1
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Hu M, Ye FY, Yu W, Sheng K, Wang W, Zheng YS. Polymorphism and Light-Driven Forward Movement of TPE Derivative Micro-Crystal due to ArH-pi Interactions Difference. Chemistry 2023; 29:e202302567. [PMID: 37709727 DOI: 10.1002/chem.202302567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 09/13/2023] [Accepted: 09/14/2023] [Indexed: 09/16/2023]
Abstract
Aggregation-induced emission (AIE) and aggregation-caused quenching (ACQ) are two classes of opposite luminescence phenomena. It is almost impossible to show both AIE and ACQ effect simultaneously by the same molecule. However, here we report that a simple TPE derivative TAP-TPE grows into both AIE crystals and ACQ ones. It is found that equatorial, contact distance-longer and weak ArH-π interactions exist in AIE crystals while vertical, contact distance-shorter and strong ArH-π interactions appear in ACQ crystals. Theoretical calculation of electron density on the interaction atoms unveils that ACQ crystals have much larger change in electron density than AIE ones, suggesting that the intermolecular electron transfer aroused by the strong ArH-π hydrogen bonds leads to ACQ phenomenon. This result provides a new insight into the emission mechanism in aggregation state. Interestingly, due to the ArH-pi interactions difference, only one of five kinds of crystals shows rapid photochromism, and can act as multimode anti-counterfeiting materials. Very exceptionally, for the first time we find that the photochromic micrometric rod-like crystal even makes forward rolling movement as it repeatedly bends and straightens by responding to on and off of the ultraviolet light irradiation, displaying potential for photo-actuator and light-driven micro-vehicle.
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Affiliation(s)
- Ming Hu
- Key Laboratory of Material Chemistry for Energy Conversion and Storage, Ministry of Education, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Feng-Ying Ye
- Key Laboratory of Material Chemistry for Energy Conversion and Storage, Ministry of Education, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Wei Yu
- Key Laboratory of Material Chemistry for Energy Conversion and Storage, Ministry of Education, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Kang Sheng
- Key Laboratory of Material Chemistry for Energy Conversion and Storage, Ministry of Education, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Weizhou Wang
- College of Chemistry and Chemical Engineering, Henan Key Laboratory of Function-Oriented Porous Materials, Luoyang Normal University, Luoyang, 471934, China
| | - Yan-Song Zheng
- Key Laboratory of Material Chemistry for Energy Conversion and Storage, Ministry of Education, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan, 430074, China
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2
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Deng Y, Tan Y, Zhang Y, Zhang L, Zhang C, Ke Y, Su X. Design of Uracil-Modified DNA Nanotubes for Targeted Drug Release via DNA-Modifying Enzyme Reactions. ACS APPLIED MATERIALS & INTERFACES 2022; 14:34470-34479. [PMID: 35867518 DOI: 10.1021/acsami.2c09488] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
DNA nanostructure-based responsive drug delivery has become an increasingly potent method in cancer therapy. However, a variety of important cancer biomarkers have not been explored in searching of new and efficient targeted delivery systems. Uracil degradation glycosylase and human apurinic/apyrimidinic endonuclease are significantly more active in cancer cells. Here, we developed uracil-modified DNA nanotubes that can deliver drugs to tumor cells through an enzyme-induced disassembly process. Although the reaction of these enzymes on their natural DNA substrates has been established, their reactivity on self-assembled nanostructures of nucleic acids is not well understood. We leveraged molecular dynamic simulation based on coarse-grained model to forecast the enzyme reactivity on different DNA designs. The experimental data are highly consistent with the simulation results. It is the first example of molecule simulation being used to guide the design of enzyme-responsive DNA nano-delivery systems. Importantly, we found that the efficiency of drug release from the nanotubes can be regulated by tuning the positions of uracil modification. The DNA nanotubes equipped with cancer-specific aptamer AS1411 are used to deliver doxorubicin to tumor-bearing mice not only effectively inhibiting tumor growth but also protecting major organs from drug-caused damage. We believe that this work provides new knowledge on and insights into future design of enzyme-responsive DNA-based nanocarriers for drug delivery.
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Affiliation(s)
- Yingnan Deng
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Yuanhang Tan
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - YingWei Zhang
- College of Material Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Linghao Zhang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - ChunYi Zhang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Yonggang Ke
- Wallance H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30322, United States
| | - Xin Su
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
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3
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Abstract
Bacteria are continuously exposed to numerous endogenous and exogenous DNA-damaging agents. To maintain genome integrity and ensure cell survival, bacteria have evolved several DNA repair pathways to correct different types of DNA damage and non-canonical bases, including strand breaks, nucleotide modifications, cross-links, mismatches and ribonucleotide incorporations. Recent advances in genome-wide screens, the availability of thousands of whole-genome sequences and advances in structural biology have enabled the rapid discovery and characterization of novel bacterial DNA repair pathways and new enzymatic activities. In this Review, we discuss recent advances in our understanding of base excision repair and nucleotide excision repair, and we discuss several new repair processes including the EndoMS mismatch correction pathway and the MrfAB excision repair system.
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Affiliation(s)
- Katherine J Wozniak
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Lyle A Simmons
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA.
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4
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Bradley NP, Wahl KL, Steenwyk JL, Rokas A, Eichman BF. Resistance-Guided Mining of Bacterial Genotoxins Defines a Family of DNA Glycosylases. mBio 2022; 13:e0329721. [PMID: 35311535 PMCID: PMC9040887 DOI: 10.1128/mbio.03297-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 02/22/2022] [Indexed: 11/20/2022] Open
Abstract
Unique DNA repair enzymes that provide self-resistance against therapeutically important, genotoxic natural products have been discovered in bacterial biosynthetic gene clusters (BGCs). Among these, the DNA glycosylase AlkZ is essential for azinomycin B production and belongs to the HTH_42 superfamily of uncharacterized proteins. Despite their widespread existence in antibiotic producers and pathogens, the roles of these proteins in production of other natural products are unknown. Here, we determine the evolutionary relationship and genomic distribution of all HTH_42 proteins from Streptomyces and use a resistance-based genome mining approach to identify homologs associated with known and uncharacterized BGCs. We find that AlkZ-like (AZL) proteins constitute one distinct HTH_42 subfamily and are highly enriched in BGCs and variable in sequence, suggesting each has evolved to protect against a specific secondary metabolite. As a validation of the approach, we show that the AZL protein, HedH4, associated with biosynthesis of the alkylating agent hedamycin, excises hedamycin-DNA adducts with exquisite specificity and provides resistance to the natural product in cells. We also identify a second, phylogenetically and functionally distinct subfamily whose proteins are never associated with BGCs, are highly conserved with respect to sequence and genomic neighborhood, and repair DNA lesions not associated with a particular natural product. This work delineates two related families of DNA repair enzymes-one specific for complex alkyl-DNA lesions and involved in self-resistance to antimicrobials and the other likely involved in protection against an array of genotoxins-and provides a framework for targeted discovery of new genotoxic compounds with therapeutic potential. IMPORTANCE Bacteria are rich sources of secondary metabolites that include DNA-damaging genotoxins with antitumor/antibiotic properties. Although Streptomyces produce a diverse number of therapeutic genotoxins, efforts toward targeted discovery of biosynthetic gene clusters (BGCs) producing DNA-damaging agents is lacking. Moreover, work on toxin-resistance genes has lagged behind our understanding of those involved in natural product synthesis. Here, we identified over 70 uncharacterized BGCs producing potentially novel genotoxins through resistance-based genome mining using the azinomycin B-resistance DNA glycosylase AlkZ. We validate our analysis by characterizing the enzymatic activity and cellular resistance of one AlkZ ortholog in the BGC of hedamycin, a potent DNA alkylating agent. Moreover, we uncover a second, phylogenetically distinct family of proteins related to Escherichia coli YcaQ, a DNA glycosylase capable of unhooking interstrand DNA cross-links, which differs from the AlkZ-like family in sequence, genomic location, proximity to BGCs, and substrate specificity. This work defines two families of DNA glycosylase for specialized repair of complex genotoxic natural products and generalized repair of a broad range of alkyl-DNA adducts and provides a framework for targeted discovery of new compounds with therapeutic potential.
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Affiliation(s)
- Noah P. Bradley
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA
| | - Katherine L. Wahl
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA
| | - Jacob L. Steenwyk
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Brandt F. Eichman
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
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5
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Chen X, Bradley NP, Lu W, Wahl KL, Zhang M, Yuan H, Hou XF, Eichman B, Tang GL. Base excision repair system targeting DNA adducts of trioxacarcin/LL-D49194 antibiotics for self-resistance. Nucleic Acids Res 2022; 50:2417-2430. [PMID: 35191495 PMCID: PMC8934636 DOI: 10.1093/nar/gkac085] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 01/10/2022] [Accepted: 01/27/2022] [Indexed: 12/25/2022] Open
Abstract
Two families of DNA glycosylases (YtkR2/AlkD, AlkZ/YcaQ) have been found to remove bulky and crosslinking DNA adducts produced by bacterial natural products. Whether DNA glycosylases eliminate other types of damage formed by structurally diverse antibiotics is unknown. Here, we identify four DNA glycosylases-TxnU2, TxnU4, LldU1 and LldU5-important for biosynthesis of the aromatic polyketide antibiotics trioxacarcin A (TXNA) and LL-D49194 (LLD), and show that the enzymes provide self-resistance to the producing strains by excising the intercalated guanine adducts of TXNA and LLD. These enzymes are highly specific for TXNA/LLD-DNA lesions and have no activity toward other, less stable alkylguanines as previously described for YtkR2/AlkD and AlkZ/YcaQ. Similarly, TXNA-DNA adducts are not excised by other alkylpurine DNA glycosylases. TxnU4 and LldU1 possess unique active site motifs that provide an explanation for their tight substrate specificity. Moreover, we show that abasic (AP) sites generated from TxnU4 excision of intercalated TXNA-DNA adducts are incised by AP endonuclease less efficiently than those formed by 7mG excision. This work characterizes a distinct class of DNA glycosylase acting on intercalated DNA adducts and furthers our understanding of specific DNA repair self-resistance activities within antibiotic producers of structurally diverse, highly functionalized DNA damaging agents.
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Affiliation(s)
- Xiaorong Chen
- School of Chemistry and Materials Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, 1 Sub-lane Xiangshan, Hangzhou 310024, China
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Noah P Bradley
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232, USA
| | - Wei Lu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Katherine L Wahl
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232, USA
| | - Mei Zhang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Hua Yuan
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Xian-Feng Hou
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Brandt F Eichman
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232, USA
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA
| | - Gong-Li Tang
- School of Chemistry and Materials Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, 1 Sub-lane Xiangshan, Hangzhou 310024, China
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200032, China
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6
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Structural evolution of a DNA repair self-resistance mechanism targeting genotoxic secondary metabolites. Nat Commun 2021; 12:6942. [PMID: 34836957 PMCID: PMC8626424 DOI: 10.1038/s41467-021-27284-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 11/10/2021] [Indexed: 01/09/2023] Open
Abstract
Microbes produce a broad spectrum of antibiotic natural products, including many DNA-damaging genotoxins. Among the most potent of these are DNA alkylating agents in the spirocyclopropylcyclohexadienone (SCPCHD) family, which includes the duocarmycins, CC-1065, gilvusmycin, and yatakemycin. The yatakemycin biosynthesis cluster in Streptomyces sp. TP-A0356 contains an AlkD-related DNA glycosylase, YtkR2, that serves as a self-resistance mechanism against yatakemycin toxicity. We previously reported that AlkD, which is not present in an SCPCHD producer, provides only limited resistance against yatakemycin. We now show that YtkR2 and C10R5, a previously uncharacterized homolog found in the CC-1065 biosynthetic gene cluster of Streptomyces zelensis, confer far greater resistance against their respective SCPCHD natural products. We identify a structural basis for substrate specificity across gene clusters and show a correlation between in vivo resistance and in vitro enzymatic activity indicating that reduced product affinity-not enhanced substrate recognition-is the evolutionary outcome of selective pressure to provide self-resistance against yatakemycin and CC-1065.
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7
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Ahmadi A, Till K, Backe PH, Blicher P, Diekmann R, Schüttpelz M, Glette K, Tørresen J, Bjørås M, Rowe AD, Dalhus B. Non-flipping DNA glycosylase AlkD scans DNA without formation of a stable interrogation complex. Commun Biol 2021; 4:876. [PMID: 34267321 PMCID: PMC8282808 DOI: 10.1038/s42003-021-02400-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 06/25/2021] [Indexed: 11/09/2022] Open
Abstract
The multi-step base excision repair (BER) pathway is initiated by a set of enzymes, known as DNA glycosylases, able to scan DNA and detect modified bases among a vast number of normal bases. While DNA glycosylases in the BER pathway generally bend the DNA and flip damaged bases into lesion specific pockets, the HEAT-like repeat DNA glycosylase AlkD detects and excises bases without sequestering the base from the DNA helix. We show by single-molecule tracking experiments that AlkD scans DNA without forming a stable interrogation complex. This contrasts with previously studied repair enzymes that need to flip bases into lesion-recognition pockets and form stable interrogation complexes. Moreover, we show by design of a loss-of-function mutant that the bimodality in scanning observed for the structural homologue AlkF is due to a key structural differentiator between AlkD and AlkF; a positively charged β-hairpin able to protrude into the major groove of DNA.
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Affiliation(s)
- Arash Ahmadi
- Department of Medical Biochemistry, Institute for Clinical Medicine, University of Oslo, Oslo, Norway
| | - Katharina Till
- FOM Institute AMOLF, Science Park 104, Amsterdam, The Netherlands.,Biomolecular Photonics, Department of Physics, University of Bielefeld, Bielefeld, Germany
| | - Paul Hoff Backe
- Department of Medical Biochemistry, Institute for Clinical Medicine, University of Oslo, Oslo, Norway.,Department of Microbiology, Oslo University Hospital HF, Rikshospitalet and University of Oslo, Oslo, Norway
| | - Pernille Blicher
- Department of Medical Biochemistry, Institute for Clinical Medicine, University of Oslo, Oslo, Norway
| | - Robin Diekmann
- Biomolecular Photonics, Department of Physics, University of Bielefeld, Bielefeld, Germany
| | - Mark Schüttpelz
- Biomolecular Photonics, Department of Physics, University of Bielefeld, Bielefeld, Germany
| | - Kyrre Glette
- Department of Informatics, University of Oslo, Oslo, Norway
| | - Jim Tørresen
- Department of Informatics, University of Oslo, Oslo, Norway
| | - Magnar Bjørås
- Department of Microbiology, Oslo University Hospital HF, Rikshospitalet and University of Oslo, Oslo, Norway.,Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Alexander D Rowe
- Department of Medical Biochemistry, Institute for Clinical Medicine, University of Oslo, Oslo, Norway.,Department of Newborn Screening, Division of Child and Adolescent Medicine, Oslo University Hospital, Oslo, Norway
| | - Bjørn Dalhus
- Department of Medical Biochemistry, Institute for Clinical Medicine, University of Oslo, Oslo, Norway. .,Department of Microbiology, Oslo University Hospital HF, Rikshospitalet and University of Oslo, Oslo, Norway.
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8
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Wang J, Yao L. Dissecting C-H∙∙∙π and N-H∙∙∙π Interactions in Two Proteins Using a Combined Experimental and Computational Approach. Sci Rep 2019; 9:20149. [PMID: 31882834 PMCID: PMC6934659 DOI: 10.1038/s41598-019-56607-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 12/12/2019] [Indexed: 01/27/2023] Open
Abstract
C−H∙∙∙π and N−H∙∙∙π interactions can have an important contribution for protein stability. However, direct measurements of these interactions in proteins are rarely reported. In this work, we combined the mutant cycle experiments and molecular dynamics (MD) simulations to characterize C−H∙∙∙π and N−H∙∙∙π interactions and their cooperativity in two model proteins. It is shown that the average C−H∙∙∙π interaction per residue pair is ~ −0.5 kcal/mol while the N−H∙∙∙π interaction is slightly stronger. The triple mutant box measurement indicates that N−H∙∙∙π∙∙∙C−H∙∙∙π and C−H∙∙∙π∙∙∙C−H∙∙∙π can have a positive or negative cooperativity. MD simulations suggest that the cooperativity, depending on the local environment of the interactions, mainly arises from the geometric rearrangement when the nearby interaction is perturbed.
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Affiliation(s)
- Jia Wang
- Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China.,Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lishan Yao
- Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China. .,Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China.
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9
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Jebastin Andrews S, Benita Jeba Silviya S, Bhuvanesh NS, Janet Sylvia Jaba Rose J, Winfred Jebaraj J, Balakrishnan C. Crystal structure and evaluating C H⋯π (aryl/chelate) interactions in bis(2-{[(2-hydroxyethyl)imino]-methyl}-4,6-diiodophenolato)-palladium(II) Schiff base complex derived from (E)-2-(((2-hydroxyethyl)imino)methyl)-4,6-diiodophenol. Inorganica Chim Acta 2019. [DOI: 10.1016/j.ica.2019.119118] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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10
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El-Desoky ESI, El-Sawi AA, Abozeid MA, Abdelmoteleb M, Shaaban M, Keshk EM, Abdel-Rahman ARH. Synthesis, antimicrobial evaluation, and molecular docking of some new angular allylbenzochromone derivatives. Med Chem Res 2019. [DOI: 10.1007/s00044-019-02397-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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11
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Njuma OJ, Su Y, Guengerich FP. The abundant DNA adduct N 7-methyl deoxyguanosine contributes to miscoding during replication by human DNA polymerase η. J Biol Chem 2019; 294:10253-10265. [PMID: 31101656 DOI: 10.1074/jbc.ra119.008986] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 05/16/2019] [Indexed: 12/14/2022] Open
Abstract
Aside from abasic sites and ribonucleotides, the DNA adduct N 7-methyl deoxyguanosine (N7 -CH3 dG) is one of the most abundant lesions in mammalian DNA. Because N7 -CH3 dG is unstable, leading to deglycosylation and ring-opening, its miscoding potential is not well-understood. Here, we employed a 2'-fluoro isostere approach to synthesize an oligonucleotide containing an analog of this lesion (N7 -CH3 2'-F dG) and examined its miscoding potential with four Y-family translesion synthesis DNA polymerases (pols): human pol (hpol) η, hpol κ, and hpol ι and Dpo4 from the archaeal thermophile Sulfolobus solfataricus We found that hpol η and Dpo4 can bypass the N7 -CH3 2'-F dG adduct, albeit with some stalling, but hpol κ is strongly blocked at this lesion site, whereas hpol ι showed no distinction with the lesion and the control templates. hpol η yielded the highest level of misincorporation opposite the adduct by inserting dATP or dTTP. Moreover, hpol η did not extend well past an N 7-CH3 2'-F dG:dT mispair. MS-based sequence analysis confirmed that hpol η catalyzes mainly error-free incorporation of dC, with misincorporation of dA and dG in 5-10% of products. We conclude that N 7-CH3 2'-F dG and, by inference, N 7-CH3 dG have miscoding and mutagenic potential. The level of misincorporation arising from this abundant adduct can be considered as potentially mutagenic as a highly miscoding but rare lesion.
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Affiliation(s)
- Olive J Njuma
- From the Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146
| | - Yan Su
- From the Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146
| | - F Peter Guengerich
- From the Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146
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12
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Mullins EA, Rodriguez AA, Bradley NP, Eichman BF. Emerging Roles of DNA Glycosylases and the Base Excision Repair Pathway. Trends Biochem Sci 2019; 44:765-781. [PMID: 31078398 DOI: 10.1016/j.tibs.2019.04.006] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Revised: 04/09/2019] [Accepted: 04/10/2019] [Indexed: 12/20/2022]
Abstract
The base excision repair (BER) pathway historically has been associated with maintaining genome integrity by eliminating nucleobases with small chemical modifications. In the past several years, however, BER was found to play additional roles in genome maintenance and metabolism, including sequence-specific restriction modification and repair of bulky adducts and interstrand crosslinks. Central to this expanded biological utility are specialized DNA glycosylases - enzymes that selectively excise damaged, modified, or mismatched nucleobases. In this review we discuss the newly identified roles of the BER pathway and examine the structural and mechanistic features of the DNA glycosylases that enable these functions.
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Affiliation(s)
- Elwood A Mullins
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232, USA
| | - Alyssa A Rodriguez
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232, USA
| | - Noah P Bradley
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232, USA
| | - Brandt F Eichman
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232, USA; Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA.
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13
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Votaw KA, McCullagh M. Characterization of the Search Complex and Recognition Mechanism of the AlkD-DNA Glycosylase. J Phys Chem B 2018; 123:95-105. [PMID: 30525620 DOI: 10.1021/acs.jpcb.8b09555] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
DNA damage is a routine problem for cells, and pathways such as base excision repair have evolved to protect the genome by using DNA glycosylases to first recognize and excise lesions. The search mechanism of these enzymes is of particular interest due to the seemingly intractable problem of probing the billions of base pairs in the genome for potential damage. It has been hypothesized that glycosylases form multiple protein-DNA conformational states to efficiently search and recognize DNA lesions, ultimately only flipping out the damaged substrate into the active site. A unique DNA glycosylase, the Bacillus cereus AlkD enzyme, has been shown to excise damaged DNA without flipping the nucleobase into a protein binding pocket following lesion recognition. Here, we use microsecond-scale all-atom molecular dynamics simulations to characterize the AlkD recognition mechanism, putting it in perspective with other DNA glycosylases. We first identify and describe two distinct enzyme-DNA conformations of AlkD: the search complex (SC) and excision complex (EC). The SC is distinguished by the linearity of DNA, changes in four helical parameters in the vicinity of the lesion, and changes in distance between active site residues and the DNA. Free DNA simulations are used to demonstrate that the DNA structural deviations and increased active site interactions present in the EC are initiated by the recognition of a methylation-induced signal in the rises both 5' to the methylation and opposing this base. Our results support the hypothesis that subtle geometric distortions in DNA are recognized by AlkD and are consequently probed to initiate concerted protein and DNA conformational changes which prime excise without additional intermediate states. This mechanism is shown to be consistent among the three methylated DNA sequences that have been crystallized bound to AlkD.
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Affiliation(s)
- Kevin A Votaw
- Department of Chemistry , Colorado State University , Fort Collins , Colorado 80523, United States
| | - Martin McCullagh
- Department of Chemistry , Colorado State University , Fort Collins , Colorado 80523, United States
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14
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Shi R, Shen XX, Rokas A, Eichman BF. Structural Biology of the HEAT-Like Repeat Family of DNA Glycosylases. Bioessays 2018; 40:e1800133. [PMID: 30264543 DOI: 10.1002/bies.201800133] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 08/27/2018] [Indexed: 11/08/2022]
Abstract
DNA glycosylases remove aberrant DNA nucleobases as the first enzymatic step of the base excision repair (BER) pathway. The alkyl-DNA glycosylases AlkC and AlkD adopt a unique structure based on α-helical HEAT repeats. Both enzymes identify and excise their substrates without a base-flipping mechanism used by other glycosylases and nucleic acid processing proteins to access nucleobases that are otherwise stacked inside the double-helix. Consequently, these glycosylases act on a variety of cationic nucleobase modifications, including bulky adducts, not previously associated with BER. The related non-enzymatic HEAT-like repeat (HLR) proteins, AlkD2, and AlkF, have unique nucleic acid binding properties that expand the functions of this relatively new protein superfamily beyond DNA repair. Here, we review the phylogeny, biochemistry, and structures of the HLR proteins, which have helped broaden our understanding of the mechanisms by which DNA glycosylases locate and excise chemically modified DNA nucleobases.
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Affiliation(s)
- Rongxin Shi
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, 37232, USA
| | - Xing-Xing Shen
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, 37232, USA
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, 37232, USA
| | - Brandt F Eichman
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, 37232, USA
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15
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Silvestrov P, Cisneros GA. Insights into conformational changes in AlkD bound to DNA with a yatakemycin adduct from computational simulations. Theor Chem Acc 2018; 137:78. [PMID: 30078993 PMCID: PMC6071674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Structural integrity of DNA molecules is necessary for their information storage function. Cells rely on a number of pathways to ensure that the damage to DNA induced by endogenous and exogenous reagents is repaired. AlkD, a base excision enzyme, removes a damaged nucleobase by cleaving a glycosidic bond. Unlike many other base excision enzymes, AlkD does not flip a damaged nucleobase into a designated reaction pocket, and as such can repair nucleobases with larger adducts, such as yatakemycin. In this study, the structure and dynamics of AlkD have been investigated by classical molecular dynamics simulations. Several systems including apo-AlkD, and AlkD in complex with DNA, both with and without the yatakemycin adduct have been simulated. Comparison of the results for the apo-AlkD with AlkD with substrate (damaged or undamaged) indicates a high degree of motion of helix αB in apo-AlkD, whereas this helix is observed to form various contacts when the substrate is bound. The calculated results are consistent with previous experimental studies that have suggested various residues involved in damage recognition, DNA binding, and base excision catalysis.
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Affiliation(s)
- Pavel Silvestrov
- Department of Chemistry, University of North Texas, Denton, TX 76201, USA
| | - G Andrés Cisneros
- Department of Chemistry, University of North Texas, Denton, TX 76201, USA
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16
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Silvestrov P, Cisneros GA. Insights into conformational changes in AlkD bound to DNA with a yatakemycin adduct from computational simulations. Theor Chem Acc 2018. [DOI: 10.1007/s00214-018-2255-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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17
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Shi R, Mullins EA, Shen XX, Lay KT, Yuen PK, David SS, Rokas A, Eichman BF. Selective base excision repair of DNA damage by the non-base-flipping DNA glycosylase AlkC. EMBO J 2018; 37:63-74. [PMID: 29054852 PMCID: PMC5753038 DOI: 10.15252/embj.201797833] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2017] [Revised: 09/11/2017] [Accepted: 09/22/2017] [Indexed: 01/07/2023] Open
Abstract
DNA glycosylases preserve genome integrity and define the specificity of the base excision repair pathway for discreet, detrimental modifications, and thus, the mechanisms by which glycosylases locate DNA damage are of particular interest. Bacterial AlkC and AlkD are specific for cationic alkylated nucleobases and have a distinctive HEAT-like repeat (HLR) fold. AlkD uses a unique non-base-flipping mechanism that enables excision of bulky lesions more commonly associated with nucleotide excision repair. In contrast, AlkC has a much narrower specificity for small lesions, principally N3-methyladenine (3mA). Here, we describe how AlkC selects for and excises 3mA using a non-base-flipping strategy distinct from that of AlkD. A crystal structure resembling a catalytic intermediate complex shows how AlkC uses unique HLR and immunoglobulin-like domains to induce a sharp kink in the DNA, exposing the damaged nucleobase to active site residues that project into the DNA This active site can accommodate and excise N3-methylcytosine (3mC) and N1-methyladenine (1mA), which are also repaired by AlkB-catalyzed oxidative demethylation, providing a potential alternative mechanism for repair of these lesions in bacteria.
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Affiliation(s)
- Rongxin Shi
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Elwood A Mullins
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Xing-Xing Shen
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Kori T Lay
- Department of Chemistry, University of California, Davis, CA, USA
| | - Philip K Yuen
- Department of Chemistry, University of California, Davis, CA, USA
| | - Sheila S David
- Department of Chemistry, University of California, Davis, CA, USA
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Brandt F Eichman
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
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18
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Maity T, Mandal H, Bauzá A, Samanta BC, Frontera A, Seth SK. Quantifying conventional C–H⋯π(aryl) and unconventional C–H⋯π(chelate) interactions in dinuclear Cu(ii) complexes: experimental observations, Hirshfeld surface and theoretical DFT study. NEW J CHEM 2018. [DOI: 10.1039/c8nj00747k] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Conventional C–H⋯π(aryl) and unconventional C–H⋯π(chelate) interactions are explored in detail.
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Affiliation(s)
- Tithi Maity
- Department of Chemistry
- P. K. College
- Purba Medinipur
- India
| | - Haridas Mandal
- Chemical División
- Geological Survey of India
- Hyderabad-500068
- India
| | - Antonio Bauzá
- Department of Chemistry
- Universitat de les Illes Balears
- 07122 Palma de Mallorca (Baleares)
- Spain
| | | | - Antonio Frontera
- Department of Chemistry
- Universitat de les Illes Balears
- 07122 Palma de Mallorca (Baleares)
- Spain
| | - Saikat Kumar Seth
- Department of Chemistry
- Universitat de les Illes Balears
- 07122 Palma de Mallorca (Baleares)
- Spain
- Department of Physics
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19
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Mullins EA, Shi R, Eichman BF. Toxicity and repair of DNA adducts produced by the natural product yatakemycin. Nat Chem Biol 2017; 13:1002-1008. [PMID: 28759018 PMCID: PMC5657529 DOI: 10.1038/nchembio.2439] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 06/20/2017] [Indexed: 12/22/2022]
Abstract
Yatakemycin (YTM) is an extraordinarily toxic DNA alkylating agent with potent antimicrobial and antitumor properties and the most recent addition to the CC-1065 and duocarmycin family of natural products. While bulky DNA lesions the size of those produced by YTM are normally removed from the genome by the nucleotide excision repair (NER) pathway, YTM adducts are also a substrate for the bacterial DNA glycosylases AlkD and YtkR2, unexpectedly implicating base excision repair (BER) in their elimination. The reason for the extreme toxicity of these lesions and the molecular basis for how they are eliminated by BER have been unclear. Here, we describe the structural and biochemical properties of YTM adducts responsible for their toxicity, and define the mechanism by which they are excised by AlkD. These findings delineate an alternative strategy for repair of bulky DNA damage and establish the cellular utility of this pathway relative to that of NER.
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Affiliation(s)
- Elwood A Mullins
- Department of Biological Sciences and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, USA
| | - Rongxin Shi
- Department of Biological Sciences and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, USA
| | - Brandt F Eichman
- Department of Biological Sciences and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, USA
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20
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Baker EG, Williams C, Hudson KL, Bartlett GJ, Heal JW, Porter Goff KL, Sessions RB, Crump MP, Woolfson DN. Engineering protein stability with atomic precision in a monomeric miniprotein. Nat Chem Biol 2017; 13:764-770. [PMID: 28530710 DOI: 10.1038/nchembio.2380] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 02/27/2017] [Indexed: 02/04/2023]
Abstract
Miniproteins simplify the protein-folding problem, allowing the dissection of forces that stabilize protein structures. Here we describe PPα-Tyr, a designed peptide comprising an α-helix buttressed by a polyproline II helix. PPα-Tyr is water soluble and monomeric, and it unfolds cooperatively with a midpoint unfolding temperature (TM) of 39 °C. NMR structures of PPα-Tyr reveal proline residues docked between tyrosine side chains, as designed. The stability of PPα is sensitive to modifications in the aromatic residues: replacing tyrosine with phenylalanine, i.e., changing three solvent-exposed hydroxyl groups to protons, reduces the TM to 20 °C. We attribute this result to the loss of CH-π interactions between the aromatic and proline rings, which we probe by substituting the aromatic residues with nonproteinogenic side chains. In analyses of natural protein structures, we find a preference for proline-tyrosine interactions over other proline-containing pairs, and observe abundant CH-π interactions in biologically important complexes between proline-rich ligands and SH3 and similar domains.
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Affiliation(s)
- Emily G Baker
- School of Chemistry, University of Bristol, Bristol, UK
| | - Christopher Williams
- School of Chemistry, University of Bristol, Bristol, UK.,BrisSynBio, University of Bristol, Bristol, UK
| | | | | | - Jack W Heal
- School of Chemistry, University of Bristol, Bristol, UK
| | | | - Richard B Sessions
- BrisSynBio, University of Bristol, Bristol, UK.,School of Biochemistry, University of Bristol, Bristol, UK
| | - Matthew P Crump
- School of Chemistry, University of Bristol, Bristol, UK.,BrisSynBio, University of Bristol, Bristol, UK
| | - Derek N Woolfson
- School of Chemistry, University of Bristol, Bristol, UK.,BrisSynBio, University of Bristol, Bristol, UK.,School of Biochemistry, University of Bristol, Bristol, UK
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21
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Wilson KA, Wetmore SD. Combining crystallographic and quantum chemical data to understand DNA-protein π-interactions in nature. Struct Chem 2017. [DOI: 10.1007/s11224-017-0954-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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22
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Abstract
DNA glycosylases are important editing enzymes that protect genomic stability by excising chemically modified nucleobases that alter normal DNA metabolism. These enzymes have been known only to initiate base excision repair of small adducts by extrusion from the DNA helix. However, recent reports have described both vertebrate and microbial DNA glycosylases capable of unhooking highly toxic interstrand cross-links (ICLs) and bulky minor groove adducts normally recognized by Fanconi anemia and nucleotide excision repair machinery, although the mechanisms of these activities are unknown. Here we report the crystal structure of Streptomyces sahachiroi AlkZ (previously Orf1), a bacterial DNA glycosylase that protects its host by excising ICLs derived from azinomycin B (AZB), a potent antimicrobial and antitumor genotoxin. AlkZ adopts a unique fold in which three tandem winged helix-turn-helix motifs scaffold a positively charged concave surface perfectly shaped for duplex DNA. Through mutational analysis, we identified two glutamine residues and a β-hairpin within this putative DNA-binding cleft that are essential for catalytic activity. Additionally, we present a molecular docking model for how this active site can unhook either or both sides of an AZB ICL, providing a basis for understanding the mechanisms of base excision repair of ICLs. Given the prevalence of this protein fold in pathogenic bacteria, this work also lays the foundation for an emerging role of DNA repair in bacteria-host pathogenesis.
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23
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Yang Z, Nejad MI, Varela JG, Price NE, Wang Y, Gates KS. A role for the base excision repair enzyme NEIL3 in replication-dependent repair of interstrand DNA cross-links derived from psoralen and abasic sites. DNA Repair (Amst) 2017; 52:1-11. [PMID: 28262582 PMCID: PMC5424475 DOI: 10.1016/j.dnarep.2017.02.011] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2017] [Accepted: 02/13/2017] [Indexed: 12/23/2022]
Abstract
Interstrand DNA-DNA cross-links are highly toxic lesions that are important in medicinal chemistry, toxicology, and endogenous biology. In current models of replication-dependent repair, stalling of a replication fork activates the Fanconi anemia pathway and cross-links are "unhooked" by the action of structure-specific endonucleases such as XPF-ERCC1 that make incisions flanking the cross-link. This process generates a double-strand break, which must be subsequently repaired by homologous recombination. Recent work provided evidence for a new, incision-independent unhooking mechanism involving intrusion of a base excision repair (BER) enzyme, NEIL3, into the world of cross-link repair. The evidence suggests that the glycosylase action of NEIL3 unhooks interstrand cross-links derived from an abasic site or the psoralen derivative trioxsalen. If the incision-independent NEIL3 pathway is blocked, repair reverts to the incision-dependent route. In light of the new model invoking participation of NEIL3 in cross-link repair, we consider the possibility that various BER glycosylases or other DNA-processing enzymes might participate in the unhooking of chemically diverse interstrand DNA cross-links.
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Affiliation(s)
- Zhiyu Yang
- University of Missouri Department of Chemistry, 125 Chemistry Building Columbia, MO 65211, United States
| | - Maryam Imani Nejad
- University of Missouri Department of Chemistry, 125 Chemistry Building Columbia, MO 65211, United States
| | - Jacqueline Gamboa Varela
- University of Missouri Department of Chemistry, 125 Chemistry Building Columbia, MO 65211, United States
| | - Nathan E Price
- University of California-Riverside, Department of Chemistry, 501 Big Springs Road Riverside, CA 92521-0403, United States
| | - Yinsheng Wang
- University of California-Riverside, Department of Chemistry, 501 Big Springs Road Riverside, CA 92521-0403, United States
| | - Kent S Gates
- University of Missouri Department of Chemistry, 125 Chemistry Building Columbia, MO 65211, United States; University of Missouri Department of Biochemistry, 125 Chemistry Building Columbia, MO 65211, United States.
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