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Cellini A, Yuan Wahlgren W, Henry L, Pandey S, Ghosh S, Castillon L, Claesson E, Takala H, Kübel J, Nimmrich A, Kuznetsova V, Nango E, Iwata S, Owada S, Stojković EA, Schmidt M, Ihalainen JA, Westenhoff S. The three-dimensional structure of Drosophila melanogaster (6-4) photolyase at room temperature. Acta Crystallogr D Struct Biol 2021; 77:1001-1009. [PMID: 34342273 PMCID: PMC8329860 DOI: 10.1107/s2059798321005830] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 06/06/2021] [Indexed: 11/10/2022] Open
Abstract
(6-4) photolyases are flavoproteins that belong to the photolyase/cryptochrome family. Their function is to repair DNA lesions using visible light. Here, crystal structures of Drosophila melanogaster (6-4) photolyase [Dm(6-4)photolyase] at room and cryogenic temperatures are reported. The room-temperature structure was solved to 2.27 Å resolution and was obtained by serial femtosecond crystallography (SFX) using an X-ray free-electron laser. The crystallization and preparation conditions are also reported. The cryogenic structure was solved to 1.79 Å resolution using conventional X-ray crystallography. The structures agree with each other, indicating that the structural information obtained from crystallography at cryogenic temperature also applies at room temperature. Furthermore, UV-Vis absorption spectroscopy confirms that Dm(6-4)photolyase is photoactive in the crystals, giving a green light to time-resolved SFX studies on the protein, which can reveal the structural mechanism of the photoactivated protein in DNA repair.
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Affiliation(s)
- Andrea Cellini
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 405 30 Gothenburg, Sweden
| | - Weixiao Yuan Wahlgren
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 405 30 Gothenburg, Sweden
| | - Léocadie Henry
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 405 30 Gothenburg, Sweden
| | - Suraj Pandey
- Physics Department, University of Wisconsin-Milwaukee, 3135 North Maryland Avenue, Milwaukee, WI 53211, USA
| | - Swagatha Ghosh
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 405 30 Gothenburg, Sweden
| | - Leticia Castillon
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 405 30 Gothenburg, Sweden
| | - Elin Claesson
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 405 30 Gothenburg, Sweden
| | - Heikki Takala
- Department of Biological and Environmental Science, Nanoscience Center, University of Jyvaskyla, 40014 Jyvaskyla, Finland
- Department of Anatomy, Faculty of Medicine, University of Helsinki, Box 63, 00014 Helsinki, Finland
| | - Joachim Kübel
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 405 30 Gothenburg, Sweden
| | - Amke Nimmrich
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 405 30 Gothenburg, Sweden
| | - Valentyna Kuznetsova
- Department of Biological and Environmental Science, Nanoscience Center, University of Jyvaskyla, 40014 Jyvaskyla, Finland
| | - Eriko Nango
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577, Japan
| | - So Iwata
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Shigeki Owada
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Emina A. Stojković
- Department of Biology, Northeastern Illinois University, 5500 North St Louis Avenue, Chicago, IL 60625, USA
| | - Marius Schmidt
- Physics Department, University of Wisconsin-Milwaukee, 3135 North Maryland Avenue, Milwaukee, WI 53211, USA
| | - Janne A. Ihalainen
- Department of Biological and Environmental Science, Nanoscience Center, University of Jyvaskyla, 40014 Jyvaskyla, Finland
| | - Sebastian Westenhoff
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 405 30 Gothenburg, Sweden
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Abstract
Anthozoan corals are an ecologically important group of cnidarians, which power the productivity of reef ecosystems. They are sessile, inhabit shallow, tropical oceans and are highly dependent on sun- and moonlight to regulate sexual reproduction, phototaxis, and photosymbiosis. However, their exposure to high levels of sunlight also imposes an increased risk of UV-induced DNA damage. How have these challenging photic environments influenced photoreceptor evolution and function in these animals? To address this question, we initially screened the cnidarian photoreceptor repertoire for Anthozoa-specific signatures by a broad-scale evolutionary analysis. We compared transcriptomic data of more than 36 cnidarian species and revealed a more diverse photoreceptor repertoire in the anthozoan subphylum than in the subphylum Medusozoa. We classified the three principle opsin classes into distinct subtypes and showed that Anthozoa retained all three classes, which diversified into at least six subtypes. In contrast, in Medusozoa, only one class with a single subtype persists. Similarly, in Anthozoa, we documented three photolyase classes and two cryptochrome (CRY) classes, whereas CRYs are entirely absent in Medusozoa. Interestingly, we also identified one anthozoan CRY class, which exhibited unique tandem duplications of the core functional domains. We next explored the functionality of anthozoan photoreceptors in the model species Exaiptasia diaphana (Aiptasia), which recapitulates key photo-behaviors of corals. We show that the diverse opsin genes are differentially expressed in important life stages common to reef-building corals and Aiptasia and that CRY expression is light regulated. We thereby provide important clues linking coral evolution with photoreceptor diversification.
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Affiliation(s)
- Sebastian G Gornik
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
| | | | - Benoit Morel
- Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
| | - Alexandros Stamatakis
- Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany.,Institute for Theoretical Informatics, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Nicholas S Foulkes
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany.,Institute of Biological and Chemical Systems, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
| | - Annika Guse
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
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Abstract
The adverse effects of global climate change combined with an exponentially increasing human population have put substantial constraints on agriculture, accelerating efforts towards ensuring food security for a sustainable future. Conventional plant breeding and modern technologies have led to the creation of plants with better traits and higher productivity. Most crop improvement approaches (conventional breeding, genome modification, and gene editing) primarily rely on DNA repair and recombination (DRR). Studying plant DRR can provide insights into designing new strategies or improvising the present techniques for crop improvement. Even though plants have evolved specialized DRR mechanisms compared to other eukaryotes, most of our insights about plant-DRRs remain rooted in studies conducted in animals. DRR mechanisms in plants include direct repair, nucleotide excision repair (NER), base excision repair (BER), mismatch repair (MMR), non-homologous end joining (NHEJ) and homologous recombination (HR). Although each DRR pathway acts on specific DNA damage, there is crosstalk between these. Considering the importance of DRR pathways as a tool in crop improvement, this review focuses on a general description of each DRR pathway, emphasizing on the structural aspects of key DRR proteins. The review highlights the gaps in our understanding and the importance of studying plant DRR in the context of crop improvement.
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Affiliation(s)
- Prabha Verma
- National Institute of Plant Genome Research, New Delhi, India
| | - Reetika Tandon
- National Institute of Plant Genome Research, New Delhi, India
| | - Gitanjali Yadav
- National Institute of Plant Genome Research, New Delhi, India
| | - Vineet Gaur
- National Institute of Plant Genome Research, New Delhi, India
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Xu L, Wen B, Shao W, Yao P, Zheng W, Zhou Z, Zhang Y, Zhu G. Impacts of Cys392, Asp393, and ATP on the FAD Binding, Photoreduction, and the Stability of the Radical State of Chlamydomonas reinhardtii Cryptochrome. Chembiochem 2019; 20:940-948. [PMID: 30548754 DOI: 10.1002/cbic.201800660] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2018] [Indexed: 12/16/2022]
Abstract
Plant cryptochromes (CRYs) are blue-light receptors that regulate light-dependent growth, development, and circadian rhythms. A flavin adenine dinucleotide (FAD) cofactor is bound to the photolyase homology region (PHR) of plant CRYs and can be photoreduced to a neutral radical state under blue light. This photoreaction can trigger subsequent signal transduction. Plant CRYs can also bind an ATP molecule adjacent to FAD in a pocket of the PHR. Chlamydomonas reinhardtii contains a single plant CRY, named Chlamydomonas photolyase homologue 1 (CPH1). In CPH1, Cys392 and Asp393 are located near the FAD cofactor. Here we have shown that replacing Cys392 with Ser has little effect on the properties of CPH1. The C392N mutant, however, showed a faster photoreduction rate than wild-type CPH1, together with a significantly lower oxidation rate of the neutral radical state. Substituting an Asn residue for Asp393 in CPH1 improved the binding affinity for FAD as well as the stability of the neutral radical, but photoreduction in the case of this mutant was severely inhibited. In the presence of ATP, CPH1 and its mutants exhibited significantly higher binding affinity for FAD and slower oxidation of the neutral radical. These results reveal that the residues at site 392 and the presence of ATP can tune the stability of the neutral radical, that the Asp residue at site 393 is crucial for photoreduction, and that the photoreduction rate is not determined merely by the stability of the neutral radical in CPH1.
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Affiliation(s)
- Lei Xu
- Anhui Province Key Laboratory of Active Biological Macromolecules, Wannan Medical College, 22# Wenchang West Road, Wuhu, 241002, Anhui, P. R. China
| | - Bin Wen
- Institute of Molecular Biology and Biotechnology, Anhui Normal University, 1# Beijing East Road, Wuhu, 241000, Anhui, P. R. China
| | - Wengui Shao
- Anhui Province Key Laboratory of Active Biological Macromolecules, Wannan Medical College, 22# Wenchang West Road, Wuhu, 241002, Anhui, P. R. China
| | - Pengcheng Yao
- Anhui Province Key Laboratory of Active Biological Macromolecules, Wannan Medical College, 22# Wenchang West Road, Wuhu, 241002, Anhui, P. R. China
| | - Wei Zheng
- Anhui Province Key Laboratory of Active Biological Macromolecules, Wannan Medical College, 22# Wenchang West Road, Wuhu, 241002, Anhui, P. R. China
| | - Zhiqiang Zhou
- Anhui Province Key Laboratory of Active Biological Macromolecules, Wannan Medical College, 22# Wenchang West Road, Wuhu, 241002, Anhui, P. R. China
| | - Yao Zhang
- Anhui Province Key Laboratory of Active Biological Macromolecules, Wannan Medical College, 22# Wenchang West Road, Wuhu, 241002, Anhui, P. R. China
| | - Guoping Zhu
- Institute of Molecular Biology and Biotechnology, Anhui Normal University, 1# Beijing East Road, Wuhu, 241000, Anhui, P. R. China
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Xu L, Wen B, Wang Y, Tian C, Wu M, Zhu G. Residues at a Single Site Differentiate Animal Cryptochromes from Cyclobutane Pyrimidine Dimer Photolyases by Affecting the Proteins' Preferences for Reduced FAD. Chembiochem 2017; 18:1129-1137. [PMID: 28393477 DOI: 10.1002/cbic.201700145] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Indexed: 12/29/2022]
Abstract
Cryptochromes (CRYs) and photolyases belong to the cryptochrome/photolyase family (CPF). Reduced FAD is essential for photolyases to photorepair UV-induced cyclobutane pyrimidine dimers (CPDs) or 6-4 photoproducts in DNA. In Drosophila CRY (dCRY, a type I animal CRY), FAD is converted to the anionic radical but not to the reduced state upon illumination, which might induce a conformational change in the protein to relay the light signal downstream. To explore the foundation of these differences, multiple sequence alignment of 650 CPF protein sequences was performed. We identified a site facing FAD (Ala377 in Escherichia coli CPD photolyase and Val415 in dCRY), hereafter referred to as "site 377", that was distinctly conserved across these sequences: CPD photolyases often had Ala, Ser, or Asn at this site, whereas animal CRYs had Ile, Leu, or Val. The binding affinity for reduced FAD, but not the photorepair activity of E. coli photolyase, was dramatically impaired when replacing Ala377 with any of the three CRY residues. Conversely, in V415S and V415N mutants of dCRY, FAD was photoreduced to its fully reduced state after prolonged illumination, and light-dependent conformational changes of these mutants were severely inhibited. We speculate that the residues at site 377 play a key role in the different preferences of CPF proteins for reduced FAD, which differentiate animal CRYs from CPD photolyases.
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Affiliation(s)
- Lei Xu
- Institute of Molecular Biology and Biotechnology, Anhui Normal University, 1# Beijing East Road, Wuhu, 241000, Anhui, China.,Anhui Province Key Laboratory of Active Biological Macro-Molecules, Wannan Medical College, 22# Wenchang West Road, Wuhu, 241002, Anhui, China
| | - Bin Wen
- Institute of Molecular Biology and Biotechnology, Anhui Normal University, 1# Beijing East Road, Wuhu, 241000, Anhui, China.,Anhui Province Key Laboratory of Active Biological Macro-Molecules, Wannan Medical College, 22# Wenchang West Road, Wuhu, 241002, Anhui, China
| | - Yuan Wang
- Institute of Molecular Biology and Biotechnology, Anhui Normal University, 1# Beijing East Road, Wuhu, 241000, Anhui, China
| | - Changqing Tian
- Institute of Molecular Biology and Biotechnology, Anhui Normal University, 1# Beijing East Road, Wuhu, 241000, Anhui, China
| | - Mingcai Wu
- Institute of Molecular Biology and Biotechnology, Anhui Normal University, 1# Beijing East Road, Wuhu, 241000, Anhui, China.,Anhui Province Key Laboratory of Active Biological Macro-Molecules, Wannan Medical College, 22# Wenchang West Road, Wuhu, 241002, Anhui, China
| | - Guoping Zhu
- Institute of Molecular Biology and Biotechnology, Anhui Normal University, 1# Beijing East Road, Wuhu, 241000, Anhui, China
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Abstract
In 1942, Walls described the concept of a 'nocturnal bottleneck' in placental mammals, where these species could survive only by avoiding daytime activity during times in which dinosaurs were the dominant taxon. Walls based this concept of a longer episode of nocturnality in early eutherian mammals by comparing the visual systems of reptiles, birds and all three extant taxa of the mammalian lineage, namely the monotremes, marsupials (now included in the metatherians) and placentals (included in the eutherians). This review describes the status of what has become known as the nocturnal bottleneck hypothesis, giving an overview of the chronobiological patterns of activity. We review the ecological plausibility that the activity patterns of (early) eutherian mammals were restricted to the night, based on arguments relating to endothermia, energy balance, foraging and predation, taking into account recent palaeontological information. We also assess genes, relating to light detection (visual and non-visual systems) and the photolyase DNA protection system that were lost in the eutherian mammalian lineage. Our conclusion presently is that arguments in favour of the nocturnal bottleneck hypothesis in eutherians prevail.
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Affiliation(s)
- Menno P Gerkema
- Centre for Behaviour and Neuroscience, Department of Chronobiology, University of Groningen, Groningen, The Netherlands.
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7
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Faraji S, Wirz L, Dreuw A. Quantum chemical study of the enzymatic repair of T(6-4)C/C(6-4)T UV-photolesions by DNA photolyases. Chemphyschem 2013; 14:2817-24. [PMID: 23821498 DOI: 10.1002/cphc.201300223] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2013] [Indexed: 11/10/2022]
Abstract
Several strategies have evolved to repair one of the abundant UV radiation-induced damages caused to DNA, namely the mutagenic pyrimidine (6-4) pyrimidone photolesions. DNA (6-4)-photolyases are enzymes repairing these lesions by a photoinitiated electron transfer. An important aspect of a possible repair mechanism is its generality and transferability to different (6-4) lesions. Therefore, previously suggested mechanisms for the repair of the T(6-4)T lesion are here transferred to the T(6-4)C and C(6-4)T lesions and investigated theoretically using quantum chemical methods. Despite the different functional groups of the pyrimidine bases involved, a general valid molecular mechanism was identified, in which the initial step is an electron transfer coupled to a proton transfer from the protonated HIS365 to the N3(') nitrogen of the 3(') pyrimidine, followed by an intramolecular OH/NH2 transfer in one concerted step, which does not require an oxetane/azetidine or isolated water/ammonia intermediate.
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Affiliation(s)
- Shirin Faraji
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 368, 69120 Heidelberg, Germany.
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Yamamoto J, Martin R, Iwai S, Plaza P, Brettel K. Repair of the (6-4) photoproduct by DNA photolyase requires two photons. Angew Chem Int Ed Engl 2013; 52:7432-6. [PMID: 23761226 DOI: 10.1002/anie.201301567] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2013] [Revised: 04/06/2013] [Indexed: 11/06/2022]
Abstract
It takes two (photons) to tango: Single-turnover flash experiments showed that the flavoenzyme (6-4) photolyase uses a successive two-photon mechanism to repair the UV-induced T(6-4)T lesion in DNA (see picture). The intermediate (X) formed by the first photoreaction is likely to be the oxetane-bridged dimer T(ox)T. The enzyme could stabilize the normally short-lived T(ox)T, allowing repair to be completed by the second photoreaction.
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Affiliation(s)
- Junpei Yamamoto
- Division of Chemistry, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan.
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Affiliation(s)
- Anja Schwögler
- Fachbereich Chemie Philipps-Universität Marburg Hans-Meerwein-Strasse, 35032 Marburg (Germany) Fax: (+49) 6421-2822189
| | - Lars T Burgdorf
- Fachbereich Chemie Philipps-Universität Marburg Hans-Meerwein-Strasse, 35032 Marburg (Germany) Fax: (+49) 6421-2822189
| | - Thomas Carell
- Fachbereich Chemie Philipps-Universität Marburg Hans-Meerwein-Strasse, 35032 Marburg (Germany) Fax: (+49) 6421-2822189
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