setembro, 87, Fundos, Vila Isabel, Rio de Janeiro, 20551030, Brazil
| | - Andre Luiz Mencalha
- Departamento de Biofísica e Biometria, Instituto de Biologia Roberto Alcantara Gomes, Universidade do Estado do Rio de Janeiro, Boulevard Vinte e Oito de Setembro, 87, Fundos, Vila Isabel, Rio de Janeiro, 20551030, Brazil
| | - Adenilson de Souza da Fonseca
- Departamento de Biofísica e Biometria, Instituto de Biologia Roberto Alcantara Gomes, Universidade do Estado do Rio de Janeiro, Boulevard Vinte e Oito de Setembro, 87, Fundos, Vila Isabel, Rio de Janeiro, 20551030, Brazil.
- Departamento de Ciências Fisiológicas, Instituto Biomédico, Universidade Federal do Estado do Rio de Janeiro, Rua Frei Caneca, 94, Rio de Janeiro, 20211040, Brazil.
- Centro de Ciências da Saúde, Centro Universitário Serra dos Órgãos, Avenida Alberto Torres, Teresópolis, Rio de Janeiro, 11125964004, Brazil.
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7
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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] [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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8
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Bayram ÖS, Bayram Ö. An Anatomy of Fungal Eye: Fungal Photoreceptors and Signalling Mechanisms. J Fungi (Basel) 2023; 9:jof9050591. [PMID: 37233302 DOI: 10.3390/jof9050591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Revised: 05/08/2023] [Accepted: 05/15/2023] [Indexed: 05/27/2023] Open
Abstract
Organisms have developed different features to capture or sense sunlight. Vertebrates have evolved specialized organs (eyes) which contain a variety of photosensor cells that help them to see the light to aid orientation. Opsins are major photoreceptors found in the vertebrate eye. Fungi, with more than five million estimated members, represent an important clade of living organisms which have important functions for the sustainability of life on our planet. Light signalling regulates a range of developmental and metabolic processes including asexual sporulation, sexual fruit body formation, pigment and carotenoid production and even production of secondary metabolites. Fungi have adopted three groups of photoreceptors: (I) blue light receptors, White Collars, vivid, cryptochromes, blue F proteins and DNA photolyases, (II) red light sensors, phytochromes and (III) green light sensors and microbial rhodopsins. Most mechanistic data were elucidated on the roles of the White Collar Complex (WCC) and the phytochromes in the fungal kingdom. The WCC acts as both photoreceptor and transcription factor by binding to target genes, whereas the phytochrome initiates a cascade of signalling by using mitogen-activated protein kinases to elicit its cellular responses. Although the mechanism of photoreception has been studied in great detail, fungal photoreception has not been compared with vertebrate vision. Therefore, this review will mainly focus on mechanistic findings derived from two model organisms, namely Aspergillus nidulans and Neurospora crassa and comparison of some mechanisms with vertebrate vision. Our focus will be on the way light signalling is translated into changes in gene expression, which influences morphogenesis and metabolism in fungi.
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Affiliation(s)
| | - Özgür Bayram
- Biology Department, Maynooth University, W23 F2K8 Maynooth, Co. Kildare, Ireland
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9
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Wang P, Ouyang J, Jia Z, Zhang A, Yang Y. Roles of DNA damage in renal tubular epithelial cells injury. Front Physiol 2023; 14:1162546. [PMID: 37089416 PMCID: PMC10117683 DOI: 10.3389/fphys.2023.1162546] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 03/29/2023] [Indexed: 04/09/2023] Open
Abstract
The prevalence of renal diseases including acute kidney injury (AKI) and chronic kidney disease (CKD) is increasing worldwide. However, the pathogenesis of most renal diseases is still unclear and effective treatments are still lacking. DNA damage and the related DNA damage response (DDR) have been confirmed as common pathogenesis of acute kidney injury and chronic kidney disease. Reactive oxygen species (ROS) induced DNA damage is one of the most common types of DNA damage involved in the pathogenesis of acute kidney injury and chronic kidney disease. In recent years, several developments have been made in the field of DNA damage. Herein, we review the roles and developments of DNA damage and DNA damage response in renal tubular epithelial cell injury in acute kidney injury and chronic kidney disease. In this review, we conclude that focusing on DNA damage and DNA damage response may provide valuable diagnostic biomarkers and treatment strategies for renal diseases including acute kidney injury and chronic kidney disease.
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Affiliation(s)
- Peipei Wang
- Department of Nephrology, Children’s Hospital of Nanjing Medical University, Nanjing, China
- Nanjing Key Laboratory of Pediatrics, Children’s Hospital of Nanjing Medical University, Nanjing, China
- Jiangsu Key Laboratory of Pediatrics, Nanjing Medical University, Nanjing, China
| | - Jing Ouyang
- Department of Nephrology, Children’s Hospital of Nanjing Medical University, Nanjing, China
- Nanjing Key Laboratory of Pediatrics, Children’s Hospital of Nanjing Medical University, Nanjing, China
- Jiangsu Key Laboratory of Pediatrics, Nanjing Medical University, Nanjing, China
| | - Zhanjun Jia
- Department of Nephrology, Children’s Hospital of Nanjing Medical University, Nanjing, China
- Nanjing Key Laboratory of Pediatrics, Children’s Hospital of Nanjing Medical University, Nanjing, China
- Jiangsu Key Laboratory of Pediatrics, Nanjing Medical University, Nanjing, China
| | - Aihua Zhang
- Department of Nephrology, Children’s Hospital of Nanjing Medical University, Nanjing, China
- Nanjing Key Laboratory of Pediatrics, Children’s Hospital of Nanjing Medical University, Nanjing, China
- Jiangsu Key Laboratory of Pediatrics, Nanjing Medical University, Nanjing, China
- *Correspondence: Yunwen Yang, ; Aihua Zhang,
| | - Yunwen Yang
- Department of Nephrology, Children’s Hospital of Nanjing Medical University, Nanjing, China
- Nanjing Key Laboratory of Pediatrics, Children’s Hospital of Nanjing Medical University, Nanjing, China
- Jiangsu Key Laboratory of Pediatrics, Nanjing Medical University, Nanjing, China
- *Correspondence: Yunwen Yang, ; Aihua Zhang,
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10
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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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11
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Li R, Kong W, An Z. Enzyme Catalysis for Reversible Deactivation Radical Polymerization. Angew Chem Int Ed Engl 2022; 61:e202202033. [PMID: 35212121 DOI: 10.1002/anie.202202033] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Indexed: 12/31/2022]
Abstract
Enzyme catalysis has been increasingly utilized in reversible deactivation radical polymerization (Enz-RDRP) on account of its mildness, efficiency, and sustainability. In this Minireview we discuss the key roles enzymes play in RDRP, including their ATRPase, initiase, deoxygenation, and photoenzyme activities. We use selected examples to highlight applications of Enz-RDRP in surface brush fabrication, sensing, polymerization-induced self-assembly, and high-throughput synthesis. We also give our reflections on the challenges and future directions of this emerging area.
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Affiliation(s)
- Ruoyu Li
- State Key Laboratory of Supramolecular Structure and Materials College of Chemistry, Jilin University, Changchun, 130012, China
| | - Weina Kong
- State Key Laboratory of Supramolecular Structure and Materials College of Chemistry, Jilin University, Changchun, 130012, China
| | - Zesheng An
- State Key Laboratory of Supramolecular Structure and Materials College of Chemistry, Jilin University, Changchun, 130012, China.,Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun, 130012, China
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12
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Wen B, Xu L, Tang Y, Jiang Z, Ge M, Liu L, Zhu G. A single amino acid residue tunes the stability of the fully reduced flavin cofactor and photorepair activity in photolyases. J Biol Chem 2022; 298:102188. [PMID: 35753350 PMCID: PMC9356274 DOI: 10.1016/j.jbc.2022.102188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 06/14/2022] [Accepted: 06/15/2022] [Indexed: 11/25/2022] Open
Abstract
The ultraviolet-induced DNA lesions, cyclobutane pyrimidine dimers (CPDs) and pyrimidine (6-4) pyrimidone photoproducts (6-4 photoproducts), can be directly photorepaired by CPD photolyases and 6-4 photolyases, respectively. The fully reduced flavin (hydroquinone, HQ) cofactor is required for the catalysis of both types of these photolyases. On the other hand, flavin cofactor in the semi-reduced state, semiquinone (SQ), can be utilized by photolyase homologs, the cryptochromes. However, the evolutionary process of the transition of the functional states of` flavin cofactors in photolyases and cryptochromes remains mysterious. In this work, we investigated three representative photolyases (Escherichia coli CPD photolyase, Microcystis aeruginosa DASH, and Phaeodactylum tricornutum 6-4 photolyase). We show that the residue at a single site adjacent to the flavin cofactor (corresponding to Ala377 in E. coli CPD photolyase, hereafter referred to as site 377) can fine-tune the stability of the HQ cofactor. We found that, in the presence of a polar residue (such as Ser or Asn) at site 377, HQ was stabilized against oxidation. Furthermore, this polar residue enhanced the photorepair activity of these photolyases both in vitro and in vivo. In constrast, substitution of hydrophobic residues, such as Ile, at site 377 in these photolyases adversely affected the stability of HQ. We speculate that these differential residue preferences at site 377 in photolyase proteins might reflect an important evolutionary event that altered the stability of HQ on the timeline from expression of photolyases to that of cryptochromes.
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Affiliation(s)
- Bin Wen
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal University, Wuhu 241000, Anhui, China
| | - Lei Xu
- Anhui Province Key Laboratory of Active Biological Macro-molecules, Wannan Medical College, Wuhu 241002, Anhui, China
| | - Yawei Tang
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal University, Wuhu 241000, Anhui, China
| | - Zhen Jiang
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal University, Wuhu 241000, Anhui, China
| | - Mengting Ge
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal University, Wuhu 241000, Anhui, China
| | - Li Liu
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal University, Wuhu 241000, Anhui, China
| | - Guoping Zhu
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal University, Wuhu 241000, Anhui, China.
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13
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An Z, Li R, Kong W. Enzyme Catalysis for Reversible Deactivation Radical Polymerization. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202202033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Zesheng An
- Jilin University State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry 2699 Qianjin Street, Changchun 130012, China 130012 Changchun CHINA
| | - Ruoyu Li
- Jilin University College of Chemistry CHINA
| | - Weina Kong
- Jilin University College of Chemistry CHINA
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14
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Application of 233 nm far-UVC LEDs for eradication of MRSA and MSSA and risk assessment on skin models. Sci Rep 2022; 12:2587. [PMID: 35173210 PMCID: PMC8850561 DOI: 10.1038/s41598-022-06397-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 01/25/2022] [Indexed: 11/08/2022] Open
Abstract
A newly developed UVC LED source with an emission wavelength of 233 nm was proved on bactericidal efficacy and skin tolerability. The bactericidal efficacy was qualitatively analysed using blood agar test. Subsequently, quantitative analyses were performed on germ carrier tests using the MRSA strain DSM11822, the MSSA strain DSM799, S. epidermidis DSM1798 with various soil loads. Additionally, the compatibility of the germicidal radiation doses on excised human skin and reconstructed human epidermis was proved. Cell viability, DNA damage and production of radicals were assessed in comparison to typical UVC radiation from discharge lamps (222 nm, 254 nm) and UVB (280–380 nm) radiation for clinical assessment. At a dose of 40 mJ/cm2, the 233 nm light source reduced the viable microorganisms by a log10 reduction (LR) of 5 log10 levels if no soil load was present. Mucin and protein containing soil loads diminished the effect to an LR of 1.5–3.3. A salt solution representing artificial sweat (pH 8.4) had only minor effects on the reduction. The viability of the skin models was not reduced and the DNA damage was far below the damage evoked by 0.1 UVB minimal erythema dose, which can be regarded as safe. Furthermore, the induced damage vanished after 24 h. Irradiation on four consecutive days also did not evoke DNA damage. The radical formation was far lower than 20 min outdoor visible light would cause, which is classified as low radical load and can be compensated by the antioxidant defence system.
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15
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Matafonova G, Batoev V. Dual-wavelength light radiation for synergistic water disinfection. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 806:151233. [PMID: 34715208 DOI: 10.1016/j.scitotenv.2021.151233] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 10/18/2021] [Accepted: 10/22/2021] [Indexed: 06/13/2023]
Abstract
Development of the narrow-band mercury-free light sources, such as light emitting diodes (LEDs) and excilamps, has stimulated research on inactivation of pathogenic microorganisms by dual-wavelength light radiation. To date, dual-wavelength light radiation has emerged as an advanced tool for enhancing microbial inactivation in water in view of potential synergistic effect. This is the first review that aims at elucidating its mechanisms under dual-wavelength light exposure and surveying a body of related literature in terms of yes-or-no synergy. We have proposed three key inactivation mechanisms, which function in the estimated spectrum ranges I (190-254 nm), II (250-320 nm) and III (300-405 nm) and provide a synergistic effect when combined. These mechanisms involve proteins damage and DNA repair suppression (I), direct and indirect DNA damage (II) and generation of reactive oxygen species (ROS) by endogenous photosensitizers (III), such as porphyrins and flavins. A synergy under dual-wavelength light irradiation simultaneously or sequentially occurs if coupling two wavelengths of different ranges (I + II, I + III, II + III) in order to trigger different inactivation mechanisms. Recent advances of dual-wavelength light strategy in photodynamic therapy could be applied for water disinfection. They bring opportunities for applying the sources of near-UV and visible radiation and making the disinfection processes more energy- and cost-effective. From this standpoint, the synergistically efficient dual-wavelength combinations II + III and the combinations within the extended to 700 nm range III (near-UV + VIS) appear to be promising for developing novel advanced oxidation processes for disinfection of real turbid waters.
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Affiliation(s)
- Galina Matafonova
- Laboratory of Engineering Ecology, Baikal Institute of Nature Management, Siberian Branch of Russian Academy of Sciences, Ulan-Ude, Russia.
| | - Valeriy Batoev
- Laboratory of Engineering Ecology, Baikal Institute of Nature Management, Siberian Branch of Russian Academy of Sciences, Ulan-Ude, Russia
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16
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Lechner VM, Nappi M, Deneny PJ, Folliet S, Chu JCK, Gaunt MJ. Visible-Light-Mediated Modification and Manipulation of Biomacromolecules. Chem Rev 2021; 122:1752-1829. [PMID: 34546740 DOI: 10.1021/acs.chemrev.1c00357] [Citation(s) in RCA: 67] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Chemically modified biomacromolecules-i.e., proteins, nucleic acids, glycans, and lipids-have become crucial tools in chemical biology. They are extensively used not only to elucidate cellular processes but also in industrial applications, particularly in the context of biopharmaceuticals. In order to enable maximum scope for optimization, it is pivotal to have a diverse array of biomacromolecule modification methods at one's disposal. Chemistry has driven many significant advances in this area, and especially recently, numerous novel visible-light-induced photochemical approaches have emerged. In these reactions, light serves as an external source of energy, enabling access to highly reactive intermediates under exceedingly mild conditions and with exquisite spatiotemporal control. While UV-induced transformations on biomacromolecules date back decades, visible light has the unmistakable advantage of being considerably more biocompatible, and a spectrum of visible-light-driven methods is now available, chiefly for proteins and nucleic acids. This review will discuss modifications of native functional groups (FGs), including functionalization, labeling, and cross-linking techniques as well as the utility of oxidative degradation mediated by photochemically generated reactive oxygen species. Furthermore, transformations at non-native, bioorthogonal FGs on biomacromolecules will be addressed, including photoclick chemistry and DNA-encoded library synthesis as well as methods that allow manipulation of the activity of a biomacromolecule.
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Affiliation(s)
- Vivian M Lechner
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Manuel Nappi
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Patrick J Deneny
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Sarah Folliet
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - John C K Chu
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Matthew J Gaunt
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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17
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Osswald M, Fingerhut BP. Electron Transfer-Induced Active Site Structural Relaxation in 64-Photolyase of Drosophila melanogaster. J Phys Chem B 2021; 125:8690-8702. [PMID: 34323497 DOI: 10.1021/acs.jpcb.1c02951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
While catalytic electron flow and photoreactivation of CPD-photolyases are increasingly understood, the microscopic details of the 64-photolyase repair mechanism are perpetually debated. Here, we investigate in long-time (μs) molecular dynamics simulations combined with extensive quantum mechanical/molecular mechanical (QM/MM) simulations the primary electron transfer (ET) reactions in 64-photolyase of Drosophila melanogaster (D. melanogaster). The characterization of the relative energetics of locally excited and charge separated states in the (6-4) photoproduct enzyme repair complex reveals a charge-separated state involving the adenine moiety of the FADH- cofactor that facilitates reduction of the photoproduct. Microscopic details of the collective reaction coordinate of ET reactions are identified that involve the reorganization of the hydrogen bond network and structural relaxation of the active site. The simulations reveal complex active site relaxation dynamics involving distinguished amino acids (Lys246, His365, and His369), conformational reorganization of the hydroxyl group of the (6-4) photoproduct, and a strengthening of hydrogen bonds with immobilized water molecules. In particular, rotation of the Lys246 side chain is found to impose a double-well character along the reaction coordinate of the ET reaction. Our findings suggest that the primary ET reactions in the (6-4) photoproduct enzyme repair complex of D. melanogaster are governed by a complex multi-minima active site relaxation dynamics and potentially precede the equilibration of the protein. ET pathways mediated by the adenine moiety and the 5' side of the photoproduct are proposed to be relevant for triggering the catalytic (6-4) photoproduct reactivation.
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Affiliation(s)
- Mara Osswald
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, D-12489 Berlin, Germany
| | - Benjamin P Fingerhut
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, D-12489 Berlin, Germany
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18
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Li RY, An ZS. Photoenzymatic RAFT Emulsion Polymerization with Oxygen Tolerance. CHINESE JOURNAL OF POLYMER SCIENCE 2021. [DOI: 10.1007/s10118-021-2556-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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19
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How (5'S) and (5'R) 5',8-Cyclo-2'-Deoxypurines Affect Base Excision Repair of Clustered DNA Damage in Nuclear Extracts of xrs5 Cells? A Biochemical Study. Cells 2021; 10:cells10040725. [PMID: 33805115 PMCID: PMC8064110 DOI: 10.3390/cells10040725] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 03/20/2021] [Accepted: 03/22/2021] [Indexed: 12/17/2022] Open
Abstract
The clustered DNA lesions (CDLs) are a characteristic feature of ionizing radiation’s impact on the human genetic material. CDLs impair the efficiency of cellular repair machinery, especially base excision repair (BER). When CDLs contain a lesion repaired by BER (e.g., apurinic/apyrimidinic (AP) sites) and a bulkier 5′,8-cyclo-2′-deoxypurine (cdPu), which is not a substrate for BER, the repair efficiency of the first one may be affected. The cdPus’ influence on the efficiency of nuclear BER in xrs5 cells have been investigated using synthetic oligonucleotides with bi-stranded CDL (containing (5′S) 5′,8-cyclo-2′-deoxyadenosine (ScdA), (5′R) 5′,8-cyclo-2′-deoxyadenosine (RcdA), (5′S) 5′,8-cyclo-2′-deoxyguanosine (ScdG) or (5′R) 5′,8-cyclo-2′-deoxyguanosine (RcdG) in one strand and an AP site in the other strand at different interlesion distances). Here, for the first time, the impact of ScdG and RcdG was experimentally tested in the context of nuclear BER. This study shows that the presence of RcdA inhibits BER more than ScdA; however, ScdG decreases repair level more than RcdG. Moreover, AP sites located ≤10 base pairs to the cdPu on its 5′-end side were repaired less efficiently than AP sites located ≤10 base pairs on the 3′-end side of cdPu. The strand with an AP site placed opposite cdPu or one base in the 5′-end direction was not reconstituted for cdA nor cdG. CdPus affect the repair of the other lesion within the CDL. It may translate to a prolonged lifetime of unrepaired lesions leading to mutations and impaired cellular processes. Therefore, future research should focus on exploring this subject in more detail.
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DNA photolyase from Antarctic marine bacterium Rhodococcus sp. NJ-530 can repair DNA damage caused by ultraviolet. 3 Biotech 2021; 11:102. [PMID: 33552830 DOI: 10.1007/s13205-021-02660-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 01/13/2021] [Indexed: 10/22/2022] Open
Abstract
Marine bacterium Rhodococcus sp. NJ-530 has developed several ultraviolet (UV) adaptive characteristics for survival and growth in extreme Antarctic environment. Rhodococcus sp. NJ-530 DNA photolyase encoded by a 1146 bp photolyase-homologous region (phr) was identified in genome. Quantitative real-time PCR demonstrated that transcriptional levels of phr were highly up-regulated by ultraviolet-B (UV-B) radiation (90 μW·cm-2) and increased to a maximum of 149.17-fold after exposure for 20 min. According to the results of SDS-PAGE and western blot, PHR was effectively induced by isopropyl-β-d-1-thiogalactopyranoside (IPTG) at the genetically engineered BL21(DE3)-pET-32a( +)-phr construct under the condition of 15 °C for 16 h and 37 °C for 4 h. In terms of in vivo activity, compared with a phr-defective E. coli strain, phr-transformed E. coli exhibited higher survival rate under high UV-B intensity of 90 μW·cm-2. Meanwhile, the purified PHR, with blue light, presented obvious photorepair activity toward UV-induced DNA damage in vitro assays. To sum up, studying the mechanisms of Rhodococcus sp. NJ-530 photolyase is of great interest to understand the adaptation of polar bacteria to high UV radiation, and such data present important therapeutic value for further UV-induced human skin and genetic damage diseases. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-021-02660-8.
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21
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Sandoval BA, Clayman PD, Oblinsky DG, Oh S, Nakano Y, Bird M, Scholes GD, Hyster TK. Photoenzymatic Reductions Enabled by Direct Excitation of Flavin-Dependent “Ene”-Reductases. J Am Chem Soc 2020; 143:1735-1739. [DOI: 10.1021/jacs.0c11494] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Braddock A. Sandoval
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544 United States
| | - Phillip D. Clayman
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544 United States
| | - Daniel G. Oblinsky
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544 United States
| | - Seokjoon Oh
- Chemistry Division, Brookhaven National Laboratory, Upton, New York 11973-5000, United States
| | - Yuji Nakano
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544 United States
| | - Matthew Bird
- Chemistry Division, Brookhaven National Laboratory, Upton, New York 11973-5000, United States
| | - Gregory D. Scholes
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544 United States
| | - Todd K. Hyster
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544 United States
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22
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Amador-Castro F, Rodriguez-Martinez V, Carrillo-Nieves D. Robust natural ultraviolet filters from marine ecosystems for the formulation of environmental friendlier bio-sunscreens. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 749:141576. [PMID: 33370909 DOI: 10.1016/j.scitotenv.2020.141576] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 08/06/2020] [Accepted: 08/07/2020] [Indexed: 05/20/2023]
Abstract
Ultraviolet radiation (UVR) has detrimental effects on human health. It induces oxidative stress, deregulates signaling mechanisms, and produces DNA mutations, factors that ultimately can lead to the development of skin cancer. Therefore, reducing exposure to UVR is of major importance. Among available measures to diminish exposure is the use of sunscreens. However, recent studies indicate that several of the currently used filters have adverse effects on marine ecosystems and human health. This situation leads to the search for new photoprotective compounds that, apart from offering protection, are environmentally friendly. The answer may lie in the same marine ecosystems since molecules such as mycosporine-like amino acids (MAAs) and scytonemin can serve as the defense system of some marine organisms against UVR. This review will discuss the harmful effects of UVR and the mechanisms that microalgae have developed to cope with it. Then it will focus on the biological distribution, characteristics, extraction, and purification methods of MAAs and scytonemin molecules to finally assess its potential as new filters for sunscreen formulation.
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Affiliation(s)
- Fernando Amador-Castro
- Tecnologico de Monterrey, Escuela de Ingenieria y Ciencias, Av. General Ramon Corona No. 2514, 45201 Zapopan, Jal., Mexico
| | - Veronica Rodriguez-Martinez
- Tecnologico de Monterrey, Escuela de Ingenieria y Ciencias, Av. General Ramon Corona No. 2514, 45201 Zapopan, Jal., Mexico
| | - Danay Carrillo-Nieves
- Tecnologico de Monterrey, Escuela de Ingenieria y Ciencias, Av. General Ramon Corona No. 2514, 45201 Zapopan, Jal., Mexico.
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23
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Sato R, Mori Y, Matsui R, Okimoto N, Yamamoto J, Taiji M. Theoretical insights into the DNA repair function of Arabidopsis thaliana cryptochrome-DASH. Biophys Physicobiol 2020; 17:113-124. [PMID: 33194514 PMCID: PMC7610064 DOI: 10.2142/biophysico.bsj-2020010] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 08/28/2020] [Indexed: 12/01/2022] Open
Abstract
Following the discovery of cryptochrome-DASH (CRYD) as a new type of blue-light receptor cryptochrome, theoretical and experimental findings on CRYD have been reported. Early studies identified CRYD as highly homologous to the DNA repair enzyme photolyases (PLs), suggesting the involvement of CRYD in DNA repair. However, an experimental study reported that CRYD does not exhibit DNA repair activity in vivo. Successful PL-mediated DNA repair requires: (i) the recognition of UV-induced DNA lesions and (ii) an electron transfer reaction. If either of them is inefficient, the DNA repair activity will be low. To elucidate the functional differences between CRYD and PL, we theoretically investigated the electron transfer reactivity and DNA binding affinity of CRYD and also performed supplementary experiments. The average electronic coupling matrix elements value for Arabidopsis thaliana CRYD (AtCRYD) was estimated to be 5.3 meV, comparable to that of Anacystis nidulans cyclobutane pyrimidine dimer PLs (AnPL) at 4.5 meV, indicating similar electron transfer reactivities. We also confirmed the DNA repair activity of AtCRYD for UV-damaged single-stranded DNA by the experimental analysis. In addition, we investigated the dynamic behavior of AtCRYD and AnPL in complex with double-stranded DNA using molecular dynamics simulations and observed the formation of a transient salt bridge between protein and DNA in AtCRYD, in contrast to AnPL in which it was formed stably. We suggested that the instability of the salt bridge between protein and DNA will lead to reduced DNA binding affinity for AtCRYD.
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Affiliation(s)
- Ryuma Sato
- Center for Biosystems Dynamics Research, RIKEN, Suita, Osaka 565-0874, Japan
| | - Yoshiharu Mori
- School of Pharmacy, Kitasato University, Minato-ku, Tokyo 108-8641, Japan
| | - Risa Matsui
- Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Noriaki Okimoto
- Center for Biosystems Dynamics Research, RIKEN, Suita, Osaka 565-0874, Japan
| | - Junpei Yamamoto
- Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Makoto Taiji
- Center for Biosystems Dynamics Research, RIKEN, Suita, Osaka 565-0874, Japan
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24
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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] [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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25
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Kciuk M, Marciniak B, Mojzych M, Kontek R. Focus on UV-Induced DNA Damage and Repair-Disease Relevance and Protective Strategies. Int J Mol Sci 2020; 21:ijms21197264. [PMID: 33019598 PMCID: PMC7582305 DOI: 10.3390/ijms21197264] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 09/28/2020] [Accepted: 09/29/2020] [Indexed: 02/06/2023] Open
Abstract
The protective ozone layer is continually depleting due to the release of deteriorating environmental pollutants. The diminished ozone layer contributes to excessive exposure of cells to ultraviolet (UV) radiation. This leads to various cellular responses utilized to restore the homeostasis of exposed cells. DNA is the primary chromophore of the cells that absorbs sunlight energy. Exposure of genomic DNA to UV light leads to the formation of multitude of types of damage (depending on wavelength and exposure time) that are removed by effectively working repair pathways. The aim of this review is to summarize current knowledge considering cellular response to UV radiation with special focus on DNA damage and repair and to give a comprehensive insight for new researchers in this field. We also highlight most important future prospects considering application of the progressing knowledge of UV response for the clinical control of diverse pathologies.
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Affiliation(s)
- Mateusz Kciuk
- Doctoral School of Exact and Natural Sciences, University of Lodz, Banacha Street 12/16, 90-237 Lodz, Poland
- Department of Molecular Biotechnology and Genetics, Faculty of Biology and Environmental Protection, University of Lodz, 12/16 Banacha St., 90-237 Lodz, Poland; (B.M.); (R.K.)
- Correspondence:
| | - Beata Marciniak
- Department of Molecular Biotechnology and Genetics, Faculty of Biology and Environmental Protection, University of Lodz, 12/16 Banacha St., 90-237 Lodz, Poland; (B.M.); (R.K.)
| | - Mariusz Mojzych
- Department of Chemistry, Siedlce University of Natural Sciences and Humanities, 3 Maja 54, 08-110 Siedlce, Poland;
| | - Renata Kontek
- Department of Molecular Biotechnology and Genetics, Faculty of Biology and Environmental Protection, University of Lodz, 12/16 Banacha St., 90-237 Lodz, Poland; (B.M.); (R.K.)
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26
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Luze H, Nischwitz SP, Zalaudek I, Müllegger R, Kamolz LP. DNA repair enzymes in sunscreens and their impact on photoageing-A systematic review. PHOTODERMATOLOGY PHOTOIMMUNOLOGY & PHOTOMEDICINE 2020; 36:424-432. [PMID: 32772409 PMCID: PMC7693079 DOI: 10.1111/phpp.12597] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Revised: 07/06/2020] [Accepted: 08/02/2020] [Indexed: 01/02/2023]
Abstract
BACKGROUND DNA damage is one of the main factors responsible for photoageing and is predominantly attributed to ultraviolet irradiation (UV-R). Photoprotection by conventional sunscreens is exclusively prophylactic, and of no value, once DNA damage has occurred. As a result, the demand for DNA repair mechanisms inhibiting, reversing or delaying the pathologic events in UV-exposed skin has sparked research on anti-photoageing and strategies to improve the effect of conventional sunscreens. This review provides an overview of recent developments in DNA repair enzymes used in sunscreens and their impact on photoageing. METHODS A systematic review of the literature, up to March 2019, was conducted using the electronic databases, PubMed and Web of Science. Quality assessment was carried out using the Newcastle-Ottawa scale (NOS) to ensure inclusion of adequate quality studies only (NOS > 5). RESULTS Out of the 352 publications, 52 were considered relevant to the key question and included in the present review. Two major enzymes were found to play a major role in DNA damage repair in sunscreens: photolyase and T4 endonuclease V. These enzymes are capable of identifying and removing UV-R-induced dimeric photoproducts. Clinical studies revealed that sunscreens with liposome-encapsulated types of photolyase and/or T4 endonuclease V can enhance these repair mechanisms. CONCLUSION There is a lack of randomized controlled trials demonstrating the efficacy of DNA repair enzymes on photoageing, or a superiority of sunscreens with DNA repair enzymes compared to conventional sunscreens. Further studies are mandatory to further reveal pathogenic factors of photoageing and possible therapeutic strategies against it.
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Affiliation(s)
- Hanna Luze
- COREMED-Cooperative Centre for Regenerative Medicine, JOANNEUM RESEARCH Forschungsgesellschaft mbH, Graz, Austria.,Division of Plastic, Aesthetic and Reconstructive Surgery, Department of Surgery, Medical University of Graz, Graz, Austria
| | - Sebastian Philipp Nischwitz
- COREMED-Cooperative Centre for Regenerative Medicine, JOANNEUM RESEARCH Forschungsgesellschaft mbH, Graz, Austria.,Division of Plastic, Aesthetic and Reconstructive Surgery, Department of Surgery, Medical University of Graz, Graz, Austria
| | - Iris Zalaudek
- Clinica Dermatologica, Dipartimento di Scienze Mediche Chirurgiche e della Salute, Università degli Studi di Trieste, Trieste, Italy
| | - Robert Müllegger
- Department of Dermatology and Venereology, Federal Hospital Wiener Neustadt, Wiener Neustadt, Austria
| | - Lars Peter Kamolz
- COREMED-Cooperative Centre for Regenerative Medicine, JOANNEUM RESEARCH Forschungsgesellschaft mbH, Graz, Austria.,Division of Plastic, Aesthetic and Reconstructive Surgery, Department of Surgery, Medical University of Graz, Graz, Austria
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27
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Pilzecker B, Buoninfante OA, Jacobs H. DNA damage tolerance in stem cells, ageing, mutagenesis, disease and cancer therapy. Nucleic Acids Res 2019; 47:7163-7181. [PMID: 31251805 PMCID: PMC6698745 DOI: 10.1093/nar/gkz531] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 05/22/2019] [Accepted: 06/26/2019] [Indexed: 12/12/2022] Open
Abstract
The DNA damage response network guards the stability of the genome from a plethora of exogenous and endogenous insults. An essential feature of the DNA damage response network is its capacity to tolerate DNA damage and structural impediments during DNA synthesis. This capacity, referred to as DNA damage tolerance (DDT), contributes to replication fork progression and stability in the presence of blocking structures or DNA lesions. Defective DDT can lead to a prolonged fork arrest and eventually cumulate in a fork collapse that involves the formation of DNA double strand breaks. Four principal modes of DDT have been distinguished: translesion synthesis, fork reversal, template switching and repriming. All DDT modes warrant continuation of replication through bypassing the fork stalling impediment or repriming downstream of the impediment in combination with filling of the single-stranded DNA gaps. In this way, DDT prevents secondary DNA damage and critically contributes to genome stability and cellular fitness. DDT plays a key role in mutagenesis, stem cell maintenance, ageing and the prevention of cancer. This review provides an overview of the role of DDT in these aspects.
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Affiliation(s)
- Bas Pilzecker
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Olimpia Alessandra Buoninfante
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Heinz Jacobs
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
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28
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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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29
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Zhou F, Li R, Wang X, Du S, An Z. Non‐natural Photoenzymatic Controlled Radical Polymerization Inspired by DNA Photolyase. Angew Chem Int Ed Engl 2019; 58:9479-9484. [DOI: 10.1002/anie.201904413] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Indexed: 12/20/2022]
Affiliation(s)
- Fanfan Zhou
- Institute of Nanochemistry and NanobiologyCollege of Environmental and Chemical EngineeringShanghai University Shanghai 200444 China
| | - Ruoyu Li
- Institute of Nanochemistry and NanobiologyCollege of Environmental and Chemical EngineeringShanghai University Shanghai 200444 China
| | - Xiao Wang
- Institute of Nanochemistry and NanobiologyCollege of Environmental and Chemical EngineeringShanghai University Shanghai 200444 China
| | - Simin Du
- Qianweichang CollegeShanghai University Shanghai 200444 China
| | - Zesheng An
- Institute of Nanochemistry and NanobiologyCollege of Environmental and Chemical EngineeringShanghai University Shanghai 200444 China
- State Key Laboratory of Supramolecular Structure and Materials College of ChemistryJilin University Changchun 130012 China
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30
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Li C, Wong JTY. DNA Damage Response Pathways in Dinoflagellates. Microorganisms 2019; 7:microorganisms7070191. [PMID: 31284474 PMCID: PMC6680887 DOI: 10.3390/microorganisms7070191] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 06/29/2019] [Accepted: 07/01/2019] [Indexed: 12/17/2022] Open
Abstract
Dinoflagellates are a general group of phytoplankton, ubiquitous in aquatic environments. Most dinoflagellates are non-obligate autotrophs, subjected to potential physical and chemical DNA-damaging agents, including UV irradiation, in the euphotic zone. Delay of cell cycles by irradiation, as part of DNA damage responses (DDRs), could potentially lead to growth inhibition, contributing to major errors in the estimation of primary productivity and interpretations of photo-inhibition. Their liquid crystalline chromosomes (LCCs) have large amount of abnormal bases, restricted placement of coding sequences at the chromosomes periphery, and tandem repeat-encoded genes. These chromosome characteristics, their large genome sizes, as well as the lack of architectural nucleosomes, likely contribute to possible differential responses to DNA damage agents. In this study, we sought potential dinoflagellate orthologues of eukaryotic DNA damage repair pathways, and the linking pathway with cell-cycle control in three dinoflagellate species. It appeared that major orthologues in photoreactivation, base excision repair, nucleotide excision repair, mismatch repair, double-strand break repair and homologous recombination repair are well represented in dinoflagellate genomes. Future studies should address possible differential DNA damage responses of dinoflagellates over other planktonic groups, especially in relation to possible shift of life-cycle transitions in responses to UV irradiation. This may have a potential role in the persistence of dinoflagellate red tides with the advent of climatic change.
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Affiliation(s)
- Chongping Li
- Department of Ocean Science, The Hong Kong University of Science and Technology, Clearwater Bay, Kowloon, Hong Kong, China.
- Division of Life Science, The Hong Kong University of Science and Technology, Clearwater Bay, Kowloon, Hong Kong, China.
| | - Joseph Tin Yum Wong
- Division of Life Science, The Hong Kong University of Science and Technology, Clearwater Bay, Kowloon, Hong Kong, China.
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31
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Zhou F, Li R, Wang X, Du S, An Z. Non‐natural Photoenzymatic Controlled Radical Polymerization Inspired by DNA Photolyase. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201904413] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Fanfan Zhou
- Institute of Nanochemistry and NanobiologyCollege of Environmental and Chemical EngineeringShanghai University Shanghai 200444 China
| | - Ruoyu Li
- Institute of Nanochemistry and NanobiologyCollege of Environmental and Chemical EngineeringShanghai University Shanghai 200444 China
| | - Xiao Wang
- Institute of Nanochemistry and NanobiologyCollege of Environmental and Chemical EngineeringShanghai University Shanghai 200444 China
| | - Simin Du
- Qianweichang CollegeShanghai University Shanghai 200444 China
| | - Zesheng An
- Institute of Nanochemistry and NanobiologyCollege of Environmental and Chemical EngineeringShanghai University Shanghai 200444 China
- State Key Laboratory of Supramolecular Structure and Materials College of ChemistryJilin University Changchun 130012 China
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32
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Schmermund L, Jurkaš V, Özgen FF, Barone GD, Büchsenschütz HC, Winkler CK, Schmidt S, Kourist R, Kroutil W. Photo-Biocatalysis: Biotransformations in the Presence of Light. ACS Catal 2019. [DOI: 10.1021/acscatal.9b00656] [Citation(s) in RCA: 147] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Luca Schmermund
- Institute of Chemistry, University of Graz, NAWI Graz, BioTechMed Graz, BioHealth, Heinrichstrasse 28, 8010 Graz, Austria
| | - Valentina Jurkaš
- Institute of Chemistry, University of Graz, NAWI Graz, BioTechMed Graz, BioHealth, Heinrichstrasse 28, 8010 Graz, Austria
| | - F. Feyza Özgen
- Institute of Molecular Biotechnology, Graz University of Technology, NAWI Graz, Petersgasse 14, 8010 Graz, Austria
| | - Giovanni D. Barone
- Institute of Molecular Biotechnology, Graz University of Technology, NAWI Graz, Petersgasse 14, 8010 Graz, Austria
| | - Hanna C. Büchsenschütz
- Institute of Molecular Biotechnology, Graz University of Technology, NAWI Graz, Petersgasse 14, 8010 Graz, Austria
| | - Christoph K. Winkler
- Institute of Chemistry, University of Graz, NAWI Graz, BioTechMed Graz, BioHealth, Heinrichstrasse 28, 8010 Graz, Austria
| | - Sandy Schmidt
- Institute of Molecular Biotechnology, Graz University of Technology, NAWI Graz, Petersgasse 14, 8010 Graz, Austria
| | - Robert Kourist
- Institute of Molecular Biotechnology, Graz University of Technology, NAWI Graz, Petersgasse 14, 8010 Graz, Austria
| | - Wolfgang Kroutil
- Institute of Chemistry, University of Graz, NAWI Graz, BioTechMed Graz, BioHealth, Heinrichstrasse 28, 8010 Graz, Austria
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33
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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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34
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Portero LR, Alonso-Reyes DG, Zannier F, Vazquez MP, Farías ME, Gärtner W, Albarracín VH. Photolyases and Cryptochromes in UV-resistant Bacteria from High-altitude Andean Lakes. Photochem Photobiol 2019; 95:315-330. [DOI: 10.1111/php.13061] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 11/18/2018] [Indexed: 11/30/2022]
Affiliation(s)
- Luciano Raúl Portero
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas (LIMLA); Planta Piloto de Procesos Industriales y Microbiológicos (PROIMI); CCT; CONICET; Tucumán Argentina
- Centro de Investigaciones y Servicios de Microscopía Electrónica (CISME-CONICET-UNT); CCT, CONICET; Tucumán Argentina
| | - Daniel G. Alonso-Reyes
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas (LIMLA); Planta Piloto de Procesos Industriales y Microbiológicos (PROIMI); CCT; CONICET; Tucumán Argentina
- Centro de Investigaciones y Servicios de Microscopía Electrónica (CISME-CONICET-UNT); CCT, CONICET; Tucumán Argentina
| | - Federico Zannier
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas (LIMLA); Planta Piloto de Procesos Industriales y Microbiológicos (PROIMI); CCT; CONICET; Tucumán Argentina
- Centro de Investigaciones y Servicios de Microscopía Electrónica (CISME-CONICET-UNT); CCT, CONICET; Tucumán Argentina
| | - Martín P. Vazquez
- Instituto de Agrobiotecnología de Rosario (INDEAR); Predio CCT Rosario; Santa Fe Argentina
| | - María Eugenia Farías
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas (LIMLA); Planta Piloto de Procesos Industriales y Microbiológicos (PROIMI); CCT; CONICET; Tucumán Argentina
| | - Wolfgang Gärtner
- Institute for Analytical Chemistry; University of Leipzig; Leipzig Germany
| | - Virginia Helena Albarracín
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas (LIMLA); Planta Piloto de Procesos Industriales y Microbiológicos (PROIMI); CCT; CONICET; Tucumán Argentina
- Centro de Investigaciones y Servicios de Microscopía Electrónica (CISME-CONICET-UNT); CCT, CONICET; Tucumán Argentina
- Facultad de Ciencias Naturales; Instituto Miguel Lillo; Universidad Nacional de Tucumán; Tucumán Argentina
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35
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Wang L, Liu L, Ma Y, Li S, Dong S, Zu W. Transcriptome profilling analysis characterized the gene expression patterns responded to combined drought and heat stresses in soybean. Comput Biol Chem 2018; 77:413-429. [PMID: 30476702 DOI: 10.1016/j.compbiolchem.2018.09.012] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Revised: 09/14/2018] [Accepted: 09/15/2018] [Indexed: 12/17/2022]
Abstract
Heat and drought are the two major abiotic stress limiting soybean growth and output worldwide. Knowledge of the molecular mechanisms underlying the responses to heat, drought, and combined stress is essential for soybean molecular breeding. In this study, RNA-sequencing was used to determine the transcriptional responses of soybean to heat, drought and combined stress. RNA-sequencing analysis demonstrated that many genes involved in the defense response, photosynthesis, metabolic process, etc. are differentially expressed in response to drought and heat. However, 1468 and 1220 up-regulated and 1146 and 686 down-regulated genes were confirmed as overlapping differentially expressed genes at 8 h and 24 h after treatment, and these genes are mainly involved in transport, binding and defense response. Furthermore, we compared the heat, drought and the combined stress-responsive genes and identified potential new targets for enhancing stress tolerance of soybean. Comparison of single and combined stress suggests the combined stress did not result in a simple additive response, and that there may be a synergistic response to the combination of drought and heat in soybean.
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Affiliation(s)
- Libin Wang
- College of Agriculture, Northeast Agricultural University, Harbin, 150030, China
| | - Lijun Liu
- College of Agriculture, Northeast Agricultural University, Harbin, 150030, China
| | - Yuling Ma
- College of Agriculture, Northeast Agricultural University, Harbin, 150030, China
| | - Shuang Li
- College of Agriculture, Northeast Agricultural University, Harbin, 150030, China
| | - Shoukun Dong
- College of Agriculture, Northeast Agricultural University, Harbin, 150030, China.
| | - Wei Zu
- College of Agriculture, Northeast Agricultural University, Harbin, 150030, China.
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36
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Röttger K, Marroux HJB, Böhnke H, Morris DTJ, Voice AT, Temps F, Roberts GM, Orr-Ewing AJ. Probing the excited state relaxation dynamics of pyrimidine nucleosides in chloroform solution. Faraday Discuss 2018; 194:683-708. [PMID: 27711889 DOI: 10.1039/c6fd00068a] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Ultrafast transient electronic and vibrational absorption spectroscopy (TEAS and TVAS) of 2'-deoxy-cytidine (dC) and 2'-deoxy-thymidine (dT) dissolved in chloroform examines their excited-state dynamics and the recovery of ground electronic state molecules following absorption of ultraviolet light. The chloroform serves as a weakly interacting solvent, allowing comparisons to be drawn with prior experimental studies of the photodynamics of these nucleosides in the gas phase and in polar solvents such as water. The pyrimidine base nucleosides have some propensity to dimerize in aprotic solvents, but the monomer photochemistry can be resolved clearly and is the focus of this study. UV absorption at a wavelength of 260 nm excites a 1ππ* ← S0 transition, but prompt crossing of a significant fraction (50% in dC, 17% in dT) of the 1ππ* population into a nearby 1nπ* state is too fast for the experiments to resolve. The remaining flux on the 1ππ* state leaves the vertical Franck-Condon region and encounters a conical intersection with the ground electronic state of ethylenic twist character. In dC, the 1ππ* state decays to the ground state with a time constant of 1.1 ± 0.1 ps. The lifetime of the 1nπ* state is much longer in the canonical forms of both molecules: recovery of the ground state population from these states occurs with time constants of 18.6 ± 1.1 ps in amino-oxo dC and ∼114 ps in dT, indicating potential energy barriers to the 1nπ*/S0 conical intersections. The small fraction of the imino-oxo tautomer of dC present in solution has a longer-lived 1nπ* state with a lifetime for ground state recovery of 193 ± 55 ps. No evidence is found for photo-induced tautomerization of amino-oxo dC to the imino-oxo form, or for population of low lying triplet states of this nucleoside. In contrast, ∼8% of the UV-excited dT molecules access the long-lived T1 (3ππ*) state through the 1nπ* state. The primary influence of the solvent appears to be the degree to which it destabilizes the states of 1nπ* character, with consequences for the lifetimes of these states as well as the triplet state yields.
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Affiliation(s)
- Katharina Röttger
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK. and Institut für Physikalische Chemie, Christian-Albrechts-Universität zu Kiel, Olshausenstr. 40, D-24098 Kiel, Germany
| | - Hugo J B Marroux
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK.
| | - Hendrik Böhnke
- Institut für Physikalische Chemie, Christian-Albrechts-Universität zu Kiel, Olshausenstr. 40, D-24098 Kiel, Germany
| | - David T J Morris
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK.
| | - Angus T Voice
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK.
| | - Friedrich Temps
- Institut für Physikalische Chemie, Christian-Albrechts-Universität zu Kiel, Olshausenstr. 40, D-24098 Kiel, Germany
| | - Gareth M Roberts
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK.
| | - Andrew J Orr-Ewing
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK.
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37
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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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38
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Shoguchi E, Beedessee G, Tada I, Hisata K, Kawashima T, Takeuchi T, Arakaki N, Fujie M, Koyanagi R, Roy MC, Kawachi M, Hidaka M, Satoh N, Shinzato C. Two divergent Symbiodinium genomes reveal conservation of a gene cluster for sunscreen biosynthesis and recently lost genes. BMC Genomics 2018; 19:458. [PMID: 29898658 PMCID: PMC6001144 DOI: 10.1186/s12864-018-4857-9] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 06/06/2018] [Indexed: 11/10/2022] Open
Abstract
Background The marine dinoflagellate, Symbiodinium, is a well-known photosynthetic partner for coral and other diverse, non-photosynthetic hosts in subtropical and tropical shallows, where it comprises an essential component of marine ecosystems. Using molecular phylogenetics, the genus Symbiodinium has been classified into nine major clades, A-I, and one of the reported differences among phenotypes is their capacity to synthesize mycosporine-like amino acids (MAAs), which absorb UV radiation. However, the genetic basis for this difference in synthetic capacity is unknown. To understand genetics underlying Symbiodinium diversity, we report two draft genomes, one from clade A, presumed to have been the earliest branching clade, and the other from clade C, in the terminal branch. Results The nuclear genome of Symbiodinium clade A (SymA) has more gene families than that of clade C, with larger numbers of organelle-related genes, including mitochondrial transcription terminal factor (mTERF) and Rubisco. While clade C (SymC) has fewer gene families, it displays specific expansions of repeat domain-containing genes, such as leucine-rich repeats (LRRs) and retrovirus-related dUTPases. Interestingly, the SymA genome encodes a gene cluster for MAA biosynthesis, potentially transferred from an endosymbiotic red alga (probably of bacterial origin), while SymC has completely lost these genes. Conclusions Our analysis demonstrates that SymC appears to have evolved by losing gene families, such as the MAA biosynthesis gene cluster. In contrast to the conservation of genes related to photosynthetic ability, the terminal clade has suffered more gene family losses than other clades, suggesting a possible adaptation to symbiosis. Overall, this study implies that Symbiodinium ecology drives acquisition and loss of gene families. Electronic supplementary material The online version of this article (10.1186/s12864-018-4857-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Eiichi Shoguchi
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan.
| | - Girish Beedessee
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
| | - Ipputa Tada
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan.,Present address: Department of Genetics, School of Life Science, The Graduate University for Advanced Studies, 1111, Yata, Mishima-shi, Shizuoka, 411-8540, Japan
| | - Kanako Hisata
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
| | - Takeshi Kawashima
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan.,Present address: Center for Information Biology, National Institute of Genetics, Mishima, 411-8540, Japan
| | - Takeshi Takeuchi
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
| | - Nana Arakaki
- DNA Sequencing Section, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
| | - Manabu Fujie
- DNA Sequencing Section, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
| | - Ryo Koyanagi
- DNA Sequencing Section, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
| | - Michael C Roy
- Instrumental Analysis Section, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
| | - Masanobu Kawachi
- Center for Environmental Biology and Ecosystem Studies, National Institute for Environmental Studies, Tsukuba, 305-8506, Japan
| | - Michio Hidaka
- Department of Chemistry, Biology and Marine Science, University of the Ryukyus, Nishihara, Okinawa, 903-0213, Japan
| | - Noriyuki Satoh
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
| | - Chuya Shinzato
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan. .,Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwanoha, Kashiwa, 277-8564, Japan.
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39
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Zwang T, Tse ECM, Zhong D, Barton JK. A Compass at Weak Magnetic Fields Using Thymine Dimer Repair. ACS CENTRAL SCIENCE 2018; 4:405-412. [PMID: 29632887 PMCID: PMC5879481 DOI: 10.1021/acscentsci.8b00008] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Indexed: 05/05/2023]
Abstract
How birds sense the variations in Earth's magnetic field for navigation is poorly understood, although cryptochromes, proteins homologous to photolyases, have been proposed to participate in this magnetic sensing. Here, in electrochemical studies with an applied magnetic field, we monitor the repair of cyclobutane pyrimidine dimer lesions in duplex DNA by photolyase, mutants of photolyase, and a modified cryptochrome. We find that the yield of dimer repair is dependent on the strength and angle of the applied magnetic field even when using magnetic fields weaker than 1 gauss. This high sensitivity to weak magnetic fields depends upon a fast radical pair reaction on the thymines leading to repair. These data illustrate chemically how cyclobutane pyrimidine dimer repair may be used in a biological compass informed by variations in Earth's magnetic field.
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Affiliation(s)
- Theodore
J. Zwang
- Division
of Chemistry and Chemical Engineering, California
Institute of Technology, Pasadena, California 91125, United States
| | - Edmund C. M. Tse
- Division
of Chemistry and Chemical Engineering, California
Institute of Technology, Pasadena, California 91125, United States
| | - Dongping Zhong
- Departments
of Chemistry and Physics, The Ohio State
University, Columbus, Ohio 43210, United
States
- E-mail:
| | - Jacqueline K. Barton
- Division
of Chemistry and Chemical Engineering, California
Institute of Technology, Pasadena, California 91125, United States
- E-mail:
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40
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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: 11] [Impact Index Per Article: 1.8] [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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41
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Kopka B, Magerl K, Savitsky A, Davari MD, Röllen K, Bocola M, Dick B, Schwaneberg U, Jaeger KE, Krauss U. Electron transfer pathways in a light, oxygen, voltage (LOV) protein devoid of the photoactive cysteine. Sci Rep 2017; 7:13346. [PMID: 29042655 PMCID: PMC5645311 DOI: 10.1038/s41598-017-13420-1] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 09/21/2017] [Indexed: 11/17/2022] Open
Abstract
Blue-light absorption by the flavin chromophore in light, oxygen, voltage (LOV) photoreceptors triggers photochemical reactions that lead to the formation of a flavin-cysteine adduct. While it has long been assumed that adduct formation is essential for signaling, it was recently shown that LOV photoreceptor variants devoid of the photoactive cysteine can elicit a functional response and that flavin photoreduction to the neutral semiquinone radical is sufficient for signal transduction. Currently, the mechanistic basis of the underlying electron- (eT) and proton-transfer (pT) reactions is not well understood. We here reengineered pT into the naturally not photoreducible iLOV protein, a fluorescent reporter protein derived from the Arabidopsis thaliana phototropin-2 LOV2 domain. A single amino-acid substitution (Q489D) enabled efficient photoreduction, suggesting that an eT pathway is naturally present in the protein. By using a combination of site-directed mutagenesis, steady-state UV/Vis, transient absorption and electron paramagnetic resonance spectroscopy, we investigate the underlying eT and pT reactions. Our study provides strong evidence that several Tyr and Trp residues, highly conserved in all LOV proteins, constitute the eT pathway for flavin photoreduction, suggesting that the propensity for photoreduction is evolutionary imprinted in all LOV domains, while efficient pT is needed to stabilize the neutral semiquinone radical.
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Affiliation(s)
- Benita Kopka
- Institut für Molekulare Enzymtechnologie, Heinrich-Heine-Universität Düsseldorf, Forschungszentrum Jülich, 52426, Jülich, Germany
| | - Kathrin Magerl
- Institut für Physikalische und Theoretische Chemie, Universität Regensburg, 93053, Regensburg, Germany
| | - Anton Savitsky
- Max Planck Institute for Chemical Energy Conversion, 45470, Mülheim an der Ruhr, Germany
| | - Mehdi D Davari
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074, Aachen, Germany
| | - Katrin Röllen
- Institut für Molekulare Enzymtechnologie, Heinrich-Heine-Universität Düsseldorf, Forschungszentrum Jülich, 52426, Jülich, Germany
| | - Marco Bocola
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074, Aachen, Germany
| | - Bernhard Dick
- Institut für Physikalische und Theoretische Chemie, Universität Regensburg, 93053, Regensburg, Germany
| | - Ulrich Schwaneberg
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074, Aachen, Germany.,DWI-Leibniz Institute for Interactive Materials, Forckenbeckstraße 50, 52056, Aachen, Germany
| | - Karl-Erich Jaeger
- Institut für Molekulare Enzymtechnologie, Heinrich-Heine-Universität Düsseldorf, Forschungszentrum Jülich, 52426, Jülich, Germany.,IBG-1: Biotechnologie, Forschungszentrum Jülich, 52426, Jülich, Germany
| | - Ulrich Krauss
- Institut für Molekulare Enzymtechnologie, Heinrich-Heine-Universität Düsseldorf, Forschungszentrum Jülich, 52426, Jülich, Germany.
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42
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Zhang M, Wang L, Zhong D. Photolyase: Dynamics and electron-transfer mechanisms of DNA repair. Arch Biochem Biophys 2017; 632:158-174. [PMID: 28802828 DOI: 10.1016/j.abb.2017.08.007] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Revised: 08/07/2017] [Accepted: 08/07/2017] [Indexed: 11/16/2022]
Abstract
Photolyase, a flavoenzyme containing flavin adenine dinucleotide (FAD) molecule as a catalytic cofactor, repairs UV-induced DNA damage of cyclobutane pyrimidine dimer (CPD) and pyrimidine-pyrimidone (6-4) photoproduct using blue light. The FAD cofactor, conserved in the whole protein superfamily of photolyase/cryptochromes, adopts a unique folded configuration at the active site that plays a critical functional role in DNA repair. Here, we review our comprehensive characterization of the dynamics of flavin cofactor and its repair photocycles by different classes of photolyases on the most fundamental level. Using femtosecond spectroscopy and molecular biology, significant advances have recently been made to map out the entire dynamical evolution and determine actual timescales of all the catalytic processes in photolyases. The repair of CPD reveals seven electron-transfer (ET) reactions among ten elementary steps by a cyclic ET radical mechanism through bifurcating ET pathways, a direct tunneling route mediated by the intervening adenine and a two-step hopping path bridged by the intermediate adenine from the cofactor to damaged DNA, through the conserved folded flavin at the active site. The unified, bifurcated ET mechanism elucidates the molecular origin of various repair quantum yields of different photolyases from three life kingdoms. For 6-4 photoproduct repair, a similar cyclic ET mechanism operates and a new cyclic proton transfer with a conserved histidine residue at the active site of (6-4) photolyases is revealed.
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Affiliation(s)
- Meng Zhang
- Department of Physics, Department of Chemistry and Biochemistry, Programs of Biophysics, Chemical Physics, and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Lijuan Wang
- Department of Physics, Department of Chemistry and Biochemistry, Programs of Biophysics, Chemical Physics, and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Dongping Zhong
- Department of Physics, Department of Chemistry and Biochemistry, Programs of Biophysics, Chemical Physics, and Biochemistry, The Ohio State University, Columbus, OH 43210, USA.
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43
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Spampinato CP. Protecting DNA from errors and damage: an overview of DNA repair mechanisms in plants compared to mammals. Cell Mol Life Sci 2017; 74:1693-1709. [PMID: 27999897 PMCID: PMC11107726 DOI: 10.1007/s00018-016-2436-2] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Revised: 12/01/2016] [Accepted: 12/05/2016] [Indexed: 01/10/2023]
Abstract
The genome integrity of all organisms is constantly threatened by replication errors and DNA damage arising from endogenous and exogenous sources. Such base pair anomalies must be accurately repaired to prevent mutagenesis and/or lethality. Thus, it is not surprising that cells have evolved multiple and partially overlapping DNA repair pathways to correct specific types of DNA errors and lesions. Great progress in unraveling these repair mechanisms at the molecular level has been made by several talented researchers, among them Tomas Lindahl, Aziz Sancar, and Paul Modrich, all three Nobel laureates in Chemistry for 2015. Much of this knowledge comes from studies performed in bacteria, yeast, and mammals and has impacted research in plant systems. Two plant features should be mentioned. Plants differ from higher eukaryotes in that they lack a reserve germline and cannot avoid environmental stresses. Therefore, plants have evolved different strategies to sustain genome fidelity through generations and continuous exposure to genotoxic stresses. These strategies include the presence of unique or multiple paralogous genes with partially overlapping DNA repair activities. Yet, in spite (or because) of these differences, plants, especially Arabidopsis thaliana, can be used as a model organism for functional studies. Some advantages of this model system are worth mentioning: short life cycle, availability of both homozygous and heterozygous lines for many genes, plant transformation techniques, tissue culture methods and reporter systems for gene expression and function studies. Here, I provide a current understanding of DNA repair genes in plants, with a special focus on A. thaliana. It is expected that this review will be a valuable resource for future functional studies in the DNA repair field, both in plants and animals.
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Affiliation(s)
- Claudia P Spampinato
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI), Universidad Nacional de Rosario, Suipacha 531, 2000, Rosario, Argentina.
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44
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Zhang M, Wang L, Shu S, Sancar A, Zhong D. Bifurcating electron-transfer pathways in DNA photolyases determine the repair quantum yield. Science 2017; 354:209-213. [PMID: 27738168 DOI: 10.1126/science.aah6071] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 09/15/2016] [Indexed: 11/02/2022]
Abstract
Photolyase is a blue-light-activated enzyme that repairs ultraviolet-induced DNA damage that occurs in the form of cyclobutane pyrimidine dimers (CPDs) and pyrimidine-pyrimidone (6-4) photoproducts. Previous studies on microbial photolyases have revealed an electron-tunneling pathway that is critical for the repair mechanism. In this study, we used femtosecond spectroscopy to deconvolute seven electron-transfer reactions in 10 elementary steps in all classes of CPD photolyases. We report a unified electron-transfer pathway through a conserved structural configuration that bifurcates to favor direct tunneling in prokaryotes and a two-step hopping mechanism in eukaryotes. Both bifurcation routes are operative, but their relative contributions, dictated by the reduction potentials of the flavin cofactor and the substrate, determine the overall quantum yield of repair.
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Affiliation(s)
- Meng Zhang
- Department of Physics, Department of Chemistry and Biochemistry, and Programs of Biophysics, Chemical Physics, and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Lijuan Wang
- Department of Physics, Department of Chemistry and Biochemistry, and Programs of Biophysics, Chemical Physics, and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Shi Shu
- Department of Physics, Department of Chemistry and Biochemistry, and Programs of Biophysics, Chemical Physics, and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Aziz Sancar
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Dongping Zhong
- Department of Physics, Department of Chemistry and Biochemistry, and Programs of Biophysics, Chemical Physics, and Biochemistry, The Ohio State University, Columbus, OH 43210, USA.
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45
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Zhang M, Wang L, Zhong D. Photolyase: Dynamics and Mechanisms of Repair of Sun-Induced DNA Damage. Photochem Photobiol 2017; 93:78-92. [PMID: 27991674 DOI: 10.1111/php.12695] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 12/05/2016] [Indexed: 01/26/2023]
Abstract
Photolyase, a photomachine discovered half a century ago for repair of sun-induced DNA damage of cyclobutane pyrimidine dimers (CPDs) and pyrimidine (6-4) pyrimidone photoproducts (6-4PPs), has been characterized extensively in biochemistry (function), structure and dynamics since 1980s. The molecular mechanism and repair photocycle have been revealed at the most fundamental level. Using femtosecond spectroscopy, we have mapped out the entire dynamical evolution and determined all actual timescales of the catalytic processes. Here, we review our recent efforts in studies of the dynamics of DNA repair by photolyases. The repair of CPDs in three life kingdoms includes seven electron transfer (ET) reactions among 10 elementary steps through initial bifurcating ET pathways, a direct tunneling route and a two-step hopping path both through an intervening adenine from the cofactor to CPD, with a conserved folded structure at the active site. The repair of 6-4PPs is challenging and requires similar ET reactions and a new cyclic proton transfer with a conserved histidine residue at the active site of (6-4) photolyases. Finally, we also summarize our efforts on multiple intraprotein ET of photolyases in different redox states and such mechanistic studies are critical to the functional mechanism of homologous cryptochromes of blue-light photoreceptors.
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Affiliation(s)
- Meng Zhang
- Department of Physics, The Ohio State University, Columbus, OH.,Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH.,Programs of Biophysics, Chemical Physics, and Biochemistry, The Ohio State University, Columbus, OH
| | - Lijuan Wang
- Department of Physics, The Ohio State University, Columbus, OH.,Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH.,Programs of Biophysics, Chemical Physics, and Biochemistry, The Ohio State University, Columbus, OH
| | - Dongping Zhong
- Department of Physics, The Ohio State University, Columbus, OH.,Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH.,Programs of Biophysics, Chemical Physics, and Biochemistry, The Ohio State University, Columbus, OH
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46
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Kondoh M, Terazima M. Conformational and Intermolecular Interaction Dynamics of Photolyase/Cryptochrome Proteins Monitored by the Time-Resolved Diffusion Technique. Photochem Photobiol 2017; 93:15-25. [DOI: 10.1111/php.12681] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 11/18/2016] [Indexed: 11/30/2022]
Affiliation(s)
- Masato Kondoh
- Department of Chemistry; Graduate School of Pure and Applied Sciences; University of Tsukuba; Tsukuba Ibaraki Japan
| | - Masahide Terazima
- Department of Chemistry; Graduate School of Science; Kyoto University; Sakyo-ku, Kyoto Japan
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47
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Faraji S, Dreuw A. Insights into Light-driven DNA Repair by Photolyases: Challenges and Opportunities for Electronic Structure Theory. Photochem Photobiol 2017; 93:37-50. [PMID: 27925218 DOI: 10.1111/php.12679] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 11/18/2016] [Indexed: 01/25/2023]
Abstract
Ultraviolet radiation causes two of the most abundant mutagenic and cytotoxic DNA lesions: cyclobutane pyrimidine dimers and 6-4 photoproducts. (6-4) Photolyases are light-activated enzymes that selectively bind to DNA and trigger repair of mutagenic 6-4 photoproducts via photoinduced electron transfer from flavin adenine dinucleotide anion (FADH- ) to the lesion triggering repair. This review provides an overview of the sequential steps of the repair process, that is light absorption and resonance energy transfer, photoinduced electron transfer and electron-induced splitting mechanisms, with an emphasis on the role of theory and computation. In addition, theoretical calculations and physical properties that can be used to classify specific mechanism are discussed in an effort to trace the fundamental aspects of each individual step and assist the interpretation of experimental data. The current challenges and suggested future directions are outlined for each step, concluding with a view on the future.
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Affiliation(s)
- Shirin Faraji
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls Heidelberg University, Heidelberg, Germany
| | - Andreas Dreuw
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls Heidelberg University, Heidelberg, Germany
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48
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Breker M, Lieberman K, Tulin F, Cross FR. High-Throughput Robotically Assisted Isolation of Temperature-sensitive Lethal Mutants in Chlamydomonas reinhardtii. J Vis Exp 2016. [PMID: 28060315 PMCID: PMC5226362 DOI: 10.3791/54831] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Systematic identification and characterization of genetic perturbations have proven useful to decipher gene function and cellular pathways. However, the conventional approaches of permanent gene deletion cannot be applied to essential genes. We have pioneered a unique collection of ~70 temperature-sensitive (ts) lethal mutants for studying cell cycle regulation in the unicellular green algae Chlamydomonas reinhardtii1. These mutations identify essential genes, and the ts alleles can be conditionally inactivated by temperature shift, providing valuable tools to identify and analyze essential functions. Mutant collections are much more valuable if they are close to comprehensive, since scattershot collections can miss important components. However, this requires the efficient collection of a large number of mutants, especially in a wide-target screen. Here, we describe a robotics-based pipeline for generating ts lethal mutants and analyzing their phenotype in Chlamydomonas. This technique can be applied to any microorganism that grows on agar. We have collected over 3000 ts mutants, probably including mutations in most or all cell-essential pathways, including about 200 new candidate cell cycle mutations. Subsequent molecular and cellular characterization of these mutants should provide new insights in plant cell biology; a comprehensive mutant collection is an essential prerequisite to ensure coverage of a broad range of biological pathways. These methods are integrated with downstream genetics and bioinformatics procedures for efficient mapping and identification of the causative mutations that are beyond the scope of this manuscript.
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Affiliation(s)
- Michal Breker
- Laboratory of Cell Cycle Genetics, The Rockefeller University
| | | | - Frej Tulin
- Sainsbury Laboratory, University of Cambridge
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49
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von Zadow A, Ignatz E, Pokorny R, Essen LO, Klug G. Rhodobacter sphaeroides CryB is a bacterial cryptochrome with (6-4) photolyase activity. FEBS J 2016; 283:4291-4309. [PMID: 27739235 DOI: 10.1111/febs.13924] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Revised: 09/20/2016] [Accepted: 10/11/2016] [Indexed: 11/30/2022]
Abstract
Photolyases are efficient DNA repair enzymes that specifically repair either cyclobutane pyrimidine dimers or (6-4) photoproducts in a light-dependent cleavage reaction. The closely related classical cryptochrome blue light photoreceptors do not repair DNA lesions; instead they are involved in regulatory processes. CryB of Rhodobacter sphaeroides was until now described as a cryptochrome that affects light-dependent and singlet oxygen-dependent gene expression and is unusual in terms of its cofactor composition. Here we present evidence for a repair activity of (6-4) photoproducts by CryB and suggest a dual character combining the functions of cryptochromes and photolyases. We investigated the effects of crucial amino acids involved in cofactor or DNA lesion binding on the light-dependent recovery of cells after UV light exposure (in vivo photoreactivation). Remarkably, impairment of one of the two light absorbing cofactors, FAD or 6,7-dimethyl-8-ribityllumazine, only marginally affected the final survival rate but strongly decelerated photoreactivation kinetics. The impairment of both of them together through mutagenesis decreased CryB-dependent photoreactivation to the level of the ∆cryB knockout strain. The third cofactor, a [4Fe4S] iron-sulfur cluster, is indispensable for the structural integrity of the protein. The reduction of FAD via the conserved tryptophan W338, which is crucial for in vitro reduction and consequently DNA repair, is not required for in vivo photoreactivation, suggesting that this reduction pathway to FAD is dispensable in the cellular environment. This demonstrates that in vitro experiments give only limited information on in vivo photolyase activity.
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Affiliation(s)
- Andrea von Zadow
- Institute of Microbiology and Molecular Biology, Giessen University, Germany
| | - Elisabeth Ignatz
- Structural Biochemistry, Department of Chemistry, Philipps University Marburg, Germany
| | - Richard Pokorny
- Department of Plant Physiology and Photobiology, Faculty of Biology, Philipps University Marburg, Germany
| | - Lars-Oliver Essen
- Structural Biochemistry, Department of Chemistry, Philipps University Marburg, Germany
| | - Gabriele Klug
- Institute of Microbiology and Molecular Biology, Giessen University, Germany
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50
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Pauszek RF, Kodali G, Siddiqui MSU, Stanley RJ. Overlapping Electronic States with Nearly Parallel Transition Dipole Moments in Reduced Anionic Flavin Can Distort Photobiological Dynamics. J Am Chem Soc 2016; 138:14880-14889. [PMID: 27686753 DOI: 10.1021/jacs.6b06449] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Chromophoric biomolecules are exploited as reporters of a diverse set of phenomena, acting as internal distance monitors, environment and redox sensors, and endogenous imaging probes. The extent to which they can be exploited is dependent on an accurate knowledge of their fundamental electronic properties. Arguably of greatest importance is a precise knowledge of the direction(s) of the absorption transition dipole moment(s) (TDMs) in the molecular frame of reference. Such is the case for flavins, fluorescent redox cofactors utilized for ground- and excited-state redox and photochemical processes. The directions of the TDMs in oxidized and semiquinone flavins were characterized decades ago, and the details of charge redistribution in these forms have also been studied by Stark spectroscopy. The electronic structure of the fully reduced hydroquinone anionic state, FlH-, however, has been the subject of unfounded assumptions and estimates about the number and direction of TDMs in FlH-, as well the electronic structure changes that occur upon light absorption. Here we have used Stark spectroscopy to measure the magnitude and direction of charge redistribution in FlH- upon optical excitation. These data were analyzed using TD-DFT calculations. The results show unequivocally that not one but two nearly orientation-degenerate electronic transitions are required to explain the 340-500 nm absorption spectral range, demolishing the commonly held assumption of a single transition. The difference dipole moments for these states show that electron density shifts toward the xylene ring for both transitions. These measurements force a reappraisal of previous studies that have used erroneous assumptions and unsubstantiated estimates of these quantities. The results put future optical studies of reduced flavins/flavoproteins on a firm photophysical footing.
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Affiliation(s)
- Raymond F Pauszek
- Department of Chemistry, Temple University , 250B Beury Hall, 1901 North 13th Street, Philadelphia, Pennsylvania 19122, United States
| | - Goutham Kodali
- Department of Chemistry, Temple University , 250B Beury Hall, 1901 North 13th Street, Philadelphia, Pennsylvania 19122, United States
| | - M Salim U Siddiqui
- Department of Chemistry, Temple University , 250B Beury Hall, 1901 North 13th Street, Philadelphia, Pennsylvania 19122, United States
| | - Robert J Stanley
- Department of Chemistry, Temple University , 250B Beury Hall, 1901 North 13th Street, Philadelphia, Pennsylvania 19122, United States
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