1
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Revealing intrinsic changes of DNA induced by spore photoproduct lesion through computer simulation. Biophys Chem 2023; 296:106992. [PMID: 36933500 DOI: 10.1016/j.bpc.2023.106992] [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: 11/03/2022] [Revised: 02/14/2023] [Accepted: 02/28/2023] [Indexed: 03/06/2023]
Abstract
In bacterial endospores, a cross-linked thymine dimer, 5-thyminyl-5,6-dihydrothymine, commonly referred to as the spore photoproduct (SP), is found as the dominant DNA photo lesion under UV radiation. During spore germination, SP is faithfully repaired by the spore photoproduct lyase (SPL) for normal DNA replication to resume. Despite this general mechanism, the exact way in which SP modifies the duplex DNA structure so that the damaged site can be recognized by SPL to initiate the repair process is still unclear. A previous X-ray crystallographic study, which used a reverse transcriptase as a DNA host template, captured a protein-bound duplex oligonucleotide containing two SP lesions; the study showed shortened hydrogen bonds between the AT base pairs involved in the lesions and widened minor grooves near the damaged sites. However, it remains to be determined whether the results accurately reflect the conformation of SP-containing DNA (SP-DNA) in its fully hydrated pre-repair form. To uncover the intrinsic changes in DNA conformation caused by SP lesions, we performed molecular dynamics (MD) simulations of SP-DNA duplexes in aqueous solution, using the nucleic acid portion of the previously determined crystal structure as a template. After MD relaxation, our simulated SP-DNAs showed weakened hydrogen bonds at the damaged sites compared to those in the undamaged DNA. Our analyses of the MD trajectories revealed a range of local and global structural distortions of DNA induced by SP. Specifically, the SP region displays a greater tendency to adopt an A-like-DNA conformation, and curvature analysis revealed an increase in the global bending compared to the canonical B-DNA. Although these SP-induced DNA conformational changes are relatively minor, they may provide a sufficient structural basis for SP to be recognized by SPL during the lesion repair process.
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2
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Dikec J, Pacheco M, Lavaud M, Winckler P, Perrier-Cornet JM. Uptake of UVc induced photoproducts of dipicolinic acid by Bacillus subtilis spores - Effects on the germination and UVc resistance of the spores. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY. B, BIOLOGY 2022; 236:112569. [PMID: 36152351 DOI: 10.1016/j.jphotobiol.2022.112569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 09/05/2022] [Accepted: 09/14/2022] [Indexed: 06/16/2023]
Abstract
Dipicolinic acid (DPA) is a specific molecule of bacterial spores which is essential to their resistance to various stresses such as ultraviolet (UV) exposure and to their germination. DPA has a particular photochemistry that remains imperfectly understood. In particular, due to its ability to absorb UVc radiation, it is likely to form in vitro a wide variety of photoproducts (DPAp) of which only about ten have been recently identified. The photochemical reactions resulting in DPAp, especially those inside the spores, are still poorly understood. Only one of these DPAp, which probably acts as a photosensitizer of DNA upon exposure to UVc, has been identified as having an impact on spores. However, as UVc is required to form DPAp, it is difficult to decouple the overall effect of UVc exposure from the possible effects of DPAp alone. In this study, DPAp were artificially introduced into the spores of the FB122 mutant strain of Bacillus subtilis, one that does not produce DPA. These experiments revealed that some DPAp may play a positive role for the spore. These benefits are visible in an improvement in spore germination rate and kinetics, as well as in an increase in their resistance to UVc exposure.
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Affiliation(s)
- J Dikec
- UMR Procédés Alimentaires et Microbiologiques, L'Institut Agro Dijon, Université de Bourgogne Franche-Comté, 1, Esplanade Erasme, 21000 Dijon, France
| | - M Pacheco
- UMR Procédés Alimentaires et Microbiologiques, L'Institut Agro Dijon, Université de Bourgogne Franche-Comté, 1, Esplanade Erasme, 21000 Dijon, France
| | - M Lavaud
- UMR Procédés Alimentaires et Microbiologiques, L'Institut Agro Dijon, Université de Bourgogne Franche-Comté, 1, Esplanade Erasme, 21000 Dijon, France; Dimacell Imaging Facility, L'Institut Agro Dijon, Université de Bourgogne Franche-Comté, 1 Esplanade Erasme, 21000 Dijon, France
| | - P Winckler
- UMR Procédés Alimentaires et Microbiologiques, L'Institut Agro Dijon, Université de Bourgogne Franche-Comté, 1, Esplanade Erasme, 21000 Dijon, France; Dimacell Imaging Facility, L'Institut Agro Dijon, Université de Bourgogne Franche-Comté, 1 Esplanade Erasme, 21000 Dijon, France
| | - J M Perrier-Cornet
- UMR Procédés Alimentaires et Microbiologiques, L'Institut Agro Dijon, Université de Bourgogne Franche-Comté, 1, Esplanade Erasme, 21000 Dijon, France; Dimacell Imaging Facility, L'Institut Agro Dijon, Université de Bourgogne Franche-Comté, 1 Esplanade Erasme, 21000 Dijon, France.
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3
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Chaturvedi R, Long EC. Mechanistic studies of dinucleotide and oligonucleotide model cyclobutane pyrimidine dimer (CPD) DNA lesions under alkaline conditions. Bioorg Med Chem 2021; 54:116499. [PMID: 34922308 DOI: 10.1016/j.bmc.2021.116499] [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: 08/11/2021] [Revised: 10/22/2021] [Accepted: 10/22/2021] [Indexed: 11/17/2022]
Abstract
Cyclobutane pyrimidine dimers (CPDs) are the most abundant mutagenic DNA lesions formed in mammalian cells upon exposure to UV-B radiation (280-315 nm) in sunlight. These lesions are thought to be chemically stable and to withstand high concentrations of acids and bases.While earlier investigations of DNA lesions containing saturated pyrimidines have shown that the C4 carbonyl is a potential target of nucleophilic attack, similar reactions with thymine nucleobase model CPDs clearly showed that the cis-syn CPD (major isomer) is stable in the presence of a high concentration of alkali at room temperature. Here is described the alkaline reactivity of these lesions when contained within a dinucleotide CPD model system. Results using cis-syn CPD formed from dinucleotide 5'-TpT-3' combined with [18O]-labelling indicated that CPD undergoes a water addition at the C4=O groups of these now saturated rings. The intermediate formed, however, completely reverts to the starting lesion. Along with confirming the target of water addition within CPD lesions, it was also determined that the two C4 carbonyls present on adjacent saturated pyrimidine rings of the photolesion undergo water exchange at different rates (3' > 5'). Moreover, the difference in reactivity exhibited by these two positions is not limited to a dinucleotide and was observed also in oligonucleotides. Overall, a full understanding of the chemistry of CPD lesions is crucial to our knowledge of naturally-occuring DNA modifications and may lead to further insight into their detection, modification, and biochemical recognition & repair.
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Affiliation(s)
- Ritu Chaturvedi
- Department of Chemistry & Chemical Biology, Indiana University-Purdue University Indianapolis (IUPUI), 402 N. Blackford St., Indianapolis, IN 46202, United States.
| | - Eric C Long
- Department of Chemistry & Chemical Biology, Indiana University-Purdue University Indianapolis (IUPUI), 402 N. Blackford St., Indianapolis, IN 46202, United States.
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4
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Moraskie M, Roshid MHO, O'Connor G, Dikici E, Zingg JM, Deo S, Daunert S. Microbial whole-cell biosensors: Current applications, challenges, and future perspectives. Biosens Bioelectron 2021; 191:113359. [PMID: 34098470 PMCID: PMC8376793 DOI: 10.1016/j.bios.2021.113359] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 05/13/2021] [Accepted: 05/15/2021] [Indexed: 12/22/2022]
Abstract
Microbial Whole-Cell Biosensors (MWCBs) have seen rapid development with the arrival of 21st century biological and technological capabilities. They consist of microbial species which produce, or limit the production of, a reporter protein in the presence of a target analyte. The quantifiable signal from the reporter protein can be used to determine the bioavailable levels of the target analyte in a variety of sample types at a significantly lower cost than most widely used and well-established analytical instrumentation. Furthermore, the versatile and robust nature of MWCBs shows great potential for their use in otherwise unavailable settings and environments. While MWCBs have been developed for use in biomedical, environmental, and agricultural monitoring, they still face various challenges before they can transition from the laboratory into industrialized settings like their enzyme-based counterparts. In this comprehensive and critical review, we describe the underlying working principles of MWCBs, highlight developments for their use in a variety of fields, detail challenges and current efforts to address them, and discuss exciting implementations of MWCBs helping redefine what is thought to be possible with this expeditiously evolving technology.
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Affiliation(s)
- Michael Moraskie
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL, 33136, USA; The Dr. John T. Macdonald Foundation Biomedical Nanotechnology Institute - BioNIUM, University of Miami, Miami, FL, 33136, USA
| | - Md Harun Or Roshid
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL, 33136, USA; The Dr. John T. Macdonald Foundation Biomedical Nanotechnology Institute - BioNIUM, University of Miami, Miami, FL, 33136, USA; Department of Chemistry, University of Miami, Miami, FL, 33146, USA
| | - Gregory O'Connor
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL, 33136, USA; The Dr. John T. Macdonald Foundation Biomedical Nanotechnology Institute - BioNIUM, University of Miami, Miami, FL, 33136, USA
| | - Emre Dikici
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL, 33136, USA; The Dr. John T. Macdonald Foundation Biomedical Nanotechnology Institute - BioNIUM, University of Miami, Miami, FL, 33136, USA
| | - Jean-Marc Zingg
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL, 33136, USA; The Dr. John T. Macdonald Foundation Biomedical Nanotechnology Institute - BioNIUM, University of Miami, Miami, FL, 33136, USA
| | - Sapna Deo
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL, 33136, USA; The Dr. John T. Macdonald Foundation Biomedical Nanotechnology Institute - BioNIUM, University of Miami, Miami, FL, 33136, USA
| | - Sylvia Daunert
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL, 33136, USA; The Dr. John T. Macdonald Foundation Biomedical Nanotechnology Institute - BioNIUM, University of Miami, Miami, FL, 33136, USA; Department of Chemistry, University of Miami, Miami, FL, 33146, USA; The Miami Clinical and Translational Science Institute, University of Miami, Miami, FL, 33146, USA; Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, 33146, USA.
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5
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Baptista MS, Cadet J, Greer A, Thomas AH. Photosensitization Reactions of Biomolecules: Definition, Targets and Mechanisms. Photochem Photobiol 2021; 97:1456-1483. [PMID: 34133762 DOI: 10.1111/php.13470] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 06/13/2021] [Indexed: 02/07/2023]
Abstract
Photosensitization reactions have been demonstrated to be largely responsible for the deleterious biological effects of UV and visible radiation, as well as for the curative actions of photomedicine. A large number of endogenous and exogenous photosensitizers, biological targets and mechanisms have been reported in the past few decades. Evolving from the original definitions of the type I and type II photosensitized oxidations, we now provide physicochemical frameworks, classifications and key examples of these mechanisms in order to organize, interpret and understand the vast information available in the literature and the new reports, which are in vigorous growth. This review surveys in an extended manner all identified photosensitization mechanisms of the major biomolecule groups such as nucleic acids, proteins, lipids bridging the gap with the subsequent biological processes. Also described are the effects of photosensitization in cells in which UVA and UVB irradiation triggers enzyme activation with the subsequent delayed generation of superoxide anion radical and nitric oxide. Definitions of photosensitized reactions are identified in biomolecules with key insights into cells and tissues.
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Affiliation(s)
| | - Jean Cadet
- Département de Médecine Nucléaire et de Radiobiologie, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Alexander Greer
- Department of Chemistry, Brooklyn College, Brooklyn, NY, USA.,Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, New York, NY, USA
| | - Andrés H Thomas
- Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas (INIFTA), Departamento de Química, Facultad de Ciencias Exactas, Universidad Nacional de La Plata (UNLP), CCT La Plata-CONICET, La Plata, Argentina
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6
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Nardi G, Lineros-Rosa M, Palumbo F, Miranda MA, Lhiaubet-Vallet V. Spectroscopic characterization of dipicolinic acid and its photoproducts as thymine photosensitizers. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 245:118898. [PMID: 32927302 DOI: 10.1016/j.saa.2020.118898] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 08/21/2020] [Accepted: 08/26/2020] [Indexed: 06/11/2023]
Abstract
Dipicolinic acid (DPA), present in large amount in bacterial spores, has been proposed to act as an endogenous photosensitizer in spore photoproduct formation. The proposed mechanism involves a triplet-triplet energy transfer from DPA to thymine. However, up to now, no spectroscopic studies have been performed to determine the interaction between the endogenous compound and the nucleobase, probably due to its photolability in aqueous solutions. Here, triplet excited state properties of DPA are reported together with its bimolecular quenching rate constant by thymidine, kq of ca. 5.3 × 109 M-1 s-1. To run more reliable studies, a stable methyl ester derivative of DPA, which exhibits the same spectroscopic properties as the parent compound, is also described. Finally, DPA photoproducts are characterized. Studies of their triplet excited state properties have demonstrated that, interestingly, one of them is able to photosensitize thymidine triplet excited state formation.
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Affiliation(s)
- Giacomo Nardi
- Instituto Universitario Mixto de Tecnología Química, Universitat Politècnica de València, Consejo Superior de Investigaciones Científicas, Avenida de los Naranjos s/n, 46022, Valencia, Spain
| | - Mauricio Lineros-Rosa
- Instituto Universitario Mixto de Tecnología Química, Universitat Politècnica de València, Consejo Superior de Investigaciones Científicas, Avenida de los Naranjos s/n, 46022, Valencia, Spain
| | - Fabrizio Palumbo
- Instituto Universitario Mixto de Tecnología Química, Universitat Politècnica de València, Consejo Superior de Investigaciones Científicas, Avenida de los Naranjos s/n, 46022, Valencia, Spain
| | - Miguel A Miranda
- Instituto Universitario Mixto de Tecnología Química, Universitat Politècnica de València, Consejo Superior de Investigaciones Científicas, Avenida de los Naranjos s/n, 46022, Valencia, Spain.
| | - Virginie Lhiaubet-Vallet
- Instituto Universitario Mixto de Tecnología Química, Universitat Politècnica de València, Consejo Superior de Investigaciones Científicas, Avenida de los Naranjos s/n, 46022, Valencia, Spain.
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7
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Francés-Monerris A, Hognon C, Douki T, Monari A. Photoinduced DNA Lesions in Dormant Bacteria: The Peculiar Route Leading to Spore Photoproducts Characterized by Multiscale Molecular Dynamics*. Chemistry 2020; 26:14236-14241. [PMID: 32597544 DOI: 10.1002/chem.202002484] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Indexed: 11/07/2022]
Abstract
Some bacterial species enter a dormant state in the form of spores to resist to unfavorable external conditions. Spores are resistant to a wide series of stress agents, including UV radiation, and can last for tens to hundreds of years. Due to the suspension of biological functions, such as DNA repair, they accumulate DNA damage upon exposure to UV radiation. Differently from active organisms, the most common DNA photoproducts in spores are not cyclobutane pyrimidine dimers, but rather the so-called spore photoproducts. This noncanonical photochemistry results from the dry state of DNA and its binding to small, acid-soluble proteins that drastically modify the structure and photoreactivity of the nucleic acid. Herein, multiscale molecular dynamics simulations, including extended classical molecular dynamics and quantum mechanics/molecular mechanics based dynamics, are used to elucidate the coupling of electronic and structural factors that lead to this photochemical outcome. In particular, the well-described impact of the peculiar DNA environment found in spores on the favored formation of the spore photoproduct, given the small free energy barrier found for this path, is rationalized. Meanwhile, the specific organization of spore DNA precludes the photochemical path that leads to cyclobutane pyrimidine dimer formation.
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Affiliation(s)
- Antonio Francés-Monerris
- Université de Lorraine and CNRS, LPCT UMR 7019, 54000, Nancy, France
- Departament de Química Física, Universitat de València, 46100, Burjassot, Spain
| | - Cécilia Hognon
- Université de Lorraine and CNRS, LPCT UMR 7019, 54000, Nancy, France
- Université de Lorraine and CNRS, CRAN UMR 7039, 54000, Nancy, France
| | - Thierry Douki
- SyMMES, CEA, CNRS, IRIG, University Grenoble Alpes, 38000, Grenoble, France
| | - Antonio Monari
- Université de Lorraine and CNRS, LPCT UMR 7019, 54000, Nancy, France
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Jian Y, Maximowitsch E, Liu D, Adhikari S, Li L, Domratcheva T. Indications of 5' to 3' Interbase Electron Transfer as the First Step of Pyrimidine Dimer Formation Probed by a Dinucleotide Analog. Chemistry 2017; 23:7526-7537. [PMID: 28370554 DOI: 10.1002/chem.201700045] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Indexed: 12/12/2022]
Abstract
Pyrimidine dimers are the most common DNA lesions generated under UV radiation. To reveal the molecular mechanisms behind their formation, it is of significance to reveal the roles of each pyrimidine residue. We thus replaced the 5'-pyrimidine residue with a photochemically inert xylene moiety (X). The electron-rich X can be readily oxidized but not reduced, defining the direction of interbase electron transfer (ET). Irradiation of the XpT dinucleotide under 254 nm UV light generates two major photoproducts: a pyrimidine (6-4) pyrimidone analog (6-4PP) and an analog of the so-called spore photoproduct (SP). Both products are formed by reaction at C4=O of the photo-excited 3'-thymidine (T), which indicates that excitation of a single "driver" residue is sufficient to trigger pyrimidine dimerization. Our quantum-chemical calculations demonstrated that photo-excited 3'-T accepts an electron from 5'-X. The resulting charge-separated radical pair lowers its energy upon formation of interbase covalent bonds, eventually yielding 6-4PP and SP.
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Affiliation(s)
- Yajun Jian
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis (IUPUI), 402 North Blackford Street, Indianapolis, Indiana, 46202, USA.,School of Chemistry & Chemical Engineering, Shaanxi Normal University (SNNU), No. 620, West Chang'an Avenue, Xi'an, Shaanxi, 710119, P. R. China
| | - Egle Maximowitsch
- Department of Biomolecular Mechanisms, Max-Planck Institute for Medical Research, Jahnstrasse 29, 69120, Heidelberg, Germany
| | - Degang Liu
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis (IUPUI), 402 North Blackford Street, Indianapolis, Indiana, 46202, USA
| | - Surya Adhikari
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis (IUPUI), 402 North Blackford Street, Indianapolis, Indiana, 46202, USA
| | - Lei Li
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis (IUPUI), 402 North Blackford Street, Indianapolis, Indiana, 46202, USA.,Department of Dermatology, Indiana University School of Medicine, Indianapolis, Indiana, 46202, USA
| | - Tatiana Domratcheva
- Department of Biomolecular Mechanisms, Max-Planck Institute for Medical Research, Jahnstrasse 29, 69120, Heidelberg, Germany
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Yang L, Jian Y, Setlow P, Li L. Spore photoproduct within DNA is a surprisingly poor substrate for its designated repair enzyme-The spore photoproduct lyase. DNA Repair (Amst) 2017; 53:31-42. [PMID: 28320593 DOI: 10.1016/j.dnarep.2016.11.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 05/23/2016] [Accepted: 11/15/2016] [Indexed: 12/15/2022]
Abstract
DNA repair enzymes typically recognize their substrate lesions with high affinity to ensure efficient lesion repair. In UV irradiated endospores, a special thymine dimer, 5-thyminyl-5,6-dihydrothymine, termed the spore photoproduct (SP), is the dominant DNA photolesion, which is rapidly repaired during spore outgrowth mainly by spore photoproduct lyase (SPL) using an unprecedented protein-harbored radical transfer process. Surprisingly, our in vitro studies using SP-containing short oligonucleotides, pUC 18 plasmid DNA, and E. coli genomic DNA found that they are all poor substrates for SPL in general, exhibiting turnover numbers of 0.01-0.2min-1. The faster turnover numbers are reached under single turnover conditions, and SPL activity is low with oligonucleotide substrates at higher concentrations. Moreover, SP-containing oligonucleotides do not go past one turnover. In contrast, the dinucleotide SP TpT exhibits a turnover number of 0.3-0.4min-1, and the reaction may reach up to 10 turnovers. These observations distinguish SPL from other specialized DNA repair enzymes. To the best of our knowledge, SPL represents an unprecedented example of a major DNA repair enzyme that cannot effectively repair its substrate lesion within the normal DNA conformation adopted in growing cells. Factors such as other DNA binding proteins, helicases or an altered DNA conformation may cooperate with SPL to enable efficient SP repair in germinating spores. Therefore, both SP formation and SP repair are likely to be tightly controlled by the unique cellular environment in dormant and outgrowing spore-forming bacteria, and thus SP repair may be extremely slow in non-spore-forming organisms.
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Affiliation(s)
- Linlin Yang
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis (IUPUI), 402 North Blackford Street, Indianapolis, IN 46202, United States
| | - Yajun Jian
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis (IUPUI), 402 North Blackford Street, Indianapolis, IN 46202, United States
| | - Peter Setlow
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT 06030, United States
| | - Lei Li
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis (IUPUI), 402 North Blackford Street, Indianapolis, IN 46202, United States; Department of Dermatology, Indiana University School of Medicine, Indianapolis, IN 46202, United States.
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Berteau O, Benjdia A. DNA Repair by the Radical SAM Enzyme Spore Photoproduct Lyase: From Biochemistry to Structural Investigations. Photochem Photobiol 2017; 93:67-77. [DOI: 10.1111/php.12702] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 12/19/2016] [Indexed: 10/20/2022]
Affiliation(s)
- Olivier Berteau
- Micalis Institute; INRA; ChemSyBio; AgroParisTech; Université Paris-Saclay; Jouy-en-Josas France
| | - Alhosna Benjdia
- Micalis Institute; INRA; ChemSyBio; AgroParisTech; Université Paris-Saclay; Jouy-en-Josas France
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11
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Yang L, Adhikari J, Gross ML, Li L. Kinetic Isotope Effects and Hydrogen/Deuterium Exchange Reveal Large Conformational Changes During the Catalysis of the Clostridium acetobutylicum Spore Photoproduct Lyase. Photochem Photobiol 2017; 93:331-342. [PMID: 27992649 PMCID: PMC5315627 DOI: 10.1111/php.12697] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Accepted: 11/29/2016] [Indexed: 11/30/2022]
Abstract
Spore photoproduct lyase (SPL) catalyzes the direct reversal of a thymine dimer 5-thyminyl-5,6-dihydrothymine (i.e. the spore photoproduct (SP)) to two thymine residues in germinating endospores. Previous studies suggest that SPL from the bacterium Bacillus subtilis (Bs) harbors an unprecedented radical-transfer pathway starting with cysteine 141 proceeding through tyrosine 99. However, in SPL from the bacterium Clostridium acetobutylicum (Ca), the cysteine (at position 74) and the tyrosine are located on the opposite sides of a substrate-binding pocket that has to collapse to bring the two residues into proximity, enabling the C→Y radical passage as implied in SPL(Bs) . To test this hypothesis, we adopted hydrogen/deuterium exchange mass spectrometry (HDX-MS) to show that C74(Ca) is located at a highly flexible region. The repair of dinucleotide SP TpT by SPL(Ca) is eight-fold to 10-fold slower than that by SPL(Bs) ; the process also generates a large portion of the aborted product TpTSO2- . SPL(Ca) exhibits apparent (D V) kinetic isotope effects (KIEs) of ~6 and abnormally large competitive (D V/K) KIEs (~20), both of which are much larger than the KIEs observed for SPL(Bs) . All these observations indicate that SPL(Ca) possesses a flexible active site and readily undergoes conformational changes during catalysis.
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Affiliation(s)
- Linlin Yang
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis (IUPUI), 402 North Blackford Street, Indianapolis, Indiana, 46202, USA
| | - Jagat Adhikari
- Department of Chemistry, Washington University in St. Louis, One Brookings Dr., St. Louis, MO 63130, USA
| | - Michael L. Gross
- Department of Chemistry, Washington University in St. Louis, One Brookings Dr., St. Louis, MO 63130, USA
| | - Lei Li
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis (IUPUI), 402 North Blackford Street, Indianapolis, Indiana, 46202, USA
- Department of Biochemistry and Molecular Biology & Department of Dermatology, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
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12
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Hayes EC, Jian Y, Li L, Stoll S. EPR Study of UV-Irradiated Thymidine Microcrystals Supports Radical Intermediates in Spore Photoproduct Formation. J Phys Chem B 2016; 120:10923-10931. [DOI: 10.1021/acs.jpcb.6b06587] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Ellen C. Hayes
- Department
of Chemistry, Box 351700, University of Washington, Seattle, Washington 98195, United States
| | - Yajun Jian
- Department
of Chemistry and Chemical Biology, 402 N. Blackford Street, LD 326, Indiana University—Purdue University Indianapolis, Indianapolis, Indiana 46202, United States
| | - Lei Li
- Department
of Chemistry and Chemical Biology, 402 N. Blackford Street, LD 326, Indiana University—Purdue University Indianapolis, Indianapolis, Indiana 46202, United States
| | - Stefan Stoll
- Department
of Chemistry, Box 351700, University of Washington, Seattle, Washington 98195, United States
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13
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Adhikari S, Lin G, Li L. Reversible Hydrolysis Reaction with the Spore Photoproduct under Alkaline Conditions. J Org Chem 2016; 81:8570-6. [PMID: 27537985 DOI: 10.1021/acs.joc.6b01846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
DNA lesions may reduce the electron density at the nucleobases, making them prone to further modifications upon the alkaline treatment. The dominant DNA photolesion found in UV-irradiated bacterial endospores is a thymine dimer, 5-thyminyl-5,6-dihydrothymine, i.e., the spore photoproduct (SP). Here we report a stepwise addition/elimination reaction in the SP hydrolysis product under strong basic conditions where a ureido group is added to the carboxyl moiety to form a cyclic amide, regenerating SP after eliminating a hydroxide ion. Direct amidation of carboxylic acids by reaction with amines in the presence of a catalyst is well documented; however, it is very rare for an amidation reaction to occur without activation. This uncatalyzed SP reverse reaction in aqueous solution is even more surprising because the carboxyl moiety is not a good electrophile due to the negative charge it carries. Examination of the base-catalyzed hydrolyses of two other saturated pyrimidine lesions, 5,6-dihydro-2'-deoxyuridine and pyrimidine (6-4) pyrimidone photoproduct, reveals that neither reaction is reversible even though all three hydrolysis reactions may share the same gem-diol intermediate. Therefore, the SP structure where the two thymine residues maintain a stacked conformation likely provides the needed framework enabling this highly unusual carboxyl addition/elimination reaction.
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Affiliation(s)
- Surya Adhikari
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis (IUPUI) , 402 North Blackford Street, Indianapolis, Indiana, 46202, United States
| | - Gengjie Lin
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis (IUPUI) , 402 North Blackford Street, Indianapolis, Indiana, 46202, United States
| | - Lei Li
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis (IUPUI) , 402 North Blackford Street, Indianapolis, Indiana, 46202, United States.,Department of Biochemistry and Molecular Biology & Department of Dermatology, Indiana University School of Medicine , Indianapolis, Indiana 46202, United States
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14
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Mundt R, Torres Ziegenbein C, Fröbel S, Weingart O, Gilch P. Femtosecond Spectroscopy of Calcium Dipicolinate—A Major Component of Bacterial Spores. J Phys Chem B 2016; 120:9376-86. [DOI: 10.1021/acs.jpcb.6b06230] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ramona Mundt
- Institut
für Physikalische Chemie, Heinrich-Heine-Universität Düsseldorf, Universitätstr.
1, D-40225 Düsseldorf, Germany
| | - Christian Torres Ziegenbein
- Institut
für Physikalische Chemie, Heinrich-Heine-Universität Düsseldorf, Universitätstr.
1, D-40225 Düsseldorf, Germany
| | - Sascha Fröbel
- Institut
für Physikalische Chemie, Heinrich-Heine-Universität Düsseldorf, Universitätstr.
1, D-40225 Düsseldorf, Germany
| | - Oliver Weingart
- Institut
für Theoretische Chemie und Computerchemie, Heinrich-Heine-Universität Düsseldorf, Universitätstr. 1, D-40225 Düsseldorf, Germany
| | - Peter Gilch
- Institut
für Physikalische Chemie, Heinrich-Heine-Universität Düsseldorf, Universitätstr.
1, D-40225 Düsseldorf, Germany
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15
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Wrigstedt P, Kavakka J, Heikkinen S, Nieger M, Räisänen M, Repo T. The Reactivity of Thymine and Thymidine 5,6-Epoxides with Organometallic Reagents - A Route to Thymidine (6-4) Photoproduct Analogues. J Org Chem 2016; 81:3848-59. [PMID: 27080560 DOI: 10.1021/acs.joc.6b00495] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
This report describes an efficient procedure for the generation and isolation of various thymine and thymidine 5,6-epoxides from the corresponding trans-5,6-bromohydrins by reaction with triethylamine. The quantitative isolation of the epoxides, accomplished by solvent precipitation of triethylamine hydrobromide, enabled their regiospecific ring-opening at C6 position by organometallic nucleophiles. The reaction was amenable to a broad range of alkyl, aryl, alkenyl, and alkynyl organomagnesium, -zinc, -aluminum, or -boron reagents, although the reactivity was strongly affected by the electronic effects of N3 protecting group. Additionally, the reaction featured excellent cis-diastereoselectivity providing access to C6-carbon-functionalized dihydrothymidine cis-alcohols, which are synthetic derivatives of UV-induced DNA lesions, namely, thymidine (6-4) photoproducts.
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Affiliation(s)
- Pauli Wrigstedt
- Department of Chemistry, †Laboratory of Inorganic Chemistry and ‡Laboratory of Organic Chemistry, University of Helsinki , P.O. Box 55, Helsinki FIN-00014, Finland
| | - Jari Kavakka
- Department of Chemistry, †Laboratory of Inorganic Chemistry and ‡Laboratory of Organic Chemistry, University of Helsinki , P.O. Box 55, Helsinki FIN-00014, Finland
| | - Sami Heikkinen
- Department of Chemistry, †Laboratory of Inorganic Chemistry and ‡Laboratory of Organic Chemistry, University of Helsinki , P.O. Box 55, Helsinki FIN-00014, Finland
| | - Martin Nieger
- Department of Chemistry, †Laboratory of Inorganic Chemistry and ‡Laboratory of Organic Chemistry, University of Helsinki , P.O. Box 55, Helsinki FIN-00014, Finland
| | - Minna Räisänen
- Department of Chemistry, †Laboratory of Inorganic Chemistry and ‡Laboratory of Organic Chemistry, University of Helsinki , P.O. Box 55, Helsinki FIN-00014, Finland
| | - Timo Repo
- Department of Chemistry, †Laboratory of Inorganic Chemistry and ‡Laboratory of Organic Chemistry, University of Helsinki , P.O. Box 55, Helsinki FIN-00014, Finland
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16
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De Coen LM, Heugebaert TSA, García D, Stevens CV. Synthetic Entries to and Biological Activity of Pyrrolopyrimidines. Chem Rev 2015; 116:80-139. [DOI: 10.1021/acs.chemrev.5b00483] [Citation(s) in RCA: 109] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Laurens M. De Coen
- Department of Sustainable
Organic Chemistry and Technology, Ghent University, Coupure links
653, B-9000 Ghent, Belgium
| | - Thomas S. A. Heugebaert
- Department of Sustainable
Organic Chemistry and Technology, Ghent University, Coupure links
653, B-9000 Ghent, Belgium
| | - Daniel García
- Department of Sustainable
Organic Chemistry and Technology, Ghent University, Coupure links
653, B-9000 Ghent, Belgium
| | - Christian V. Stevens
- Department of Sustainable
Organic Chemistry and Technology, Ghent University, Coupure links
653, B-9000 Ghent, Belgium
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17
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Setlow P, Li L. Photochemistry and Photobiology of the Spore Photoproduct: A 50-Year Journey. Photochem Photobiol 2015; 91:1263-90. [PMID: 26265564 PMCID: PMC4631623 DOI: 10.1111/php.12506] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Accepted: 07/21/2015] [Indexed: 02/06/2023]
Abstract
Fifty years ago, a new thymine dimer was discovered as the dominant DNA photolesion in UV-irradiated bacterial spores [Donnellan, J. E. & Setlow R. B. (1965) Science, 149, 308-310], which was later named the spore photoproduct (SP). Formation of SP is due to the unique environment in the spore core that features low hydration levels favoring an A-DNA conformation, high levels of calcium dipicolinate that acts as a photosensitizer, and DNA saturation with small, acid-soluble proteins that alters DNA structure and reduces side reactions. In vitro studies reveal that any of these factors alone can promote SP formation; however, SP formation is usually accompanied by the production of other DNA photolesions. Therefore, the nearly exclusive SP formation in spores is due to the combined effects of these three factors. Spore photoproduct photoreaction is proved to occur via a unique H-atom transfer mechanism between the two involved thymine residues. Successful incorporation of SP into an oligonucleotide has been achieved via organic synthesis, which enables structural studies that reveal minor conformational changes in the SP-containing DNA. Here, we review the progress on SP photochemistry and photobiology in the past 50 years, which indicates a very rich SP photobiology that may exist beyond endospores.
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Affiliation(s)
- Peter Setlow
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, Connecticut, USA
| | - Lei Li
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis (IUPUI), Indianapolis, Indiana, 46202
- Department of Biochemistry and Molecular Biology & Department of Dermatology, Indiana University School of Medicine, Indianapolis, Indiana 46202
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18
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Whole-cell method for phenol detection based on the color reaction of phenol with 4-aminoantipyrine catalyzed by CotA laccase on endospore surfaces. Biosens Bioelectron 2015; 69:162-6. [DOI: 10.1016/j.bios.2015.02.032] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Revised: 02/17/2015] [Accepted: 02/19/2015] [Indexed: 11/24/2022]
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19
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Benjdia A, Heil K, Winkler A, Carell T, Schlichting I. Rescuing DNA repair activity by rewiring the H-atom transfer pathway in the radical SAM enzyme, spore photoproduct lyase. Chem Commun (Camb) 2015; 50:14201-4. [PMID: 25285338 DOI: 10.1039/c4cc05158k] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The radical SAM enzyme, spore photoproduct lyase, requires an H-atom transfer (HAT) pathway to catalyze DNA repair. By rational engineering, we demonstrate that it is possible to rewire its HAT pathway, a first step toward the development of novel catalysts based on the radical SAM enzyme scaffold.
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Affiliation(s)
- Alhosna Benjdia
- Department of Biomolecular Mechanisms, Max-Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
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20
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Solar UV radiation-induced DNA Bipyrimidine photoproducts: formation and mechanistic insights. Top Curr Chem (Cham) 2015; 356:249-75. [PMID: 25370518 DOI: 10.1007/128_2014_553] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
This review chapter presents a critical survey of the main available information on the UVB and UVA bipyrimidine photoproducts which constitute the predominant recipient classes of photo-induced DNA damage. Evidence is provided that UVB irradiation of isolated DNA in aqueous solutions and in cells gives rise to the predominant generation of cis-syn cyclobutane pyrimidine dimers (CPDs) and, to a lesser extent, of pyrimidine (6-4) pyrimidone photoproducts (6-4PPs), the importance of which is strongly primary sequence dependent. A notable change in the photoproduct distribution is observed when DNA either in the dry or in desiccated microorganisms is exposed to UVC or UVB photons with an overwhelming formation of 5-(α-thymidyl)-5,6-dihydrothymidine, also called spore photoproduct (dSP), at the expense of CPDs and 6-4PPs. UVA irradiation of isolated and cellular DNA gives rise predominantly to bipyrimidine photoproducts with the overwhelming formation of thymine-containing cyclobutane pyrimidine dimers at the exclusion of 6-4PPs. UVA photons have been shown to modulate the distribution of UVB dimeric pyrimidine photoproducts by triggering isomerization of the 6-4PPs into related Dewar valence isomers. Mechanistic aspects of the formation of bipyrimidine photoproducts are discussed in the light of recent photophysical and theoretical studies.
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21
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Jian Y, Ames DM, Ouyang H, Li L. Photochemical reactions of microcrystalline thymidine. Org Lett 2015; 17:824-7. [PMID: 25668312 DOI: 10.1021/ol5036276] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Nucleoside/nucleotide/oligonucleotide photoreactions usually result in a number of products simultaneously due to a wide range of conformers existing at a given time. Such a complicated reaction pattern makes it difficult for one to focus on a single DNA photoproduct and elucidate the requirements for its formation. A rare example of thymidine photoreaction in microcrystals is reported, where 5-thyminyl-5,6-dihydrothymine, e.g., the spore photoproduct (SP), is produced as the dominant species in ∼85% yield. This unprecedented high yield clears the major obstacle for future SP photochemistry studies in detail.
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Affiliation(s)
- Yajun Jian
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis (IUPUI) , 402 North Blackford Street, Indianapolis, Indiana 46202, United States
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22
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Abstract
Ultraviolet (UV) radiation is a leading external hazard to the integrity of DNA. Exposure to UV radiation triggers a cascade of chemical reactions, and many molecular products (photolesions) have been isolated that are potentially dangerous for the cellular system. The early steps that take place after UV absorption by DNA have been studied by ultrafast spectroscopy. The review focuses on the evolution of excited electronic states, the formation of photolesions, and processes suppressing their formation. Emphasis is placed on lesions involving two thymine bases, such as the cyclobutane pyrimidine dimer, the (6-4) lesion, and its Dewar valence isomer.
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Affiliation(s)
- Wolfgang J Schreier
- Lehrstuhl für BioMolekulare Optik, Fakultät für Physik and Munich Center for Integrated Protein Science CIPSM, Ludwig-Maximilians-Universität München, 80538 München, Germany;
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23
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Weller C, Wu M. A generation-time effect on the rate of molecular evolution in bacteria. Evolution 2015; 69:643-52. [PMID: 25564727 DOI: 10.1111/evo.12597] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2014] [Accepted: 12/17/2014] [Indexed: 12/31/2022]
Abstract
Molecular evolutionary rate varies significantly among species and a strict global molecular clock has been rejected across the tree of life. Generation time is one primary life-history trait that influences the molecular evolutionary rate. Theory predicts that organisms with shorter generation times evolve faster because of the accumulation of more DNA replication errors per unit time. Although the generation-time effect has been demonstrated consistently in plants and animals, the evidence of its existence in bacteria is lacking. The bacterial phylum Firmicutes offers an excellent system for testing generation-time effect because some of its members can enter a dormant, nonreproductive endospore state in response to harsh environmental conditions. It follows that spore-forming bacteria would--with their longer generation times--evolve more slowly than their nonspore-forming relatives. It is therefore surprising that a previous study found no generation-time effect in Firmicutes. Using a phylogenetic comparative approach and leveraging on a large number of Firmicutes genomes, we found sporulation significantly reduces the genome-wide spontaneous DNA mutation rate and protein evolutionary rate. Contrary to the previous study, our results provide strong evidence that the evolutionary rates of bacteria, like those of plants and animals, are influenced by generation time.
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Affiliation(s)
- Cory Weller
- Department of Biology, University of Virginia, Charlottesville, Virginia, 22904
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24
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Abstract
Spore photoproduct lyase (SPL) repairs 5-thyminyl-5,6-dihydrothymine, a thymine dimer that is also called the spore photoproduct (SP), in germinating endospores. SPL is a radical S-adenosylmethionine (SAM) enzyme, utilizing the 5'-deoxyadenosyl radical generated by SAM reductive cleavage reaction to revert SP to two thymine residues. Here we review the current progress in SPL mechanistic studies. Protein radicals are known to be involved in SPL catalysis; however, how these radicals are quenched to close the catalytic cycle is under debate.
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Affiliation(s)
- Linlin Yang
- From the Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis (IUPUI), Indianapolis, Indiana, 46202 and
| | - Lei Li
- From the Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis (IUPUI), Indianapolis, Indiana, 46202 and Department of Biochemistry and Molecular Biology, Indiana University School of Medicine (IUSM), Indianapolis, Indiana 46202
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25
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Lin G, Jian Y, Dria KJ, Long EC, Li L. Reactivity of damaged pyrimidines: DNA cleavage via hemiaminal formation at the C4 positions of the saturated thymine of spore photoproduct and dihydrouridine. J Am Chem Soc 2014; 136:12938-46. [PMID: 25127075 PMCID: PMC4183628 DOI: 10.1021/ja505407p] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
![]()
Described
here are mechanistic details of the chemical reactivities
of two modified/saturated pyrimidine residues that represent naturally
occurring forms of DNA damage: 5-thyminyl-5,6-dihydrothymine, commonly
referred to as the “spore photoproduct” (SP), and 5,6-dihydro-2′-deoxyuridine
(dHdU), formed via ionizing radiation damage to cytosine under anoxic
conditions and also serving as a general model of saturated pyrimidine
residues. It is shown that due to the loss of the pyrimidine C5–C6
double bond and consequent loss of ring aromaticity, the C4 position
of both these saturated pyrimidines is prone to the formation of a
hemiaminal intermediate via water addition. Water addition is facilitated
by basic conditions; however, it also occurs at physiological pH at
a slower rate. The hemiaminal species so-formed subsequently converts
to a ring-opened hydrolysis product through cleavage of the pyrimidine
N3–C4 bond. Further decomposition of this ring-opened product
above physiological pH leads to DNA strand break formation. Taken
together, these results suggest that once the aromaticity of a pyrimidine
residue is lost, the C4 position becomes a “hot spot”
for the formation of a tetrahedral intermediate, the decay of which
triggers a cascade of elimination reactions that can under certain
conditions convert a simple nucleobase modification into a DNA strand
break.
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Affiliation(s)
- Gengjie Lin
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis (IUPUI) , 402 North Blackford Street, Indianapolis, Indiana 46202, United States
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26
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Ames DM, Lin G, Jian Y, Cadet J, Li L. Unusually large deuterium discrimination during spore photoproduct formation. J Org Chem 2014; 79:4843-51. [PMID: 24820206 PMCID: PMC4049236 DOI: 10.1021/jo500775b] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The deuterium-labeling strategy has been widely used and proved highly effective in mechanistic investigation of chemical and biochemical reactions. However, it is often hampered by the incomplete label transfer, which subsequently obscures the mechanistic conclusion. During the study of photoinduced generation of 5-thyminyl-5,6-dihydrothymine, which is commonly called the spore photoproduct (SP), the Cadet laboratory found an incomplete (~67%) deuterium transfer in SP formation, which contrasts to the exclusive transfer observed by the Li laboratory. Here, we investigated this discrepancy by re-examining the SP formation using d3-thymidine. We spiked the d3-thymidine with varying amounts of unlabeled thymidine before the SP photochemistry is performed. Strikingly, our data show that the reaction is highly sensitive to the trace protiated thymidine in the starting material. As many as 17-fold enrichment is detected in the formed SP, which may explain the previously observed one-third protium incorporation. Although commercially available deuterated reagents are generally satisfactory as mechanistic probes, our results argue that attention is still needed to the possible interference from the trace protiated impurity, especially when the reaction yield is low and large isotopic discrimination is involved.
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Affiliation(s)
- David M Ames
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis (IUPUI) , 402 North Blackford Street, Indianapolis, Indiana 46202, United States
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27
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Douki T. The variety of UV-induced pyrimidine dimeric photoproducts in DNA as shown by chromatographic quantification methods. Photochem Photobiol Sci 2014; 12:1286-302. [PMID: 23572060 DOI: 10.1039/c3pp25451h] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Induction of DNA damage is one of the major consequences of exposure to solar UV radiation in living organisms. UV-induced DNA photoproducts are mostly pyrimidine dimers, including cyclobutane pyrimidine dimers, pyrimidine (6-4) pyrimidone photoproducts and Dewar valence isomers. In the last few decades, a large number of methods have been developed for the quantification of these pyrimidine dimers. The present review emphasizes the contribution of chromatographic techniques to our better understanding of the basic DNA photochemistry and the better description of damage in cells.
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Affiliation(s)
- Thierry Douki
- Laboratoire 'Lésions des Acides Nucléiques', Université Joseph Fourier - Grenoble 1/CEA/Institut Nanoscience et Cryogénie/SCIB, UMR-E3, Grenoble, France.
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28
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Abstract
Solar ultraviolet (UV) radiation, mainly UV-B (280-315 nm), is one of the most potent genotoxic agents that adversely affects living organisms by altering their genomic stability. DNA through its nucleobases has absorption maxima in the UV region and is therefore the main target of the deleterious radiation. The main biological relevance of UV radiation lies in the formation of several cytotoxic and mutagenic DNA lesions such as cyclobutane pyrimidine dimers (CPDs), 6-4 photoproducts (6-4PPs), and their Dewar valence isomers (DEWs), as well as DNA strand breaks. However, to counteract these DNA lesions, organisms have developed a number of highly conserved repair mechanisms such as photoreactivation, excision repair, and mismatch repair (MMR). Photoreactivation involving the enzyme photolyase is the most frequently used repair mechanism in a number of organisms. Excision repair can be classified as base excision repair (BER) and nucleotide excision repair (NER) involving a number of glycosylases and polymerases, respectively. In addition to this, double-strand break repair, SOS response, cell-cycle checkpoints, and programmed cell death (apoptosis) are also operative in various organisms to ensure genomic stability. This review concentrates on the UV-induced DNA damage and the associated repair mechanisms as well as various damage detection methods.
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Affiliation(s)
- Richa
- Laboratory of Photobiology and Molecular Microbiology, Centre of Advanced Study in Botany, Banaras Hindu University, Varanasi, 221005, India
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29
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30
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Dong A, Xue M, Lan S, Wang Q, Zhao Y, Wang Y, Zhang Y, Gao G, Liu F, Harnoode C. Bactericidal evaluation of N-halamine-functionalized silica nanoparticles based on barbituric acid. Colloids Surf B Biointerfaces 2014; 113:450-7. [DOI: 10.1016/j.colsurfb.2013.09.048] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Revised: 09/03/2013] [Accepted: 09/24/2013] [Indexed: 12/22/2022]
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31
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Kneuttinger AC, Kashiwazaki G, Prill S, Heil K, Müller M, Carell T. Formation and Direct Repair of UV-induced Dimeric DNA Pyrimidine Lesions. Photochem Photobiol 2013; 90:1-14. [PMID: 24354557 DOI: 10.1111/php.12197] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Accepted: 10/17/2013] [Indexed: 12/11/2022]
Abstract
Direct repair of UV-induced DNA lesions represents an elegant method for many organisms to deal with these highly mutagenic and cytotoxic compounds. Although the participating proteins are structurally well investigated, the exact repair mechanism of the photolyase enzymes remains a vivid subject of current research. In this review, we summarize and highlight the recent contributions to this exciting field.
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Affiliation(s)
- Andrea Christa Kneuttinger
- Center for Integrated Protein Sciences at the Department of Chemistry, Ludwig-Maximilians Universität München, Munich, Germany
| | - Gengo Kashiwazaki
- Center for Integrated Protein Sciences at the Department of Chemistry, Ludwig-Maximilians Universität München, Munich, Germany
| | - Stefan Prill
- Center for Integrated Protein Sciences at the Department of Chemistry, Ludwig-Maximilians Universität München, Munich, Germany
| | - Korbinian Heil
- Center for Integrated Protein Sciences at the Department of Chemistry, Ludwig-Maximilians Universität München, Munich, Germany
| | - Markus Müller
- Center for Integrated Protein Sciences at the Department of Chemistry, Ludwig-Maximilians Universität München, Munich, Germany
| | - Thomas Carell
- Center for Integrated Protein Sciences at the Department of Chemistry, Ludwig-Maximilians Universität München, Munich, Germany
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32
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Du Q, Zhao H, Su H. Theoretical Investigation on the Absence of Spore Photoproduct Analogue at Cytosine‐Thymine Site. CHINESE J CHEM PHYS 2013. [DOI: 10.1063/1674-0068/26/06/661-668] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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33
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Vendrell-Criado V, Rodríguez-Muñiz GM, Yamaji M, Lhiaubet-Vallet V, Cuquerella MC, Miranda MA. Two-Photon Chemistry from Upper Triplet States of Thymine. J Am Chem Soc 2013; 135:16714-9. [DOI: 10.1021/ja408997j] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Victoria Vendrell-Criado
- Instituto
de Tecnología Química UPV-CSIC, Universitat Politècnica de València, Av. Los Naranjos s/n, 46022 Valencia, Spain
| | - Gemma M. Rodríguez-Muñiz
- Instituto
de Tecnología Química UPV-CSIC, Universitat Politècnica de València, Av. Los Naranjos s/n, 46022 Valencia, Spain
| | - Minoru Yamaji
- Division
of Molecular Science, Faculty of Science and Technology, Gunma University, Kiryu Gunma 376-8515, Japan
| | - Virginie Lhiaubet-Vallet
- Instituto
de Tecnología Química UPV-CSIC, Universitat Politècnica de València, Av. Los Naranjos s/n, 46022 Valencia, Spain
| | - M. Consuelo Cuquerella
- Instituto
de Tecnología Química UPV-CSIC, Universitat Politècnica de València, Av. Los Naranjos s/n, 46022 Valencia, Spain
| | - Miguel A. Miranda
- Instituto
de Tecnología Química UPV-CSIC, Universitat Politècnica de València, Av. Los Naranjos s/n, 46022 Valencia, Spain
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34
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Yang L, Li L. The enzyme-mediated direct reversal of a dithymine photoproduct in germinating endospores. Int J Mol Sci 2013; 14:13137-53. [PMID: 23799365 PMCID: PMC3742179 DOI: 10.3390/ijms140713137] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Revised: 06/04/2013] [Accepted: 06/07/2013] [Indexed: 11/16/2022] Open
Abstract
Spore photoproduct lyase (SPL) repairs a special thymine dimer, 5-thyminyl-5,6-dihydrothymine, which is commonly called spore photoproduct, or SP, in germinating endospores. SP is the exclusive DNA photo-damaging product found in endospores; its generation and swift repair by SPL are responsible for the spores’ extremely high UV resistance. Early in vivo studies suggested that SPL utilizes a direct reversal strategy to repair SP in the absence of light. Recently, it has been established that SPL belongs to the radical S-adenosylmethionine (SAM) superfamily. The enzymes in this superfamily utilize a tri-cysteine CXXXCXXC motif to bind a [4Fe-4S] cluster. The cluster provides an electron to the S-adenosylmethionine (SAM) to reductively cleave its C5′-S bond, generating a reactive 5′-deoxyadenosyl (5′-dA) radical. This 5′-dA radical abstracts the proR hydrogen atom from the C6 carbon of SP to initiate the repair process; the resulting SP radical subsequently fragments to generate a putative thymine methyl radical, which accepts a back-donated H atom to yield the repaired TpT. The H atom donor is suggested to be a conserved cysteine141 in B. subtilis SPL; the resulting thiyl radical likely interacts with a neighboring tyrosine99 before oxidizing the 5′-dA to 5′-dA radical and, subsequently, regenerating SAM. These findings suggest SPL to be the first enzyme in the large radical SAM superfamily (>44,000 members) to utilize a radical transfer pathway for catalysis; its study should shed light on the mechanistic understanding of the SAM regeneration process in other members of the superfamily.
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Affiliation(s)
- Linlin Yang
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis (IUPUI), 402 N Blackford Street, Indianapolis, IN 46202, USA; E-Mail:
| | - Lei Li
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis (IUPUI), 402 N Blackford Street, Indianapolis, IN 46202, USA; E-Mail:
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine (IUSM), 635 Barnhill Drive, Indianapolis, IN 46202, USA
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +1-317-278-2202; Fax: +1-317-274-4701
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Clivio P, Coantic-Castex S, Guillaume D. (3'-5')-Cyclic dinucleotides: synthetic strategies and biological potential. Chem Rev 2013; 113:7354-401. [PMID: 23767818 DOI: 10.1021/cr300011s] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Pascale Clivio
- UMR 6229, Institut de Chimie Moléculaire de Reims, CNRS-Université de Reims Champagne Ardenne , UFR Médecine-Pharmacie, 51 Rue Cognacq Jay, 51096 Reims Cedex, France
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Kneuttinger AC, Heil K, Kashiwazaki G, Carell T. The radical SAM enzyme spore photoproduct lyase employs a tyrosyl radical for DNA repair. Chem Commun (Camb) 2013; 49:722-4. [PMID: 23228940 DOI: 10.1039/c2cc37735g] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The spore photoproduct lyase is a radical SAM enzyme, which repairs 5-(α-thyminyl)-5,6-dihydrothymidine. Here we show that the enzyme establishes a complex radical transfer cascade and creates a cysteine and a tyrosyl radical dyade to establish repair. This allows the enzyme to solve topological and energetic problems associated with the radical based repair reaction.
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Affiliation(s)
- Andrea Christa Kneuttinger
- Center for Integrative Protein Science at the Department for Chemistry, Ludwig-Maximilians-Universität, Butenandtstr. 5-13, 81377 Munich, Germany
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Yang L, Nelson RS, Benjdia A, Lin G, Telser J, Stoll S, Schlichting I, Li L. A radical transfer pathway in spore photoproduct lyase. Biochemistry 2013; 52:3041-50. [PMID: 23607538 DOI: 10.1021/bi3016247] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Spore photoproduct lyase (SPL) repairs a covalent UV-induced thymine dimer, spore photoproduct (SP), in germinating endospores and is responsible for the strong UV resistance of endospores. SPL is a radical S-adenosyl-l-methionine (SAM) enzyme, which uses a [4Fe-4S](+) cluster to reduce SAM, generating a catalytic 5'-deoxyadenosyl radical (5'-dA(•)). This in turn abstracts a H atom from SP, generating an SP radical that undergoes β scission to form a repaired 5'-thymine and a 3'-thymine allylic radical. Recent biochemical and structural data suggest that a conserved cysteine donates a H atom to the thymine radical, resulting in a putative thiyl radical. Here we present structural and biochemical data that suggest that two conserved tyrosines are also critical in enzyme catalysis. One [Y99(Bs) in Bacillus subtilis SPL] is downstream of the cysteine, suggesting that SPL uses a novel hydrogen atom transfer (HAT) pathway with a pair of cysteine and tyrosine residues to regenerate SAM. The other tyrosine [Y97(Bs)] has a structural role to facilitate SAM binding; it may also contribute to the SAM regeneration process by interacting with the putative (•)Y99(Bs) and/or 5'-dA(•) intermediates to lower the energy barrier for the second H abstraction step. Our results indicate that SPL is the first member of the radical SAM superfamily (comprising more than 44000 members) to bear a catalytically operating HAT chain.
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Affiliation(s)
- Linlin Yang
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, Indianapolis, IN 46202, USA
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Abstract
5-(α-Thyminyl)-5,6-dihydrothymine, also called spore photoproduct or SP, is commonly found in the genomic DNA of UV-irradiated bacterial endospores. Despite the fact that SP was discovered nearly 50 years ago, its biochemical impact is still largely unclear due to the difficulty of preparing SP-containing oligonucleotide in high purity. Here, we report the first synthesis of the phosphoramidite derivative of dinucleotide SP TpT, which enables successful incorporation of SP TpT into oligodeoxyribonucleotides with high efficiency via standard solid-phase synthesis. This result provides the scientific community a reliable means to prepare SP-containing oligonucleotides, laying the foundation for future SP biochemical studies. Thermal denaturation studies of the SP-containing oligonucleotide found that SP destabilizes the duplex by 10-20 kJ/mol, suggesting that its presence in the spore-genomic DNA may alter the DNA local conformation.
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Affiliation(s)
- Yajun Jian
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis (IUPUI), Indianapolis, Indiana, 46202
| | - Lei Li
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis (IUPUI), Indianapolis, Indiana, 46202
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine (IUSM), 635 Barnhill Drive, Indianapolis, Indiana 46202
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Benjdia A. DNA photolyases and SP lyase: structure and mechanism of light-dependent and independent DNA lyases. Curr Opin Struct Biol 2012; 22:711-20. [PMID: 23164663 DOI: 10.1016/j.sbi.2012.10.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2012] [Revised: 09/30/2012] [Accepted: 10/02/2012] [Indexed: 10/27/2022]
Abstract
Light is essential for many critical biological processes including vision, circadian rhythms, photosynthesis and DNA repair. DNA photolyases use light energy and a fully reduced flavin cofactor to repair the major UV-induced DNA damages, the cis-syn cyclobutane pyrimidine dimers (CPDs) and the pyrimidine-pyrimidone (6-4) photoproducts. Catalysis involves two photoreactions, the photoactivation which leads to the conversion of the flavin cofactor to its catalytic active form and the photorepair whose efficiency depends on a light-harvesting antenna chromophore. Very interestingly, an alternative and light-independent direct reversal mechanism to repair a distinct photolesion is found in bacterial spores, catalyzed by spore photoproduct lyase. This radical SAM enzyme uses an iron-sulfur cluster and S-adenosyl-l-methionine (SAM) to split a specific photoproduct, the so-called spore photoproduct (SP), back to two thymidine residues. The recently solved crystal structure of SP lyase provides new insights into this unique DNA repair mechanism and allows a detailed comparison with DNA photolyases. Similarities as well as divergences between DNA photolyases and SP lyase are highlighted in this review.
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Affiliation(s)
- Alhosna Benjdia
- Department of Biomolecular Mechanisms, Max-Planck Institute for Medical Research, Jahnstrasse 29, Heidelberg, Germany.
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Li L. Mechanistic studies of the radical SAM enzyme spore photoproduct lyase (SPL). BIOCHIMICA ET BIOPHYSICA ACTA 2012; 1824:1264-77. [PMID: 22197590 PMCID: PMC3314140 DOI: 10.1016/j.bbapap.2011.11.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2011] [Accepted: 11/28/2011] [Indexed: 02/06/2023]
Abstract
Spore photoproduct lyase (SPL) repairs a special thymine dimer 5-thyminyl-5,6-dihydrothymine, which is commonly called spore photoproduct or SP at the bacterial early germination phase. SP is the exclusive DNA photo-damage product in bacterial endospores; its generation and swift repair by SPL are responsible for the spores' extremely high UV resistance. The early in vivo studies suggested that SPL utilizes a direct reversal strategy to repair the SP in the absence of light. The research in the past decade further established SPL as a radical SAM enzyme, which utilizes a tri-cysteine CXXXCXXC motif to harbor a [4Fe-4S] cluster. At the 1+ oxidation state, the cluster provides an electron to the S-adenosylmethionine (SAM), which binds to the cluster in a bidentate manner as the fourth and fifth ligands, to reductively cleave the CS bond associated with the sulfonium ion in SAM, generating a reactive 5'-deoxyadenosyl (5'-dA) radical. This 5'-dA radical abstracts the proR hydrogen atom from the C6 carbon of SP to initiate the repair process; the resulting SP radical subsequently fragments to generate a putative thymine methyl radical, which accepts a back-donated H atom to yield the repaired TpT. SAM is suggested to be regenerated at the end of each catalytic cycle; and only a catalytic amount of SAM is needed in the SPL reaction. The H atom source for the back donation step is suggested to be a cysteine residue (C141 in Bacillus subtilis SPL), and the H-atom transfer reaction leaves a thiyl radical behind on the protein. This thiyl radical thus must participate in the SAM regeneration process; however how the thiyl radical abstracts an H atom from the 5'-dA to regenerate SAM is unknown. This paper reviews and discusses the history and the latest progress in the mechanistic elucidation of SPL. Despite some recent breakthroughs, more questions are raised in the mechanistic understanding of this intriguing DNA repair enzyme. This article is part of a Special Issue entitled: Radical SAM enzymes and Radical Enzymology.
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Affiliation(s)
- Lei Li
- Department of Chemistry, Indiana University-Purdue University Indianapolis (IUPUI), 402 N Blackford Street, Indianapolis, IN 46202, USA.
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Recent advances in cyclonucleosides: C-cyclonucleosides and spore photoproducts in damaged DNA. Molecules 2012; 17:11630-54. [PMID: 23023688 PMCID: PMC6268316 DOI: 10.3390/molecules171011630] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2012] [Revised: 09/25/2012] [Accepted: 09/26/2012] [Indexed: 12/04/2022] Open
Abstract
Cyclonucleosides which are fixed in a specific conformation around the glycosyl bond by a carbon and heteroatom chain constitute a unique category of nucleoside derivatives. Because they are structural analogs, cyclonucleosides and oligodeoxynucleotides containing them would be useful tools for investigating the biological functions and conformations of DNA, RNA as well as their steric interactions with proteins. C-Cyclonucleosides bridged by a carbon chain between the base and sugar moieties are the most attractive from the synthetic points of view as well as for use as biological tools. In this review, recent progress of the synthesis of C-cyclonucleosides is surveyed. Among the C-cyclonucleosides, 5′,8-C-cyclodeoxyadenosine is one of the well-known derivatives of which the first practical synthesis was reported over 30 years ago. Recently, 5′,8-C-cyclodeoxyadenosine has attracted considerable interest as a biomarker, since its formation in oxidatively-damaged DNA is considered to be related to various diseases and aging. Another important analogue of cyclonucleosides is a unique thymidine phosphate dimer, a so-called spore photoproduct, which has been found in photo-damaged DNA. Recent advances in the synthesis, mechanism-studies, and stereochemical preference of repairing enzymes related to 5′,8-C-cyclodeoxyadenosine and spore photoproducts are also reviewed.
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Yang L, Lin G, Nelson RS, Jian Y, Telser J, Li L. Mechanistic studies of the spore photoproduct lyase via a single cysteine mutation. Biochemistry 2012; 51:7173-88. [PMID: 22906093 PMCID: PMC3448869 DOI: 10.1021/bi3010945] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
5-Thyminyl-5,6-dihydrothymine (also called spore photoproduct or SP) is the exclusive DNA photodamage product in bacterial endospores. It is repaired by a radical SAM (S-adenosylmethionine) enzyme, the spore photoproduct lyase (SPL), at the bacterial early germination phase. Our previous studies proved that SPL utilizes the 5'-dA• generated by the SAM cleavage reaction to abstract the H(6proR) atom to initiate the SP repair process. The resulting thymine allylic radical was suggested to take an H atom from an unknown protein source, most likely cysteine 141. Here we show that C141 can be readily alkylated in the native SPL by an iodoacetamide treatment, suggesting that it is accessible to the TpT radical. SP repair by the SPL C141A mutant yields TpTSO(2)(-) and TpT simultaneously from the very beginning of the reaction; no lag phase is observed for TpTSO(2)(-) formation. Should any other protein residue serve as the H donor, its presence would result in TpT being the major product at least for the first enzyme turnover. These observations provide strong evidence to support C141 as the direct H atom donor. Moreover, because of the lack of this intrinsic H donor, the C141A mutant produces TpT via an unprecedented thymine cation radical reduction (proton-coupled electron transfer) process, contrasting to the H atom transfer mechanism in the wild-type (WT) SPL reaction. The C141A mutant repairs SP at a rate that is ~3-fold slower than that of the WT enzyme. Formation of TpTSO(2)(-) and TpT exhibits a V(max) deuterium kinetic isotope effect (KIE) of 1.7 ± 0.2, which is smaller than the (D)V(max) KIE of 2.8 ± 0.3 determined for the WT SPL reaction. These findings suggest that removing the intrinsic H atom donor disturbs the rate-limiting process during enzyme catalysis. As expected, the prereduced C141A mutant supports only ~0.4 turnover, which is in sharp contrast to the >5 turnovers exhibited by the WT SPL reaction, suggesting that the enzyme catalytic cycle (SAM regeneration) is disrupted by this single mutation.
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Affiliation(s)
- Linlin Yang
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis (IUPUI), 402 N Blackford Street, Indianapolis, Indiana, 46202
| | - Gengjie Lin
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis (IUPUI), 402 N Blackford Street, Indianapolis, Indiana, 46202
| | - Renae S. Nelson
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis (IUPUI), 402 N Blackford Street, Indianapolis, Indiana, 46202
| | - Yajun Jian
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis (IUPUI), 402 N Blackford Street, Indianapolis, Indiana, 46202
| | - Joshua Telser
- Department of Biological, Chemical, and Physical Sciences, Roosevelt University, Chicago, Illinois 60605
| | - Lei Li
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis (IUPUI), 402 N Blackford Street, Indianapolis, Indiana, 46202
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine (IUSM), 635 Barnhill Drive, Indianapolis, Indiana 46202
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Du Q, Zhao H, Song D, Liu K, Su H. Consecutive Reaction Mechanism for the Formation of Spore Photoproduct in DNA Photolesion. J Phys Chem B 2012; 116:11117-23. [DOI: 10.1021/jp305915e] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Qian Du
- Beijing National
Laboratory for Molecular Sciences
(BNLMS), State Key Laboratory of Molecular Reaction Dynamics, Institute
of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Hongmei Zhao
- Beijing National
Laboratory for Molecular Sciences
(BNLMS), State Key Laboratory of Molecular Reaction Dynamics, Institute
of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Di Song
- Beijing National
Laboratory for Molecular Sciences
(BNLMS), State Key Laboratory of Molecular Reaction Dynamics, Institute
of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Kunhui Liu
- Beijing National
Laboratory for Molecular Sciences
(BNLMS), State Key Laboratory of Molecular Reaction Dynamics, Institute
of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Hongmei Su
- Beijing National
Laboratory for Molecular Sciences
(BNLMS), State Key Laboratory of Molecular Reaction Dynamics, Institute
of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
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Benjdia A, Heil K, Barends TRM, Carell T, Schlichting I. Structural insights into recognition and repair of UV-DNA damage by Spore Photoproduct Lyase, a radical SAM enzyme. Nucleic Acids Res 2012; 40:9308-18. [PMID: 22761404 PMCID: PMC3467042 DOI: 10.1093/nar/gks603] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Bacterial spores possess an enormous resistance to ultraviolet (UV) radiation. This is largely due to a unique DNA repair enzyme, Spore Photoproduct Lyase (SP lyase) that repairs a specific UV-induced DNA lesion, the spore photoproduct (SP), through an unprecedented radical-based mechanism. Unlike DNA photolyases, SP lyase belongs to the emerging superfamily of radical S-adenosyl-l-methionine (SAM) enzymes and uses a [4Fe–4S]1+ cluster and SAM to initiate the repair reaction. We report here the first crystal structure of this enigmatic enzyme in complex with its [4Fe–4S] cluster and its SAM cofactor, in the absence and presence of a DNA lesion, the dinucleoside SP. The high resolution structures provide fundamental insights into the active site, the DNA lesion recognition and binding which involve a β-hairpin structure. We show that SAM and a conserved cysteine residue are perfectly positioned in the active site for hydrogen atom abstraction from the dihydrothymine residue of the lesion and donation to the α-thyminyl radical moiety, respectively. Based on structural and biochemical characterizations of mutant proteins, we substantiate the role of this cysteine in the enzymatic mechanism. Our structure reveals how SP lyase combines specific features of radical SAM and DNA repair enzymes to enable a complex radical-based repair reaction to take place.
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Affiliation(s)
- Alhosna Benjdia
- Department of Biomolecular Mechanisms, Max-Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany.
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Lin G, Chen CH, Pink M, Pu J, Li L. Chemical synthesis, crystal structure and enzymatic evaluation of a dinucleotide spore photoproduct analogue containing a formacetal linker. Chemistry 2011; 17:9658-68. [PMID: 21780208 PMCID: PMC3180863 DOI: 10.1002/chem.201101821] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2011] [Indexed: 11/11/2022]
Abstract
Spore photoproduct (SP) is the exclusive DNA photodamage product found in bacterial endospores. Its photoformation and repair by a metalloenzyme spore photoproduct lyase (SPL) composes the unique SP biochemistry. Despite the fact that the SP was discovered almost 50 years ago, its crystal structure is still unknown and the lack of structural information greatly hinders the study of SP biochemistry. Employing a formacetal linker and organic synthesis, we successfully prepared a dinucleotide SP isostere 5R-CH(2) SP, which contains a neutral CH(2) moiety between the two thymine residues instead of a phosphate. The neutral linker dramatically facilitates the crystallization process, allowing us to obtain the crystal structure for this intriguing thymine dimer half a century after its discovery. Further ROESY spectroscopic, DFT computational, and enzymatic studies of this 5R-CH(2) SP compound prove that it possesses similar properties with the 5R-SP species, suggesting that the revealed structure truly reflects that of SP generated in Nature.
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Affiliation(s)
- Gengjie Lin
- Department of Chemistry and Chemical Biology, Indiana University, Purdue University Indianapolis (IUPUI), 402 N. Blackford St., Indianapolis, IN 46202 (USA)
| | - Chun-Hsing Chen
- Indiana University Molecular Structure Center, Chemistry, A421, Indiana University, 800 E. Kirkwood Avenue, Bloomington, IN 47405 (USA)
| | - Maren Pink
- Indiana University Molecular Structure Center, Chemistry, A421, Indiana University, 800 E. Kirkwood Avenue, Bloomington, IN 47405 (USA)
| | - Jingzhi Pu
- Department of Chemistry and Chemical Biology, Indiana University, Purdue University Indianapolis (IUPUI), 402 N. Blackford St., Indianapolis, IN 46202 (USA)
| | - Lei Li
- Department of Chemistry and Chemical Biology, Indiana University, Purdue University Indianapolis (IUPUI), 402 N. Blackford St., Indianapolis, IN 46202 (USA)
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, 635 Barnhill Drive, Indianapolis, IN 46202 (USA)
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Heil K, Kneuttinger AC, Schneider S, Lischke U, Carell T. Crystal structures and repair studies reveal the identity and the base-pairing properties of the UV-induced spore photoproduct DNA lesion. Chemistry 2011; 17:9651-7. [PMID: 21780197 DOI: 10.1002/chem.201100177] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2011] [Revised: 05/05/2011] [Indexed: 11/11/2022]
Abstract
UV light is one of the major causes of DNA damage. In spore DNA, due to an unusual packing of the genetic material, a special spore photoproduct lesion (SP lesion) is formed, which is repaired by the enzyme spore photoproduct lyase (Spl), a radical S-adenosylmethionine (SAM) enzyme. We report here the synthesis and DNA incorporation of a DNA SP lesion analogue lacking the phosphodiester backbone. The oligonucleotides were used for repair studies and they were cocrystallized with a polymerase enzyme as a template to clarify the configuration of the SP lesion and to provide information about the base-pairing properties of the lesion. The structural analysis together with repair studies allowed us to clarify the identity of the preferentially repaired lesion diastereoisomer.
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Affiliation(s)
- Korbinian Heil
- Center for Integrated Protein Science (CiPSM) at the Department of Chemistry, Ludwig-Maximilians-University, Munich, Germany
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Yang L, Lin G, Liu D, Dria KJ, Telser J, Li L. Probing the reaction mechanism of spore photoproduct lyase (SPL) via diastereoselectively labeled dinucleotide SP TpT substrates. J Am Chem Soc 2011; 133:10434-47. [PMID: 21671623 DOI: 10.1021/ja110196d] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
5-Thyminyl-5,6-dihydrothymine (commonly called spore photoproduct or SP) is the exclusive DNA photodamage product in bacterial endospores. It is generated in the bacterial sporulation phase and repaired by a radical SAM enzyme, spore photoproduct lyase (SPL), at the early germination phase. SPL utilizes a special [4Fe-4S] cluster to reductively cleave S-adenosylmethionine (SAM) to generate a reactive 5'-dA radical. The 5'-dA radical is proposed to abstract one of the two H-atoms at the C6 carbon of SP to initiate the repair process. Via organic synthesis and DNA photochemistry, we selectively labeled the 6-H(proS) or 6-H(proR) position with a deuterium in a dinucleotide SP TpT substrate. Monitoring the deuterium migration in enzyme catalysis (employing Bacillus subtilis SPL) revealed that it is the 6-H(proR) atom of SP that is abstracted by the 5'-dA radical. Surprisingly, the abstracted deuterium was not returned to the resulting TpT after enzymatic catalysis; an H-atom from the aqueous buffer was incorporated into TpT instead. This result questions the currently hypothesized SPL mechanism which excludes the involvement of protein residue(s) in SPL reaction, suggesting that some protein residue(s), which is capable of exchanging a proton with the aqueous buffer, is involved in the enzyme catalysis. Moreover, evidence has been obtained for a possible SAM regeneration after each catalytic cycle; however, such a regeneration process is more complex than currently thought, with one or even more protein residues involved as well. These observations have enabled us to propose a modified reaction mechanism for this intriguing DNA repair enzyme.
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Affiliation(s)
- Linlin Yang
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis (IUPUI), 402 N Blackford Street, Indianapolis, Indiana 46202, USA
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Shetlar MD, Chung J. The (5‐4) and (6‐4) Adducts of 1‐Methylthymine and Their Dewar Valence Isomers. Photochem Photobiol 2011; 87:802-17. [DOI: 10.1111/j.1751-1097.2011.00932.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Lin G, Li L. Elucidation of spore-photoproduct formation by isotope labeling. Angew Chem Int Ed Engl 2011; 49:9926-9. [PMID: 21104967 DOI: 10.1002/anie.201005228] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Gengjie Lin
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, 402 North Blackford Street, Indianapolis, IN 46202, USA
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