1
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Ren Z, Zhang F, Kang W, Wang C, Shin H, Zeng X, Gunawardana S, Bowatte K, Krauß N, Lamparter T, Yang X. Spin-Coupled Electron Densities of Iron-Sulfur Cluster Imaged by In Situ Serial Laue Diffraction. Chem 2024; 10:2103-2130. [PMID: 39170732 PMCID: PMC11335340 DOI: 10.1016/j.chempr.2024.02.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/23/2024]
Abstract
Iron-sulfur clusters are inorganic cofactors found in many proteins involved in fundamental biological processes. The prokaryotic DNA repair photolyase PhrB carries a four-iron-four-sulfur cluster ([4Fe4S]) in addition to the catalytic flavin adenine dinucleotide (FAD) and a second cofactor ribolumazine. Our recent study suggested that the [4Fe4S] cluster functions as an electron cache to coordinate two interdependent photoreactions of the FAD and ribolumazine. Here we report the crystallography observations of light-induced responses in PhrB using the cryo-trapping method and in situ serial Laue diffraction at room temperature. We capture strong signals that depict electron density changes arising from quantized electronic movements in the [4Fe4S] cluster. Our data reveal the mixed valence layers of the [4Fe4S] cluster due to spin coupling and their dynamic responses to light-induced redox changes. The quantum effects imaged by decomposition of electron density changes have shed light on the emerging roles of metal clusters in proteins.
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Affiliation(s)
- Zhong Ren
- Department of Chemistry, University of Illinois Chicago, Chicago, IL 60607, USA
- Renz Research, Inc., Westmont, IL 60559, USA
- Lead contact
| | - Fan Zhang
- Botanical Institute, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Weijia Kang
- Department of Chemistry, University of Illinois Chicago, Chicago, IL 60607, USA
| | - Cong Wang
- Department of Chemistry, University of Illinois Chicago, Chicago, IL 60607, USA
| | - Heewhan Shin
- Department of Chemistry, University of Illinois Chicago, Chicago, IL 60607, USA
| | - Xiaoli Zeng
- Department of Chemistry, University of Illinois Chicago, Chicago, IL 60607, USA
| | - Semini Gunawardana
- Department of Chemistry, University of Illinois Chicago, Chicago, IL 60607, USA
| | - Kalinga Bowatte
- Department of Chemistry, University of Illinois Chicago, Chicago, IL 60607, USA
| | - Norbert Krauß
- Botanical Institute, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Tilman Lamparter
- Botanical Institute, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Xiaojing Yang
- Department of Chemistry, University of Illinois Chicago, Chicago, IL 60607, USA
- Department of Ophthalmology and Vision Sciences, University of Illinois Chicago, Chicago, IL 60607, USA
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2
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Ren Z, Yang X. Deconvolution of dynamic heterogeneity in protein structure. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2024; 11:041302. [PMID: 39165899 PMCID: PMC11335360 DOI: 10.1063/4.0000261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Accepted: 07/30/2024] [Indexed: 08/22/2024]
Abstract
Heterogeneity is intrinsic to the dynamic process of a chemical reaction. As reactants are converted to products via intermediates, the nature and extent of heterogeneity vary temporally throughout the duration of the reaction and spatially across the molecular ensemble. The goal of many biophysical techniques, including crystallography and spectroscopy, is to establish a reaction trajectory that follows an experimentally provoked dynamic process. It is essential to properly analyze and resolve heterogeneity inevitably embedded in experimental datasets. We have developed a deconvolution technique based on singular value decomposition (SVD), which we have rigorously practiced in diverse research projects. In this review, we recapitulate the motivation and challenges in addressing the heterogeneity problem and lay out the mathematical foundation of our methodology that enables isolation of chemically sensible structural signals. We also present a few case studies to demonstrate the concept and outcome of the SVD-based deconvolution. Finally, we highlight a few recent studies with mechanistic insights made possible by heterogeneity deconvolution.
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Affiliation(s)
- Zhong Ren
- Authors to whom correspondence should be addressed: and
| | - Xiaojing Yang
- Authors to whom correspondence should be addressed: and
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3
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Nascimento NS, Torres-Obreque KM, Oliveira CA, Rabelo J, Baby AR, Long PF, Young AR, Rangel-Yagui CDO. Enzymes for dermatological use. Exp Dermatol 2024; 33:e15008. [PMID: 38284197 DOI: 10.1111/exd.15008] [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: 07/12/2023] [Revised: 10/18/2023] [Accepted: 12/15/2023] [Indexed: 01/30/2024]
Abstract
Skin is the ultimate barrier between body and environment and prevents water loss and penetration of pathogens and toxins. Internal and external stressors, such as ultraviolet radiation (UVR), can damage skin integrity and lead to disorders. Therefore, skin health and skin ageing are important concerns and increased research from cosmetic and pharmaceutical sectors aims to improve skin conditions and provide new anti-ageing treatments. Biomolecules, compared to low molecular weight drugs and cosmetic ingredients, can offer high levels of specificity. Topically applied enzymes have been investigated to treat the adverse effects of sunlight, pollution and other external agents. Enzymes, with a diverse range of targets, present potential for dermatological use such as antioxidant enzymes, proteases and repairing enzymes. In this review, we discuss enzymes for dermatological applications and the challenges associated in this growing field.
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Affiliation(s)
- Natália Santos Nascimento
- Department of Biochemical and Pharmaceutical Technology, School of Pharmaceutical Sciences, University of São Paulo (USP), São Paulo, Brazil
| | - Karin Mariana Torres-Obreque
- Department of Biochemical and Pharmaceutical Technology, School of Pharmaceutical Sciences, University of São Paulo (USP), São Paulo, Brazil
| | - Camila Areias Oliveira
- Laboratory of Analytical Validation and Development, Fundação Oswaldo Cruz - FIOCRUZ, Rio de Janeiro, Brazil
| | - Jheniffer Rabelo
- Department of Biochemical and Pharmaceutical Technology, School of Pharmaceutical Sciences, University of São Paulo (USP), São Paulo, Brazil
| | - André Rolim Baby
- Department of Pharmacy, School of Pharmaceutical Sciences, University of São Paulo (USP), São Paulo, Brazil
| | - Paul F Long
- Institute of Pharmaceutical Science, King's College London, London, UK
| | - Antony R Young
- St John's Institute of Dermatology, King's College London, London, UK
| | - Carlota de Oliveira Rangel-Yagui
- Department of Biochemical and Pharmaceutical Technology, School of Pharmaceutical Sciences, University of São Paulo (USP), São Paulo, Brazil
- Institute of Pharmaceutical Science, King's College London, London, UK
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4
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Ren Z, Kang W, Gunawardana S, Bowatte K, Thoulass K, Kaeser G, Krauß N, Lamparter T, Yang X. Dynamic interplays between three redox cofactors in a DNA photolyase revealed by spectral decomposition. CELL REPORTS. PHYSICAL SCIENCE 2023; 4:101297. [PMID: 37064408 PMCID: PMC10104447 DOI: 10.1016/j.xcrp.2023.101297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
DNA repair catalyzed by photolyases is accomplished by a light-dependent electron transfer event from a fully reduced flavin adenine dinucleotide to a DNA lesion site. Prokaryotic DNA photolyase, PhrB, possesses a ribolumazine cofactor and a four-iron-four-sulfur cluster in addition to the catalytic flavin, but their functional roles are poorly understood. Here, we employ time-resolved absorption spectroscopy to probe light-induced responses in both solution and single crystals of PhrB. We jointly analyze a large collection of light-induced difference spectra from the wild-type and mutant PhrB obtained under different light and redox conditions. By applying singular value decomposition to 159 time series, we dissect light-induced spectral changes and examine the dynamic interplay between three cofactors. Our findings suggest that these cofactors form an interdependent redox network to coordinate light-induced redox responses. We propose that the ribolumazine cofactor serves as a photoprotective pigment under intense light or prolonged illumination, while the iron-sulfur cluster acts as a transient electron cache to maintain balance between two otherwise independent photoreactions of the flavin and ribolumazine.
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Affiliation(s)
- Zhong Ren
- Department of Chemistry, University of Illinois Chicago, Chicago, IL, USA
- Lead contact
| | - Weijia Kang
- Department of Chemistry, University of Illinois Chicago, Chicago, IL, USA
| | - Semini Gunawardana
- Department of Chemistry, University of Illinois Chicago, Chicago, IL, USA
| | - Kalinga Bowatte
- Department of Chemistry, University of Illinois Chicago, Chicago, IL, USA
| | - Katharina Thoulass
- Botanical Institute, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Gero Kaeser
- Botanical Institute, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Norbert Krauß
- Botanical Institute, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Tilman Lamparter
- Botanical Institute, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Xiaojing Yang
- Department of Chemistry, University of Illinois Chicago, Chicago, IL, USA
- Department of Ophthalmology and Vision Sciences, University of Illinois Chicago, Chicago, IL, USA
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5
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Ren Z, Zhang F, Kang W, Wang C, Shin H, Zeng X, Gunawardana S, Bowatte K, Krau Ü N, Lamparter T, Yang X. Spin-Coupled Electron Densities of Iron-Sulfur Cluster Imaged by In Situ Serial Laue Diffraction. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.09.523341. [PMID: 36711581 PMCID: PMC9882091 DOI: 10.1101/2023.01.09.523341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Iron-sulfur clusters are inorganic cofactors found in many proteins involved in fundamental biological processes including DNA processing. The prokaryotic DNA repair enzyme PhrB, a member of the protein family of cryptochromes and photolyases, carries a four-iron-four-sulfur cluster [4Fe4S] in addition to the catalytic cofactor flavin adenine dinucleotide (FAD) and a second pigment 6,7-dimethyl-8-ribityllumazine (DMRL). The light-induced redox reactions of this multi-cofactor protein complex were recently shown as two interdependent photoreductions of FAD and DMRL mediated by the [4Fe4S] cluster functioning as an electron cache to hold a fine balance of electrons. Here, we apply the more traditional temperature-scan cryo-trapping technique in protein crystallography and the newly developed technology of in situ serial Laue diffraction at room temperature. These diffraction methods in dynamic crystallography enable us to capture strong signals of electron density changes in the [4Fe4S] cluster that depict quantized electronic movements. The mixed valence layers of the [4Fe4S] cluster due to spin coupling and their dynamic responses to light illumination are observed directly in our difference maps between its redox states. These direct observations of the quantum effects in a protein bound iron-sulfur cluster have thus opened a window into the mechanistic understanding of metal clusters in biological systems.
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Fernández MB, Latorre L, Correa-Aragunde N, Cassia R. A putative bifunctional CPD/ (6-4) photolyase from the cyanobacteria Synechococcus sp. PCC 7335 is encoded by a UV-B inducible operon: New insights into the evolution of photolyases. Front Microbiol 2022; 13:981788. [DOI: 10.3389/fmicb.2022.981788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 09/26/2022] [Indexed: 11/13/2022] Open
Abstract
Photosynthetic organisms are continuously exposed to solar ultraviolet radiation-B (UV-B) because of their autotrophic lifestyle. UV-B provokes DNA damage, such as cyclobutane pyrimidine dimers (CPD) or pyrimidine (6-4) pyrimidone photoproducts (6-4 PPs). The cryptochrome/photolyase family (CPF) comprises flavoproteins that can bind damaged or undamaged DNA. Photolyases (PHRs) are enzymes that repair either CPDs or 6-4 PPs. A natural bifunctional CPD/(6-4)- PHR (PhrSph98) was recently isolated from the UV-resistant bacteria Sphingomonas sp. UV9. In this work, phylogenetic studies of bifunctional CPD/(6-4)- photolyases and their evolutionary relationship with other CPF members were performed. Amino acids involved in electron transfer and binding to FAD cofactor and DNA lesions were conserved in proteins from proteobacteria, planctomycete, bacteroidete, acidobacteria and cyanobacteria clades. Genome analysis revealed that the cyanobacteria Synechococcus sp. PCC 7335 encodes a two-gene assembly operon coding for a PHR and a bifunctional CPD/(6-4) PHR- like. Operon structure was validated by RT-qPCR analysis and the polycistronic transcript accumulated after 15 min of UV-B irradiation. Conservation of structure and evolution is discussed. This study provides evidence for a UV-B inducible PHR operon that encodes a CPD/(6-4)- photolyase homolog with a putative bifunctional role in the repair of CPDs and 6-4 PPs damages in oxygenic photosynthetic organisms.
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7
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Alonso-Reyes DG, Galván FS, Irazoqui JM, Amadio A, Tschoeke D, Thompson F, Albarracín VH, Farias ME. Dissecting Light Sensing and Metabolic Pathways on the Millimeter Scale in High-Altitude Modern Stromatolites. MICROBIAL ECOLOGY 2022:10.1007/s00248-022-02112-7. [PMID: 36161499 DOI: 10.1007/s00248-022-02112-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 09/13/2022] [Indexed: 06/16/2023]
Abstract
Modern non-lithifying stromatolites on the shore of the volcanic lake Socompa (SST) in the Puna are affected by several extreme conditions. The present study assesses for the first time light utilization and functional metabolic stratification of SST on a millimeter scale through shotgun metagenomics. In addition, a scanning-electron-microscopy approach was used to explore the community. The analysis on SST unveiled the profile of a photosynthetic mat, with cyanobacteria not directly exposed to light, but placed just below a high-UV-resistant community. Calvin-Benson and 3-hydroxypropinate cycles for carbon fixation were abundant in upper, oxic layers, while the Wood-Ljungdahl pathway was dominant in the deeper anoxic strata. The high abundance of genes for UV-screening and oxidant-quenching pigments and CPF (photoreactivation) in the UV-stressed layers could indicate that the zone itself works as a UV shield. There is a remarkable density of sequences associated with photoreceptors in the first two layers. Also, genetic evidence of photosynthesis split in eukaryotic (layer 1) and prokaryotic (layer 2). Photoheterotrophic bacteria, aerobic photoautotrophic bacteria, and anaerobic photoautotrophic bacteria coexist by selectively absorbing different parts of the light spectrum (blue, red, and IR respectively) at different positions of the mat. Genes for oxygen, nitrogen, and sulfur metabolism account for the microelectrode chemical data and pigment measurements performed in previous publications. We also provide here an explanation for the vertical microbial mobility within the SST described previously. Finally, our study points to SST as ideal modern analogues of ancient ST.
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Affiliation(s)
- Daniel Gonzalo Alonso-Reyes
- Laboratorio de Microbiología Ultraestructural Y Molecular, Centro Integral de Microscopía Electrónica (CIME,), CONICET-Universidad Nacional de Tucumán, Camino de Sirga s/n, Finca El Manantial, Yerba Buena (4107), San Miguel de Tucumán, Tucumán, Argentina
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas (LIMLA), Planta Piloto de Procesos Industriales y Microbiológicos (PROIMI), CCT, CONICET, Tucumán, Argentina
| | - Fátima Silvina Galván
- Laboratorio de Microbiología Ultraestructural Y Molecular, Centro Integral de Microscopía Electrónica (CIME,), CONICET-Universidad Nacional de Tucumán, Camino de Sirga s/n, Finca El Manantial, Yerba Buena (4107), San Miguel de Tucumán, Tucumán, Argentina
| | - José Matías Irazoqui
- Instituto de Investigación de La Cadena Láctea (INTA-CONICET), Rafaela, Argentina
| | - Ariel Amadio
- Instituto de Investigación de La Cadena Láctea (INTA-CONICET), Rafaela, Argentina
| | - Diogo Tschoeke
- Institute of Biology and Coppe, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Fabiano Thompson
- Institute of Biology and Coppe, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Virginia Helena Albarracín
- Laboratorio de Microbiología Ultraestructural Y Molecular, Centro Integral de Microscopía Electrónica (CIME,), CONICET-Universidad Nacional de Tucumán, Camino de Sirga s/n, Finca El Manantial, Yerba Buena (4107), San Miguel de Tucumán, Tucumán, Argentina.
- Facultad de Ciencias Naturales e Instituto Miguel Lillo, Universidad Nacional de Tucumán, Tucumán, Argentina.
| | - María Eugenia Farias
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas (LIMLA), Planta Piloto de Procesos Industriales y Microbiológicos (PROIMI), CCT, CONICET, Tucumán, Argentina
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8
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Ramírez-Gamboa D, Díaz-Zamorano AL, Meléndez-Sánchez ER, Reyes-Pardo H, Villaseñor-Zepeda KR, López-Arellanes ME, Sosa-Hernández JE, Coronado-Apodaca KG, Gámez-Méndez A, Afewerki S, Iqbal HMN, Parra-Saldivar R, Martínez-Ruiz M. Photolyase Production and Current Applications: A Review. Molecules 2022; 27:molecules27185998. [PMID: 36144740 PMCID: PMC9505440 DOI: 10.3390/molecules27185998] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 08/20/2022] [Accepted: 08/24/2022] [Indexed: 11/16/2022] Open
Abstract
The photolyase family consists of flavoproteins with enzyme activity able to repair ultraviolet light radiation damage by photoreactivation. DNA damage by the formation of a cyclobutane pyrimidine dimer (CPD) and a pyrimidine-pyrimidone (6-4) photoproduct can lead to multiple affections such as cellular apoptosis and mutagenesis that can evolve into skin cancer. The development of integrated applications to prevent the negative effects of prolonged sunlight exposure, usually during outdoor activities, is imperative. This study presents the functions, characteristics, and types of photolyases, their therapeutic and cosmetic applications, and additionally explores some photolyase-producing microorganisms and drug delivery systems.
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Affiliation(s)
- Diana Ramírez-Gamboa
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey 64849, Mexico
| | | | | | - Humberto Reyes-Pardo
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey 64849, Mexico
| | | | | | - Juan Eduardo Sosa-Hernández
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey 64849, Mexico
- Tecnologico de Monterrey, Institute of Advanced Materials for Sustainable Manufacturing, Monterrey 64849, Mexico
| | - Karina G. Coronado-Apodaca
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey 64849, Mexico
- Tecnologico de Monterrey, Institute of Advanced Materials for Sustainable Manufacturing, Monterrey 64849, Mexico
| | - Ana Gámez-Méndez
- Department of Basic Sciences, Universidad de Monterrey, Av. Ignacio Morones Prieto 4500 Pte, San Pedro Garza Garcia 66238, Mexico
| | - Samson Afewerki
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
- Division of Gastroenterology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Hafiz M. N. Iqbal
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey 64849, Mexico
- Tecnologico de Monterrey, Institute of Advanced Materials for Sustainable Manufacturing, Monterrey 64849, Mexico
| | - Roberto Parra-Saldivar
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey 64849, Mexico
- Tecnologico de Monterrey, Institute of Advanced Materials for Sustainable Manufacturing, Monterrey 64849, Mexico
- Correspondence: (R.P.-S.); (M.M.-R.)
| | - Manuel Martínez-Ruiz
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey 64849, Mexico
- Tecnologico de Monterrey, Institute of Advanced Materials for Sustainable Manufacturing, Monterrey 64849, Mexico
- Correspondence: (R.P.-S.); (M.M.-R.)
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9
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An ML, Miao JL. Genetic and Molecular Characterization of a Dash Cryptochrome Homologous Gene from Antarctic Diatom Phaeodactylum tricornutum ICE-H. Mol Biol 2022. [DOI: 10.1134/s0026893322060024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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10
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Chen S, Liu C, Zhou C, Wei Z, Li Y, Xiong L, Yan L, Lv J, Shen L, Xu L. Identification and characterization of a prokaryotic 6-4 photolyase from Synechococcus elongatus with a deazariboflavin antenna chromophore. Nucleic Acids Res 2022; 50:5757-5771. [PMID: 35639925 PMCID: PMC9178010 DOI: 10.1093/nar/gkac416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Revised: 04/16/2022] [Accepted: 05/09/2022] [Indexed: 11/23/2022] Open
Abstract
Synechococcus elongatus, formerly known as Anacystis nidulans, is a representative species of cyanobacteria. It is also a model organism for the study of photoreactivation, which can be fully photoreactivated even after receiving high UV doses. However, for a long time, only one photolyase was found in S. elongatus that is only able to photorepair UV induced cyclobutane pyrimidine dimers (CPDs) in DNA. Here, we characterize another photolyase in S. elongatus, which belongs to iron-sulfur bacterial cryptochromes and photolyases (FeS-BCP), a subtype of prokaryotic 6–4 photolyases. This photolyase was named SePhrB that could efficiently photorepair 6–4 photoproducts in DNA. Chemical analyses revealed that SePhrB contains a catalytic FAD cofactor and an iron-sulfur cluster. All of previously reported FeS-BCPs contain 6,7-dimethyl-8-ribityllumazine (DMRL) as their antenna chromophores. Here, we first demonstrated that SePhrB possesses 7,8-didemethyl-8-hydroxy-5-deazariboflavin (8-HDF) as an antenna chromophore. Nevertheless, SePhrB could be photoreduced without external electron donors. After being photoreduced, the reduced FAD cofactor in SePhrB was extremely stable against air oxidation. These results suggest that FeS-BCPs are more diverse than expected which deserve further investigation.
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Affiliation(s)
- Simeng Chen
- Anhui Province Key Laboratory of Active Biological Macro-molecules, Wannan Medical College, Wuhu, Anhui 241002, China
| | - Chenxi Liu
- Anhui Province Key Laboratory of Active Biological Macro-molecules, Wannan Medical College, Wuhu, Anhui 241002, China
| | - Chenchen Zhou
- Anhui Province Key Laboratory of Active Biological Macro-molecules, Wannan Medical College, Wuhu, Anhui 241002, China
| | - Zhihui Wei
- Anhui Province Key Laboratory of Active Biological Macro-molecules, Wannan Medical College, Wuhu, Anhui 241002, China
| | - Yuting Li
- Anhui Province Key Laboratory of Active Biological Macro-molecules, Wannan Medical College, Wuhu, Anhui 241002, China
| | - Lei Xiong
- Anhui Province Key Laboratory of Active Biological Macro-molecules, Wannan Medical College, Wuhu, Anhui 241002, China
| | - Liang Yan
- Anhui Province Key Laboratory of Active Biological Macro-molecules, Wannan Medical College, Wuhu, Anhui 241002, China
| | - Jun Lv
- Anhui Province Key Laboratory of Active Biological Macro-molecules, Wannan Medical College, Wuhu, Anhui 241002, China
| | - Liang Shen
- College of Life Sciences, Anhui Normal University, Wuhu, Anhui 241000, China
| | - Lei Xu
- Anhui Province Key Laboratory of Active Biological Macro-molecules, Wannan Medical College, Wuhu, Anhui 241002, China
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11
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Xu L, Chen S, Wen B, Shi H, Chi C, Liu C, Wang K, Tao X, Wang M, Lv J, Yan L, Ling L, Zhu G. Identification of a Novel Class of Photolyases as Possible Ancestors of Their Family. Mol Biol Evol 2021; 38:4505-4519. [PMID: 34175934 PMCID: PMC8476157 DOI: 10.1093/molbev/msab191] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
UV irradiation induces the formation of cyclobutane pyrimidine dimers (CPDs) and 6-4 photoproducts in DNA. These two types of lesions can be directly photorepaired by CPD photolyases and 6-4 photolyases, respectively. Recently, a new class of 6-4 photolyases named iron–sulfur bacterial cryptochromes and photolyases (FeS-BCPs) were found, which were considered as the ancestors of all photolyases and their homologs—cryptochromes. However, a controversy exists regarding 6-4 photoproducts only constituting ∼10–30% of the total UV-induced lesions that primordial organisms would hardly survive without a CPD repair enzyme. By extensive phylogenetic analyses, we identified a novel class of proteins, all from eubacteria. They have relatively high similarity to class I/III CPD photolyases, especially in the putative substrate-binding and FAD-binding regions. However, these proteins are shorter, and they lack the “N-terminal α/β domain” of normal photolyases. Therefore, we named them short photolyase-like. Nevertheless, similar to FeS-BCPs, some of short photolyase-likes also contain four conserved cysteines, which may also coordinate an iron–sulfur cluster as FeS-BCPs. A member from Rhodococcus fascians was cloned and expressed. It was demonstrated that the protein contains a FAD cofactor and an iron–sulfur cluster, and has CPD repair activity. It was speculated that this novel class of photolyases may be the real ancestors of the cryptochrome/photolyase family.
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Affiliation(s)
- Lei Xu
- Anhui Province Key Laboratory of Active Biological Macro-molecules, Wannan Medical College, Wuhu, Anhui, 241002, China.,Key Laboratory of Biomedicine in Gene Diseases and Health of Anhui Higher Education Institutes, Anhui Normal University, Wuhu, Anhui, 241000, China
| | - Simeng Chen
- Anhui Province Key Laboratory of Active Biological Macro-molecules, Wannan Medical College, Wuhu, Anhui, 241002, China
| | - Bin Wen
- Key Laboratory of Biomedicine in Gene Diseases and Health of Anhui Higher Education Institutes, Anhui Normal University, Wuhu, Anhui, 241000, China
| | - Hao Shi
- Anhui Province Key Laboratory of Active Biological Macro-molecules, Wannan Medical College, Wuhu, Anhui, 241002, China
| | - Changbiao Chi
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230027, China
| | - Chenxi Liu
- Anhui Province Key Laboratory of Active Biological Macro-molecules, Wannan Medical College, Wuhu, Anhui, 241002, China
| | - Kangyu Wang
- Anhui Province Key Laboratory of Active Biological Macro-molecules, Wannan Medical College, Wuhu, Anhui, 241002, China
| | - Xianglin Tao
- Anhui Province Key Laboratory of Active Biological Macro-molecules, Wannan Medical College, Wuhu, Anhui, 241002, China
| | - Ming Wang
- Anhui Province Key Laboratory of Active Biological Macro-molecules, Wannan Medical College, Wuhu, Anhui, 241002, China
| | - Jun Lv
- Anhui Province Key Laboratory of Active Biological Macro-molecules, Wannan Medical College, Wuhu, Anhui, 241002, China
| | - Liang Yan
- Anhui Province Key Laboratory of Active Biological Macro-molecules, Wannan Medical College, Wuhu, Anhui, 241002, China
| | - Liefeng Ling
- Anhui Province Key Laboratory of Active Biological Macro-molecules, Wannan Medical College, Wuhu, Anhui, 241002, China
| | - Guoping Zhu
- Key Laboratory of Biomedicine in Gene Diseases and Health of Anhui Higher Education Institutes, Anhui Normal University, Wuhu, Anhui, 241000, China
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12
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Vanoni MA. Iron-sulfur flavoenzymes: the added value of making the most ancient redox cofactors and the versatile flavins work together. Open Biol 2021; 11:210010. [PMID: 33947244 PMCID: PMC8097209 DOI: 10.1098/rsob.210010] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Iron-sulfur (Fe-S) flavoproteins form a broad and growing class of complex, multi-domain and often multi-subunit proteins coupling the most ancient cofactors (the Fe-S clusters) and the most versatile coenzymes (the flavin coenzymes, FMN and FAD). These enzymes catalyse oxidoreduction reactions usually acting as switches between donors of electron pairs and acceptors of single electrons, and vice versa. Through selected examples, the enzymes' structure−function relationships with respect to rate and directionality of the electron transfer steps, the role of the apoprotein and its dynamics in modulating the electron transfer process will be discussed.
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Affiliation(s)
- Maria Antonietta Vanoni
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy
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13
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A (6-4)-photolyase from the Antarctic bacterium Sphingomonas sp. UV9: recombinant production and in silico features. Extremophiles 2020; 24:887-896. [PMID: 32960344 DOI: 10.1007/s00792-020-01202-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 09/07/2020] [Indexed: 10/23/2022]
Abstract
Photolyases are proteins that enzymatically repair the UV-induced DNA damage by a protein-DNA electron transfer mechanism. They repair either cyclobutane pyrimidine dimers or pyrimidine (6-4) pyrimidone photoproducts or just (6-4)-photoproducts. In this work, we report the production and partial characterization of a recombinant (6-4)-photolyase (SphPhrB97) from a bacterial psychrotolerant Antarctic isolate identified as Sphingomonas sp. strain UV9. The spectrum analysis and the in silico study of SphPhrB97 suggest that this enzyme has similar features as compared to the (6-4)-photolyase from Agrobacterium tumefaciens (4DJA; PhrB), including the presence of three cofactors: FAD, DMRL (6,7-dimethyl-8-(1'-D-ribityl) lumazine), and an Fe-S cluster. The homology model of SphPhrB97 predicts that the DNA-binding pocket (area and volume) is larger as compared to (6-4)-photolyases from mesophilic microbes. Based on sequence comparison and on the homology model, we propose an electron transfer pathway towards the FAD cofactor involving the residues Trp342, Trp390, Tyr40, Tyr391, and Tyr399. The phylogenetic tree performed using curated and well-characterized prokaryotic (6-4)-photolyases suggests that SphPhrB97 may have an ancient evolutionary origin. The results suggest that SphPhrB97 is a cold-adapted enzyme, ready to cope with the UV irradiation stress found in a hostile environment, such as Antarctica.
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14
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Zhang X, Zheng Z, He Y, Liu L, Qu C, Miao J. Molecular Cloning and Expression of a Cryptochrome Gene CiCRY-DASH1 from the Antarctic microalga Chlamydomonas sp. ICE-L. Mol Biotechnol 2020; 62:91-103. [PMID: 31863411 DOI: 10.1007/s12033-019-00225-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Cryptochromes (CRYs) are flavin-binding proteins that sense blue and near-ultraviolet light and participate in the photoreactions of organisms and the regulation of biological clocks. In this study, the complete open reading frame (ORF) of CiCRY-DASH1 (GenBank ID MK392361), encoding one kind of cryptochrome, was cloned from the Antarctic microalga Chlamydomonas sp. ICE-L. The quantitative real-time PCR study showed that the CiCRY-DASH1 had the highest expression at 5 °C and salinity of 32‰. The CiCRY-DASH1 was positively regulated by blue, yellow, or red light. Moreover, the CiCRY-DASH1 can positively respond to extreme polar day and night treatment and exhibit a certain circadian rhythm, which indicated that CiCRY-DASH1 participated in the circadian clock and its expression was regulated by circadian rhythms. And the CiCRY-DASH1 was more noticeably affected by ultraviolet-B radiation than ultraviolet-A radiation, indicating ultraviolet-B light does obvious damage to Antarctic microalgae.
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Affiliation(s)
- Xin Zhang
- School of Basic Medicine, Qingdao University, Qingdao, 266071, China
| | - Zhou Zheng
- First Institute of Oceanography, Ministry of Natural Resource, Qingdao, 266061, China.,Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
| | - Yingying He
- School of Basic Medicine, Qingdao University, Qingdao, 266071, China
| | - Lina Liu
- School of Basic Medicine, Qingdao University, Qingdao, 266071, China
| | - Changfeng Qu
- First Institute of Oceanography, Ministry of Natural Resource, Qingdao, 266061, China.,Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
| | - Jinlai Miao
- First Institute of Oceanography, Ministry of Natural Resource, Qingdao, 266061, China. .,Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.
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15
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Vechtomova YL, Telegina TA, Kritsky MS. Evolution of Proteins of the DNA Photolyase/Cryptochrome Family. BIOCHEMISTRY (MOSCOW) 2020; 85:S131-S153. [DOI: 10.1134/s0006297920140072] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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16
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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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17
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18
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Zhao H, Di Mauro G, Lungu-Mitea S, Negrini P, Guarino AM, Frigato E, Braunbeck T, Ma H, Lamparter T, Vallone D, Bertolucci C, Foulkes NS. Modulation of DNA Repair Systems in Blind Cavefish during Evolution in Constant Darkness. Curr Biol 2018; 28:3229-3243.e4. [PMID: 30318355 DOI: 10.1016/j.cub.2018.08.039] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2018] [Revised: 07/19/2018] [Accepted: 08/16/2018] [Indexed: 11/18/2022]
Abstract
How the environment shapes the function and evolution of DNA repair systems is poorly understood. In a comparative study using zebrafish and the Somalian blind cavefish, Phreatichthys andruzzii, we reveal that during evolution for millions of years in continuous darkness, photoreactivation DNA repair function has been lost in P. andruzzii. We demonstrate that this loss results in part from loss-of-function mutations in pivotal DNA-repair genes. Specifically, C-terminal truncations in P. andruzzii DASH and 6-4 photolyase render these proteins predominantly cytoplasmic, with consequent loss in their functionality. In addition, we reveal a general absence of light-, UV-, and ROS-induced expression of P. andruzzii DNA-repair genes. This results from a loss of function of the D-box enhancer element, which coordinates and enhances DNA repair in response to sunlight. Our results point to P. andruzzii being the only species described, apart from placental mammals, that lacks the highly evolutionary conserved photoreactivation function. We predict that in the DNA repair systems of P. andruzzii, we may be witnessing the first stages in a process that previously occurred in the ancestors of placental mammals during the Mesozoic era.
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Affiliation(s)
- Haiyu Zhao
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Hermann-von-Helmholtz Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Giuseppe Di Mauro
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Hermann-von-Helmholtz Platz 1, 76344 Eggenstein-Leopoldshafen, Germany; Department of Life Science and Biotechnology, University of Ferrara, Via Luigi Borsari 46, 44121 Ferrara, Italy
| | - Sebastian Lungu-Mitea
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Hermann-von-Helmholtz Platz 1, 76344 Eggenstein-Leopoldshafen, Germany; Aquatic Ecology and Toxicology, Centre for Organismal Studies, University of Heidelberg, Im Neuenheimer Feld, 69120 Heidelberg, Germany; Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, 75007 Uppsala, Sweden
| | - Pietro Negrini
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Hermann-von-Helmholtz Platz 1, 76344 Eggenstein-Leopoldshafen, Germany; Department of Life Science and Biotechnology, University of Ferrara, Via Luigi Borsari 46, 44121 Ferrara, Italy
| | - Andrea Maria Guarino
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Hermann-von-Helmholtz Platz 1, 76344 Eggenstein-Leopoldshafen, Germany; Department of Biology, University of Naples "Federico II," 80126 Naples, Italy
| | - Elena Frigato
- Department of Life Science and Biotechnology, University of Ferrara, Via Luigi Borsari 46, 44121 Ferrara, Italy
| | - Thomas Braunbeck
- Aquatic Ecology and Toxicology, Centre for Organismal Studies, University of Heidelberg, Im Neuenheimer Feld, 69120 Heidelberg, Germany
| | - Hongju Ma
- Botanical Institute, Karlsruhe Institute of Technology, 76128 Karlsruhe, Germany
| | - Tilman Lamparter
- Botanical Institute, Karlsruhe Institute of Technology, 76128 Karlsruhe, Germany
| | - Daniela Vallone
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Hermann-von-Helmholtz Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Cristiano Bertolucci
- Department of Life Science and Biotechnology, University of Ferrara, Via Luigi Borsari 46, 44121 Ferrara, Italy
| | - Nicholas S Foulkes
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Hermann-von-Helmholtz Platz 1, 76344 Eggenstein-Leopoldshafen, Germany.
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19
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A highly efficient and cost-effective recombinant production of a bacterial photolyase from the Antarctic isolate Hymenobacter sp. UV11. Extremophiles 2018; 23:49-57. [DOI: 10.1007/s00792-018-1059-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 09/24/2018] [Indexed: 01/12/2023]
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20
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Ma H, Zhang F, Ignatz E, Suehnel M, Xue P, Scheerer P, Essen LO, Krauß N, Lamparter T. Divalent Cations Increase DNA Repair Activities of Bacterial (6-4) Photolyases. Photochem Photobiol 2018; 93:323-330. [PMID: 27992646 DOI: 10.1111/php.12698] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 12/09/2016] [Indexed: 11/29/2022]
Abstract
The (6-4) photolyases of the FeS-BCP group can be considered as the most ancient type among the large family of cryptochrome and photolyase flavoproteins. In contrast to other photolyases, they contain an Fe-S cluster of unknown function, a DMRL chromophore, an interdomain loop, which could interact with DNA, and a long C-terminal extension. We compared DNA repair and photoreduction of two members of the FeS-BCP family, Agrobacterium fabrum PhrB and Rhodobacter sphaeroides RsCryB, with a eukaryotic (6-4) photolyase from Ostreococcus, OsCPF, and a member of the class III CPD photolyases, PhrA from A. fabrum. We found that the low DNA repair effectivity of FeS-BCP proteins is largely stimulated by Mg2+ and other divalent cations, whereas no effect of divalent cations was observed in OsCPF and PhrA. The (6-4) repair activity in the presence of Mg2+ is comparable with the repair activities of the other two photolyases. The photoreduction, on the other hand, is negatively affected by Mg2+ in PhrB, but stimulated by Mg2+ in PhrA. A clear relationship of Mg2+ dependency on DNA repair with the evolutionary position conflicts with Mg2+ dependency of photoreduction. We discuss the Mg2+ effect in the context of structural data and DNA binding.
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Affiliation(s)
- Hongju Ma
- Karlsruhe Institute of Technology, Botanical Institute, Karlsruhe, Germany
| | - Fan Zhang
- China Academy of Engineering Physics, Institute of Materials, Mianyang, China
| | - Elisabeth Ignatz
- Department of Chemistry, LOEWE Center for Synthetic Microbiology, Philipps University Marburg, Marburg, Germany
| | - Martin Suehnel
- Karlsruhe Institute of Technology, Botanical Institute, Karlsruhe, Germany
| | - Peng Xue
- Karlsruhe Institute of Technology, Botanical Institute, Karlsruhe, Germany
| | - Patrick Scheerer
- Institute of Medical Physics and Biophysics (CC2), Group Protein X-ray Crystallography and Signal Transduction, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Lars Oliver Essen
- Department of Chemistry, LOEWE Center for Synthetic Microbiology, Philipps University Marburg, Marburg, Germany
| | - Norbert Krauß
- Karlsruhe Institute of Technology, Botanical Institute, Karlsruhe, Germany
| | - Tilman Lamparter
- Karlsruhe Institute of Technology, Botanical Institute, Karlsruhe, Germany
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21
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An M, Zheng Z, Qu C, Wang X, Chen H, Shi C, Miao J. The first (6-4) photolyase with DNA damage repair activity from the Antarctic microalga Chlamydomonas sp. ICE-L. Mutat Res 2018; 809:13-19. [PMID: 29625375 DOI: 10.1016/j.mrfmmm.2018.03.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Revised: 12/20/2017] [Accepted: 03/28/2018] [Indexed: 10/17/2022]
Abstract
The psychrophilic microalga, Chlamydomonas sp. ICE-L, isolated from floating ice in the Antarctic, one of the most highly UV exposed ecosystems on Earth, displays an efficient DNA photorepair capacity. Here, the first known (6-4) photolyase gene (6-4CiPhr) from C. sp. ICE-L was identified. The 6-4CiPhr encoded 559-amino acid polypeptide with a pI of 8.86, and had a predicted Mw of 64.2 kDa. Real-time PCR was carried out to investigate the response of 6-4CiPhr to UVB exposure. The transcription of 6-4CiPhr was up-regulated continuously within 6 h, achieving a maximum of 62.7-fold at 6 h. Expressing 6-4CiPhr in a photolyase-deficient Escherichia coli strain improved survival rate of the strain. In vitro activity assays of purified protein demonstrated that 6-4CiPhr was a photolyase with 6-4PP repair activity. These findings improve understanding of photoreactivation mechanisms of (6-4) photolyase.
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Affiliation(s)
- Meiling An
- Medical College, Qingdao University, Qingdao 266071, China
| | - Zhou Zheng
- Medical College, Qingdao University, Qingdao 266071, China; Key Laboratory of Marine Bioactive Substances, First Institute of Oceanography, State Oceanic Administration, Qingdao 266061, China; Laboratory for Marine Drugs and Bioproducts of Qingdao, National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Changfeng Qu
- Key Laboratory of Marine Bioactive Substances, First Institute of Oceanography, State Oceanic Administration, Qingdao 266061, China; Laboratory for Marine Drugs and Bioproducts of Qingdao, National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Xixi Wang
- Key Laboratory of Marine Bioactive Substances, First Institute of Oceanography, State Oceanic Administration, Qingdao 266061, China
| | - Hao Chen
- Medical College, Qingdao University, Qingdao 266071, China
| | - Chongli Shi
- College of Chemical Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Jinlai Miao
- Medical College, Qingdao University, Qingdao 266071, China; Key Laboratory of Marine Bioactive Substances, First Institute of Oceanography, State Oceanic Administration, Qingdao 266061, China; Laboratory for Marine Drugs and Bioproducts of Qingdao, National Laboratory for Marine Science and Technology, Qingdao 266237, China; College of Chemical Engineering, Qingdao University of Science and Technology, Qingdao 266042, China.
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22
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Holub D, Ma H, Krauß N, Lamparter T, Elstner M, Gillet N. Functional role of an unusual tyrosine residue in the electron transfer chain of a prokaryotic (6-4) photolyase. Chem Sci 2017; 9:1259-1272. [PMID: 29675172 PMCID: PMC5887102 DOI: 10.1039/c7sc03386a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Accepted: 12/09/2017] [Indexed: 11/21/2022] Open
Abstract
Cryptochromes and photolyases form a flavoprotein family in which the FAD chromophore undergoes light induced changes of its redox state. During this process, termed photoreduction, electrons flow from the surface via conserved amino acid residues to FAD. The bacterial (6-4) photolyase PhrB belongs to a phylogenetically ancient group. Photoreduction of PhrB differs from the typical pattern because the amino acid of the electron cascade next to FAD is a tyrosine (Tyr391), whereas photolyases and cryptochromes of other groups have a tryptophan as direct electron donor of FAD. Mutagenesis studies have identified Trp342 and Trp390 as essential for charge transfer. Trp342 is located at the periphery of PhrB while Trp390 connects Trp342 and Tyr391. The role of Tyr391, which lies between Trp390 and FAD, is however unclear as its replacement by phenylalanine did not block photoreduction. Experiments reported here, which replace Tyr391 by Ala, show that photoreduction is blocked, underlining the relevance of Tyr/Phe at position 391 and indicating that charge transfer occurs via the triad 391-390-342. This raises the question, why PhrB positions a tyrosine at this location, having a less favourable ionisation potential than tryptophan, which occurs at this position in many proteins of the photolyase/cryptochrome family. Tunnelling matrix calculations show that tyrosine or phenylalanine can be involved in a productive bridged electron transfer between FAD and Trp390, in line with experimental findings. Since replacement of Tyr391 by Trp resulted in loss of FAD and DMRL chromophores, electron transfer cannot be studied experimentally in this mutant, but calculations on a mutant model suggest that Trp might participate in the electron transfer cascade. Charge transfer simulations reveal an unusual stabilization of the positive charge on site 391 compared to other photolyases or cryptochromes. Water molecules near Tyr391 offer a polar environment which stabilizes the positive charge on this site, thereby lowering the energetic barrier intrinsic to tyrosine. This opens a second charge transfer channel in addition to tunnelling through the tyrosine barrier, based on hopping and therefore transient oxidation of Tyr391, which enables a fast charge transfer similar to proteins utilizing a tryptophan-triad. Our results suggest that evolution of the first site of the redox chain has just been possible by tuning the protein structure and environment to manage a downhill hole transfer process from FAD to solvent.
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Affiliation(s)
- Daniel Holub
- Department for Theoretical Chemical Biology , Institute for Physical Chemistry , Karlsruhe Institute for Technology , Kaiserstr. 12 , 76131 , Karlsruhe , Germany .
| | - Hongju Ma
- Botanical Institute , Karlsruhe Institute for Technology , Fritz Haber Weg 4 , 76131 , Karlsruhe , Germany
| | - Norbert Krauß
- Botanical Institute , Karlsruhe Institute for Technology , Fritz Haber Weg 4 , 76131 , Karlsruhe , Germany
| | - Tilman Lamparter
- Botanical Institute , Karlsruhe Institute for Technology , Fritz Haber Weg 4 , 76131 , Karlsruhe , Germany
| | - Marcus Elstner
- Department for Theoretical Chemical Biology , Institute for Physical Chemistry , Karlsruhe Institute for Technology , Kaiserstr. 12 , 76131 , Karlsruhe , Germany . .,Institute of Biological Interfaces (IGB2) , Karlsruhe Institute for Technology , Kaiserstr. 12 , 76131 , Karlsruhe , Germany
| | - Natacha Gillet
- Department for Theoretical Chemical Biology , Institute for Physical Chemistry , Karlsruhe Institute for Technology , Kaiserstr. 12 , 76131 , Karlsruhe , Germany .
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23
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Zanello P. The competition between chemistry and biology in assembling iron–sulfur derivatives. Molecular structures and electrochemistry. Part V. {[Fe4S4](SCysγ)4} proteins. Coord Chem Rev 2017. [DOI: 10.1016/j.ccr.2016.10.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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24
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Marizcurrena JJ, Morel MA, Braña V, Morales D, Martinez-López W, Castro-Sowinski S. Searching for novel photolyases in UVC-resistant Antarctic bacteria. Extremophiles 2017; 21:409-418. [DOI: 10.1007/s00792-016-0914-y] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Accepted: 12/31/2016] [Indexed: 12/31/2022]
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25
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Zhang F, Ma H, Bowatte K, Kwiatkowski D, Mittmann E, Qasem H, Krauß N, Zeng X, Ren Z, Scheerer P, Yang X, Lamparter T. Crystal Structures of Bacterial (6-4) Photolyase Mutants with Impaired DNA Repair Activity. Photochem Photobiol 2017; 93:304-314. [DOI: 10.1111/php.12699] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 11/29/2016] [Indexed: 11/27/2022]
Affiliation(s)
- Fan Zhang
- Karlsruhe Institute of Technology; Botanical Institute; Karlsruhe Germany
- Institute of Materials; China Academy of Engineering Physics; Mianyang China
| | - Hongju Ma
- Karlsruhe Institute of Technology; Botanical Institute; Karlsruhe Germany
| | - Kalinga Bowatte
- Department of Chemistry; University of Illinois at Chicago; Chicago IL
| | - Dennis Kwiatkowski
- Charité - Universitätsmedizin Berlin; Institute of Medical Physics and Biophysics (CC2); Group Protein X-ray Crystallography and Signal Transduction; Berlin Germany
| | - Esther Mittmann
- Karlsruhe Institute of Technology; Botanical Institute; Karlsruhe Germany
| | - Heba Qasem
- Karlsruhe Institute of Technology; Botanical Institute; Karlsruhe Germany
| | - Norbert Krauß
- Karlsruhe Institute of Technology; Botanical Institute; Karlsruhe Germany
| | - Xiaoli Zeng
- Department of Chemistry; University of Illinois at Chicago; Chicago IL
| | - Zhong Ren
- Department of Chemistry; University of Illinois at Chicago; Chicago IL
| | - Patrick Scheerer
- Charité - Universitätsmedizin Berlin; Institute of Medical Physics and Biophysics (CC2); Group Protein X-ray Crystallography and Signal Transduction; Berlin Germany
| | - Xiaojing Yang
- Department of Chemistry; University of Illinois at Chicago; Chicago IL
| | - Tilman Lamparter
- Karlsruhe Institute of Technology; Botanical Institute; Karlsruhe Germany
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26
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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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