1
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Venkadakrishnan J, Lahane G, Dhar A, Xiao W, Bhat KM, Pandita TK, Bhat A. Implications of Translesion DNA Synthesis Polymerases on Genomic Stability and Human Health. Mol Cell Biol 2023; 43:401-425. [PMID: 37439479 PMCID: PMC10448981 DOI: 10.1080/10985549.2023.2224199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 05/03/2023] [Accepted: 06/01/2023] [Indexed: 07/14/2023] Open
Abstract
Replication fork arrest-induced DNA double strand breaks (DSBs) caused by lesions are effectively suppressed in cells due to the presence of a specialized mechanism, commonly referred to as DNA damage tolerance (DDT). In eukaryotic cells, DDT is facilitated through translesion DNA synthesis (TLS) carried out by a set of DNA polymerases known as TLS polymerases. Another parallel mechanism, referred to as homology-directed DDT, is error-free and involves either template switching or fork reversal. The significance of the DDT pathway is well established. Several diseases have been attributed to defects in the TLS pathway, caused either by mutations in the TLS polymerase genes or dysregulation. In the event of a replication fork encountering a DNA lesion, cells switch from high-fidelity replicative polymerases to low-fidelity TLS polymerases, which are associated with genomic instability linked with several human diseases including, cancer. The role of TLS polymerases in chemoresistance has been recognized in recent years. In addition to their roles in the DDT pathway, understanding noncanonical functions of TLS polymerases is also a key to unraveling their importance in maintaining genomic stability. Here we summarize the current understanding of TLS pathway in DDT and its implication for human health.
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Affiliation(s)
| | - Ganesh Lahane
- Department of Pharmacy, Birla Institute of Technology and Sciences Pilani, Hyderabad Campus, Hyderabad, India
| | - Arti Dhar
- Department of Pharmacy, Birla Institute of Technology and Sciences Pilani, Hyderabad Campus, Hyderabad, India
| | - Wei Xiao
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Canada
| | - Krishna Moorthi Bhat
- Department of Molecular Medicine, University of South Florida, Tampa, Florida, USA
| | - Tej K. Pandita
- Center for Genomics and Precision Medicine, Texas A&M College of Medicine, Houston, Texas, USA
| | - Audesh Bhat
- Center for Molecular Biology, Central University of Jammu, UT Jammu and Kashmir, India
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2
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Peng HC, Castro GL, Karthikeyan V, Jarrett A, Katz MA, Hargrove JA, Hoang D, Hilber S, Meng W, Wang L, Fick RJ, Ahn JM, Kreutz C, Stelling AL. Measuring the Enthalpy of an Individual Hydrogen Bond in a DNA Duplex with Nucleobase Isotope Editing and Variable-Temperature Infrared Spectroscopy. J Phys Chem Lett 2023; 14:4313-4321. [PMID: 37130045 DOI: 10.1021/acs.jpclett.3c00178] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The level of interest in probing the strength of noncovalent interactions in DNA duplexes is high, as these weak forces dictate the range of suprastructures the double helix adopts under different conditions, in turn directly impacting the biological functions and industrial applications of duplexes that require making and breaking them to access the genetic code. However, few experimental tools can measure these weak forces embedded within large biological suprastructures in the native solution environment. Here, we develop experimental methods for detecting the presence of a single noncovalent interaction [a hydrogen bond (H-bond)] within a large DNA duplex in solution and measure its formation enthalpy (ΔHf). We report that introduction of a H-bond into the TC2═O group from the noncanonical nucleobase 2-aminopurine produces an expected decrease ∼10 ± 0.76 cm-1 (from ∼1720 cm-1 in Watson-Crick to ∼1710 cm-1 in 2-aminopurine), which correlates with an enthalpy of ∼0.93 ± 0.066 kcal/mol for this interaction.
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Affiliation(s)
- Hao-Che Peng
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, United States
| | - Gabrielle L Castro
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, United States
| | - Varshini Karthikeyan
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, United States
| | - Alina Jarrett
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, United States
| | - Melanie A Katz
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, United States
| | - James A Hargrove
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, United States
| | - David Hoang
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, United States
| | - Stefan Hilber
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck 6020, Austria
| | - Wenting Meng
- Department of Chemistry and Chemical Biology, Institute for Quantitative Biomedicine, Rutgers University, Piscataway, New Jersey 08854, United States
| | - Lu Wang
- Department of Chemistry and Chemical Biology, Institute for Quantitative Biomedicine, Rutgers University, Piscataway, New Jersey 08854, United States
| | - Robert J Fick
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, United States
| | - Jung-Mo Ahn
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, United States
| | - Christoph Kreutz
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck 6020, Austria
| | - Allison L Stelling
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, United States
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3
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Shi H, Kimsey IJ, Gu S, Liu HF, Pham U, Schumacher MA, Al-Hashimi HM. Revealing A-T and G-C Hoogsteen base pairs in stressed protein-bound duplex DNA. Nucleic Acids Res 2021; 49:12540-12555. [PMID: 34792150 PMCID: PMC8643651 DOI: 10.1093/nar/gkab936] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Revised: 09/25/2021] [Accepted: 11/14/2021] [Indexed: 11/17/2022] Open
Abstract
Watson–Crick base pairs (bps) are the fundamental unit of genetic information and the building blocks of the DNA double helix. However, A-T and G-C can also form alternative ‘Hoogsteen’ bps, expanding the functional complexity of DNA. We developed ‘Hoog-finder’, which uses structural fingerprints to rapidly screen Hoogsteen bps, which may have been mismodeled as Watson–Crick in crystal structures of protein–DNA complexes. We uncovered 17 Hoogsteen bps, 7 of which were in complex with 6 proteins never before shown to bind Hoogsteen bps. The Hoogsteen bps occur near mismatches, nicks and lesions and some appear to participate in recognition and damage repair. Our results suggest a potentially broad role for Hoogsteen bps in stressed regions of the genome and call for a community-wide effort to identify these bps in current and future crystal structures of DNA and its complexes.
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Affiliation(s)
- Honglue Shi
- Department of Chemistry, Duke University, Durham, NC 27710, USA
| | - Isaac J Kimsey
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
| | - Stephanie Gu
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
| | - Hsuan-Fu Liu
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
| | - Uyen Pham
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
| | - Maria A Schumacher
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
| | - Hashim M Al-Hashimi
- Department of Chemistry, Duke University, Durham, NC 27710, USA.,Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
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4
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Vaisman A, McDonald JP, Smith MR, Aspelund SL, Evans TC, Woodgate R. Identification and Characterization of Thermostable Y-Family DNA Polymerases η, ι, κ and Rev1 From a Lower Eukaryote, Thermomyces lanuginosus. Front Mol Biosci 2021; 8:778400. [PMID: 34805283 PMCID: PMC8595933 DOI: 10.3389/fmolb.2021.778400] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 10/19/2021] [Indexed: 11/13/2022] Open
Abstract
Y-family DNA polymerases (pols) consist of six phylogenetically separate subfamilies; two UmuC (polV) branches, DinB (pol IV, Dpo4, polκ), Rad30A/POLH (polη), and Rad30B/POLI (polι) and Rev1. Of these subfamilies, DinB orthologs are found in all three domains of life; eubacteria, archaea, and eukarya. UmuC orthologs are identified only in bacteria, whilst Rev1 and Rad30A/B orthologs are only detected in eukaryotes. Within eukaryotes, a wide array of evolutionary diversity exists. Humans possess all four Y-family pols (pols η, ι, κ, and Rev1), Schizosaccharomyces pombe has three Y-family pols (pols η, κ, and Rev1), and Saccharomyces cerevisiae only has polη and Rev1. Here, we report the cloning, expression, and biochemical characterization of the four Y-family pols from the lower eukaryotic thermophilic fungi, Thermomyces lanuginosus. Apart from the expected increased thermostability of the T. lanuginosus Y-family pols, their major biochemical properties are very similar to properties of their human counterparts. In particular, both Rad30B homologs (T. lanuginosus and human polɩ) exhibit remarkably low fidelity during DNA synthesis that is template sequence dependent. It was previously hypothesized that higher organisms had acquired this property during eukaryotic evolution, but these observations imply that polι originated earlier than previously known, suggesting a critical cellular function in both lower and higher eukaryotes.
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Affiliation(s)
- Alexandra Vaisman
- Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
| | - John P McDonald
- Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
| | - Mallory R Smith
- Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
| | - Sender L Aspelund
- Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
| | - Thomas C Evans
- New England Biolabs Incorporated, Ipswich, MA, United States
| | - Roger Woodgate
- Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
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5
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DNA Polymerase and dRP-lyase activities of polymorphic variants of human Pol ι. Biochem J 2021; 478:1399-1412. [PMID: 33600564 DOI: 10.1042/bcj20200491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 02/13/2021] [Accepted: 02/16/2021] [Indexed: 11/17/2022]
Abstract
Y-family DNA polymerase iota (Pol ι) is involved in DNA damage response and tolerance. Mutations and altered expression level of POLI gene are linked to a higher incidence of cancer. We biochemically characterized five active site polymorphic variants of human Pol ι: R71G (rs3218778), P118L (rs554252419), I236M (rs3218784), E251K (rs3218783) and P365R (rs200852409). We analyzed fidelity of nucleotide incorporation on undamaged DNA, efficiency and accuracy of DNA damage bypass, as well as 5'-deoxyribophosphate lyase (dRP-lyase) activity. The I236M and P118L variants were indistinguishable from the wild-type Pol ι in activity. The E251K and P365R substitutions altered the spectrum of nucleotide incorporation opposite several undamaged DNA bases. The P365R variant also reduced the dRP-lyase activity and possessed the decreased TLS activity opposite 8-oxo-G. The R71G mutation dramatically affected the catalytic activities of Pol ι. The reduced DNA polymerase activity of the R71G variant correlated with an enhanced fidelity of nucleotide incorporation on undamaged DNA, altered lesion-bypass activity and reduced dRP-lyase activity. Therefore, this amino acid substitution likely alters Pol ι functions in vivo.
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6
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Shilkin ES, Boldinova EO, Stolyarenko AD, Goncharova RI, Chuprov-Netochin RN, Khairullin RF, Smal MP, Makarova AV. Translesion DNA Synthesis and Carcinogenesis. BIOCHEMISTRY (MOSCOW) 2021; 85:425-435. [PMID: 32569550 DOI: 10.1134/s0006297920040033] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Tens of thousands of DNA lesions are formed in mammalian cells each day. DNA translesion synthesis is the main mechanism of cell defense against unrepaired DNA lesions. DNA polymerases iota (Pol ι), eta (Pol η), kappa (Pol κ), and zeta (Pol ζ) have active sites that are less stringent toward the DNA template structure and efficiently incorporate nucleotides opposite DNA lesions. However, these polymerases display low accuracy of DNA synthesis and can introduce mutations in genomic DNA. Impaired functioning of these enzymes can lead to an increased risk of cancer.
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Affiliation(s)
- E S Shilkin
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, 123182, Russia
| | - E O Boldinova
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, 123182, Russia
| | - A D Stolyarenko
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, 123182, Russia
| | - R I Goncharova
- Institute of Genetics and Cytology, National Academy of Sciences of Belarus, Minsk, 220072, Republic of Belarus
| | - R N Chuprov-Netochin
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - R F Khairullin
- Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan, 420012, Russia
| | - M P Smal
- Institute of Genetics and Cytology, National Academy of Sciences of Belarus, Minsk, 220072, Republic of Belarus.
| | - A V Makarova
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, 123182, Russia.
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7
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Saha P, Mandal T, Talukdar AD, Kumar D, Kumar S, Tripathi PP, Wang QE, Srivastava AK. DNA polymerase eta: A potential pharmacological target for cancer therapy. J Cell Physiol 2020; 236:4106-4120. [PMID: 33184862 DOI: 10.1002/jcp.30155] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 10/21/2020] [Accepted: 11/02/2020] [Indexed: 12/24/2022]
Abstract
In the last two decades, intensive research has been carried out to improve the survival rates of cancer patients. However, the development of chemoresistance that ultimately leads to tumor relapse poses a critical challenge for the successful treatment of cancer patients. Many cancer patients experience tumor relapse and ultimately die because of treatment failure associated with acquired drug resistance. Cancer cells utilize multiple lines of self-defense mechanisms to bypass chemotherapy and radiotherapy. One such mechanism employed by cancer cells is translesion DNA synthesis (TLS), in which specialized TLS polymerases bypass the DNA lesion with the help of monoubiquitinated proliferating cell nuclear antigen. Among all TLS polymerases (Pol η, Pol ι, Pol κ, REV1, Pol ζ, Pol μ, Pol λ, Pol ν, and Pol θ), DNA polymerase eta (Pol η) is well studied and majorly responsible for the bypass of cisplatin and UV-induced DNA damage. TLS polymerases contribute to chemotherapeutic drug-induced mutations as well as therapy resistance. Therefore, targeting these polymerases presents a novel therapeutic strategy to combat chemoresistance. Mounting evidence suggests that inhibition of Pol η may have multiple impacts on cancer therapy such as sensitizing cancer cells to chemotherapeutics, suppressing drug-induced mutagenesis, and inhibiting the development of secondary tumors. Herein, we provide a general introduction of Pol η and its clinical implications in blocking acquired drug resistance. In addition; this review addresses the existing gaps and challenges of Pol η mediated TLS mechanisms in human cells. A better understanding of the Pol η mediated TLS mechanism will not merely establish it as a potential pharmacological target but also open possibilities to identify novel drug targets for future therapy.
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Affiliation(s)
- Priyanka Saha
- Cancer Biology & Inflammatory Disorder Division, CSIR-Indian Institute of Chemical Biology, Kolkata, West Bengal, India
| | - Tanima Mandal
- Cancer Biology & Inflammatory Disorder Division, CSIR-Indian Institute of Chemical Biology, Kolkata, West Bengal, India
| | - Anupam D Talukdar
- Department of Life Science and Bioinformatics, Assam University, Silchar, Assam, India
| | - Deepak Kumar
- Organic & Medicinal Chemistry Division, CSIR-Indian Institute of Chemical Biology, Kolkata, West Bengal, India
| | - Sanjay Kumar
- Division of Biology, Indian Institute of Science Education and Research (IISER) Tirupati, Andhra Pradesh, India
| | - Prem P Tripathi
- Cell Biology & Physiology Division, CSIR-Indian Institute of Chemical Biology, Kolkata, West Bengal, India
| | - Qi-En Wang
- Department of Radiation Oncology, Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, USA
| | - Amit K Srivastava
- Cancer Biology & Inflammatory Disorder Division, CSIR-Indian Institute of Chemical Biology, Kolkata, West Bengal, India
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Kim DV, Makarova AV, Miftakhova RR, Zharkov DO. Base Excision DNA Repair Deficient Cells: From Disease Models to Genotoxicity Sensors. Curr Pharm Des 2020; 25:298-312. [PMID: 31198112 DOI: 10.2174/1381612825666190319112930] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 03/13/2019] [Indexed: 12/29/2022]
Abstract
Base excision DNA repair (BER) is a vitally important pathway that protects the cell genome from many kinds of DNA damage, including oxidation, deamination, and hydrolysis. It involves several tightly coordinated steps, starting from damaged base excision and followed by nicking one DNA strand, incorporating an undamaged nucleotide, and DNA ligation. Deficiencies in BER are often embryonic lethal or cause morbid diseases such as cancer, neurodegeneration, or severe immune pathologies. Starting from the early 1980s, when the first mammalian cell lines lacking BER were produced by spontaneous mutagenesis, such lines have become a treasure trove of valuable information about the mechanisms of BER, often revealing unexpected connections with other cellular processes, such as antibody maturation or epigenetic demethylation. In addition, these cell lines have found an increasing use in genotoxicity testing, where they provide increased sensitivity and representativity to cell-based assay panels. In this review, we outline current knowledge about BER-deficient cell lines and their use.
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Affiliation(s)
- Daria V Kim
- Novosibirsk State University, 2 Pirogova St., Novosibirsk 630090, Russian Federation
| | - Alena V Makarova
- RAS Institute of Molecular Genetics, 2 Kurchatova Sq., Moscow 123182, Russian Federation
| | - Regina R Miftakhova
- Kazan Federal University, 18 Kremlevsakaya St., Kazan 420008, Russian Federation
| | - Dmitry O Zharkov
- Novosibirsk State University, 2 Pirogova St., Novosibirsk 630090, Russian Federation.,SB RAS Institute of Chemical Biology and Fu ndamental Medicine, 8 Lavrentieva Ave., Novosibirsk 630090, Russian Federation
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9
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Marygold SJ, Attrill H, Speretta E, Warner K, Magrane M, Berloco M, Cotterill S, McVey M, Rong Y, Yamaguchi M. The DNA polymerases of Drosophila melanogaster. Fly (Austin) 2020; 14:49-61. [PMID: 31933406 PMCID: PMC7714529 DOI: 10.1080/19336934.2019.1710076] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
DNA synthesis during replication or repair is a fundamental cellular process that is catalyzed by a set of evolutionary conserved polymerases. Despite a large body of research, the DNA polymerases of Drosophila melanogaster have not yet been systematically reviewed, leading to inconsistencies in their nomenclature, shortcomings in their functional (Gene Ontology, GO) annotations and an under-appreciation of the extent of their characterization. Here, we describe the complete set of DNA polymerases in D. melanogaster, applying nomenclature already in widespread use in other species, and improving their functional annotation. A total of 19 genes encode the proteins comprising three replicative polymerases (alpha-primase, delta, epsilon), five translesion/repair polymerases (zeta, eta, iota, Rev1, theta) and the mitochondrial polymerase (gamma). We also provide an overview of the biochemical and genetic characterization of these factors in D. melanogaster. This work, together with the incorporation of the improved nomenclature and GO annotation into key biological databases, including FlyBase and UniProtKB, will greatly facilitate access to information about these important proteins.
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Affiliation(s)
- Steven J Marygold
- FlyBase, Department of Physiology, Development and Neuroscience, University of Cambridge , Cambridge, UK
| | - Helen Attrill
- FlyBase, Department of Physiology, Development and Neuroscience, University of Cambridge , Cambridge, UK
| | - Elena Speretta
- UniProt, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI) , Cambridgeshire, UK
| | - Kate Warner
- UniProt, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI) , Cambridgeshire, UK
| | - Michele Magrane
- UniProt, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI) , Cambridgeshire, UK
| | - Maria Berloco
- Dipartimento di Biologia, Università degli Studi di Bari "Aldo Moro" , Bari, Italy
| | - Sue Cotterill
- Department Basic Medical Sciences, St Georges University London , London, UK
| | - Mitch McVey
- Department of Biology, Tufts University , Medford, MA, USA
| | - Yikang Rong
- School of Life Sciences, Sun Yat-sen University , Guangzhou, China
| | - Masamitsu Yamaguchi
- Department of Applied Biology and Advanced Insect Research Promotion Center, Kyoto Institute of Technology , Kyoto, Japan
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Hoitsma NM, Whitaker AM, Schaich MA, Smith MR, Fairlamb MS, Freudenthal BD. Structure and function relationships in mammalian DNA polymerases. Cell Mol Life Sci 2020; 77:35-59. [PMID: 31722068 PMCID: PMC7050493 DOI: 10.1007/s00018-019-03368-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 10/11/2019] [Accepted: 10/31/2019] [Indexed: 12/19/2022]
Abstract
DNA polymerases are vital for the synthesis of new DNA strands. Since the discovery of DNA polymerase I in Escherichia coli, a diverse library of mammalian DNA polymerases involved in DNA replication, DNA repair, antibody generation, and cell checkpoint signaling has emerged. While the unique functions of these DNA polymerases are differentiated by their association with accessory factors and/or the presence of distinctive catalytic domains, atomic resolution structures of DNA polymerases in complex with their DNA substrates have revealed mechanistic subtleties that contribute to their specialization. In this review, the structure and function of all 15 mammalian DNA polymerases from families B, Y, X, and A will be reviewed and discussed with special emphasis on the insights gleaned from recently published atomic resolution structures.
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Affiliation(s)
- Nicole M Hoitsma
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS, 66160, USA
| | - Amy M Whitaker
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS, 66160, USA
| | - Matthew A Schaich
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS, 66160, USA
| | - Mallory R Smith
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS, 66160, USA
| | - Max S Fairlamb
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS, 66160, USA
| | - Bret D Freudenthal
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS, 66160, USA.
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11
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Abstract
7,8-Dihydro-8-oxoguanine (oxoG) is the most abundant oxidative DNA lesion with dual coding properties. It forms both Watson–Crick (anti)oxoG:(anti)C and Hoogsteen (syn)oxoG:(anti)A base pairs without a significant distortion of a B-DNA helix. DNA polymerases bypass oxoG but the accuracy of nucleotide incorporation opposite the lesion varies depending on the polymerase-specific interactions with the templating oxoG and incoming nucleotides. High-fidelity replicative DNA polymerases read oxoG as a cognate base for A while treating oxoG:C as a mismatch. The mutagenic effects of oxoG in the cell are alleviated by specific systems for DNA repair and nucleotide pool sanitization, preventing mutagenesis from both direct DNA oxidation and oxodGMP incorporation. DNA translesion synthesis could provide an additional protective mechanism against oxoG mutagenesis in cells. Several human DNA polymerases of the X- and Y-families efficiently and accurately incorporate nucleotides opposite oxoG. In this review, we address the mutagenic potential of oxoG in cells and discuss the structural basis for oxoG bypass by different DNA polymerases and the mechanisms of the recognition of oxoG by DNA glycosylases and dNTP hydrolases.
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12
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Zhou H, Sathyamoorthy B, Stelling A, Xu Y, Xue Y, Pigli YZ, Case DA, Rice PA, Al-Hashimi HM. Characterizing Watson-Crick versus Hoogsteen Base Pairing in a DNA-Protein Complex Using Nuclear Magnetic Resonance and Site-Specifically 13C- and 15N-Labeled DNA. Biochemistry 2019; 58:1963-1974. [PMID: 30950607 DOI: 10.1021/acs.biochem.9b00027] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
A( syn)-T and G( syn)-C+ Hoogsteen base pairs in protein-bound DNA duplexes can be difficult to resolve by X-ray crystallography due to ambiguous electron density and by nuclear magnetic resonance (NMR) spectroscopy due to poor chemical shift dispersion and size limitations with solution-state NMR spectroscopy. Here we describe an NMR strategy for characterizing Hoogsteen base pairs in protein-DNA complexes, which relies on site-specifically incorporating 13C- and 15N-labeled nucleotides into DNA duplexes for unambiguous resonance assignment and to improve spectral resolution. The approach was used to resolve the conformation of an A-T base pair in a crystal structure of an ∼43 kDa complex between a 34 bp duplex DNA and the integration host factor (IHF) protein. In the crystal structure (Protein Data Bank entry 1IHF ), this base pair adopts an unusual Hoogsteen conformation with a distorted sugar backbone that is accommodated by a nearby nick used to aid in crystallization. The NMR chemical shifts and interproton nuclear Overhauser effects indicate that this base pair predominantly adopts a Watson-Crick conformation in the intact DNA-IHF complex under solution conditions. Consistent with these NMR findings, substitution of 7-deazaadenine at this base pair resulted in only a small (∼2-fold) decrease in the IHF-DNA binding affinity. The NMR strategy provides a new approach for resolving crystallographic ambiguity and more generally for studying the structure and dynamics of protein-DNA complexes in solution.
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Affiliation(s)
- Huiqing Zhou
- Department of Biochemistry , Duke University School of Medicine , Durham , North Carolina 27710 , United States
| | - Bharathwaj Sathyamoorthy
- Department of Chemistry , Indian Institute of Science Education and Research Bhopal , Bhopal 462066 , India
| | - Allison Stelling
- Department of Biochemistry , Duke University School of Medicine , Durham , North Carolina 27710 , United States
| | - Yu Xu
- Department of Chemistry , Duke University , Durham , North Carolina 27708 , United States
| | - Yi Xue
- Tsinghua-Peking Center for Life Sciences, School of Life Sciences , Tsinghua University , Beijing 100084 , China
| | - Ying Zhang Pigli
- Biochemistry and Molecular Biology , The University of Chicago , Chicago , Illinois 60637 , United States
| | - David A Case
- Department of Chemistry and Chemical Biology , Rutgers University , Piscataway , New Jersey 08854 , United States
| | - Phoebe A Rice
- Biochemistry and Molecular Biology , The University of Chicago , Chicago , Illinois 60637 , United States
| | - Hashim M Al-Hashimi
- Department of Biochemistry , Duke University School of Medicine , Durham , North Carolina 27710 , United States.,Department of Chemistry , Duke University , Durham , North Carolina 27708 , United States
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13
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Vonk JM, Nieuwenhuis MAE, Dijk FN, Boudier A, Siroux V, Bouzigon E, Probst-Hensch N, Imboden M, Keidel D, Sin D, Bossé Y, Hao K, van den Berge M, Faiz A, Koppelman GH, Postma DS. Novel genes and insights in complete asthma remission: A genome-wide association study on clinical and complete asthma remission. Clin Exp Allergy 2018; 48:1286-1296. [PMID: 29786918 DOI: 10.1111/cea.13181] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Revised: 03/25/2018] [Accepted: 03/29/2018] [Indexed: 12/16/2022]
Abstract
BACKGROUND Asthma is a chronic respiratory disease without a cure, although there exists spontaneous remission. Genome-wide association (GWA) studies have pinpointed genes associated with asthma development, but did not investigate asthma remission. OBJECTIVE We performed a GWA study to develop insights in asthma remission. METHODS Clinical remission (ClinR) was defined by the absence of asthma treatment and wheezing in the last year and asthma attacks in the last 3 years and complete remission (ComR) similarly but additionally with normal lung function and absence of bronchial hyperresponsiveness (BHR). A GWA study on both ClinR and ComR was performed in 790 asthmatics with initial doctor diagnosis of asthma and BHR and long-term follow-up. We assessed replication of the 25 top single nucleotide polymorphisms (SNPs) in 2 independent cohorts (total n = 456), followed by expression quantitative loci (eQTL) analyses of the 4 replicated SNPs in lung tissue and epithelium. RESULTS Of the 790 asthmatics, 178 (23%) had ClinR and 55 ComR (7%) after median follow-up of 15.5 (range 3.3-47.8) years. In ClinR, 1 of the 25 SNPs, rs2740102, replicated in a meta-analysis of the replication cohorts, which was an eQTL for POLI in lung tissue. In ComR, 3 SNPs replicated in a meta-analysis of the replication cohorts. The top-hit, rs6581895, almost reached genome-wide significance (P-value 4.68 × 10-7 ) and was an eQTL for FRS2 and CCT in lung tissue. Rs1420101 was a cis-eQTL in lung tissue for IL1RL1 and IL18R1 and a trans-eQTL for IL13. CONCLUSIONS AND CLINICAL RELEVANCE By defining a strict remission phenotype, we identified 3 SNPs to be associated with complete asthma remission, where 2 SNPs have plausible biological relevance in FRS2, CCT, IL1RL1, IL18R1 and IL13.
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Affiliation(s)
- J M Vonk
- University of Groningen, University Medical Center Groningen, Department of Epidemiology, Groningen, The Netherlands.,University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, The Netherlands
| | - M A E Nieuwenhuis
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, The Netherlands.,University of Groningen, University Medical Center Groningen, Department of Pulmonology, Groningen, The Netherlands
| | - F N Dijk
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, The Netherlands.,University of Groningen, University Medical Center Groningen, Department of Pediatric Pulmonology and Pediatric Allergology, Groningen, The Netherlands
| | - A Boudier
- INSERM, Team of Environmental Epidemiology applied to Reproduction and Respiratory Health, IAB, Grenoble, France
| | - V Siroux
- INSERM, Team of Environmental Epidemiology applied to Reproduction and Respiratory Health, IAB, Grenoble, France.,Team of Environmental Epidemiology applied to Reproduction and Respiratory Health, IAB, Univ. Grenoble Alpes, Grenoble, France.,CHU de Grenoble, Team of Environmental Epidemiology applied to Reproduction and Respiratory Health, IAB, Grenoble, France
| | - E Bouzigon
- UMR-946, Inserm, Paris, France.,Sorbonne Paris Cité, Institut Universitaire d'Hématologie, Université Paris Diderot, Paris, France
| | - N Probst-Hensch
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - M Imboden
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - D Keidel
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - D Sin
- St Paul's Hospital, The University of British Columbia James Hogg Research Laboratory, Vancouver, BC, Canada.,Respiratory Division, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Y Bossé
- Institut Universitaire de Cardiologie et de Pneumologie de Québec, Department of Molecular Medicine, Laval University, Québec, QC, Canada
| | - K Hao
- Merck Research Laboratories, Boston, MA, USA
| | - M van den Berge
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, The Netherlands.,University of Groningen, University Medical Center Groningen, Department of Pulmonology, Groningen, The Netherlands
| | - A Faiz
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, The Netherlands.,University of Groningen, University Medical Center Groningen, Department of Pulmonology, Groningen, The Netherlands
| | - G H Koppelman
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, The Netherlands.,University of Groningen, University Medical Center Groningen, Department of Pediatric Pulmonology and Pediatric Allergology, Groningen, The Netherlands
| | - D S Postma
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, The Netherlands.,University of Groningen, University Medical Center Groningen, Department of Pulmonology, Groningen, The Netherlands
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14
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Miropolskaya N, Petushkov I, Kulbachinskiy A, Makarova AV. Identification of amino acid residues involved in the dRP-lyase activity of human Pol ι. Sci Rep 2017; 7:10194. [PMID: 28860552 PMCID: PMC5579206 DOI: 10.1038/s41598-017-10668-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 08/11/2017] [Indexed: 11/09/2022] Open
Abstract
Besides X-family DNA polymerases (first of all, Pol β) several other human DNA polymerases from Y- and A- families were shown to possess the dRP-lyase activity and could serve as backup polymerases in base excision repair (Pol ι, Rev1, Pol γ and Pol θ). However the exact position of the active sites and the amino acid residues involved in the dRP-lyase activity in Y- and A- family DNA polymerases are not known. Here we carried out functional analysis of fifteen amino acid residues possibly involved in the dRP-lyase activity of human Pol ι. We show that substitutions of residues Q59, K60 and K207 impair the dRP-lyase activity of Pol ι while residues in the HhH motif of the thumb domain are dispensable for this activity. While both K60G and K207A substitutions decrease Schiff-base intermediate formation during dRP group cleavage, the latter substitution also strongly affects the DNA polymerase activity of Pol ι, suggesting that it may impair DNA binding. These data are consistent with an important role of the N-terminal region in the dRP-lyase activity of Pol ι, with possible involvement of residues from the finger domain in the dRP group cleavage.
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Affiliation(s)
- Nataliya Miropolskaya
- Institute of Molecular Genetics, Russian Academy of Sciences, Kurchatov sq. 2, 123182, Moscow, Russia
| | - Ivan Petushkov
- Institute of Molecular Genetics, Russian Academy of Sciences, Kurchatov sq. 2, 123182, Moscow, Russia
| | - Andrey Kulbachinskiy
- Institute of Molecular Genetics, Russian Academy of Sciences, Kurchatov sq. 2, 123182, Moscow, Russia
| | - Alena V Makarova
- Institute of Molecular Genetics, Russian Academy of Sciences, Kurchatov sq. 2, 123182, Moscow, Russia.
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15
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Sathyamoorthy B, Shi H, Zhou H, Xue Y, Rangadurai A, Merriman DK, Al-Hashimi HM. Insights into Watson-Crick/Hoogsteen breathing dynamics and damage repair from the solution structure and dynamic ensemble of DNA duplexes containing m1A. Nucleic Acids Res 2017; 45:5586-5601. [PMID: 28369571 PMCID: PMC5435913 DOI: 10.1093/nar/gkx186] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 03/06/2017] [Accepted: 03/17/2017] [Indexed: 12/18/2022] Open
Abstract
In the canonical DNA double helix, Watson-Crick (WC) base pairs (bps) exist in dynamic equilibrium with sparsely populated (∼0.02-0.4%) and short-lived (lifetimes ∼0.2-2.5 ms) Hoogsteen (HG) bps. To gain insights into transient HG bps, we used solution-state nuclear magnetic resonance spectroscopy, including measurements of residual dipolar couplings and molecular dynamics simulations, to examine how a single HG bp trapped using the N1-methylated adenine (m1A) lesion affects the structural and dynamic properties of two duplexes. The solution structure and dynamic ensembles of the duplexes reveals that in both cases, m1A forms a m1A•T HG bp, which is accompanied by local and global structural and dynamic perturbations in the double helix. These include a bias toward the BI backbone conformation; sugar repuckering, major-groove directed kinking (∼9°); and local melting of neighboring WC bps. These results provide atomic insights into WC/HG breathing dynamics in unmodified DNA duplexes as well as identify structural and dynamic signatures that could play roles in m1A recognition and repair.
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Affiliation(s)
- Bharathwaj Sathyamoorthy
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Chemistry, Duke University, Durham, NC 27710, USA
| | - Honglue Shi
- Department of Chemistry, Duke University, Durham, NC 27710, USA
| | - Huiqing Zhou
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
| | - Yi Xue
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Chemistry, Duke University, Durham, NC 27710, USA
| | - Atul Rangadurai
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
| | | | - Hashim M. Al-Hashimi
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Chemistry, Duke University, Durham, NC 27710, USA
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16
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Kazachenko KY, Miropolskaya NA, Gening LV, Tarantul VZ, Makarova AV. Alternative splicing at exon 2 results in the loss of the catalytic activity of mouse DNA polymerase iota in vitro. DNA Repair (Amst) 2017; 50:77-82. [DOI: 10.1016/j.dnarep.2017.01.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 12/27/2016] [Accepted: 01/03/2017] [Indexed: 12/16/2022]
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17
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Ucisik MN, Hammes-Schiffer S. Effects of Active Site Mutations on Specificity of Nucleobase Binding in Human DNA Polymerase η. J Phys Chem B 2016; 121:3667-3675. [PMID: 28423907 PMCID: PMC5402696 DOI: 10.1021/acs.jpcb.6b09973] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
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Human DNA polymerase η (Pol
η) plays a vital role in
protection against skin cancer caused by damage from ultraviolet light.
This enzyme rescues stalled replication forks at cyclobutane thymine–thymine
dimers (TTDs) by inserting nucleotides opposite these DNA lesions.
Residue R61 is conserved in the Pol η enzymes across species,
but the corresponding residue, as well as its neighbor S62, is different
in other Y-family polymerases, Pol ι and Pol κ. Herein,
R61 and S62 are mutated to their Pol ι and Pol κ counterparts.
Relative binding free energies of dATP to mutant Pol η•DNA
complexes with and without a TTD were calculated using thermodynamic
integration. The binding free energies of dATP to the Pol η•DNA
complex with and without a TTD are more similar for all of these mutants
than for wild-type Pol η, suggesting that these mutations decrease
the ability of this enzyme to distinguish between a TTD lesion and
undamaged DNA. Molecular dynamics simulations of the mutant systems
provide insights into the molecular level basis for the changes in
relative binding free energies. The simulations identified differences
in hydrogen-bonding, cation−π, and π–π
interactions of the side chains with the dATP and the TTD or thymine–thymine
(TT) motif. The simulations also revealed that R61 and Q38 act as
a clamp to position the dATP and the TTD or TT and that the mutations
impact the balance among the interactions related to this clamp. Overall,
these calculations suggest that R61 and S62 play key roles in the
specificity and effectiveness of Pol η for bypassing TTD lesions
during DNA replication. Understanding the basis for this specificity
is important for designing drugs aimed at cancer treatment.
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Affiliation(s)
- Melek N Ucisik
- Department of Chemistry, University of Illinois at Urbana-Champaign , 600 South Mathews Avenue, Urbana, Illinois 61801-3364, United States
| | - Sharon Hammes-Schiffer
- Department of Chemistry, University of Illinois at Urbana-Champaign , 600 South Mathews Avenue, Urbana, Illinois 61801-3364, United States
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18
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Belousova EA, Lavrik OI. Repair of Clustered Damage and DNA Polymerase Iota. BIOCHEMISTRY (MOSCOW) 2016; 80:1010-8. [PMID: 26547069 DOI: 10.1134/s0006297915080064] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Multiple DNA lesions occurring within one or two turns of the DNA helix known as clustered damage are a source of double-stranded DNA breaks, which represent a serious threat to the cells. Repair of clustered lesions is accomplished in several steps. If a clustered lesion contains oxidized bases, an individual DNA lesion is repaired by the base excision repair (BER) mechanism involving a specialized DNA polymerase after excising DNA damage. Here, we investigated DNA synthesis catalyzed by DNA polymerase iota using damaged DNA templates. Two types of DNA substrates were used as model DNAs: partial DNA duplexes containing breaks of different length, and DNA duplexes containing 5-formyluracil (5-foU) and uracil as a precursor of apurinic/apyrimidinic sites (AP) in opposite DNA strands. For the first time, we showed that DNA polymerase iota is able to catalyze DNA synthesis using partial DNA duplexes having breaks of different length as substrates. In addition, we found that DNA polymerase iota could catalyze DNA synthesis during repair of clustered damage via the BER system by using both undamaged and 5-foU-containing templates. We found that hPCNA (human proliferating cell nuclear antigen) increased efficacy of DNA synthesis catalyzed by DNA polymerase iota.
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Affiliation(s)
- E A Belousova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia.
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19
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Zhou H, Kimsey IJ, Nikolova EN, Sathyamoorthy B, Grazioli G, McSally J, Bai T, Wunderlich CH, Kreutz C, Andricioaei I, Al-Hashimi HM. m(1)A and m(1)G disrupt A-RNA structure through the intrinsic instability of Hoogsteen base pairs. Nat Struct Mol Biol 2016; 23:803-10. [PMID: 27478929 PMCID: PMC5016226 DOI: 10.1038/nsmb.3270] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Accepted: 07/05/2016] [Indexed: 12/13/2022]
Abstract
The B-DNA double helix can dynamically accommodate G-C and A-T base pairs in either Watson-Crick or Hoogsteen configurations. Here, we show that G-C(+) (in which + indicates protonation) and A-U Hoogsteen base pairs are strongly disfavored in A-RNA. As a result,N(1)-methyladenosine and N(1)-methylguanosine, which occur in DNA as a form of alkylation damage and in RNA as post-transcriptional modifications, have dramatically different consequences. Whereas they create G-C(+) and A-T Hoogsteen base pairs in duplex DNA, thereby maintaining the structural integrity of the double helix, they block base-pairing and induce local duplex melting in RNA. These observations provide a mechanism for disrupting RNA structure through post-transcriptional modifications. The different propensities to form Hoogsteen base pairs in B-DNA and A-RNA may help cells meet the opposing requirements of maintaining genome stability, on the one hand, and of dynamically modulating the structure of the epitranscriptome, on the other.
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Affiliation(s)
- Huiqing Zhou
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina USA
| | - Isaac J. Kimsey
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina USA
| | - Evgenia N. Nikolova
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, California USA
| | | | - Gianmarc Grazioli
- Department of Chemistry, University of California Irvine, Irvine, California USA
| | - James McSally
- Department of Chemistry, University of California Irvine, Irvine, California USA
| | - Tianyu Bai
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina USA
| | | | - Christoph Kreutz
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck Austria
| | - Ioan Andricioaei
- Department of Chemistry, University of California Irvine, Irvine, California USA
| | - Hashim M. Al-Hashimi
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina USA
- Department of Chemistry, Duke University, Durham, North Carolina USA
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20
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DNA damage tolerance pathway involving DNA polymerase ι and the tumor suppressor p53 regulates DNA replication fork progression. Proc Natl Acad Sci U S A 2016; 113:E4311-9. [PMID: 27407148 DOI: 10.1073/pnas.1605828113] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
DNA damage tolerance facilitates the progression of replication forks that have encountered obstacles on the template strands. It involves either translesion DNA synthesis initiated by proliferating cell nuclear antigen monoubiquitination or less well-characterized fork reversal and template switch mechanisms. Herein, we characterize a novel tolerance pathway requiring the tumor suppressor p53, the translesion polymerase ι (POLι), the ubiquitin ligase Rad5-related helicase-like transcription factor (HLTF), and the SWI/SNF catalytic subunit (SNF2) translocase zinc finger ran-binding domain containing 3 (ZRANB3). This novel p53 activity is lost in the exonuclease-deficient but transcriptionally active p53(H115N) mutant. Wild-type p53, but not p53(H115N), associates with POLι in vivo. Strikingly, the concerted action of p53 and POLι decelerates nascent DNA elongation and promotes HLTF/ZRANB3-dependent recombination during unperturbed DNA replication. Particularly after cross-linker-induced replication stress, p53 and POLι also act together to promote meiotic recombination enzyme 11 (MRE11)-dependent accumulation of (phospho-)replication protein A (RPA)-coated ssDNA. These results implicate a direct role of p53 in the processing of replication forks encountering obstacles on the template strand. Our findings define an unprecedented function of p53 and POLι in the DNA damage response to endogenous or exogenous replication stress.
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21
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Nikolova EN, Zhou H, Gottardo FL, Alvey HS, Kimsey IJ, Al-Hashimi HM. A historical account of Hoogsteen base-pairs in duplex DNA. Biopolymers 2016; 99:955-68. [PMID: 23818176 DOI: 10.1002/bip.22334] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2013] [Accepted: 06/17/2013] [Indexed: 11/05/2022]
Abstract
In 1957, a unique pattern of hydrogen bonding between N3 and O4 on uracil and N7 and N6 on adenine was proposed to explain how poly(rU) strands can associate with poly(rA)-poly(rU) duplexes to form triplexes. Two years later, Karst Hoogsteen visualized such a noncanonical A-T base-pair through X-ray analysis of co-crystals containing 9-methyladenine and 1-methylthymine. Subsequent X-ray analyses of guanine and cytosine derivatives yielded the expected Watson-Crick base-pairing, but those of adenine and thymine (or uridine) did not yield Watson-Crick base-pairs, instead favoring "Hoogsteen" base-pairing. More than two decades ensued without experimental "proof" for A-T Watson-Crick base-pairs, while Hoogsteen base-pairs continued to surface in AT-rich sequences, closing base-pairs of apical loops, in structures of DNA bound to antibiotics and proteins, damaged and chemically modified DNA, and in polymerases that replicate DNA via Hoogsteen pairing. Recently, NMR studies have shown that base-pairs in duplex DNA exist as a dynamic equilibrium between Watson-Crick and Hoogsteen forms. There is now little doubt that Hoogsteen base-pairs exist in significant abundance in genomic DNA, where they can expand the structural and functional versatility of duplex DNA beyond that which can be achieved based only on Watson-Crick base-pairing. Here, we provide a historical account of the discovery and characterization of Hoogsteen base-pairs, hoping that this will inform future studies exploring the occurrence and functional importance of these alternative base-pairs.
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Affiliation(s)
- Evgenia N Nikolova
- Department of Chemistry & Biophysics, The University of Michigan, 930 North University Avenue, Ann Arbor, MI, 48109-1055; Integrative Structural & Computational Biology Department, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037
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22
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Zhou H, Hintze BJ, Kimsey IJ, Sathyamoorthy B, Yang S, Richardson JS, Al-Hashimi HM. New insights into Hoogsteen base pairs in DNA duplexes from a structure-based survey. Nucleic Acids Res 2015; 43:3420-33. [PMID: 25813047 PMCID: PMC4402545 DOI: 10.1093/nar/gkv241] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Accepted: 03/01/2015] [Indexed: 11/14/2022] Open
Abstract
Hoogsteen (HG) base pairs (bps) provide an alternative pairing geometry to Watson-Crick (WC) bps and can play unique functional roles in duplex DNA. Here, we use structural features unique to HG bps (syn purine base, HG hydrogen bonds and constricted C1'-C1' distance across the bp) to search for HG bps in X-ray structures of DNA duplexes in the Protein Data Bank. The survey identifies 106 A•T and 34 G•C HG bps in DNA duplexes, many of which are undocumented in the literature. It also uncovers HG-like bps with syn purines lacking HG hydrogen bonds or constricted C1'-C1' distances that are analogous to conformations that have been proposed to populate the WC-to-HG transition pathway. The survey reveals HG preferences similar to those observed for transient HG bps in solution by nuclear magnetic resonance, including stronger preferences for A•T versus G•C bps, TA versus GG steps, and also suggests enrichment at terminal ends with a preference for 5'-purine. HG bps induce small local perturbations in neighboring bps and, surprisingly, a small but significant degree of DNA bending (∼14°) directed toward the major groove. The survey provides insights into the preferences and structural consequences of HG bps in duplex DNA.
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Affiliation(s)
- Huiqing Zhou
- Department of Biochemistry, Duke University, Durham, NC 27710, USA
| | - Bradley J Hintze
- Department of Biochemistry, Duke University, Durham, NC 27710, USA
| | - Isaac J Kimsey
- Department of Biochemistry, Duke University, Durham, NC 27710, USA
| | | | - Shan Yang
- Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
| | | | - Hashim M Al-Hashimi
- Department of Biochemistry, Duke University, Durham, NC 27710, USA Department of Chemistry, Duke University, Durham, NC 27708, USA
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23
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Nikolova EN, Stull F, Al-Hashimi HM. Guanine to inosine substitution leads to large increases in the population of a transient G·C Hoogsteen base pair. Biochemistry 2014; 53:7145-7. [PMID: 25339065 PMCID: PMC4245982 DOI: 10.1021/bi5011909] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
![]()
We
recently showed that Watson–Crick base pairs in canonical
duplex DNA exist in dynamic equilibrium with G(syn)·C+ and A(syn)·T Hoogsteen
base pairs that have minute populations of ∼1%. Here, using
nuclear magnetic resonance R1ρ relaxation
dispersion, we show that substitution of guanine with the naturally
occurring base inosine results in an ∼17-fold increase in the
population of transient Hoogsteen base pairs, which can be rationalized
by the loss of a Watson–Crick hydrogen bond. These results
provide further support for transient Hoogsteen base pairs and demonstrate
that their population can increase significantly upon damage or chemical
modification of the base.
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Affiliation(s)
- Evgenia N Nikolova
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute , La Jolla, California 92037, United States
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24
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Alvey HS, Gottardo FL, Nikolova EN, Al-Hashimi HM. Widespread transient Hoogsteen base pairs in canonical duplex DNA with variable energetics. Nat Commun 2014; 5:4786. [PMID: 25185517 DOI: 10.1038/ncomms5786] [Citation(s) in RCA: 96] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Accepted: 07/23/2014] [Indexed: 12/21/2022] Open
Abstract
Hoogsteen (HG) base pairing involves a 180° rotation of the purine base relative to Watson-Crick (WC) base pairing within DNA duplexes, creating alternative DNA conformations that can play roles in recognition, damage induction and replication. Here, using nuclear magnetic resonance R1ρ relaxation dispersion, we show that transient HG base pairs occur across more diverse sequence and positional contexts than previously anticipated. We observe sequence-specific variations in HG base pair energetic stabilities that are comparable with variations in WC base pair stability, with HG base pairs being more abundant for energetically less favourable WC base pairs. Our results suggest that the variations in HG stabilities and rates of formation are dominated by variations in WC base pair stability, suggesting a late transition state for the WC-to-HG conformational switch. The occurrence of sequence and position-dependent HG base pairs provide a new potential mechanism for achieving sequence-dependent DNA transactions.
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Affiliation(s)
- Heidi S Alvey
- Department of Chemistry and Biophysics, University of Michigan, 930 N. University Avenue, Ann Arbor, Michigan 48109, USA
| | - Federico L Gottardo
- Department of Chemistry and Biophysics, University of Michigan, 930 N. University Avenue, Ann Arbor, Michigan 48109, USA
| | - Evgenia N Nikolova
- Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
| | - Hashim M Al-Hashimi
- Department of Biochemistry and Chemistry, Duke University School of Medicine, 307 Research Dr, Nanaline H. Duke Building, Durham, North Carolina 27710, USA
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25
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Makarova AV, Ignatov A, Miropolskaya N, Kulbachinskiy A. Roles of the active site residues and metal cofactors in noncanonical base-pairing during catalysis by human DNA polymerase iota. DNA Repair (Amst) 2014; 22:67-76. [PMID: 25108837 DOI: 10.1016/j.dnarep.2014.07.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Revised: 07/12/2014] [Accepted: 07/14/2014] [Indexed: 12/15/2022]
Abstract
Human DNA polymerase iota (Pol ι) is a Y-family polymerase that can bypass various DNA lesions but possesses very low fidelity of DNA synthesis in vitro. Structural analysis of Pol ι revealed a narrow active site that promotes noncanonical base-pairing during catalysis. To better understand the structure-function relationships in the active site of Pol ι we investigated substitutions of individual amino acid residues in its fingers domain that contact either the templating or the incoming nucleotide. Two of the substitutions, Y39A and Q59A, significantly decreased the catalytic activity but improved the fidelity of Pol ι. Surprisingly, in the presence of Mn(2+) ions, the wild-type and mutant Pol ι variants efficiently incorporated nucleotides opposite template purines containing modifications that disrupted either Hoogsteen or Watson-Crick base-pairing, suggesting that Pol ι may use various types of interactions during nucleotide addition. In contrast, in Mg(2+) reactions, wild-type Pol ι was dependent on Hoogsteen base-pairing, the Y39A mutant was essentially inactive, and the Q59A mutant promoted Watson-Crick interactions with template purines. The results suggest that Pol ι utilizes distinct mechanisms of nucleotide incorporation depending on the metal cofactor and reveal important roles of specific residues from the fingers domain in base-pairing and catalysis.
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Affiliation(s)
- Alena V Makarova
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow 123182, Russia.
| | - Artem Ignatov
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow 123182, Russia
| | | | - Andrey Kulbachinskiy
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow 123182, Russia.
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Kimsey I, Al-Hashimi HM. Increasing occurrences and functional roles for high energy purine-pyrimidine base-pairs in nucleic acids. Curr Opin Struct Biol 2014; 24:72-80. [PMID: 24721455 DOI: 10.1016/j.sbi.2013.12.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Accepted: 12/13/2013] [Indexed: 10/25/2022]
Abstract
There are a growing number of studies reporting the observation of purine-pyrimidine base-pairs that are seldom observed in unmodified nucleic acids because they entail the loss of energetically favorable interactions or require energetically costly base ionization or tautomerization. These high energy purine-pyrimidine base-pairs include G•C(+) and A•T Hoogsteen base-pairs, which entail ∼180° rotation of the purine base in a Watson-Crick base-pair, protonation of cytosine N3, and constriction of the C1'-C1' distance by ∼2.5Å. Other high energy pure-pyrimidine base-pairs include G•T, G•U, and A•C mispairs that adopt Watson-Crick like geometry through either base ionization or tautomerization. Although difficult to detect and characterize using biophysical methods, high energy purine-pyrimidine base-pairs appear to be more common than once thought. They further expand the structural and functional diversity of canonical and non-canonical nucleic acid base-pairs.
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Affiliation(s)
- Isaac Kimsey
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, United States
| | - Hashim M Al-Hashimi
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, United States.
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