1
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Tessmer I, Margison GP. The DNA Alkyltransferase Family of DNA Repair Proteins: Common Mechanisms, Diverse Functions. Int J Mol Sci 2023; 25:463. [PMID: 38203633 PMCID: PMC10779285 DOI: 10.3390/ijms25010463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 12/22/2023] [Accepted: 12/27/2023] [Indexed: 01/12/2024] Open
Abstract
DNA alkyltransferase and alkyltransferase-like family proteins are responsible for the repair of highly mutagenic and cytotoxic O6-alkylguanine and O4-alkylthymine bases in DNA. Their mechanism involves binding to the damaged DNA and flipping the base out of the DNA helix into the active site pocket in the protein. Alkyltransferases then directly and irreversibly transfer the alkyl group from the base to the active site cysteine residue. In contrast, alkyltransferase-like proteins recruit nucleotide excision repair components for O6-alkylguanine elimination. One or more of these proteins are found in all kingdoms of life, and where this has been determined, their overall DNA repair mechanism is strictly conserved between organisms. Nevertheless, between species, subtle as well as more extensive differences that affect target lesion preferences and/or introduce additional protein functions have evolved. Examining these differences and their functional consequences is intricately entwined with understanding the details of their DNA repair mechanism(s) and their biological roles. In this review, we will present and discuss various aspects of the current status of knowledge on this intriguing protein family.
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Affiliation(s)
- Ingrid Tessmer
- Rudolf Virchow Center, University of Würzburg, Josef-Schneider-Strasse 2, 97080 Würzburg, Germany
| | - Geoffrey P. Margison
- School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK;
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2
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Abdelhady R, Senthong P, Eyers CE, Reamtong O, Cowley E, Cannizzaro L, Stimpson J, Cain K, Wilkinson OJ, Williams NH, Barran PE, Margison GP, Williams DM, Povey AC. Mass Spectrometric Analysis of the Active Site Tryptic Peptide of Recombinant O6-Methylguanine-DNA Methyltransferase Following Incubation with Human Colorectal DNA Reveals the Presence of an O6-Alkylguanine Adductome. Chem Res Toxicol 2023; 36:1921-1929. [PMID: 37983188 PMCID: PMC10731659 DOI: 10.1021/acs.chemrestox.3c00207] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 10/31/2023] [Accepted: 11/01/2023] [Indexed: 11/22/2023]
Abstract
Human exposure to DNA alkylating agents is poorly characterized, partly because only a limited range of specific alkyl DNA adducts have been quantified. The human DNA repair protein, O6-methylguanine O6-methyltransferase (MGMT), irreversibly transfers the alkyl group from DNA O6-alkylguanines (O6-alkGs) to an acceptor cysteine, allowing the simultaneous detection of multiple O6-alkG modifications in DNA by mass spectrometric analysis of the MGMT active site peptide (ASP). Recombinant MGMT was incubated with oligodeoxyribonucleotides (ODNs) containing different O6-alkGs, Temozolomide-methylated calf thymus DNA (Me-CT-DNA), or human colorectal DNA of known O6-MethylG (O6-MeG) levels. It was digested with trypsin, and ASPs were detected and quantified by matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry. ASPs containing S-methyl, S-ethyl, S-propyl, S-hydroxyethyl, S-carboxymethyl, S-benzyl, and S-pyridyloxobutyl cysteine groups were detected by incubating MGMT with ODNs containing the corresponding O6-alkGs. The LOQ of ASPs containing S-methylcysteine detected after MGMT incubation with Me-CT-DNA was <0.05 pmol O6-MeG per mg CT-DNA. Incubation of MGMT with human colorectal DNA produced ASPs containing S-methylcysteine at levels that correlated with those of O6-MeG determined previously by HPLC-radioimmunoassay (r2 = 0.74; p = 0.014). O6-CMG, a putative O6-hydroxyethylG adduct, and other potential unidentified MGMT substrates were also detected in human DNA samples. This novel approach to the identification and quantitation of O6-alkGs in human DNA has revealed the existence of a human DNA alkyl adductome that remains to be fully characterized. The methodology establishes a platform for characterizing the human DNA O6-alkG adductome and, given the mutagenic potential of O6-alkGs, can provide mechanistic information about cancer pathogenesis.
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Affiliation(s)
- Rasha Abdelhady
- Epidemiology
and Public Health Group, Division of Population Health, Health Services
Research and Primary Care, School of Health Sciences, Faculty of Biology,
Medicine and Health, University of Manchester, Manchester M13 9PL, U.K.
| | - Pattama Senthong
- Epidemiology
and Public Health Group, Division of Population Health, Health Services
Research and Primary Care, School of Health Sciences, Faculty of Biology,
Medicine and Health, University of Manchester, Manchester M13 9PL, U.K.
| | - Claire E. Eyers
- Department
of Chemistry and Manchester Institute of Biotechnology, University of Manchester, Manchester M1 7DN, U.K.
| | - Onrapak Reamtong
- Department
of Chemistry and Manchester Institute of Biotechnology, University of Manchester, Manchester M1 7DN, U.K.
| | - Elizabeth Cowley
- Epidemiology
and Public Health Group, Division of Population Health, Health Services
Research and Primary Care, School of Health Sciences, Faculty of Biology,
Medicine and Health, University of Manchester, Manchester M13 9PL, U.K.
| | - Luca Cannizzaro
- Department
of Chemistry and Manchester Institute of Biotechnology, University of Manchester, Manchester M1 7DN, U.K.
| | - Joanna Stimpson
- Department
of Chemistry and Manchester Institute of Biotechnology, University of Manchester, Manchester M1 7DN, U.K.
| | - Kathleen Cain
- Department
of Chemistry and Manchester Institute of Biotechnology, University of Manchester, Manchester M1 7DN, U.K.
| | - Oliver J. Wilkinson
- Centre
for Chemical Biology, Department of Chemistry, Sheffield Institute
for Nucleic Acids, University of Sheffield, Sheffield S3 7HF, U.K.
| | - Nicholas H. Williams
- Centre
for Chemical Biology, Department of Chemistry, Sheffield Institute
for Nucleic Acids, University of Sheffield, Sheffield S3 7HF, U.K.
| | - Perdita E. Barran
- Department
of Chemistry and Manchester Institute of Biotechnology, University of Manchester, Manchester M1 7DN, U.K.
| | - Geoffrey P. Margison
- Epidemiology
and Public Health Group, Division of Population Health, Health Services
Research and Primary Care, School of Health Sciences, Faculty of Biology,
Medicine and Health, University of Manchester, Manchester M13 9PL, U.K.
| | - David M. Williams
- Centre
for Chemical Biology, Department of Chemistry, Sheffield Institute
for Nucleic Acids, University of Sheffield, Sheffield S3 7HF, U.K.
| | - Andrew C. Povey
- Epidemiology
and Public Health Group, Division of Population Health, Health Services
Research and Primary Care, School of Health Sciences, Faculty of Biology,
Medicine and Health, University of Manchester, Manchester M13 9PL, U.K.
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3
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Aloisi CMN, Escher NA, Kim HS, Geisen SM, Fontana GA, Yeo JE, Schärer OD, Sturla SJ. A combination of direct reversion and nucleotide excision repair counters the mutagenic effects of DNA carboxymethylation. DNA Repair (Amst) 2022; 110:103262. [PMID: 35030424 PMCID: PMC9232693 DOI: 10.1016/j.dnarep.2021.103262] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 12/20/2021] [Accepted: 12/20/2021] [Indexed: 02/03/2023]
Abstract
Distinct cellular DNA damage repair pathways maintain the structural integrity of DNA and protect it from the mutagenic effects of genotoxic exposures and processes. The occurrence of O6-carboxymethylguanine (O6-CMG) has been linked to meat consumption and hypothesized to contribute to the development of colorectal cancer. However, the cellular fate of O6-CMG is poorly characterized and there is contradictory data in the literature as to how repair pathways may protect cells from O6-CMG mutagenicity. To better address how cells detect and remove O6-CMG, we evaluated the role of two DNA repair pathways in counteracting the accumulation and toxic effects of O6-CMG. We found that cells deficient in either the direct repair protein O6-methylguanine-DNA methyltransferase (MGMT), or key components of the nucleotide excision repair (NER) pathway, accumulate higher levels O6-CMG DNA adducts than wild type cells. Furthermore, repair-deficient cells were more sensitive to carboxymethylating agents and displayed an increased mutation rate. These findings suggest that a combination of direct repair and NER circumvent the effects O6-CMG DNA damage.
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Affiliation(s)
- Claudia M N Aloisi
- Department of Health Sciences and Technology, ETH Zurich, 8092 Zurich, Switzerland
| | - Nora A Escher
- Department of Health Sciences and Technology, ETH Zurich, 8092 Zurich, Switzerland
| | - Hyun Suk Kim
- Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea
| | - Susanne M Geisen
- Department of Health Sciences and Technology, ETH Zurich, 8092 Zurich, Switzerland
| | - Gabriele A Fontana
- Department of Health Sciences and Technology, ETH Zurich, 8092 Zurich, Switzerland
| | - Jung-Eun Yeo
- Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea; Department of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Orlando D Schärer
- Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea; Department of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea.
| | - Shana J Sturla
- Department of Health Sciences and Technology, ETH Zurich, 8092 Zurich, Switzerland.
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4
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Aloisi CMN, Sandell ES, Sturla SJ. A Chemical Link between Meat Consumption and Colorectal Cancer Development? Chem Res Toxicol 2021; 34:12-23. [PMID: 33417435 DOI: 10.1021/acs.chemrestox.0c00395] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
O6-carboxymethylguanine (O6-CMG) is a mutagenic DNA adduct that forms at increased levels when people eat meat. It has been studied as a potential initiating event in colorectal carcinogenesis. It can arise from alkylation of guanine in DNA by electrophilic degradation products of N-nitroso compounds. There is significant data regarding biochemical and cellular process, including DNA repair and translesion DNA synthesis that control O6-CMG accumulation, persistence, and mutagenicity. Mutation spectra arising from the adduct closely resemble common mutations in colorectal cancer; however, gaps remain in understanding the biochemical processes that regulate how and where the damage persists in the genome. Addressing such questions relies on advances in chemistry such as synthesis approaches and bioanalytical methods. Results of research in this area help advance our understanding of the toxicological relevance of O6-CMG-modified DNA. Further attention should focus on understanding how a combination of genetic and environmental factors control its biological persistence and how this information can be used as a basis of biomoniotoring and prevention efforts to help mitigate colon cancer risk.
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Affiliation(s)
- Claudia M N Aloisi
- Department of Health Sciences and Technology, ETH Zürich, Schmelzbergstrasse 9, 8092 Zürich, Switzerland
| | - Emma S Sandell
- Department of Health Sciences and Technology, ETH Zürich, Schmelzbergstrasse 9, 8092 Zürich, Switzerland
| | - Shana J Sturla
- Department of Health Sciences and Technology, ETH Zürich, Schmelzbergstrasse 9, 8092 Zürich, Switzerland
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5
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Envisioning how the prototypic molecular machine TFIIH functions in transcription initiation and DNA repair. DNA Repair (Amst) 2020; 96:102972. [PMID: 33007515 DOI: 10.1016/j.dnarep.2020.102972] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 09/02/2020] [Accepted: 09/07/2020] [Indexed: 12/22/2022]
Abstract
Critical for transcription initiation and bulky lesion DNA repair, TFIIH provides an exemplary system to connect molecular mechanisms to biological outcomes due to its strong genetic links to different specific human diseases. Recent advances in structural and computational biology provide a unique opportunity to re-examine biologically relevant molecular structures and develop possible mechanistic insights for the large dynamic TFIIH complex. TFIIH presents many puzzles involving how its two SF2 helicase family enzymes, XPB and XPD, function in transcription initiation and repair: how do they initiate transcription, detect and verify DNA damage, select the damaged strand for incision, coordinate repair with transcription and cell cycle through Cdk-activating-kinase (CAK) signaling, and result in very different specific human diseases associated with cancer, aging, and development from single missense mutations? By joining analyses of breakthrough cryo-electron microscopy (cryo-EM) structures and advanced computation with data from biochemistry and human genetics, we develop unified concepts and molecular level understanding for TFIIH functions with a focus on structural mechanisms. We provocatively consider that TFIIH may have first evolved from evolutionary pressure for TCR to resolve arrested transcription blocks to DNA replication and later added its key roles in transcription initiation and global DNA repair. We anticipate that this level of mechanistic information will have significant impact on thinking about TFIIH, laying a robust foundation suitable to develop new paradigms for DNA transcription initiation and repair along with insights into disease prevention, susceptibility, diagnosis and interventions.
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6
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Abdu K, Aiertza MK, Wilkinson OJ, Senthong P, Craggs TD, Povey AC, Margison GP, Williams DM. Synthesis of oligodeoxyribonucleotides containing a tricyclic thio analogue of O6-methylguanine and their recognition by MGMT and Atl1. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2020; 39:1108-1121. [PMID: 32449465 DOI: 10.1080/15257770.2020.1764971] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Promutagenic O6-alkylguanine adducts in DNA are repaired in humans by O6-methylguanine-DNA-methyltransferase (MGMT) in an irreversible reaction. Here we describe the synthesis of a phosphoramidite that allows the preparation of oligodeoxyribonucleotides (ODNs) containing a novel tricyclic thio analogue of O6-methylguanine in which the third ring bridges the 6-thio group and C7 of a 7-deazapurine. These ODNs are very poor substrates for MGMT and poorly recognised by the alkyltransferase-like protein, Atl1. Examination of the active sites of both MGMT and Atl1 suggest large steric clashes hindering binding of the analogue. Such analogues, if mutagenic, are likely to be highly toxic.
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Affiliation(s)
- Kabir Abdu
- Department of Pure and Industrial Chemistry, Faculty of Physical Sciences, Bayero University, Kano, Nigeria
| | - Miren K Aiertza
- Centre for Chemical Biology, Department of Chemistry, Sheffield Institute for Nucleic Acids, University of Sheffield, Sheffield, UK
| | - Oliver J Wilkinson
- Centre for Chemical Biology, Department of Chemistry, Sheffield Institute for Nucleic Acids, University of Sheffield, Sheffield, UK
| | | | - Timothy D Craggs
- Centre for Chemical Biology, Department of Chemistry, Sheffield Institute for Nucleic Acids, University of Sheffield, Sheffield, UK
| | - Andrew C Povey
- Centre of Epidemiology, Faculty of Biology, Medicine and Health
| | | | - David M Williams
- Centre for Chemical Biology, Department of Chemistry, Sheffield Institute for Nucleic Acids, University of Sheffield, Sheffield, UK
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7
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Alkyltransferase-like protein clusters scan DNA rapidly over long distances and recruit NER to alkyl-DNA lesions. Proc Natl Acad Sci U S A 2020; 117:9318-9328. [PMID: 32273391 DOI: 10.1073/pnas.1916860117] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Alkylation of guanine bases in DNA is detrimental to cells due to its high mutagenic and cytotoxic potential and is repaired by the alkyltransferase AGT. Additionally, alkyltransferase-like proteins (ATLs), which are structurally similar to AGTs, have been identified in many organisms. While ATLs are per se catalytically inactive, strong evidence has suggested that ATLs target alkyl lesions to the nucleotide excision repair system (NER). Using a combination of single-molecule and ensemble approaches, we show here recruitment of UvrA, the initiating enzyme of prokaryotic NER, to an alkyl lesion by ATL. We further characterize lesion recognition by ATL and directly visualize DNA lesion search by highly motile ATL and ATL-UvrA complexes on DNA at the molecular level. Based on the high similarity of ATLs and the DNA-interacting domain of AGTs, our results provide important insight in the lesion search mechanism, not only by ATL but also by AGT, thus opening opportunities for controlling the action of AGT for therapeutic benefit during chemotherapy.
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8
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Thapar R, Bacolla A, Oyeniran C, Brickner JR, Chinnam NB, Mosammaparast N, Tainer JA. RNA Modifications: Reversal Mechanisms and Cancer. Biochemistry 2018; 58:312-329. [PMID: 30346748 DOI: 10.1021/acs.biochem.8b00949] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
An emerging molecular understanding of RNA alkylation and its removal is transforming our knowledge of RNA biology and its interplay with cancer chemotherapy responses. DNA modifications are known to perform critical functions depending on the genome template, including gene expression, DNA replication timing, and DNA damage protection, yet current results suggest that the chemical diversity of DNA modifications pales in comparison to those on RNA. More than 150 RNA modifications have been identified to date, and their complete functional implications are still being unveiled. These include intrinsic roles such as proper processing and RNA maturation; emerging evidence has furthermore uncovered RNA modification "readers", seemingly analogous to those identified for histone modifications. These modification recognition factors may regulate mRNA stability, localization, and interaction with translation machinery, affecting gene expression. Not surprisingly, tumors differentially modulate factors involved in expressing these marks, contributing to both tumorigenesis and responses to alkylating chemotherapy. Here we describe the current understanding of RNA modifications and their removal, with a focus primarily on methylation and alkylation as functionally relevant changes to the transcriptome. Intriguingly, some of the same RNA modifications elicited by physiological processes are also produced by alkylating agents, thus blurring the lines between what is a physiological mark and a damage-induced modification. Furthermore, we find that a high level of gene expression of enzymes with RNA dealkylation activity is a sensitive readout for poor survival in four different cancer types, underscoring the likely importance of examining RNA dealkylation mechanisms to cancer biology and for cancer treatment and prognosis.
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Affiliation(s)
- Roopa Thapar
- Department of Molecular and Cellular Oncology , University of Texas M. D. Anderson Cancer Center , Houston , Texas 77030 , United States
| | - Albino Bacolla
- Department of Molecular and Cellular Oncology , University of Texas M. D. Anderson Cancer Center , Houston , Texas 77030 , United States
| | - Clement Oyeniran
- Department of Pathology and Immunology, Siteman Cancer Center , Washington University in St. Louis School of Medicine , St. Louis , Missouri 63110 , United States
| | - Joshua R Brickner
- Department of Pathology and Immunology, Siteman Cancer Center , Washington University in St. Louis School of Medicine , St. Louis , Missouri 63110 , United States
| | - Naga Babu Chinnam
- Department of Molecular and Cellular Oncology , University of Texas M. D. Anderson Cancer Center , Houston , Texas 77030 , United States
| | - Nima Mosammaparast
- Department of Pathology and Immunology, Siteman Cancer Center , Washington University in St. Louis School of Medicine , St. Louis , Missouri 63110 , United States
| | - John A Tainer
- Department of Molecular and Cellular Oncology , University of Texas M. D. Anderson Cancer Center , Houston , Texas 77030 , United States
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9
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Sacre L, Wilds CJ. Fluorine at the C5 Position of 2′-Deoxyuridine Enhances Repair of a O
4
-Methyl Adduct by O
6
-Alkylguanine DNA Alkyltransferases. European J Org Chem 2017. [DOI: 10.1002/ejoc.201700466] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Lauralicia Sacre
- Department of Chemistry and Biochemistry and Centre for Structural and Functional Genomics; Concordia University; 7141 Sherbrooke St. West H4B 1R6 Montréal Québec Canada
| | - Christopher J. Wilds
- Department of Chemistry and Biochemistry and Centre for Structural and Functional Genomics; Concordia University; 7141 Sherbrooke St. West H4B 1R6 Montréal Québec Canada
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10
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Vettone A, Serpe M, Hidalgo A, Berenguer J, del Monaco G, Valenti A, Rossi M, Ciaramella M, Perugino G. A novel thermostable protein-tag: optimization of the Sulfolobus solfataricus DNA- alkyl-transferase by protein engineering. Extremophiles 2016; 20:1-13. [PMID: 26499124 DOI: 10.1007/s00792-015-0791-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 10/03/2015] [Indexed: 12/12/2022]
Abstract
In the last decade, a powerful biotechnological tool for the in vivo and in vitro specific labeling of proteins (SNAP-tag™ technology) was proposed as a valid alternative to classical protein-tags (green fluorescent proteins, GFPs). This was made possible by the discovery of the irreversible reaction of the human alkylguanine-DNA-alkyl-transferase (hAGT) in the presence of benzyl-guanine derivatives. However, the mild reaction conditions and the general instability of the mesophilic SNAP-tag™ make this new approach not fully applicable to (hyper-)thermophilic and, in general, extremophilic organisms. Here, we introduce an engineered variant of the thermostable alkylguanine-DNA-alkyl-transferase from the Archaea Sulfolobus solfataricus (SsOGT-H5), which displays a catalytic efficiency comparable to the SNAP-tag™ protein, but showing high intrinsic stability typical of proteins from this organism. The successful heterologous expression obtained in a thermophilic model organism makes SsOGT-H5 a valid candidate as protein-tag for organisms living in extreme environments.
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Affiliation(s)
- Antonella Vettone
- Institute of Biosciences and BioResources, National Council of Research of Italy, Via P. Castellino 111, 80131 Naples, Italy
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11
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Martins-Pinheiro M, Schons-Fonseca L, da Silva JB, Domingos RH, Momo LHS, Simões ACQ, Ho PL, da Costa RMA. Genomic survey and expression analysis of DNA repair genes in the genus Leptospira. Mol Genet Genomics 2015; 291:703-22. [PMID: 26527082 DOI: 10.1007/s00438-015-1135-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Accepted: 10/16/2015] [Indexed: 10/22/2022]
Abstract
Leptospirosis is an emerging zoonosis with important economic and public health consequences and is caused by pathogenic leptospires. The genus Leptospira belongs to the order Spirochaetales and comprises saprophytic (L. biflexa), pathogenic (L. interrogans) and host-dependent (L. borgpetersenii) members. Here, we present an in silico search for DNA repair pathways in Leptospira spp. The relevance of such DNA repair pathways was assessed through the identification of mRNA levels of some genes during infection in animal model and after exposition to spleen cells. The search was performed by comparison of available Leptospira spp. genomes in public databases with known DNA repair-related genes. Leptospires exhibit some distinct and unexpected characteristics, for instance the existence of a redundant mechanism for repairing a chemically diverse spectrum of alkylated nucleobases, a new mutS-like gene and a new shorter version of uvrD. Leptospira spp. shares some characteristics from Gram-positive, as the presence of PcrA, two RecQ paralogs and two SSB proteins; the latter is considered a feature shared by naturally competent bacteria. We did not find a significant reduction in the number of DNA repair-related genes in both pathogenic and host-dependent species. Pathogenic leptospires were enriched for genes dedicated to base excision repair and non-homologous end joining. Their evolutionary history reveals a remarkable importance of lateral gene transfer events for the evolution of the genus. Up-regulation of specific DNA repair genes, including components of SOS regulon, during infection in animal model validates the critical role of DNA repair mechanisms for the complex interplay between host/pathogen.
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Affiliation(s)
- Marinalva Martins-Pinheiro
- Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, 05508-900, Brazil.,Departamento de Engenharia Química, Escola Politécnica, Universidade de São Paulo, São Paulo, São Paulo, Brazil
| | - Luciane Schons-Fonseca
- Centro de Biotecnologia, Instituto Butantan, São Paulo, 05503-900, Brazil.,Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, 05508-000, Brazil
| | - Josefa B da Silva
- Centro de Biotecnologia, Instituto Butantan, São Paulo, 05503-900, Brazil
| | - Renan H Domingos
- Centro de Biotecnologia, Instituto Butantan, São Paulo, 05503-900, Brazil
| | | | - Ana Carolina Quirino Simões
- Centro de Engenharia, Modelagem e Ciências Sociais Aplicadas, Universidade Federal do ABC, Santo André, 09210-170, Brazil
| | - Paulo Lee Ho
- Centro de Biotecnologia, Instituto Butantan, São Paulo, 05503-900, Brazil.,Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, 05508-000, Brazil
| | - Renata M A da Costa
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Santo André, 09210-170, Brazil.
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12
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Mullins EA, Shi R, Parsons ZD, Yuen PK, David SS, Igarashi Y, Eichman BF. The DNA glycosylase AlkD uses a non-base-flipping mechanism to excise bulky lesions. Nature 2015; 527:254-8. [PMID: 26524531 DOI: 10.1038/nature15728] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Accepted: 09/18/2015] [Indexed: 01/10/2023]
Abstract
Threats to genomic integrity arising from DNA damage are mitigated by DNA glycosylases, which initiate the base excision repair pathway by locating and excising aberrant nucleobases. How these enzymes find small modifications within the genome is a current area of intensive research. A hallmark of these and other DNA repair enzymes is their use of base flipping to sequester modified nucleotides from the DNA helix and into an active site pocket. Consequently, base flipping is generally regarded as an essential aspect of lesion recognition and a necessary precursor to base excision. Here we present the first, to our knowledge, DNA glycosylase mechanism that does not require base flipping for either binding or catalysis. Using the DNA glycosylase AlkD from Bacillus cereus, we crystallographically monitored excision of an alkylpurine substrate as a function of time, and reconstructed the steps along the reaction coordinate through structures representing substrate, intermediate and product complexes. Instead of directly interacting with the damaged nucleobase, AlkD recognizes aberrant base pairs through interactions with the phosphoribose backbone, while the lesion remains stacked in the DNA duplex. Quantum mechanical calculations revealed that these contacts include catalytic charge-dipole and CH-π interactions that preferentially stabilize the transition state. We show in vitro and in vivo how this unique means of recognition and catalysis enables AlkD to repair large adducts formed by yatakemycin, a member of the duocarmycin family of antimicrobial natural products exploited in bacterial warfare and chemotherapeutic trials. Bulky adducts of this or any type are not excised by DNA glycosylases that use a traditional base-flipping mechanism. Hence, these findings represent a new model for DNA repair and provide insights into catalysis of base excision.
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Affiliation(s)
- Elwood A Mullins
- Department of Biological Sciences and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37232, USA
| | - Rongxin Shi
- Department of Biological Sciences and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37232, USA
| | - Zachary D Parsons
- Department of Biological Sciences and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37232, USA
| | - Philip K Yuen
- Department of Chemistry, University of California, Davis, California 95616, USA
| | - Sheila S David
- Department of Chemistry, University of California, Davis, California 95616, USA
| | - Yasuhiro Igarashi
- Biotechnology Research Center, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Brandt F Eichman
- Department of Biological Sciences and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37232, USA
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Tomaszowski KH, Aasland D, Margison GP, Williams E, Pinder SI, Modesti M, Fuchs RP, Kaina B. The bacterial alkyltransferase-like (eATL) protein protects mammalian cells against methylating agent-induced toxicity. DNA Repair (Amst) 2015; 28:14-20. [PMID: 25703834 DOI: 10.1016/j.dnarep.2015.01.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Revised: 12/13/2014] [Accepted: 01/22/2015] [Indexed: 11/16/2022]
Abstract
In both pro- and eukaryotes, the mutagenic and toxic DNA adduct O(6)-methylguanine (O(6)MeG) is subject to repair by alkyltransferase proteins via methyl group transfer. In addition, in prokaryotes, there are proteins with sequence homology to alkyltransferases, collectively designated as alkyltransferase-like (ATL) proteins, which bind to O(6)-alkylguanine adducts and mediate resistance to alkylating agents. Whether such proteins might enable similar protection in higher eukaryotes is unknown. Here we expressed the ATL protein of Escherichia coli (eATL) in mammalian cells and addressed the question whether it is able to protect them against the cytotoxic effects of alkylating agents. The Chinese hamster cell line CHO-9, the nucleotide excision repair (NER) deficient derivative 43-3B and the DNA mismatch repair (MMR) impaired derivative Tk22-C1 were transfected with eATL cloned in an expression plasmid and the sensitivity to N-methyl-N'-nitro-N-nitrosoguanidine (MNNG) was determined in reproductive survival, DNA double-strand break (DSB) and apoptosis assays. The results indicate that eATL expression is tolerated in mammalian cells and conferes protection against killing by MNNG in both wild-type and 43-3B cells, but not in the MMR-impaired cell line. The protection effect was dependent on the expression level of eATL and was completely ablated in cells co-expressing the human O(6)-methylguanine-DNA methyltransferase (MGMT). eATL did not protect against cytotoxicity induced by the chloroethylating agent lomustine, suggesting that O(6)-chloroethylguanine adducts are not target of eATL. To investigate the mechanism of protection, we determined O(6)MeG levels in DNA after MNNG treatment and found that eATL did not cause removal of the adduct. However, eATL expression resulted in a significantly lower level of DSBs in MNNG-treated cells, and this was concomitant with attenuation of G2 blockage and a lower level of apoptosis. The results suggest that eATL confers protection against methylating agents by masking O(6)MeG/thymine mispaired adducts, preventing them from becoming a substrate for mismatch repair-mediated DSB formation and cell death.
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Affiliation(s)
- Karl-Heinz Tomaszowski
- Department of Toxicology, University Medical Center, Obere Zahlbacher Strasse 67, D-55131 Mainz, Germany
| | - Dorthe Aasland
- Department of Toxicology, University Medical Center, Obere Zahlbacher Strasse 67, D-55131 Mainz, Germany
| | - Geoffrey P Margison
- Paterson Institute for Cancer Research, University of Manchester, Wilmslow Road, Manchester, M20 4BX Manchester, UK
| | - Emma Williams
- Paterson Institute for Cancer Research, University of Manchester, Wilmslow Road, Manchester, M20 4BX Manchester, UK
| | - Sarah I Pinder
- Paterson Institute for Cancer Research, University of Manchester, Wilmslow Road, Manchester, M20 4BX Manchester, UK
| | - Mauro Modesti
- Centre de Recherche en Cancérologie de Marseille, CNRS-UMR7258, Inserm-U1068, Institut Paoli-Calmettes, Université Aix-Marseille, France
| | - Robert P Fuchs
- Centre de Recherche en Cancérologie de Marseille, CNRS-UMR7258, Inserm-U1068, Institut Paoli-Calmettes, Université Aix-Marseille, France
| | - Bernd Kaina
- Department of Toxicology, University Medical Center, Obere Zahlbacher Strasse 67, D-55131 Mainz, Germany.
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Abstract
TET-mediated 5-methyl cytosine (5mC) oxidation acts in epigenetic regulation, stem cell development, and cancer. Hu et al. now determine the crystal structure of the TET2 catalytic domain bound to DNA, shedding light on 5mC-DNA substrate recognition and the catalytic mechanism of 5mC oxidation.
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Affiliation(s)
- Chi-Lin Tsai
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - John A Tainer
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Department of Molecular Biology, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
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Da Pieve C, Sahgal N, Moore SA, Velasco-Garcia MN. Development of a liquid chromatography/tandem mass spectrometry method to investigate the presence of biomarkers of DNA damage in urine related to red meat consumption and risk of colorectal cancer. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2013; 27:2493-2503. [PMID: 24097406 DOI: 10.1002/rcm.6709] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Revised: 07/19/2013] [Accepted: 08/04/2013] [Indexed: 06/02/2023]
Abstract
RATIONALE The consumption of red meat is known to enhance the endogenous formation of N-nitroso compounds (NOCs), which are potent carcinogens. DNA damage related to NOCs, and hence red meat, has been detected in colorectal cells and in blood. We proposed to extend previous studies to a non-invasive approach for the detection of O(6)-carboxymethylguanine (O(6)CMG) and O(6)-carboxymethyl-2'-deoxyguanosine (O(6)CMdG) in urine in relation to red meat intake using liquid chromatography/tandem mass spectrometry (LC/MS/MS). The presence of the adduct in urine samples either as the free base or as 2'-deoxynucleoside could help in determining the repair mechanism involved when such lesions are produced. A non-invasive assessment of DNA adducts could also allow for large-scale analyses in the population and cancer prevention dietary strategies. METHODS An LC/MS/MS method for the quantitation of O(6)CMG and O(6)CMdG was developed. Urine samples collected from healthy volunteers on red meat and vegetarian diets were analysed either by direct injection or after purification by solid-phase extraction (SPE). A separate LC/MS/MS method for O(6)-methylguanine (O(6)MeG) and O(6)-methyl-2'-deoxyguanosine (O(6)MedG), which are possible hydrolysis products forming during the sample pre-treatment, was also developed. RESULTS The developed LC/MS/MS method allowed the simultaneous measurement of O(6)CMG and O(6)CMdG. The limits of detection (LODs) were 0.38 ng/mL for O(6)CMG and 0.18 ng/mL for O(6)CMdG. The direct injection analysis of the clinical samples showed low sensitivity due to high background signal that was improved by SPE purification. However, the concentrations of the adducts in clinical samples were still found to be below the LOD. CONCLUSIONS Novel, reproducible, and accurate LC/MS/MS methods were developed for the determination of the urinary content of O(6)CMG and O(6)CMdG, and of the possible formation of O(6)MeG and O(6)MedG by decarboxylation. Clinical samples from volunteers on different diets were analysed. Further studies are required to discover a link between the presence of these biomarkers in urine and red meat consumption.
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Affiliation(s)
- Chiara Da Pieve
- Department of Life, Health and Chemical Sciences, Faculty of Science, The Open University, Walton Hall, Milton Keynes, MK7 6AA, UK
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Stewart M, Dunlap T, Dourlain E, Grant B, McFail-Isom L. Cations form sequence selective motifs within DNA grooves via a combination of cation-pi and ion-dipole/hydrogen bond interactions. PLoS One 2013; 8:e71420. [PMID: 23940752 PMCID: PMC3735504 DOI: 10.1371/journal.pone.0071420] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2013] [Accepted: 07/02/2013] [Indexed: 11/19/2022] Open
Abstract
The fine conformational subtleties of DNA structure modulate many fundamental cellular processes including gene activation/repression, cellular division, and DNA repair. Most of these cellular processes rely on the conformational heterogeneity of specific DNA sequences. Factors including those structural characteristics inherent in the particular base sequence as well as those induced through interaction with solvent components combine to produce fine DNA structural variation including helical flexibility and conformation. Cation-pi interactions between solvent cations or their first hydration shell waters and the faces of DNA bases form sequence selectively and contribute to DNA structural heterogeneity. In this paper, we detect and characterize the binding patterns found in cation-pi interactions between solvent cations and DNA bases in a set of high resolution x-ray crystal structures. Specifically, we found that monovalent cations (Tl+) and the polarized first hydration shell waters of divalent cations (Mg2+, Ca2+) form cation-pi interactions with DNA bases stabilizing unstacked conformations. When these cation-pi interactions are combined with electrostatic interactions a pattern of specific binding motifs is formed within the grooves.
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Affiliation(s)
- Mikaela Stewart
- Department of Chemistry, University of Central Arkansas, Conway, Arkansas, United States of America
| | - Tori Dunlap
- Department of Chemistry, University of Central Arkansas, Conway, Arkansas, United States of America
| | - Elizabeth Dourlain
- Department of Chemistry, University of Central Arkansas, Conway, Arkansas, United States of America
| | - Bryce Grant
- Department of Chemistry, University of Central Arkansas, Conway, Arkansas, United States of America
| | - Lori McFail-Isom
- Department of Chemistry, University of Central Arkansas, Conway, Arkansas, United States of America
- * E-mail:
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Biochemical and structural studies of the Mycobacterium tuberculosis O6-methylguanine methyltransferase and mutated variants. J Bacteriol 2013; 195:2728-36. [PMID: 23564173 DOI: 10.1128/jb.02298-12] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Mycobacterium tuberculosis displays remarkable genetic stability despite continuous exposure to the hostile environment represented by the host's infected macrophages. Similarly to other organisms, M. tuberculosis possesses multiple systems to counteract the harmful potential of DNA alkylation. In particular, the suicidal enzyme O(6)-methylguanine-DNA methyltransferase (OGT) is responsible for the direct repair of O(6)-alkylguanine in double-stranded DNA and is therefore supposed to play a central role in protecting the mycobacterial genome from the risk of G · C-to-A · T transition mutations. Notably, a number of geographically widely distributed M. tuberculosis strains shows nonsynonymous single-nucleotide polymorphisms in their OGT-encoding gene, leading to amino acid substitutions at position 15 (T15S) or position 37 (R37L) of the N-terminal domain of the corresponding protein. However, the role of these mutations in M. tuberculosis pathogenesis is unknown. We describe here the in vitro characterization of M. tuberculosis OGT (MtOGT) and of two point-mutated versions of the protein mimicking the naturally occurring ones, revealing that both mutated proteins are impaired in their activity as a consequence of their lower affinity for alkylated DNA than the wild-type protein. The analysis of the crystal structures of MtOGT and MtOGT-R37L confirms the high level of structural conservation of members of this protein family and provides clues to an understanding of the molecular bases for the reduced affinity for the natural substrate displayed by mutated MtOGT. Our in vitro results could contribute to validate the inferred participation of mutated OGTs in M. tuberculosis phylogeny and biology.
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Abdu K, Aiertza MK, Wilkinson OJ, Grasby JA, Senthong P, Povey AC, Margison GP, Williams DM. Synthesis of oligodeoxyribonucleotides containing a conformationally-locked anti analogue of O6-methyl-2'-deoxyguanosine and their recognition by MGMT and Atl1. Chem Commun (Camb) 2012; 48:11214-6. [PMID: 23059787 DOI: 10.1039/c2cc36252j] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
We show that DNA containing a conformationally-locked anti analogue of O(6)-alkylguanine is a poor substrate for human O(6)-methylguanine-DNA methyltransferase (MGMT) and the alkyltransferase-like protein, Atl1. This highlights the requirement for the syn conformation and rationalises why certain O(6)-alkylguanines are poor MGMT substrates.
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Affiliation(s)
- Kabir Abdu
- Centre for Chemical Biology, Department of Chemistry, Krebs Institute, University of Sheffield, Sheffield, S3 7HF, UK
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