Visualizing the DNA repair process by a photolyase at atomic resolution-Reference-Cited by-同舟云学术

Visualizing the DNA repair process by a photolyase at atomic resolution

Published:2023-12 Issue:6674 Volume:382 Page:
ISSN:0036-8075
Container-title:Science
language:en
Short-container-title:Science

Author:

Maestre-Reyna Manuel¹²^ORCID,Wang Po-Hsun¹^ORCID,Nango Eriko³⁴^ORCID,Hosokawa Yuhei¹²⁵^ORCID,Saft Martin⁶^ORCID,Furrer Antonia⁷^ORCID,Yang Cheng-Han¹^ORCID,Gusti Ngurah Putu Eka Putra¹^ORCID,Wu Wen-Jin¹^ORCID,Emmerich Hans-Joachim⁶^ORCID,Caramello Nicolas⁸⁹^ORCID,Franz-Badur Sophie⁶^ORCID,Yang Chao¹⁰^ORCID,Engilberge Sylvain⁸¹¹^ORCID,Wranik Maximilian⁷^ORCID,Glover Hannah Louise⁷^ORCID,Weinert Tobias⁷^ORCID,Wu Hsiang-Yi¹^ORCID,Lee Cheng-Chung¹^ORCID,Huang Wei-Cheng¹^ORCID,Huang Kai-Fa¹^ORCID,Chang Yao-Kai¹^ORCID,Liao Jiahn-Haur¹^ORCID,Weng Jui-Hung¹^ORCID,Gad Wael¹^ORCID,Chang Chiung-Wen¹,Pang Allan H.¹^ORCID,Yang Kai-Chun²,Lin Wei-Ting²^ORCID,Chang Yu-Chen²^ORCID,Gashi Dardan⁷,Beale Emma⁷^ORCID,Ozerov Dmitry⁷^ORCID,Nass Karol⁷^ORCID,Knopp Gregor⁷^ORCID,Johnson Philip J. M.⁷^ORCID,Cirelli Claudio⁷^ORCID,Milne Chris⁷^ORCID,Bacellar Camila⁷^ORCID,Sugahara Michihiro³,Owada Shigeki³¹²^ORCID,Joti Yasumasa³¹²^ORCID,Yamashita Ayumi³¹³^ORCID,Tanaka Rie³¹³^ORCID,Tanaka Tomoyuki³¹³,Luo Fangjia¹²^ORCID,Tono Kensuke³¹²^ORCID,Zarzycka Wiktoria¹⁴,Müller Pavel¹⁴^ORCID,Alahmad Maisa Alkheder⁶^ORCID,Bezold Filipp⁶^ORCID,Fuchs Valerie⁶^ORCID,Gnau Petra⁶,Kiontke Stephan⁶^ORCID,Korf Lukas⁶^ORCID,Reithofer Viktoria⁶^ORCID,Rosner Christian Joshua⁶,Seiler Elisa Marie⁶^ORCID,Watad Mohamed⁶,Werel Laura⁶,Spadaccini Roberta⁶¹⁵^ORCID,Yamamoto Junpei⁵^ORCID,Iwata So³¹³^ORCID,Zhong Dongping¹⁰¹⁶¹⁷^ORCID,Standfuss Jörg⁷^ORCID,Royant Antoine⁸¹¹^ORCID,Bessho Yoshitaka¹³^ORCID,Essen Lars-Oliver⁶^ORCID,Tsai Ming-Daw¹¹⁸^ORCID

Affiliation:

1. Institute of Biological Chemistry, Academia Sinica, 128 Academia Rd. Sec. 2, Nankang, Taipei 115, Taiwan.

2. Department of Chemistry, National Taiwan University, 1, Roosevelt Rd. Sec. 4, Taipei 106, Taiwan.

3. RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan.

4. Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577, Japan.

5. Division of Chemistry, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan.

6. Department of Chemistry, Philipps University Marburg, Hans-Meerwein Strasse 4, Marburg 35032, Germany.

7. Paul Scherrer Institute, Forschungstrasse 111, 5232 Villigen PSI, Switzerland.

8. European Synchrotron Radiation Facility, 38043 Grenoble, France.

9. Hamburg Centre for Ultrafast Imaging, Universität Hamburg, 22761 Hamburg, Germany.

10. Department of Physics, The Ohio State University, Columbus, OH 43210, USA.

11. Université Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), 38044 Grenoble, France.

12. Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5198, Japan.

13. Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan.

14. Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France.

15. Dipartimento di Scienze e tecnologie, Universita degli studi del Sannio, Benevento, Italy.

16. Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA.

17. Center for Ultrafast Science and Technology, Shanghai Jiao Tong University, Shanghai 200240, China.

18. Institute of Biochemical Sciences, National Taiwan University, 1, Roosevelt Rd. Sec. 4, Taipei 106, Taiwan.

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.

Publisher

American Association for the Advancement of Science (AAAS)

Subject

Multidisciplinary

Link

https://www.science.org/doi/pdf/10.1126/science.add7795

Reference93 articles.

1. Photolyase: Dynamics and electron-transfer mechanisms of DNA repair

2. Light-driven DNA repair by photolyases

3. Influence of cytosine methylation on ultraviolet-induced cyclobutane pyrimidine dimer formation in genomic DNA

4. Direct observation of thymine dimer repair in DNA by photolyase

5. Reaction mechanisms of DNA photolyase

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