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Abdelmageed M, Palanisamy P, Vernail V, Silberman Y, Paul S, Paul A. An altered cell-specific subcellular distribution of translesion synthesis DNA polymerase kappa (POLK) in aging neurons. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.09.27.559771. [PMID: 39026788 PMCID: PMC11257472 DOI: 10.1101/2023.09.27.559771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Genomic stability is critical for cellular function, however, in the central nervous system highly metabolically active differentiated neurons are challenged to maintain their genome over the organismal lifespan without replication. DNA damage in neurons increases with chronological age and accelerates in neurodegenerative disorders, resulting in cellular and systemic dysregulation. Distinct DNA damage response strategies have evolved with a host of polymerases. The Y-family translesion synthesis (TLS) polymerases are well known for bypassing and repairing damaged DNA in dividing cells. However, their expression, dynamics, and role if any, in enduring postmitotic differentiated neurons of the brain are completely unknown. We show through systematic longitudinal studies for the first time that DNA polymerase kappa (POLK), a member of the Y-family polymerases, is highly expressed in neurons. With chronological age, there is a progressive and significant reduction of nuclear POLK with a concomitant accumulation in the cytoplasm that is predictive of brain tissue age. The reduction of nuclear POLK in old brains is congruent with an increase in DNA damage markers. The nuclear POLK colocalizes with damaged sites and DNA repair proteins. The cytoplasmic POLK accumulates with stress granules and endo/lysosomal markers. Nuclear POLK expression is significantly higher in GABAergic interneurons compared to excitatory pyramidal neurons and lowest in non-neurons, possibly reflective of the inherent biological differences such as firing rates and neuronal activity. Interneurons associated with microglia have significantly higher levels of cytoplasmic POLK in old age. Finally, we show that neuronal activity itself can lead to an increase in nuclear POLK levels and a reduction of the cytoplasmic fraction. Our findings open a new avenue in understanding how different classes of postmitotic neurons deploy TLS polymerase(s) to maintain their genomic integrity over time, which will help design strategies for longevity, healthspan, and prevention of neurodegeneration.
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Vassel FM, Laverty DJ, Bian K, Piett CG, Hemann MT, Walker GC, Nagel ZD. REV7 Monomer Is Unable to Participate in Double Strand Break Repair and Translesion Synthesis but Suppresses Mitotic Errors. Int J Mol Sci 2023; 24:15799. [PMID: 37958783 PMCID: PMC10649693 DOI: 10.3390/ijms242115799] [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: 09/02/2023] [Revised: 10/19/2023] [Accepted: 10/24/2023] [Indexed: 11/15/2023] Open
Abstract
Rev7 is a regulatory protein with roles in translesion synthesis (TLS), double strand break (DSB) repair, replication fork protection, and cell cycle regulation. Rev7 forms a homodimer in vitro using its HORMA (Hop, Rev7, Mad2) domain; however, the functional importance of Rev7 dimerization has been incompletely understood. We analyzed the functional properties of cells expressing either wild-type mouse Rev7 or Rev7K44A/R124A/A135D, a mutant that cannot dimerize. The expression of wild-type Rev7, but not the mutant, rescued the sensitivity of Rev7-/- cells to X-rays and several alkylating agents and reversed the olaparib resistance phenotype of Rev7-/- cells. Using a novel fluorescent host-cell reactivation assay, we found that Rev7K44A/R124A/A135D is unable to promote gap-filling TLS opposite an abasic site analog. The Rev7 dimerization interface is also required for shieldin function, as both Rev7-/- cells and Rev7-/- cells expressing Rev7K44A/R124A/A135D exhibit decreased proficiency in rejoining some types of double strand breaks, as well as increased homologous recombination. Interestingly, Rev7K44A/R124A/A135D retains some function in cell cycle regulation, as it maintains an interaction with Ras-related nuclear protein (Ran) and partially rescues the formation of micronuclei. The mutant Rev7 also rescues the G2/M accumulation observed in Rev7-/- cells but does not affect progression through mitosis following nocodazole release. We conclude that while Rev7 dimerization is required for its roles in TLS, DSB repair, and regulation of the anaphase promoting complex, dimerization is at least partially dispensable for promoting mitotic spindle assembly through its interaction with Ran.
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Affiliation(s)
- Faye M. Vassel
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; (F.M.V.)
| | - Daniel J. Laverty
- Department of Environmental Health, Harvard TH Chan School of Public Health, Boston, MA 02115, USA
| | - Ke Bian
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; (F.M.V.)
| | - Cortt G. Piett
- Department of Environmental Health, Harvard TH Chan School of Public Health, Boston, MA 02115, USA
| | - Michael T. Hemann
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; (F.M.V.)
| | - Graham C. Walker
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; (F.M.V.)
| | - Zachary D. Nagel
- Department of Environmental Health, Harvard TH Chan School of Public Health, Boston, MA 02115, USA
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3
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Deshmukh PU, Lad SB, Sudarsan A, Sudhakar S, Aggarwal T, Mandal S, Bagale SS, Kondabagil K, Pradeepkumar PI. Human Translesion Synthesis Polymerases polκ and polη Perform Error-Free Replication across N2-dG Methyleugenol and Estragole DNA Adducts. Biochemistry 2023; 62:2391-2406. [PMID: 37486230 DOI: 10.1021/acs.biochem.2c00663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/25/2023]
Abstract
The secondary metabolites of polypropanoids, methyleugenol (MEG), and estragole (EG), found in many herbs and spices, are commonly used as food flavoring agents and as ingredients in cosmetics. MEG and EG have been reported to cause hepatocarcinogenicity in rodents, human livers, and lung cells. The formation of N2-dG and N6-dA DNA adducts is primarily attributed to the carcinogenicity of these compounds. Therefore, these compounds have been classified as "possible human carcinogens" by the International Agency for Research on Cancer and "reasonably anticipated to be a human carcinogen" by the National Toxicology Program. Herein, we report the synthesis of the N2-MEG-dG and N2-EG-dG modified oligonucleotides to study the mutagenicity of these DNA adducts. Our studies show that N2-MEG-dG and N2-EG-dG could be bypassed by human translesion synthesis (TLS) polymerases hpolκ and hpolη in an error-free manner. The steady-state kinetics of dCTP incorporation by hpolκ across N2-MEG-dG and N2-EG-dG adducts show that the catalytic efficiencies (kcat/Km) were ∼2.5- and ∼4.4-fold higher, respectively, compared to the unmodified dG template. A full-length primer extension assay demonstrates that hpolκ exhibits better catalytic efficiency than hpolη. Molecular modeling and dynamics studies capturing pre-insertion, insertion, and post-insertion steps reveal the structural features associated with the efficient bypass of the N2-MEG-dG adduct by hpolκ and indicate the reorientation of the adduct in the active site allowing the successful insertion of the incoming nucleotide. Together, these results suggest that though hpolκ and hpolη perform error-free TLS across MEG and EG during DNA replication, the observed carcinogenicity of these adducts could be attributed to the involvement of other low fidelity polymerases.
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Affiliation(s)
- Priyanka U Deshmukh
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Shailesh B Lad
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Akhil Sudarsan
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Sruthi Sudhakar
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Tanvi Aggarwal
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Soumyadeep Mandal
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | | | - Kiran Kondabagil
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - P I Pradeepkumar
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
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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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Ishii Y, Takasu S, Grúz P, Masumura K, Ogawa K, Nohmi T, Umemura T. The role of DNA polymerase ζ in benzo[a]pyrene-induced mutagenesis in the mouse lung. Mutagenesis 2021; 36:155-164. [PMID: 33544859 DOI: 10.1093/mutage/geab007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 02/02/2021] [Indexed: 11/12/2022] Open
Abstract
DNA polymerase zeta (Polζ) is a heterotetramer composed of the catalytic subunit Rev3l, Rev7 and two subunits of Polδ (PolD2/Pol31 and PolD3/Pol32), and this polymerase exerts translesion DNA synthesis (TLS) in yeast. Because Rev3l knockout results in embryonic lethality in mice, the functions of Polζ need further investigation in vivo. Then, we noted the two facts that substitution of leucine 979 of yeast Rev3l with methionine reduces Polζ replication fidelity and that reporter gene transgenic rodents are able to provide the detailed mutation status. Here, we established gpt delta mouse knocked in the constructed gene encoding methionine instead of leucine at residue 2610 of Rev3l (Rev3l L2610M gpt delta mice), to clarify the role of Polζ in TLS of chemical-induced bulky DNA adducts in vivo. Eight-week-old gpt delta mice and Rev3l L2610M gpt delta mice were treated with benzo[a]pyrene (BaP) at 0, 40, 80, or 160 mg/kg via single intraperitoneal injection. At necropsy 31 days after treatment, lungs were collected for reporter gene mutation assays. Although the gpt mutant frequency was significantly increased by BaP in both mouse genotypes, it was three times higher in Rev3l L2610M gpt delta than gpt delta mice after treatment with 160 mg/kg BaP. The frequencies of G:C base substitutions and characteristic complex mutations were significantly increased in Rev3l L2610M gpt delta mice compared with gpt delta mice. The BaP dose-response relationship suggested that Polζ plays a central role in TLS when protective mechanisms against BaP mutagenesis, such as error-free TLS, are saturated. Overall, Polζ may incorporate incorrect nucleotides at the sites opposite to BaP-modified guanines and extend short DNA sequences from the resultant terminal mismatches only when DNA is heavily damaged.
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Affiliation(s)
- Yuji Ishii
- Division of Pathology, National Institute of Health Sciences, Tonomachi, Kawasaki-shi, Kawasaki-ku, Kanagawa, Japan
| | - Shinji Takasu
- Division of Pathology, National Institute of Health Sciences, Tonomachi, Kawasaki-shi, Kawasaki-ku, Kanagawa, Japan
| | - Petr Grúz
- Division of Genetics and Mutagenesis, National Institute of Health Sciences, Tonomachi, Kawasaki-shi, Kawasaki-ku, Kanagawa, Japan
| | - Kenichi Masumura
- Division of Genetics and Mutagenesis, National Institute of Health Sciences, Tonomachi, Kawasaki-shi, Kawasaki-ku, Kanagawa, Japan
| | - Kumiko Ogawa
- Division of Pathology, National Institute of Health Sciences, Tonomachi, Kawasaki-shi, Kawasaki-ku, Kanagawa, Japan
| | - Takehiko Nohmi
- Division of Pathology, National Institute of Health Sciences, Tonomachi, Kawasaki-shi, Kawasaki-ku, Kanagawa, Japan
| | - Takashi Umemura
- Division of Pathology, National Institute of Health Sciences, Tonomachi, Kawasaki-shi, Kawasaki-ku, Kanagawa, Japan
- Faculty of Animal Health Technology, Yamazaki University of Animal Health Technology, Minami-osawa, Hachihoji, Tokyo, Japan
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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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Feher KM, Kolbanovskiy A, Durandin A, Shim Y, Min JH, Lee YC, Shafirovich V, Mu H, Broyde S, Geacintov NE. The DNA damage-sensing NER repair factor XPC-RAD23B does not recognize bulky DNA lesions with a missing nucleotide opposite the lesion. DNA Repair (Amst) 2020; 96:102985. [PMID: 33035795 PMCID: PMC8423485 DOI: 10.1016/j.dnarep.2020.102985] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 08/27/2020] [Accepted: 09/21/2020] [Indexed: 11/23/2022]
Abstract
The Nucleotide Excision Repair (NER) mechanism removes a wide spectrum of structurally different lesions that critically depend on the binding of the DNA damage sensing NER factor XPC-RAD23B (XPC) to the lesions. The bulky mutagenic benzo[a]pyrene diol epoxide metabolite-derived cis- and trans-B[a]P-dG lesions (G*) adopt base-displaced intercalative (cis) or minor groove (trans) conformations in fully paired DNA duplexes with the canonical C opposite G* (G*:C duplexes). While XPC has a high affinity for binding to these DNA lesions in fully complementary double-stranded DNA, we show here that deleting only the C in the complementary strand opposite the lesion G* embedded in 50-mer duplexes, fully abrogates XPC binding. Accurate values of XPC dissociation constants (KD) were determined by employing an excess of unmodified DNA as a competitor; this approach eliminated the binding and accumulation of multiple XPC molecules to the same DNA duplexes, a phenomenon that prevented the accurate estimation of XPC binding affinities in previous studies. Surprisingly, a detailed comparison of XPC dissociation constants KD of unmodified and lesion-containing G*:Del complexes, showed that the KD values were -2.5-3.6 times greater in the case of G*:Del than in the unmodified G:Del and fully base-paired G:C duplexes. The origins of this unexpected XPC lesion avoidance effect is attributed to the intercalation of the bulky, planar B[a]P aromatic ring system between adjacent DNA bases that thermodynamically stabilize the G*:Del duplexes. The strong lesion-base stacking interactions associated with the absence of the partner base, prevent the DNA structural distortions needed for the binding of the BHD2 and BHD3 β-hairpins of XPC to the deletion duplexes, thus accounting for the loss of XPC binding and the known NER-resistance of G*:Del duplexes.
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Affiliation(s)
- Katie M Feher
- Chemistry Department, New York University, 100 Washington East, New York, NY, 10003-5180, USA
| | - Alexander Kolbanovskiy
- Chemistry Department, New York University, 100 Washington East, New York, NY, 10003-5180, USA
| | - Alexander Durandin
- Chemistry Department, New York University, 100 Washington East, New York, NY, 10003-5180, USA
| | - Yoonjung Shim
- Department of Chemistry & Biochemistry, Baylor University, Waco, TX, 76706, USA
| | - Jung-Hyun Min
- Department of Chemistry & Biochemistry, Baylor University, Waco, TX, 76706, USA
| | - Yuan Cho Lee
- Chemistry Department, New York University, 100 Washington East, New York, NY, 10003-5180, USA
| | - Vladimir Shafirovich
- Chemistry Department, New York University, 100 Washington East, New York, NY, 10003-5180, USA
| | - Hong Mu
- Department of Biology, New York University, 100 Washington Square East, New York, N.Y., 10003-5180, USA
| | - Suse Broyde
- Department of Biology, New York University, 100 Washington Square East, New York, N.Y., 10003-5180, USA
| | - Nicholas E Geacintov
- Chemistry Department, New York University, 100 Washington East, New York, NY, 10003-5180, USA.
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8
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Ghodke PP, Pradeepkumar PI. Site‐Specific
N
2
‐dG DNA Adducts: Formation, Synthesis, and TLS Polymerase‐Mediated Bypass. European J Org Chem 2020. [DOI: 10.1002/ejoc.202000298] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Pratibha P. Ghodke
- Department of Biochemistry Vanderbilt University School of Medicine 638B Robinson Research Building 2200 Pierce Avenue 37323‐0146 Nashville Tennessee United States
- Department of Chemistry Indian Institute of Technology Bombay 400076 Mumbai Powai India
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9
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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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10
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Feng X, Liu X, Xu R, Zhao R, Feng W, Liao J, Han W, She Q. A Unique B-Family DNA Polymerase Facilitating Error-Prone DNA Damage Tolerance in Crenarchaeota. Front Microbiol 2020; 11:1585. [PMID: 32793138 PMCID: PMC7390963 DOI: 10.3389/fmicb.2020.01585] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Accepted: 06/17/2020] [Indexed: 12/20/2022] Open
Abstract
Sulfolobus islandicus codes for four DNA polymerases: three are of the B-family (Dpo1, Dpo2, and Dpo3), and one is of the Y-family (Dpo4). Western analysis revealed that among the four polymerases, only Dpo2 exhibited DNA damage-inducible expression. To investigate how these DNA polymerases could contribute to DNA damage tolerance in S. islandicus, we conducted genetic analysis of their encoding genes in this archaeon. Plasmid-borne gene expression revealed that Dpo2 increases cell survival upon DNA damage at the expense of mutagenesis. Gene deletion studies showed although dpo1 is essential, the remaining three genes are dispensable. Furthermore, although Dpo4 functions in housekeeping translesion DNA synthesis (TLS), Dpo2, a B-family DNA polymerase once predicted to be inactive, functions as a damage-inducible TLS enzyme solely responsible for targeted mutagenesis, facilitating GC to AT/TA conversions in the process. Together, our data indicate that Dpo2 is the main DNA polymerase responsible for DNA damage tolerance and is the primary source of targeted mutagenesis. Given that crenarchaea encoding a Dpo2 also have a low-GC composition genome, the Dpo2-dependent DNA repair pathway may be conserved in this archaeal lineage.
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Affiliation(s)
- Xu Feng
- CRISPR and Archaea Biology Research Center, Microbial Technology Institute and State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Xiaotong Liu
- CRISPR and Archaea Biology Research Center, Microbial Technology Institute and State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Ruyi Xu
- CRISPR and Archaea Biology Research Center, Microbial Technology Institute and State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Ruiliang Zhao
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Wenqian Feng
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jianglan Liao
- CRISPR and Archaea Biology Research Center, Microbial Technology Institute and State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Wenyuan Han
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Qunxin She
- CRISPR and Archaea Biology Research Center, Microbial Technology Institute and State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
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11
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Zhang H. Mechanisms of mutagenesis induced by DNA lesions: multiple factors affect mutations in translesion DNA synthesis. Crit Rev Biochem Mol Biol 2020; 55:219-251. [PMID: 32448001 DOI: 10.1080/10409238.2020.1768205] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Environmental mutagens lead to mutagenesis. However, the mechanisms are very complicated and not fully understood. Environmental mutagens produce various DNA lesions, including base-damaged or sugar-modified DNA lesions, as well as epigenetically modified DNA. DNA polymerases produce mutation spectra in translesion DNA synthesis (TLS) through misincorporation of incorrect nucleotides, frameshift deletions, blockage of DNA replication, imbalance of leading- and lagging-strand DNA synthesis, and genome instability. Motif or subunit in DNA polymerases further affects the mutations in TLS. Moreover, protein interactions and accessory proteins in DNA replisome also alter mutations in TLS, demonstrated by several representative DNA replisomes. Finally, in cells, multiple DNA polymerases or cellular proteins collaborate in TLS and reduce in vivo mutagenesis. Summaries and perspectives were listed. This review shows mechanisms of mutagenesis induced by DNA lesions and the effects of multiple factors on mutations in TLS in vitro and in vivo.
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Affiliation(s)
- Huidong Zhang
- Key Laboratory of Environment and Female Reproductive Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
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12
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Abstract
DNA contains information that must be safeguarded, but also accessed for transcription and replication. To perform replication, eukaryotic cells use the B-family DNA polymerase enzymes Polδ and Polɛ, which are optimized for accuracy, speed, and processivity. The molecular basis of these high-performance characteristics causes these replicative polymerases to fail at sites of DNA damage (lesions), which would lead to genomic instability and cell death. To avoid this, cells possess additional DNA polymerases such as the Y-family of polymerases and the B-family member Polζ that can replicate over sites of DNA damage in a process called translesion synthesis (TLS). While able to replicate over DNA lesions, the TLS polymerases exhibit low-fidelity on undamaged DNA and, consequently, must be prevented from replicating DNA under normal circumstances and recruited only when necessary. The replicative bypass of most types of DNA lesions requires the consecutive action of these specialized TLS polymerases assembled into a dynamic multiprotein complex called the Rev1/Polζ mutasome. To this end, posttranslational modifications and a network of protein-protein interactions mediated by accessory domains/subunits of the TLS polymerases control the assembly and rearrangements of the Rev1/Polζ mutasome and recruitment of TLS proteins to sites of DNA damage. This chapter focuses on the structures and interactions that control these processes underlying the function of the Rev1/Polζ mutasome, as well as the development of small molecule inhibitors of the Rev1/Polζ-dependent TLS holding promise as a potential anticancer therapy.
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Affiliation(s)
- Alessandro A Rizzo
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, CT, United States
| | - Dmitry M Korzhnev
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, CT, United States.
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13
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Mammalian DNA Polymerase Kappa Activity and Specificity. Molecules 2019; 24:molecules24152805. [PMID: 31374881 PMCID: PMC6695781 DOI: 10.3390/molecules24152805] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 07/27/2019] [Accepted: 07/30/2019] [Indexed: 12/31/2022] Open
Abstract
DNA polymerase (pol) kappa is a Y-family translesion DNA polymerase conserved throughout all domains of life. Pol kappa is special6 ized for the ability to copy DNA containing minor groove DNA adducts, especially N2-dG adducts, as well as to extend primer termini containing DNA damage or mismatched base pairs. Pol kappa generally cannot copy DNA containing major groove modifications or UV-induced photoproducts. Pol kappa can also copy structured or non-B-form DNA, such as microsatellite DNA, common fragile sites, and DNA containing G quadruplexes. Thus, pol kappa has roles both in maintaining and compromising genomic integrity. The expression of pol kappa is altered in several different cancer types, which can lead to genome instability. In addition, many cancer-associated single-nucleotide polymorphisms have been reported in the POLK gene, some of which are associated with poor survival and altered chemotherapy response. Because of this, identifying inhibitors of pol kappa is an active area of research. This review will address these activities of pol kappa, with a focus on lesion bypass and cellular mutagenesis.
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14
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Wojtaszek JL, Chatterjee N, Najeeb J, Ramos A, Lee M, Bian K, Xue JY, Fenton BA, Park H, Li D, Hemann MT, Hong J, Walker GC, Zhou P. A Small Molecule Targeting Mutagenic Translesion Synthesis Improves Chemotherapy. Cell 2019; 178:152-159.e11. [PMID: 31178121 DOI: 10.1016/j.cell.2019.05.028] [Citation(s) in RCA: 116] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 03/06/2019] [Accepted: 05/14/2019] [Indexed: 10/26/2022]
Abstract
Intrinsic and acquired drug resistance and induction of secondary malignancies limit successful chemotherapy. Because mutagenic translesion synthesis (TLS) contributes to chemoresistance as well as treatment-induced mutations, targeting TLS is an attractive avenue for improving chemotherapeutics. However, development of small molecules with high specificity and in vivo efficacy for mutagenic TLS has been challenging. Here, we report the discovery of a small-molecule inhibitor, JH-RE-06, that disrupts mutagenic TLS by preventing recruitment of mutagenic POL ζ. Remarkably, JH-RE-06 targets a nearly featureless surface of REV1 that interacts with the REV7 subunit of POL ζ. Binding of JH-RE-06 induces REV1 dimerization, which blocks the REV1-REV7 interaction and POL ζ recruitment. JH-RE-06 inhibits mutagenic TLS and enhances cisplatin-induced toxicity in cultured human and mouse cell lines. Co-administration of JH-RE-06 with cisplatin suppresses the growth of xenograft human melanomas in mice, establishing a framework for developing TLS inhibitors as a novel class of chemotherapy adjuvants.
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Affiliation(s)
- Jessica L Wojtaszek
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA
| | - Nimrat Chatterjee
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Javaria Najeeb
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA
| | - Azucena Ramos
- The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Minhee Lee
- Department of Chemistry, Duke University, Durham, NC 27708, USA
| | - Ke Bian
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, RI 02881, USA
| | - Jenny Y Xue
- Trinity College of Arts & Sciences, Duke University, Durham, NC 27708, USA
| | - Benjamin A Fenton
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA
| | - Hyeri Park
- Department of Chemistry, Duke University, Durham, NC 27708, USA
| | - Deyu Li
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, RI 02881, USA
| | - Michael T Hemann
- The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| | - Jiyong Hong
- Department of Chemistry, Duke University, Durham, NC 27708, USA; Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC 27710, USA.
| | - Graham C Walker
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| | - Pei Zhou
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA.
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15
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Hakura A, Sui H, Sonoda J, Matsuda T, Nohmi T. DNA polymerase kappa counteracts inflammation-induced mutagenesis in multiple organs of mice. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2019; 60:320-330. [PMID: 30620413 DOI: 10.1002/em.22272] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 12/26/2018] [Accepted: 12/28/2018] [Indexed: 05/07/2023]
Abstract
In vitro studies indicate that DNA polymerase kappa (Polκ) is able to accurately and efficiently perform DNA synthesis using templates containing various types of DNA damage, including benzo[a]pyrene (BP)-induced N2 -deoxyguanosine adducts. In this study, we examined sensitivity of inactivated Polk knock-in (Polk-/- ) mice to BP carcinogenicity in the colon by administering an oral dose of BP plus dextran sulfate sodium (DSS), an inflammation causing promoter of carcinogenesis. Although colon cancer was successfully induced by BP plus DSS, there was no significant difference in tumor incidence or multiplicity between Polk-/- and Polk+/+ mice. Malignant lymphoma was induced in thymus by the treatment only in Polk-/- mice, but it lacked statistical significance. Mutant frequencies (MFs) in the gpt reporter gene were strongly enhanced in colon; almost to the same extent in both types of mice. Micronucleus formation in bone marrow at the high dose of BP and DNA adducts in colon and lung was not significantly different between two types of mice. Surprisingly, however, Polk-/- mice exhibited significantly higher MFs in colon and lung than did Polk+/+ mice when they were treated with DSS alone. The most prominent mutation induced by DSS treatment was G:C to C:G transversion, whose specific MF in proximal colon was 30 times higher in Polk-/- than in Polk+/+ mice. DSS alone did not enhance MF at all in Polk+/+ mice. The results indicate that Polκ does not suppress BP-induced mutagenesis and carcinogenesis in the colon, but counteracts inflammation-induced mutagenesis in multiple organs. Environ. Mol. Mutagen. 60:320-330, 2019. © 2019 Wiley Periodicals, Inc.
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Affiliation(s)
- Atsushi Hakura
- Tsukuba Drug Safety, Eisai Co., Ltd., Tsukuba-shi, Ibaraki, Japan
| | - Hajime Sui
- Food and Drug Safety Center, Hatano Research Institute, Hadano, Kanagawa, Japan
| | - Jiro Sonoda
- GLP, Eisai Co., Ltd., Tsukuba-shi, Ibaraki, Japan
| | - Tomonari Matsuda
- Research Center for Environmental Quality Management, Kyoto University, Otsu, Shiga, Japan
| | - Takehiko Nohmi
- Biological Safety Research Center, National Institute of Health Sciences, Kawasaki-ku, Kawasaki-shi, Kanagawa, Japan
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16
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Tsao WC, Eckert KA. Detours to Replication: Functions of Specialized DNA Polymerases during Oncogene-induced Replication Stress. Int J Mol Sci 2018; 19:ijms19103255. [PMID: 30347795 PMCID: PMC6214091 DOI: 10.3390/ijms19103255] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2018] [Revised: 10/15/2018] [Accepted: 10/15/2018] [Indexed: 01/10/2023] Open
Abstract
Incomplete and low-fidelity genome duplication contribute to genomic instability and cancer development. Difficult-to-Replicate Sequences, or DiToRS, are natural impediments in the genome that require specialized DNA polymerases and repair pathways to complete and maintain faithful DNA synthesis. DiToRS include non B-DNA secondary structures formed by repetitive sequences, for example within chromosomal fragile sites and telomeres, which inhibit DNA replication under endogenous stress conditions. Oncogene activation alters DNA replication dynamics and creates oncogenic replication stress, resulting in persistent activation of the DNA damage and replication stress responses, cell cycle arrest, and cell death. The response to oncogenic replication stress is highly complex and must be tightly regulated to prevent mutations and tumorigenesis. In this review, we summarize types of known DiToRS and the experimental evidence supporting replication inhibition, with a focus on the specialized DNA polymerases utilized to cope with these obstacles. In addition, we discuss different causes of oncogenic replication stress and its impact on DiToRS stability. We highlight recent findings regarding the regulation of DNA polymerases during oncogenic replication stress and the implications for cancer development.
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Affiliation(s)
- Wei-Chung Tsao
- Department of Pathology, The Jake Gittlen Laboratories for Cancer Research, Hershey, PA 17033, USA.
| | - Kristin A Eckert
- Department of Pathology, The Jake Gittlen Laboratories for Cancer Research, Hershey, PA 17033, USA.
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Robinson M, Shah P, Cui YH, He YY. The Role of Dynamic m 6 A RNA Methylation in Photobiology. Photochem Photobiol 2018; 95:95-104. [PMID: 29729018 DOI: 10.1111/php.12930] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 04/24/2018] [Indexed: 02/06/2023]
Abstract
N6 -methyladenosine (m6 A) is the most abundant internal RNA modification among numerous post-transcriptional modifications identified in eukaryotic mRNA. m6 A modification of RNA is catalyzed by the "writer" m6 A methyltransferase enzyme complex, consisting of METTL3, METTL14, WTAP and KIAA1429. The m6 A modification is reversible and can be removed by "eraser" m6 A demethylase enzymes, namely, FTO and ALKBH5. The biological function of m6 A modification on RNA is carried out by RNA-binding effector proteins called "readers." Varied functions of the reader proteins regulate mRNA metabolism by affecting stability, translation, splicing or nuclear export. The epitranscriptomic gene regulation by m6 A RNA methylation regulates various pathways, which contribute to basic cellular processes essential for cell maintenance, development and cell fate, and affect response to external stimuli and stressors. In this review, we summarize the recent advances in the regulation and function of m6 A RNA methylation, with a focus on UV-induced DNA damage response and the circadian clock machinery. Insights into the mechanisms of m6 A RNA regulation and post-transcriptional regulatory function in these biological processes may facilitate the development of new preventive and therapeutic strategies for various diseases related to dysregulation of UV damage response and circadian rhythm.
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Affiliation(s)
- Myles Robinson
- Department of Medicine, Section of Dermatology, University of Chicago, Chicago, IL.,Pritzker School of Medicine, University of Chicago, Chicago, IL
| | - Palak Shah
- Department of Medicine, Section of Dermatology, University of Chicago, Chicago, IL
| | - Yan-Hong Cui
- Department of Medicine, Section of Dermatology, University of Chicago, Chicago, IL
| | - Yu-Ying He
- Department of Medicine, Section of Dermatology, University of Chicago, Chicago, IL
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18
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Coordinated Activity of Y Family TLS Polymerases and EXO1 Protects Non-S Phase Cells from UV-Induced Cytotoxic Lesions. Mol Cell 2018; 70:34-47.e4. [PMID: 29551515 DOI: 10.1016/j.molcel.2018.02.017] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 12/18/2017] [Accepted: 02/08/2018] [Indexed: 11/23/2022]
Abstract
UV-induced photoproducts are responsible for the pathological effects of sunlight. Mutations in nucleotide excision repair (NER) cause severe pathologies characterized by sunlight sensitivity, coupled to elevated predisposition to cancer and/or neurological dysfunctions. We have previously shown that in UV-irradiated non-cycling cells, only a particular subset of lesions activates the DNA damage response (DDR), and this requires NER and EXO1 activities. To define the molecular mechanism acting at these lesions, we demonstrate that Y family TLS polymerases are recruited at NER- and EXO1-positive lesion sites in non-S phase cells. The coordinated action of EXO1 and Y family TLS polymerases promotes checkpoint activation, leads to lesion repair, and is crucial to prevent cytotoxic double-strand break (DSB) formation.
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19
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Masumura K, Toyoda-Hokaiwado N, Niimi N, Grúz P, Wada NA, Takeiri A, Jishage KI, Mishima M, Nohmi T. Limited ability of DNA polymerase kappa to suppress benzo[a]pyrene-induced genotoxicity in vivo. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2017; 58:644-653. [PMID: 29076178 DOI: 10.1002/em.22146] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 08/20/2017] [Accepted: 09/20/2017] [Indexed: 05/07/2023]
Abstract
DNA polymerase kappa (Polk) is a specialized DNA polymerase involved in translesion DNA synthesis. To understand the protective roles against genotoxins in vivo, we established inactivated Polk knock-in gpt delta (inactivated Polk KI) mice that possessed reporter genes for mutations and expressed inactive Polk. In this study, we examined genotoxicity of benzo[a]pyrene (BP) to determine whether Polk actually suppressed BP-induced genotoxicity as predicted by biochemistry and in vitro cell culture studies. Seven-week-old inactivated Polk KI and wild-type (WT) mice were treated with BP at doses of 5, 15, or 50 mg/(kg·day) for three consecutive days by intragastric gavage, and mutations in the colon and micronucleus formation in the peripheral blood were examined. Surprisingly, no differences were observed in the frequencies of mutations and micronucleus formation at 5 or 50 mg/kg doses. Inactivated Polk KI mice exhibited approximately two times higher gpt mutant frequency than did WT mice only at the 15 mg/kg dose. The frequency of micronucleus formation was slightly higher in inactivated Polk KI than in WT mice at the same dose, but it was statistically insignificant. The results suggest that Polk has a limited ability to suppress BP-induced genotoxicity in the colon and bone marrow and also that the roles of specialized DNA polymerases in mutagenesis and carcinogenesis should be examined not only by in vitro assays but also by in vivo mouse studies. We also report the spontaneous mutagenesis in inactivated Polk KI mice at young and old ages. Environ. Mol. Mutagen. 58:644-653, 2017. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Kenichi Masumura
- Division of Genetics and Mutagenesis, National Institute of Health Sciences, 1-18-1 Kamiyoga, Setagaya-ku, Tokyo, 158-8501, Japan
| | - Naomi Toyoda-Hokaiwado
- Division of Genetics and Mutagenesis, National Institute of Health Sciences, 1-18-1 Kamiyoga, Setagaya-ku, Tokyo, 158-8501, Japan
| | - Naoko Niimi
- Division of Genetics and Mutagenesis, National Institute of Health Sciences, 1-18-1 Kamiyoga, Setagaya-ku, Tokyo, 158-8501, Japan
| | - Petr Grúz
- Division of Genetics and Mutagenesis, National Institute of Health Sciences, 1-18-1 Kamiyoga, Setagaya-ku, Tokyo, 158-8501, Japan
| | - Naoko A Wada
- Research Division, Chugai Pharmaceutical Co., Ltd., 1-135 Komakado, Gotemba, Shizuoka, 412-8513, Japan
| | - Akira Takeiri
- Research Division, Chugai Pharmaceutical Co., Ltd., 1-135 Komakado, Gotemba, Shizuoka, 412-8513, Japan
| | - Kou-Ichi Jishage
- Research Division, Chugai Pharmaceutical Co., Ltd., 1-135 Komakado, Gotemba, Shizuoka, 412-8513, Japan
| | - Masayuki Mishima
- Research Division, Chugai Pharmaceutical Co., Ltd., 1-135 Komakado, Gotemba, Shizuoka, 412-8513, Japan
| | - Takehiko Nohmi
- Division of Genetics and Mutagenesis, National Institute of Health Sciences, 1-18-1 Kamiyoga, Setagaya-ku, Tokyo, 158-8501, Japan
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20
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Prakasha Gowda AS, Spratt TE. Active Site Interactions Impact Phosphoryl Transfer during Replication of Damaged and Undamaged DNA by Escherichia coli DNA Polymerase I. Chem Res Toxicol 2017; 30:2033-2043. [PMID: 29053918 DOI: 10.1021/acs.chemrestox.7b00257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Replicative DNA polymerases are able to discriminate between very similar substrates with high accuracy. One mechanism by which E. coli DNA polymerase I checks for Watson-Crick geometry is through a hydrogen bonding fork between Arg668 and the incoming dNTP and the minor groove of the primer terminus. The importance of the Arg-fork was examined by disrupting it with either a guanine to 3-deazaguanine substitution at the primer terminus or the use of a carbocyclic deoxyribose analog of dUTP. Using thio-substituted dNTPs and differential quench techniques, we determined that when the Arg-fork was disrupted, the rate-limiting step changed from a conformational change to phosphodiester bond formation. This result indicates that Arg668 is involved in the phosphoryl transfer step. We examined the role of the Arg-fork in the replication of four DNA damaged templates, O6-methylguanine (O6-mG), 8-oxo-7,8-dihydroguanine (oxoG), O2-[4-(3-pyridyl)-4-oxobutyl]thymine (O2-POB-T), and N2-[(7S,8R,9S,10R)-7,8,9,10-tetrahydro-8,9,10-trihydroxybenzo[a]pyren-7-yl]-guanine (N2-BP-G). In general, the guanine to 3-deazaguanine substitution caused a decrease in kpol that was proportional to kpol over five orders of magnitude. The linear relationship indicates that the Arg668-fork helps catalyze phosphoryl transfer by the same mechanism with all the substrates. Exceptions to the linear relationship were the incorporations of dTTP opposite G, oxoG, and O6mG, which showed large decreases in kpol, similar to that exhibited by the Watson-Crick base pairs. It was proposed that the incorporation of dTTP opposite G, oxoG, and O6mG occurred via Watson-Crick-like structures.
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Affiliation(s)
- A S Prakasha Gowda
- Department of Biochemistry and Molecular Biology, Milton S. Hershey Medical Center, Pennsylvania State University College of Medicine , Hershey, Pennsylvania 17033, United States
| | - Thomas E Spratt
- Department of Biochemistry and Molecular Biology, Milton S. Hershey Medical Center, Pennsylvania State University College of Medicine , Hershey, Pennsylvania 17033, United States
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21
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Yockey OP, Jha V, Ghodke PP, Xu T, Xu W, Ling H, Pradeepkumar PI, Zhao L. Mechanism of Error-Free DNA Replication Past Lucidin-Derived DNA Damage by Human DNA Polymerase κ. Chem Res Toxicol 2017; 30:2023-2032. [PMID: 28972744 DOI: 10.1021/acs.chemrestox.7b00227] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
DNA damage impinges on genetic information flow and has significant implications in human disease and aging. Lucidin-3-O-primeveroside (LuP) is an anthraquinone derivative present in madder root, which has been used as a coloring agent and food additive. LuP can be metabolically converted to genotoxic compound lucidin, which subsequently forms lucidin-specific N2-2'-deoxyguanosine (N2-dG) and N6-2'-deoxyadenosine (N6-dA) DNA adducts. Lucidin is mutagenic and carcinogenic in rodents but has low carcinogenic risks in humans. To understand the molecular mechanism of low carcinogenicity of lucidin in humans, we performed DNA replication assays using site-specifically modified oligodeoxynucleotides containing a structural analogue (LdG) of lucidin-N2-dG DNA adduct and determined the crystal structures of DNA polymerase (pol) κ in complex with LdG-bearing DNA and an incoming nucleotide. We examined four human pols (pol η, pol ι, pol κ, and Rev1) in their efficiency and accuracy during DNA replication with LdG; these pols are key players in translesion DNA synthesis. Our results demonstrate that pol κ efficiently and accurately replicates past the LdG adduct, whereas DNA replication by pol η, pol ι is compromised to different extents. Rev1 retains its ability to incorporate dCTP opposite the lesion albeit with decreased efficiency. Two ternary crystal structures of pol κ illustrate that the LdG adduct is accommodated by pol κ at the enzyme active site during insertion and postlesion-extension steps. The unique open active site of pol κ allows the adducted DNA to adopt a standard B-form for accurate DNA replication. Collectively, these biochemical and structural data provide mechanistic insights into the low carcinogenic risk of lucidin in humans.
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Affiliation(s)
| | - Vikash Jha
- Department of Biochemistry, Schulich School of Medicine & Dentistry, University of Western Ontario , London, Ontario N6A 5C1, Canada
| | - Pratibha P Ghodke
- Department of Chemistry, Indian Institute of Technology Bombay , Mumbai 400076, India
| | | | | | - Hong Ling
- Department of Biochemistry, Schulich School of Medicine & Dentistry, University of Western Ontario , London, Ontario N6A 5C1, Canada
| | - P I Pradeepkumar
- Department of Chemistry, Indian Institute of Technology Bombay , Mumbai 400076, India
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22
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Mechanism of error-free replication across benzo[a]pyrene stereoisomers by Rev1 DNA polymerase. Nat Commun 2017; 8:965. [PMID: 29042535 PMCID: PMC5645340 DOI: 10.1038/s41467-017-01013-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 08/11/2017] [Indexed: 12/21/2022] Open
Abstract
Benzo[a]pyrene (BP) is a carcinogen in cigarette smoke which, after metabolic activation, can react with the exocyclic N2 amino group of guanine to generate four stereoisomeric BP-N2-dG adducts. Rev1 is unique among translesion synthesis DNA polymerases in employing a protein-template-directed mechanism of DNA synthesis opposite undamaged and damaged guanine. Here we report high-resolution structures of yeast Rev1 with three BP-N2-dG adducts, namely the 10S (+)-trans-BP-N2-dG, 10R (+)-cis-BP-N2-dG, and 10S ( − )-cis-BP-N2-dG. Surprisingly, in all three structures, the bulky and hydrophobic BP pyrenyl residue is entirely solvent-exposed in the major groove of the DNA. This is very different from the adduct alignments hitherto observed in free or protein-bound DNA. All complexes are well poised for dCTP insertion. Our structures provide a view of cis-BP-N2-dG adducts in a DNA polymerase active site, and offer a basis for understanding error-free replication of the BP-derived stereoisomeric guanine adducts. Benzo[a]pyrene (BP) is a carcinogen in cigarette smoke that upon metabolic activation reacts with guanine. Here, the authors present the structures of the translesion DNA synthesis polymerase Rev1 in complex with three of the four possible stereoisomeric BP-N2 -dG adducts, which gives insights how Rev1 achieves error-free replication.
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23
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Zafar MK, Eoff RL. Translesion DNA Synthesis in Cancer: Molecular Mechanisms and Therapeutic Opportunities. Chem Res Toxicol 2017; 30:1942-1955. [PMID: 28841374 DOI: 10.1021/acs.chemrestox.7b00157] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The genomic landscape of cancer is one marred by instability, but the mechanisms that underlie these alterations are multifaceted and remain a topic of intense research. Cellular responses to DNA damage and/or replication stress can affect genome stability in tumors and influence the response of patients to therapy. In addition to direct repair, DNA damage tolerance (DDT) is an element of genomic maintenance programs that contributes to the etiology of several types of cancer. DDT mechanisms primarily act to resolve replication stress, and this can influence the effectiveness of genotoxic drugs. Translesion DNA synthesis (TLS) is an important component of DDT that facilitates direct bypass of DNA adducts and other barriers to replication. The central role of TLS in the bypass of drug-induced DNA lesions, the promotion of tumor heterogeneity, and the involvement of these enzymes in the maintenance of the cancer stem cell niche presents an opportunity to leverage inhibition of TLS as a way of improving existing therapies. In the review that follows, we summarize mechanisms of DDT, misregulation of TLS in cancer, and discuss the potential for targeting these pathways as a means of improving cancer therapies.
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Affiliation(s)
- Maroof K Zafar
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences , Little Rock, Arkansas 72205-7199, United States
| | - Robert L Eoff
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences , Little Rock, Arkansas 72205-7199, United States
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24
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Abstract
The eukaryotic global genomic nucleotide excision repair (GG-NER) pathway is the major mechanism that removes most bulky and some nonbulky lesions from cellular DNA. There is growing evidence that certain DNA lesions are repaired slowly or are entirely resistant to repair in cells, tissues, and in cell extract model assay systems. It is well established that the eukaryotic DNA lesion-sensing proteins do not detect the damaged nucleotide, but recognize the distortions/destabilizations in the native DNA structure caused by the damaged nucleotides. In this article, the nature of the structural features of certain bulky DNA lesions that render them resistant to NER, or cause them to be repaired slowly, is compared to that of those that are good-to-excellent NER substrates. Understanding the structural features that distinguish NER-resistant DNA lesions from good NER substrates may be useful for interpreting the biological significance of biomarkers of exposure of human populations to genotoxic environmental chemicals. NER-resistant lesions can survive to replication and cause mutations that can initiate cancer and other diseases. Furthermore, NER diminishes the efficacy of certain chemotherapeutic drugs, and the design of more potent pharmaceuticals that resist repair can be advanced through a better understanding of the structural properties of DNA lesions that engender repair-resistance.
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Affiliation(s)
- Nicholas E. Geacintov
- Chemistry and Biology Departments, New York University, New York, New York 10003-5180, United States
| | - Suse Broyde
- Chemistry and Biology Departments, New York University, New York, New York 10003-5180, United States
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25
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Gowda ASP, Krzeminski J, Amin S, Suo Z, Spratt TE. Mutagenic Replication of N 2-Deoxyguanosine Benzo[a]pyrene Adducts by Escherichia coli DNA Polymerase I and Sulfolobus solfataricus DNA Polymerase IV. Chem Res Toxicol 2017; 30:1168-1176. [PMID: 28402640 DOI: 10.1021/acs.chemrestox.6b00466] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Benzo[a]pyrene, a potent human carcinogen, is metabolized in vivo to a diol epoxide that reacts with the N2-position of guanine to produce N2-BP-dG adducts. These adducts are mutagenic causing G to T transversions. These adducts block replicative polymerases but can be bypassed by the Y-family translesion synthesis polymerases. The mechanisms by which mutagenic bypass occurs is not well-known. We have evaluated base pairing structures using atomic substitution of the dNTP with two stereoisomers, 2'-deoxy-N-[(7R,8S,9R,10S)-7,8,9,10-tetrahydro-7,8,9-trihydroxybenzo[a]pyren-10-yl]guanosine and 2'-deoxy-N-[(7S,8R,9S,10R)-7,8,9,10-tetrahydro-7,8,9-trihydroxybenzo[a]pyren-10-yl]guanosine. We have examined the kinetics of incorporation of 1-deaza-dATP, 7-deaza-dATP, 2'-deoxyinosine triphosphate, and 7-deaza-dGTP, analogues of dATP and dGTP in which single atoms are changed. Changes in rate will occur if that atom provided a critical interaction in the transition state of the reaction. We examined two polymerases, Escherichia coli DNA polymerase I (Kf) and Sulfolobus solfataricus DNA polymerase IV (Dpo4), as models of a high fidelity and TLS polymerase, respectively. We found that with Kf, substitution of the nitrogens on the Watson-Crick face of the dNTPs resulted in decreased rate of reactions. This result is consistent with a Hoogsteen base pair in which the template N2-BP-dG flipped from the anti to syn conformation. With Dpo4, while the substitution did not affect the rate of reaction, the amplitude of the reaction decreased with all substitutions. This result suggests that Dpo4 bypasses N2-BP-dG via Hoogsteen base pairs but that the flipped nucleotide can be either the dNTP or the template.
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Affiliation(s)
- A S Prakasha Gowda
- Department of Biochemistry and Molecular Biology, Milton S. Hershey Medical Center, Pennsylvania State University College of Medicine , Hershey, Pennsylvania 17033, United States
| | - Jacek Krzeminski
- Department of Pharmacology, Milton S. Hershey Medical Center, Pennsylvania State University College of Medicine , Hershey, Pennsylvania 17033, United States
| | - Shantu Amin
- Department of Pharmacology, Milton S. Hershey Medical Center, Pennsylvania State University College of Medicine , Hershey, Pennsylvania 17033, United States
| | - Zucai Suo
- Department of Chemistry and Biochemistry, The Ohio State University , Columbus, Ohio 43210, United States
| | - Thomas E Spratt
- Department of Biochemistry and Molecular Biology, Milton S. Hershey Medical Center, Pennsylvania State University College of Medicine , Hershey, Pennsylvania 17033, United States
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Gowda ASP, Lee M, Spratt TE. N 2
-Substituted 2′-Deoxyguanosine Triphosphate Derivatives as Selective Substrates for Human DNA Polymerase κ. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201611607] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- A. S. Prakasha Gowda
- Department of Biochemistry and Molecular Biology; Pennsylvania State University; 500 University Dr. Hershey PA 17033 USA
| | - Marietta Lee
- Department of Biochemistry and Molecular Biology; New York Medical College; Valhalla NY 10595 USA
| | - Thomas E. Spratt
- Department of Biochemistry and Molecular Biology; Pennsylvania State University; 500 University Dr. Hershey PA 17033 USA
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27
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White PA, Douglas GR, Phillips DH, Arlt VM. Quantitative relationships between lacZ mutant frequency and DNA adduct frequency in Muta™Mouse tissues and cultured cells exposed to 3-nitrobenzanthrone. Mutagenesis 2017; 32:299-312. [PMID: 28096451 PMCID: PMC5638019 DOI: 10.1093/mutage/gew067] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Accepted: 12/13/2016] [Indexed: 02/07/2023] Open
Abstract
The frequency of stable DNA adducts in a target tissue can be used to assess biologically effective dose; however, the utility of the metric in a risk assessment context depends on the likelihood that the DNA damage will be manifested as mutation. Previously, we employed the Muta™Mouse system to examine the induction of lacZ mutants and DNA adducts following exposure to the well-studied mutagenic carcinogen 3-nitrobenzanthrone (3-NBA). In this follow-up work, we examined the empirical relationships between total adduct frequency and mutant frequency (MF) in tissues and cultured cells following acute 3-NBA exposure. The results show a significant induction of DNA damage and lacZ mutants in liver, colon and bone marrow, as well as FE1 pulmonary epithelial cells. In contrast, lung and small intestine samples had low, but significantly elevated adduct levels, with no significant increases in lacZ MF. Additional analyses showed a significant relationship between the mutagenic efficiency of total adducts, measured as the slope of the relationships between MF and total adduct frequency, and tissue-specific mitotic index (MI). The lack of mutation response in lung, in contrast to the high in vitro MF in FE-1 lung cells, is likely related to the 100-fold difference in MI. The lack of small intestine mutagenic response may be related to limited metabolic capacity, differences in DNA repair, and /or chemically induced apoptosis that has been observed for other potent mutagens. The results indicate that interpretation of adduct frequency values in a risk assessment context can be improved by considering the MI of the target tissue; however, more generalised interpretation is hampered by tissue-specific variations in metabolic capacity and damage processing. The work provides a proof of principle regarding the use of the Muta™Mouse system to critically examine the health risks associated with tissue-specific adduct loads.
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Affiliation(s)
- Paul A White
- Environmental Health Science and Research Bureau, Health Canada, Tunney’s Pasture, Colombine Driveway, Ottawa, Ontario, Canada
| | - George R Douglas
- Environmental Health Science and Research Bureau, Health Canada, Tunney’s Pasture, Colombine Driveway, Ottawa, Ontario, Canada
| | - David H Phillips
- King’s College London, Analytical and Environmental Sciences Division, MRC-PHE Centre for Environment and Health, Franklin-Wilkins Building, London, UK
| | - Volker M Arlt
- King’s College London, Analytical and Environmental Sciences Division, MRC-PHE Centre for Environment and Health, Franklin-Wilkins Building, London, UK
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28
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Gowda ASP, Lee M, Spratt TE. N 2 -Substituted 2'-Deoxyguanosine Triphosphate Derivatives as Selective Substrates for Human DNA Polymerase κ. Angew Chem Int Ed Engl 2017; 56:2628-2631. [PMID: 28140505 DOI: 10.1002/anie.201611607] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Revised: 01/12/2017] [Indexed: 11/09/2022]
Abstract
N2 -Alkyl-2'-deoxyguanosine triphosphate (N2 -alkyl-dGTP) derivatives with methyl, butyl, benzyl, or 4-ethynylbenzyl substituents were prepared and tested as substrates for human DNA polymerases. N2 -Benzyl-dGTP was equal to dGTP as a substrate for DNA polymerase κ (pol κ), but was a poor substrate for pols β, δ, η, ι, or ν. In vivo reactivity was evaluated through incubation of N2 -4-ethynylbenzyl-dG with wild-type and pol κ deficient mouse embryonic fibroblasts. CuAAC reaction with 5(6)-FAM-azide demonstrated that only cells containing pol κ were able to incorporate N2 -4-ethynylbenzyl-dG into the nucleus. This is the first instance of a Y-family-polymerase-specific dNTP, and this method could be used to probe the activity of pol κ in vivo.
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Affiliation(s)
- A S Prakasha Gowda
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, 500 University Dr., Hershey, PA, 17033, USA
| | - Marietta Lee
- Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla, NY, 10595, USA
| | - Thomas E Spratt
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, 500 University Dr., Hershey, PA, 17033, USA
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29
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Zhao L, Washington MT. Translesion Synthesis: Insights into the Selection and Switching of DNA Polymerases. Genes (Basel) 2017; 8:genes8010024. [PMID: 28075396 PMCID: PMC5295019 DOI: 10.3390/genes8010024] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 01/04/2017] [Accepted: 01/04/2017] [Indexed: 01/05/2023] Open
Abstract
DNA replication is constantly challenged by DNA lesions, noncanonical DNA structures and difficult-to-replicate DNA sequences. Two major strategies to rescue a stalled replication fork and to ensure continuous DNA synthesis are: (1) template switching and recombination-dependent DNA synthesis; and (2) translesion synthesis (TLS) using specialized DNA polymerases to perform nucleotide incorporation opposite DNA lesions. The former pathway is mainly error-free, and the latter is error-prone and a major source of mutagenesis. An accepted model of translesion synthesis involves DNA polymerase switching steps between a replicative DNA polymerase and one or more TLS DNA polymerases. The mechanisms that govern the selection and exchange of specialized DNA polymerases for a given DNA lesion are not well understood. In this review, recent studies concerning the mechanisms of selection and switching of DNA polymerases in eukaryotic systems are summarized.
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Affiliation(s)
- Linlin Zhao
- Department of Chemistry and Biochemistry, Central Michigan University, Mount Pleasant, MI 48859, USA.
- Science of Advanced Materials Program, Central Michigan University, Mount Pleasant, MI 48859, USA.
| | - M Todd Washington
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA.
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30
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Kanemaru Y, Suzuki T, Sassa A, Matsumoto K, Adachi N, Honma M, Numazawa S, Nohmi T. DNA polymerase kappa protects human cells against MMC-induced genotoxicity through error-free translesion DNA synthesis. Genes Environ 2017; 39:6. [PMID: 28077981 PMCID: PMC5219776 DOI: 10.1186/s41021-016-0067-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 12/08/2016] [Indexed: 12/16/2022] Open
Abstract
Background Interactions between genes and environment are critical factors for causing cancer in humans. The genotoxicity of environmental chemicals can be enhanced via the modulation of susceptible genes in host human cells. DNA polymerase kappa (Pol κ) is a specialized DNA polymerase that plays an important role in DNA damage tolerance through translesion DNA synthesis. To better understand the protective roles of Pol κ, we previously engineered two human cell lines either deficient in expression of Pol κ (KO) or expressing catalytically dead Pol κ (CD) in Nalm-6-MSH+ cells and examined cytotoxic sensitivity against various genotoxins. In this study, we set up several genotoxicity assays with cell lines possessing altered Pol κ activities and investigated the protective roles of Pol κ in terms of genotoxicity induced by mitomycin C (MMC), a therapeutic agent that induces bulky DNA adducts and crosslinks in DNA. Results We introduced a frameshift mutation in one allele of the thymidine kinase (TK) gene of the KO, CD, and wild-type Pol κ cells (WT), thereby establishing cell lines for the TK gene mutation assay, namely TK+/- cells. In addition, we formulated experimental conditions to conduct chromosome aberration (CA) and sister chromatid exchange (SCE) assays with cells. By using the WT TK+/- and KO TK+/- cells, we assayed genotoxicity of MMC. In the TK gene mutation assay, the cytotoxic and mutagenic sensitivities of KO TK+/- cells were higher than those of WT TK+/- cells. MMC induced loss of heterozygosity (LOH), base pair substitutions at CpG sites and tandem mutations at GpG sites in both cell lines. However, the frequencies of LOH and base substitutions at CpG sites were significantly higher in KO TK+/- cells than in WT TK+/- cells. MMC also induced CA and SCE in both cell lines. The KO TK+/- cells displayed higher sensitivity than that displayed by WT TK+/- cells in the SCE assay. Conclusions These results suggest that Pol κ is a modulating factor for the genotoxicity of MMC and also that the established cell lines are useful for evaluating the genotoxicity of chemicals from multiple endpoints in different genetic backgrounds of Pol κ. Electronic supplementary material The online version of this article (doi:10.1186/s41021-016-0067-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yuki Kanemaru
- Division of Genetics and Mutagenesis, National Institute of Health Sciences, 1-18-1 Kamiyoga, Setagaya-ku, Tokyo, 158-8501 Japan ; Division of Toxicology, Department of Pharmacology, Toxicology and Therapeutics, Showa University School of Pharmacy, 1-5-8 Hatanodai, Shinagawa-ku, Tokyo, 142-0064 Japan
| | - Tetsuya Suzuki
- Division of Genetics and Mutagenesis, National Institute of Health Sciences, 1-18-1 Kamiyoga, Setagaya-ku, Tokyo, 158-8501 Japan ; Present Addresses: Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima 734-8553 Japan
| | - Akira Sassa
- Division of Genetics and Mutagenesis, National Institute of Health Sciences, 1-18-1 Kamiyoga, Setagaya-ku, Tokyo, 158-8501 Japan
| | - Kyomu Matsumoto
- Toxicology Division, The Institute of Environmental Toxicology, 4321 Uchimoriya-machi, Joso-shi, Ibaraki 303-0043 Japan
| | - Noritaka Adachi
- Graduate School of Nanobioscience, Yokohama City University, 22-2 Seto, Kanazawa-ku, Yokohama, 236-0027 Japan
| | - Masamitsu Honma
- Division of Genetics and Mutagenesis, National Institute of Health Sciences, 1-18-1 Kamiyoga, Setagaya-ku, Tokyo, 158-8501 Japan
| | - Satoshi Numazawa
- Division of Toxicology, Department of Pharmacology, Toxicology and Therapeutics, Showa University School of Pharmacy, 1-5-8 Hatanodai, Shinagawa-ku, Tokyo, 142-0064 Japan
| | - Takehiko Nohmi
- Division of Genetics and Mutagenesis, National Institute of Health Sciences, 1-18-1 Kamiyoga, Setagaya-ku, Tokyo, 158-8501 Japan ; Present Addresses: Biological Safety Research Center, National Institute of Health Sciences, 1-18-1 Kamiyoga, Setagaya-ku, Tokyo, 158-8501 Japan
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31
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Jha V, Ling H. Structural basis of accurate replication beyond a bulky major benzo[a]pyrene adduct by human DNA polymerase kappa. DNA Repair (Amst) 2016; 49:43-50. [PMID: 27894903 DOI: 10.1016/j.dnarep.2016.11.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Revised: 11/14/2016] [Accepted: 11/14/2016] [Indexed: 12/19/2022]
Abstract
Human Y-family DNA polymerase kappa (polκ) is specialized to bypass bulky lesions in DNA in an error-free way, thus protecting cells from carcinogenic bulky DNA adducts. Benzo[a]pyrene (BP) is one of the most ubiquitous polycyclic aromatic hydrocarbons and an environmental carcinogen. BP covalently modifies DNA and generates mutagenic, bulky adducts. The major BP adduct formed in cells is 10S (+)-trans-anti-BP-N2-dG adduct (BP-dG), which is associated with cancer. The molecular mechanism of how polκ replicates BP-dG accurately is not clear. Here we report the structure of polκ captured at the lesion-extension stage: the enzyme is extending the primer strand after the base pair containing the BP-dG adduct in the template strand at the -1 position. Polκ accommodates the BP adduct in the nascent DNA's minor groove and keeps the adducted DNA helix in a B-form. Two water molecules cover the edge of the minor groove of the replicating base pair (0 position), which is secured by the BP ring in the -1 position in a 5' orientation. The 5' oriented BP adduct keeps correct Watson-Crick base pairing in the active site and promotes high fidelity replication. Our structural and biochemical data reveal a unique molecular basis for accurate DNA replication right after the bulky lesion BP-dG.
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Affiliation(s)
- Vikash Jha
- Department of Biochemistry, Schulich School of Medicine & Dentistry, University of Western Ontario, London, Ontario, N6A 5C1, Canada
| | - Hong Ling
- Department of Biochemistry, Schulich School of Medicine & Dentistry, University of Western Ontario, London, Ontario, N6A 5C1, Canada.
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32
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O'Brien JM, Beal MA, Yauk CL, Marchetti F. Next generation sequencing of benzo(a)pyrene-induced lacZ mutants identifies a germ cell-specific mutation spectrum. Sci Rep 2016; 6:36743. [PMID: 27829668 PMCID: PMC5103183 DOI: 10.1038/srep36743] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 10/14/2016] [Indexed: 12/19/2022] Open
Abstract
De novo mutations are implicated in a variety of genetic diseases and arise primarily in the male germline. We investigated whether male germ cells have unique mechanisms for spontaneous or chemically-induced mutation relative to somatic cells using the MutaMouse model. We recovered lacZ transgenes from sperm 42 days after a 28-day exposure to benzo(a)pyrene (BaP, 100 mg/kg/day) to assess mutations arising in dividing spermatogonia. BaP caused a 3.4-fold increase in lacZ mutant frequency over controls which increased to 4.1-fold after clonal correction. We then used next generation sequencing to compare the spontaneous and BaP-induced mutation spectra in sperm and bone marrow. The spontaneous spectrum in sperm had significantly more G:C to A:T transitions and fewer mutations at A:T basepairs than bone marrow. BaP predominantly induced G:C to T:A transversions in both cell types, and both were enriched for mutations at CpG dinucleotides. However, BaP induced significantly more deletions in sperm, but more G:C to A:T transitions and G:C to C:G transversions in bone marrow. Differences in error-prone translesion DNA synthesis polymerases may underlie the observed spectrum differences between sperm and bone marrow. These findings suggest that mutations in sperm can arise via mechanisms that are unique to male germ cells.
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Affiliation(s)
- Jason M O'Brien
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, ON, K1A 0K9, Canada
| | - Marc A Beal
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, ON, K1A 0K9, Canada
| | - Carole L Yauk
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, ON, K1A 0K9, Canada
| | - Francesco Marchetti
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, ON, K1A 0K9, Canada
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33
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Basu AK, Pande P, Bose A. Translesion Synthesis of 2'-Deoxyguanosine Lesions by Eukaryotic DNA Polymerases. Chem Res Toxicol 2016; 30:61-72. [PMID: 27760288 PMCID: PMC5241707 DOI: 10.1021/acs.chemrestox.6b00285] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
![]()
With the discovery
of translesion synthesis DNA polymerases, great
strides have been made in the last two decades in understanding the
mode of replication of various DNA lesions in prokaryotes and eukaryotes.
A database search indicated that approximately 2000 articles on this
topic have been published in this period. This includes research involving
genetic and structural studies as well as in vitro experiments using purified DNA polymerases and accessory proteins.
It is a daunting task to comprehend this exciting and rapidly emerging
area of research. Even so, as the majority of DNA damage occurs at
2′-deoxyguanosine residues, this perspective attempts to summarize
a subset of this field, focusing on the most relevant eukaryotic DNA
polymerases responsible for their bypass.
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Affiliation(s)
- Ashis K Basu
- Department of Chemistry, University of Connecticut , Storrs, Connecticut 06269, United States
| | - Paritosh Pande
- Department of Chemistry, University of Connecticut , Storrs, Connecticut 06269, United States
| | - Arindam Bose
- Department of Chemistry, University of Connecticut , Storrs, Connecticut 06269, United States
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34
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Kim JK, Yeom M, Hong JK, Song I, Lee YS, Guengerich FP, Choi JY. Six Germline Genetic Variations Impair the Translesion Synthesis Activity of Human DNA Polymerase κ. Chem Res Toxicol 2016; 29:1741-1754. [PMID: 27603496 DOI: 10.1021/acs.chemrestox.6b00244] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
DNA polymerase (pol) κ efficiently catalyzes error-free translesion DNA synthesis (TLS) opposite bulky N2-guanyl lesions induced by carcinogens such as polycyclic aromatic hydrocarbons. We investigated the biochemical effects of nine human nonsynonymous germline POLK variations on the TLS properties of pol κ, utilizing recombinant pol κ (residues 1-526) enzymes and DNA templates containing an N2-CH2(9-anthracenyl)G (N2-AnthG), 8-oxo-7,8-dihydroguanine (8-oxoG), O6-methyl(Me)G, or an abasic site. In steady-state kinetic analyses, the R246X, R298H, T473A, and R512W variants displayed 7- to 18-fold decreases in kcat/Km for dCTP insertion opposite G and N2-AnthG, with 2- to 3-fold decreases in DNA binding affinity, compared to that of the wild-type, and further showed 5- to 190-fold decreases in kcat/Km for next-base extension from C paired with N2-AnthG. The A471V variant showed 2- to 4-fold decreases in kcat/Km for correct nucleotide insertion opposite and beyond G (or N2-AnthG) compared to that of the wild-type. These five hypoactive variants also showed similar patterns of attenuation of TLS activity opposite 8-oxoG, O6-MeG, and abasic lesions. By contrast, the T44M variant exhibited 7- to 11-fold decreases in kcat/Km for dCTP insertion opposite N2-AnthG and O6-MeG (as well as for dATP insertion opposite an abasic site) but not opposite both G and 8-oxoG, nor beyond N2-AnthG, compared to that of the wild-type. These results suggest that the R246X, R298H, T473A, R512W, and A471V variants cause a general catalytic impairment of pol κ opposite G and all four lesions, whereas the T44M variant induces opposite lesion-dependent catalytic impairment, i.e., only opposite O6-MeG, abasic, and bulky N2-G lesions but not opposite G and 8-oxoG, in pol κ, which might indicate that these hypoactive pol κ variants are genetic factors in modifying individual susceptibility to genotoxic carcinogens in certain subsets of populations.
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Affiliation(s)
- Jae-Kwon Kim
- Division of Pharmacology, Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine , Suwon, Gyeonggi-do 16419, Republic of Korea
| | - Mina Yeom
- Division of Pharmacology, Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine , Suwon, Gyeonggi-do 16419, Republic of Korea
| | - Jin-Kyung Hong
- Division of Pharmacology, Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine , Suwon, Gyeonggi-do 16419, Republic of Korea
| | - Insil Song
- Division of Pharmacology, Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine , Suwon, Gyeonggi-do 16419, Republic of Korea
| | - Young-Sam Lee
- Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology , Daegu 42988, Republic of Korea
| | - F Peter Guengerich
- Department of Biochemistry, Vanderbilt University School of Medicine , Nashville, Tennessee 37232-0146, United States
| | - Jeong-Yun Choi
- Division of Pharmacology, Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine , Suwon, Gyeonggi-do 16419, Republic of Korea
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Bose A, Millsap AD, DeLeon A, Rizzo C, Basu AK. Translesion Synthesis of the N(2)-2'-Deoxyguanosine Adduct of the Dietary Mutagen IQ in Human Cells: Error-Free Replication by DNA Polymerase κ and Mutagenic Bypass by DNA Polymerases η, ζ, and Rev1. Chem Res Toxicol 2016; 29:1549-59. [PMID: 27490094 PMCID: PMC5031085 DOI: 10.1021/acs.chemrestox.6b00221] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Indexed: 12/18/2022]
Abstract
Translesion synthesis (TLS) of the N(2)-2'-deoxyguanosine (dG-N(2)-IQ) adduct of the carcinogen 2-amino-3-methylimidazo[4,5-f]quinoline (IQ) was investigated in human embryonic kidney 293T cells by replicating plasmid constructs in which the adduct was individually placed at each guanine (G1, G2, or G3) of the NarI sequence (5'-CG1G2CG3CC-3'). TLS efficiency was 38%, 29%, and 25% for the dG-N(2)-IQ located at G1, G2, and G3, respectively, which suggests that dG-N(2)-IQ is bypassed more efficiently by one or more DNA polymerases at G1 than at either G2 or G3. TLS efficiency was decreased 8-35% in cells with knockdown of pol η, pol κ, pol ι, pol ζ, or Rev1. Up to 75% reduction in TLS occurred when pol η, pol ζ, and Rev1 were simultaneously knocked down, suggesting that these three polymerases play important roles in dG-N(2)-IQ bypass. Mutation frequencies (MFs) of dG-N(2)-IQ at G1, G2, and G3 were 23%, 17%, and 11%, respectively, exhibiting a completely reverse trend of the previously reported MF of the C8-dG adduct of IQ (dG-C8-IQ), which is most mutagenic at G3 ( ( 2015 ) Nucleic Acids Res. 43 , 8340 - 8351 ). The major type of mutation induced by dG-N(2)-IQ was targeted G → T, as was reported for dG-C8-IQ. In each site, knockdown of pol κ resulted in an increase in MF, whereas MF was reduced when pol η, pol ι, pol ζ, or Rev1 was knocked down. The reduction in MF was most pronounced when pol η, pol ζ, and Rev1 were simultaneously knocked down and especially when the adduct was located at G3, where MF was reduced by 90%. We conclude that pol κ predominantly performs error-free TLS of the dG-N(2)-IQ adduct, whereas pols η, pol ζ, and Rev1 cooperatively carry out the error-prone TLS. However, in vitro experiments using yeast pol ζ and κ showed that the former was inefficient in full-length primer extension on dG-N(2)-IQ templates, whereas the latter was efficient in both error-free and error-prone extensions. We believe that the observed differences between the in vitro experiments using purified DNA polymerases, and the cellular results may arise from several factors including the crucial roles played by the accessory proteins in TLS.
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Affiliation(s)
- Arindam Bose
- Department
of Chemistry, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Amy D. Millsap
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Arnie DeLeon
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Carmelo
J. Rizzo
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Ashis K. Basu
- Department
of Chemistry, University of Connecticut, Storrs, Connecticut 06269, United States
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36
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Choi JY, Patra A, Yeom M, Lee YS, Zhang Q, Egli M, Guengerich FP. Kinetic and Structural Impact of Metal Ions and Genetic Variations on Human DNA Polymerase ι. J Biol Chem 2016; 291:21063-21073. [PMID: 27555320 DOI: 10.1074/jbc.m116.748285] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Indexed: 12/13/2022] Open
Abstract
DNA polymerase (pol) ι is a Y-family polymerase involved in translesion synthesis, exhibiting higher catalytic activity with Mn2+ than Mg2+ The human germline R96G variant impairs both Mn2+-dependent and Mg2+-dependent activities of pol ι, whereas the Δ1-25 variant selectively enhances its Mg2+-dependent activity. We analyzed pre-steady-state kinetic and structural effects of these two metal ions and genetic variations on pol ι using pol ι core (residues 1-445) proteins. The presence of Mn2+ (0.15 mm) instead of Mg2+ (2 mm) caused a 770-fold increase in efficiency (kpol/Kd,dCTP) of pol ι for dCTP insertion opposite G, mainly due to a 450-fold decrease in Kd,dCTP The R96G and Δ1-25 variants displayed a 53-fold decrease and a 3-fold increase, respectively, in kpol/Kd,dCTP for dCTP insertion opposite G with Mg2+ when compared with wild type, substantially attenuated by substitution with Mn2+ Crystal structures of pol ι ternary complexes, including the primer terminus 3'-OH and a non-hydrolyzable dCTP analogue opposite G with the active-site Mg2+ or Mn2+, revealed that Mn2+ achieves more optimal octahedral coordination geometry than Mg2+, with lower values in average coordination distance geometry in the catalytic metal A-site. Crystal structures of R96G revealed the loss of three H-bonds of residues Gly-96 and Tyr-93 with an incoming dNTP, due to the lack of an arginine, as well as a destabilized Tyr-93 side chain secondary to the loss of a cation-π interaction between both side chains. These results provide a mechanistic basis for alteration in pol ι catalytic function with coordinating metals and genetic variation.
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Affiliation(s)
- Jeong-Yun Choi
- From the Division of Pharmacology, Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Gyeonggi-do 16419, Republic of Korea
| | - Amritaj Patra
- the Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, and
| | - Mina Yeom
- From the Division of Pharmacology, Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Gyeonggi-do 16419, Republic of Korea
| | - Young-Sam Lee
- the Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology, Daegu 42988, Republic of Korea
| | - Qianqian Zhang
- the Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, and
| | - Martin Egli
- the Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, and
| | - F Peter Guengerich
- the Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, and
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Bostian ACL, Eoff RL. Aberrant Kynurenine Signaling Modulates DNA Replication Stress Factors and Promotes Genomic Instability in Gliomas. Chem Res Toxicol 2016; 29:1369-80. [PMID: 27482758 DOI: 10.1021/acs.chemrestox.6b00255] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Metabolism of the essential amino acid L-tryptophan (TRP) is implicated in a number of neurological conditions including depression, neurodegenerative diseases, and cancer. The TRP catabolite kynurenine (KYN) has recently emerged as an important neuroactive factor in brain tumor pathogenesis, with additional studies implicating KYN in other types of cancer. Often highlighted as a modulator of the immune response and a contributor to immune escape for malignant tumors, it is well-known that KYN has effects on the production of the coenzyme nicotinamide adenine dinucleotide (NAD(+)), which can have a direct impact on DNA repair, replication, cell division, redox signaling, and mitochondrial function. Additional effects of KYN signaling are imparted through its role as an endogenous agonist for the aryl hydrocarbon receptor (AhR), and it is largely through activation of the AhR that KYN appears to mediate malignant progression in gliomas. We have recently reported on the ability of KYN signaling to modulate expression of human DNA polymerase kappa (hpol κ), a translesion enzyme involved in bypass of bulky DNA lesions and activation of the replication stress response. Given the impact of KYN on NAD(+) production, AhR signaling, and translesion DNA synthesis, it follows that dysregulation of KYN signaling in cancer may promote malignancy through alterations in the level of endogenous DNA damage and replication stress. In this perspective, we discuss the connections between KYN signaling, DNA damage tolerance, and genomic instability, as they relate to cancer.
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Affiliation(s)
- April C L Bostian
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences , 4301 W. Markham Street, Little Rock, Arkansas 72205-7199, United States
| | - Robert L Eoff
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences , 4301 W. Markham Street, Little Rock, Arkansas 72205-7199, United States
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38
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Korzhnev DM, Hadden MK. Targeting the Translesion Synthesis Pathway for the Development of Anti-Cancer Chemotherapeutics. J Med Chem 2016; 59:9321-9336. [PMID: 27362876 DOI: 10.1021/acs.jmedchem.6b00596] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Human cells possess tightly controlled mechanisms to rescue DNA replication following DNA damage caused by environmental and endogenous carcinogens using a set of low-fidelity translesion synthesis (TLS) DNA polymerases. These polymerases can copy over replication blocking DNA lesions while temporarily leaving them unrepaired, preventing cell death at the expense of increasing mutation rates and contributing to the onset and progression of cancer. In addition, TLS has been implicated as a major cellular mechanism promoting acquired resistance to genotoxic chemotherapy. Owing to its central role in mutagenesis and cell survival after DNA damage, inhibition of the TLS pathway has emerged as a potential target for the development of anticancer agents. This review will recap our current understanding of the structure and regulation of DNA polymerase complexes that mediate TLS and describe how this knowledge is beginning to translate into the development of small molecule TLS inhibitors.
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Affiliation(s)
- Dmitry M Korzhnev
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center , Farmington, Connecticut 06030, United States
| | - M Kyle Hadden
- Department of Pharmaceutical Sciences, University of Connecticut , 69 North Eagleville Road, Unit 3092, Storrs, Connecticut 06269, United States
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Bose A, Surugihalli C, Pande P, Champeil E, Basu AK. Comparative Error-Free and Error-Prone Translesion Synthesis of N(2)-2'-Deoxyguanosine Adducts Formed by Mitomycin C and Its Metabolite, 2,7-Diaminomitosene, in Human Cells. Chem Res Toxicol 2016; 29:933-9. [PMID: 27082015 PMCID: PMC4871107 DOI: 10.1021/acs.chemrestox.6b00087] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Indexed: 11/28/2022]
Abstract
Mitomycin C (MC) is a cytotoxic and mutagenic antitumor agent that alkylates DNA upon reductive activation. 2,7-Diaminomitosene (2,7-DAM) is a major metabolite of MC in tumor cells, which also alkylates DNA. MC forms seven DNA adducts, including monoadducts and inter- and intrastrand cross-links, whereas 2,7-DAM forms two monoadducts. Herein, the biological effects of the dG-N(2) adducts formed by MC and 2,7-DAM have been compared by constructing single-stranded plasmids containing these adducts and replicating them in human embryonic kidney 293T cells. Translesion synthesis (TLS) efficiencies of dG-N(2)-MC and dG-N(2)-2,7-DAM were 38 ± 3 and 27 ± 3%, respectively, compared to that of a control plasmid. This indicates that both adducts block DNA synthesis and that dG-N(2)-2,7-DAM is a stronger replication block than dG-N(2)-MC. TLS of each adducted construct was reduced upon siRNA knockdown of pol η, pol κ, or pol ζ. For both adducts, the most significant reduction occurred with knockdown of pol κ, which suggests that pol κ plays a major role in TLS of these dG-N(2) adducts. Analysis of the progeny showed that both adducts were mutagenic, and the mutation frequencies (MF) of dG-N(2)-MC and dG-N(2)-2,7-DAM were 18 ± 3 and 10 ± 1%, respectively. For both adducts, the major type of mutation was G → T transversions. Knockdown of pol η and pol ζ reduced the MF of dG-N(2)-MC and dG-N(2)-2,7-DAM, whereas knockdown of pol κ increased the MF of these adducts. This suggests that pol κ predominantly carries out error-free TLS, whereas pol η and pol ζ are involved in error-prone TLS. The largest reduction in MF by 78 and 80%, respectively, for dG-N(2)-MC and dG-N(2)-2,7-DAM constructs occurred when pol η, pol ζ, and Rev1 were simultaneously knocked down. This result strongly suggests that, unlike pol κ, these three TLS polymerases cooperatively perform the error-prone TLS of these adducts.
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Affiliation(s)
- Arindam Bose
- Department
of Chemistry, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Chaitra Surugihalli
- Department
of Chemistry, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Paritosh Pande
- Department
of Chemistry, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Elise Champeil
- Department
of Science, John Jay College of Criminal
Justice, New York, New York 10019, United
States
| | - Ashis K. Basu
- Department
of Chemistry, University of Connecticut, Storrs, Connecticut 06269, United States
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40
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Jha V, Bian C, Xing G, Ling H. Structure and mechanism of error-free replication past the major benzo[a]pyrene adduct by human DNA polymerase κ. Nucleic Acids Res 2016; 44:4957-67. [PMID: 27034468 PMCID: PMC4889944 DOI: 10.1093/nar/gkw204] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2015] [Accepted: 03/16/2016] [Indexed: 01/28/2023] Open
Abstract
Benzo[a]pyrene (BP) is a well-known and frequently encountered carcinogen which generates a bulky DNA adduct (+)-trans-10S-BP-N(2)-dG (BP-dG) in cells. DNA polymerase kappa (polκ) is the only known Y-family polymerase that bypasses BP-dG accurately and thus protects cells from genotoxic BP. Here, we report the structures of human polκ in complex with DNA containing either a normal guanine (G) base or a BP-dG adduct at the active site and a correct deoxycytidine. The structures and supporting biochemical data reveal a unique mechanism for accurate replication by translesion synthesis past the major bulky adduct. The active site of polκ opens at the minor groove side of the DNA substrate to accommodate the bulky BP-dG that is attached there. More importantly, polκ stabilizes the lesion DNA substrate in the same active conformation as for regular B-form DNA substrates and the bulky BPDE ring in a 5' end pointing conformation. The BP-dG adducted DNA substrate maintains a Watson-Crick (BP-dG:dC) base pair within the active site, governing correct nucleotide insertion opposite the bulky adduct. In addition, polκ's unique N-clasp domain supports the open conformation of the enzyme and the extended conformation of the single-stranded template to allow bypass of the bulky lesion. This work illustrates the first molecular mechanism for how a bulky major adduct is replicated accurately without strand misalignment and mis-insertion.
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Affiliation(s)
- Vikash Jha
- Department of Biochemistry, Schulich School of Medicine & Dentistry, University of Western Ontario, London, Ontario, N6A 5C1, Canada
| | - Chuanbing Bian
- Department of Biochemistry, Schulich School of Medicine & Dentistry, University of Western Ontario, London, Ontario, N6A 5C1, Canada
| | - Guangxin Xing
- Department of Biochemistry, Schulich School of Medicine & Dentistry, University of Western Ontario, London, Ontario, N6A 5C1, Canada
| | - Hong Ling
- Department of Biochemistry, Schulich School of Medicine & Dentistry, University of Western Ontario, London, Ontario, N6A 5C1, Canada
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Pustovalova Y, Magalhães MTQ, D'Souza S, Rizzo AA, Korza G, Walker GC, Korzhnev DM. Interaction between the Rev1 C-Terminal Domain and the PolD3 Subunit of Polζ Suggests a Mechanism of Polymerase Exchange upon Rev1/Polζ-Dependent Translesion Synthesis. Biochemistry 2016; 55:2043-53. [PMID: 26982350 DOI: 10.1021/acs.biochem.5b01282] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Translesion synthesis (TLS) is a mutagenic branch of cellular DNA damage tolerance that enables bypass replication over DNA lesions carried out by specialized low-fidelity DNA polymerases. The replicative bypass of most types of DNA damage is performed in a two-step process of Rev1/Polζ-dependent TLS. In the first step, a Y-family TLS enzyme, typically Polη, Polι, or Polκ, inserts a nucleotide across a DNA lesion. In the second step, a four-subunit B-family DNA polymerase Polζ (Rev3/Rev7/PolD2/PolD3 complex) extends the distorted DNA primer-template. The coordinated action of error-prone TLS enzymes is regulated through their interactions with the two scaffold proteins, the sliding clamp PCNA and the TLS polymerase Rev1. Rev1 interactions with all other TLS enzymes are mediated by its C-terminal domain (Rev1-CT), which can simultaneously bind the Rev7 subunit of Polζ and Rev1-interacting regions (RIRs) from Polη, Polι, or Polκ. In this work, we identified a previously unknown RIR motif in the C-terminal part of PolD3 subunit of Polζ whose interaction with the Rev1-CT is among the tightest mediated by RIR motifs. Three-dimensional structure of the Rev1-CT/PolD3-RIR complex determined by NMR spectroscopy revealed a structural basis for the relatively high affinity of this interaction. The unexpected discovery of PolD3-RIR motif suggests a mechanism of "inserter" to "extender" DNA polymerase switch upon Rev1/Polζ-dependent TLS, in which the PolD3-RIR binding to the Rev1-CT (i) helps displace the "inserter" Polη, Polι, or Polκ from its complex with Rev1, and (ii) facilitates assembly of the four-subunit "extender" Polζ through simultaneous interaction of Rev1-CT with Rev7 and PolD3 subunits.
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Affiliation(s)
- Yulia Pustovalova
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center , Farmington, Connecticut 06030, United States
| | - Mariana T Q Magalhães
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center , Farmington, Connecticut 06030, United States
| | - Sanjay D'Souza
- Department of Biology, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States
| | - Alessandro A Rizzo
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center , Farmington, Connecticut 06030, United States
| | - George Korza
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center , Farmington, Connecticut 06030, United States
| | - Graham C Walker
- Department of Biology, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States
| | - Dmitry M Korzhnev
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center , Farmington, Connecticut 06030, United States
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42
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Gowda ASP, Spratt TE. DNA Polymerases η and ζ Combine to Bypass O(2)-[4-(3-Pyridyl)-4-oxobutyl]thymine, a DNA Adduct Formed from Tobacco Carcinogens. Chem Res Toxicol 2016; 29:303-16. [PMID: 26868090 PMCID: PMC5081176 DOI: 10.1021/acs.chemrestox.5b00468] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
4-(Methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK) and N'-nitrosonornicotine (NNN) are important human carcinogens in tobacco products. They are metabolized to produce a variety 4-(3-pyridyl)-4-oxobutyl (POB) DNA adducts including O(2)-[4-(3-pyridyl)-4-oxobut-1-yl]thymidine (O(2)-POB-dT), the most abundant POB adduct in NNK- and NNN-treated rodents. To evaluate the mutagenic properties of O(2)-POB-dT, we measured the rate of insertion of dNTPs opposite and extension past O(2)-POB-dT and O(2)-Me-dT by purified human DNA polymerases η, κ, ι, and yeast polymerase ζ in vitro. Under conditions of polymerase in excess, polymerase η was most effective at the insertion of dNTPs opposite O(2)-alkyl-dTs. The time courses were biphasic suggesting the formation of inactive DNA-polymerase complexes. The kpol parameter was reduced approximately 100-fold in the presence of the adduct for pol η, κ, and ι. Pol η was the most reactive polymerase for the adducts due to a higher burst amplitude. For all three polymerases, the nucleotide preference was dATP > dTTP ≫ dGTP and dCTP. Yeast pol ζ was most effective in bypassing the adducts; the kcat/Km values were reduced only 3-fold in the presence of the adducts. The identity of the nucleotide opposite the O(2)-alkyl-dT did not significantly affect the ability of pol ζ to bypass the adducts. The data support a model in which pol η inserts ATP or dTTP opposite O(2)-POB-dT, and then, pol ζ extends past the adduct.
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Affiliation(s)
- A. S. Prakasha Gowda
- Department of Biochemistry and Molecular Biology Penn State Hershey Cancer Institute, Milton S. Hershey Medical Center, Pennsylvania State University College of Medicine, Hershey, Pennsylvania 17033, United States
| | - Thomas E. Spratt
- Department of Biochemistry and Molecular Biology Penn State Hershey Cancer Institute, Milton S. Hershey Medical Center, Pennsylvania State University College of Medicine, Hershey, Pennsylvania 17033, United States
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43
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Bostian ACL, Maddukuri L, Reed MR, Savenka T, Hartman JH, Davis L, Pouncey DL, Miller GP, Eoff RL. Kynurenine Signaling Increases DNA Polymerase Kappa Expression and Promotes Genomic Instability in Glioblastoma Cells. Chem Res Toxicol 2015; 29:101-8. [PMID: 26651356 DOI: 10.1021/acs.chemrestox.5b00452] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Overexpression of the translesion synthesis polymerase hpol κ in glioblastomas has been linked to poor patient prognosis; however, the mechanism promoting higher expression in these tumors remains unknown. We determined that activation of the aryl hydrocarbon receptor (AhR) pathway in glioblastoma cells leads to increased hpol κ mRNA and protein levels. We blocked nuclear translocation and DNA binding by AhR in glioblastoma cells using a small-molecule and observed decreased hpol κ expression. Pharmacological inhibition of tryptophan-2,3-dioxygenase (TDO), the enzyme largely responsible for activating AhR in glioblastoma, led to a decrease in the endogenous AhR agonist kynurenine and a corresponding decrease in hpol κ protein levels. Importantly, we discovered that inhibiting TDO activity, AhR signaling, or suppressing hpol κ expression with RNA interference led to decreased chromosomal damage in glioblastoma cells. Epistasis assays further supported the idea that TDO activity, activation of AhR signaling, and the resulting overexpression of hpol κ function primarily in the same pathway to increase endogenous DNA damage. These findings indicate that upregulation of hpol κ through glioblastoma-specific TDO activity and activation of AhR signaling likely contributes to the high levels of replication stress and genomic instability observed in these tumors.
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Affiliation(s)
- April C L Bostian
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences , Little Rock, Arkansas 72205-7199, United States
| | - Leena Maddukuri
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences , Little Rock, Arkansas 72205-7199, United States
| | - Megan R Reed
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences , Little Rock, Arkansas 72205-7199, United States
| | - Tatsiana Savenka
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences , Little Rock, Arkansas 72205-7199, United States
| | - Jessica H Hartman
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences , Little Rock, Arkansas 72205-7199, United States
| | - Lauren Davis
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences , Little Rock, Arkansas 72205-7199, United States
| | - Dakota L Pouncey
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences , Little Rock, Arkansas 72205-7199, United States
| | - Grover P Miller
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences , Little Rock, Arkansas 72205-7199, United States
| | - Robert L Eoff
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences , Little Rock, Arkansas 72205-7199, United States
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44
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Liu Y, Ma X, Guo C. Effects of the N terminus of mouse DNA polymerase κ on the bypass of a guanine-benzo[a]pyrenyl adduct. J Biochem 2015; 159:471-9. [PMID: 26634445 DOI: 10.1093/jb/mvv118] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Accepted: 11/14/2015] [Indexed: 12/15/2022] Open
Abstract
DNA polymerase κ (Polκ), one of the typical member of the Y-family DNA polymerases, has been demonstrated to bypass the 10S(+)-trans-anti-benzo[a]pyrene diol epoxide-N(2)-deoxyguanine adducts (BPDE-dG) efficiently and accurately. A large structural gap between the core and little finger as well as an N-clasp domain are essential to its unique translesion capability. However, whether the extreme N-terminus of Polκ is required for its activity is unclear. In this work, we constructed two mouse Polκ deletions, which have either a catalytic core (mPolκ1-516) or a core without the first 21-residues (mPolκ22-516), and tested their activities in the replication of normal and BPDE-DNA. These two Polκ deletions are nearly as efficient as the full length protein (Polκ1-852) in normal DNA synthesis. However, steady-state kinetics reveals a significant reduction in efficiency of dCTP incorporation opposite the lesion by Polκ22-516, along with increased frequencies for misinsertion compared with Polκ1-852 The next nucleotide insertion opposite the template C immediately following the BPDE-dG was also examined, and the bypass differences induced by deletions were highlighted in both insertion and extension step. We conclude that the extreme N-terminal part of Polκ is required for the processivity and fidelity of Polκ during translesion synthesis of BPDE-dG lesions.
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Affiliation(s)
- Yang Liu
- Key Laboratory of Genomic and Precision Medicine, China Gastrointestinal Cancer Research Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiaolu Ma
- Key Laboratory of Genomic and Precision Medicine, China Gastrointestinal Cancer Research Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Caixia Guo
- Key Laboratory of Genomic and Precision Medicine, China Gastrointestinal Cancer Research Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
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45
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Richter KS, Götz M, Winter S, Jeske H. The contribution of translesion synthesis polymerases on geminiviral replication. Virology 2015; 488:137-48. [PMID: 26638018 DOI: 10.1016/j.virol.2015.10.027] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 10/26/2015] [Accepted: 10/28/2015] [Indexed: 12/25/2022]
Abstract
Geminiviruses multiply primarily in the plant phloem, but never in meristems. Their Rep protein can activate DNA synthesis in differentiated cells. However, when their single-stranded DNA is injected into the phloem by insects, no Rep is present for inducing initial complementary strand replication. Considering a contribution of translesion synthesis (TLS) polymerases in plants, four of them (Polη, Polζ, Polκ, Rev1) are highly and constitutively expressed in differentiated tissues like the phloem. Two geminiviruses (Euphorbia yellow mosaic virus, Cleome leaf crumple virus), inoculated either biolistically or by whiteflies, replicated in Arabidopsis thaliana mutant lines of these genes to the same extent as in wild type plants. Comparative deep sequencing of geminiviral DNAs, however, showed a high exchange rate (10(-4)-10(-3)) similar to the phylogenetic variation described before and a significant difference in nucleotide substation rates if Polη and Polζ were absent, with a differential response to the viral DNA components.
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Affiliation(s)
- Kathrin S Richter
- Institute of Biomaterials and Biomolecular Systems, Department of Molecular Biology and Plant Virology, University of Stuttgart, Pfaffenwaldring 57, D-70550 Stuttgart, Germany
| | - Monika Götz
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Messeweg 11-12, D-38104 Braunschweig, Germany
| | - Stephan Winter
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Messeweg 11-12, D-38104 Braunschweig, Germany
| | - Holger Jeske
- Institute of Biomaterials and Biomolecular Systems, Department of Molecular Biology and Plant Virology, University of Stuttgart, Pfaffenwaldring 57, D-70550 Stuttgart, Germany.
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46
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Zhang X, Chen Q, Chen J, He C, Mao J, Dai Y, Yang X, Hu W, Zhu C, Chen B. Association of polymorphisms in translesion synthesis genes with prognosis of advanced non-small-cell lung cancer patients treated with platinum-based chemotherapy. J Surg Oncol 2015; 113:17-23. [PMID: 26611653 DOI: 10.1002/jso.24103] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 11/11/2015] [Indexed: 01/04/2023]
Abstract
BACKGROUND AND OBJECTIVES Translesion synthesis (TLS) polymerases enable cells to bypass or overcome DNA damage during DNA replication and contributes to genomic instability and cancer. Inhibition of the expression of TLS genes enhances the sensitivity of cancer cells to cisplatin. This study aimed to investigate the relationship between single nucleotide polymorphisms (SNPs) in the TLS genes and clinical outcome of advanced non-small-cell lung cancer (NSCLC) patients treated with platinum-based chemotherapy. METHODS A total of 16 SNPs were genotyped and analyzed in 302 advanced NSCLC patients (discovery set), and the results were further validated in additional 428 NSCLC patients (validation set). RESULTS Analyses revealed significant associations of two SNPs, rs3213801 and rs3792136, with overall survival, with the lowest combined P values of 0.003 and 0.016, respectively. These effects also remained in stratification analyses by clinical variables. Furthermore, the number of risk genotypes of the two SNPs showed a cumulative effect on overall survival (P = 0.03). CONCLUSIONS Genetic polymorphisms in the TLS genes might serve as potential predictive biomarkers of prognosis of advanced NSCLC patients treated with platinum-based chemotherapy.
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Affiliation(s)
- Xuelin Zhang
- Department of Thoracic Surgery, Taizhou Central Hospital, Taizhou, Zhejiang, China
| | - Qun Chen
- Department of Oncology, Fuzhou Pulmonary Hospital, Fujian Medical University, Fuzhou, Fujian, China
| | - Jia Chen
- School of Medical Laboratory Science, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Chunya He
- Department of Surgical Oncology, Taizhou Central Hospital, Taizhou, Zhejiang, China
| | - Jianlin Mao
- Department of Thoracic Surgery, Taizhou Central Hospital, Taizhou, Zhejiang, China
| | - Yuechu Dai
- Department of Surgical Oncology, Taizhou Central Hospital, Taizhou, Zhejiang, China
| | - Xi Yang
- Department of Respiratory Medicine, Taizhou Central Hospital, Taizhou, Zhejiang, China
| | - Wei Hu
- Department of Respiratory Medicine, Taizhou Central Hospital, Taizhou, Zhejiang, China
| | - Chengchu Zhu
- Department of Radiotherapy, Taizhou Central Hospital, Taizhou, Zhejiang, China
| | - Baofu Chen
- Department of Radiotherapy, Taizhou Central Hospital, Taizhou, Zhejiang, China.,Department of Thoracic Surgery, Taizhou Hospital, Taizhou, Zhejiang, China
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Yagi T, Fujikawa Y, Sawai T, Takamura-Enya T, Ito-Harashima S, Kawanishi M. Error-Prone and Error-Free Translesion DNA Synthesis over Site-Specifically Created DNA Adducts of Aryl Hydrocarbons (3-Nitrobenzanthrone and 4-Aminobiphenyl). Toxicol Res 2015; 33:265-272. [PMID: 29071010 PMCID: PMC5654197 DOI: 10.5487/tr.2017.33.4.265] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2017] [Revised: 09/20/2017] [Accepted: 09/25/2017] [Indexed: 01/05/2023] Open
Abstract
Aryl hydrocarbons such as 3-nitrobenzanthrone (NBA), 4-aminobiphenyl (ABP), acetylaminofluorene (AAF), benzo(a)pyrene (BaP), and 1-nitropyrene (NP) form bulky DNA adducts when absorbed by mammalian cells. These chemicals are metabolically activated to reactive forms in mammalian cells and preferentially get attached covalently to the N2 or C8 positions of guanine or the N6 position of adenine. The proportion of N2 and C8 guanine adducts in DNA differs among chemicals. Although these adducts block DNA replication, cells have a mechanism allowing to continue replication by bypassing these adducts: translesion DNA synthesis (TLS). TLS is performed by translesion DNA polymerases—Pol η, κ, ι, and ζ and Rev1—in an error-free or error-prone manner. Regarding the NBA adducts, namely, 2-(2′-deoxyguanosin-N2-yl)-3-aminobenzanthrone (dG-N2-ABA) and N-(2′-deoxyguanosin-8-yl)-3-aminobenzanthrone (dG-C8-ABA), dG-N2-ABA is produced more often than dG-C8-ABA, whereas dG-C8-ABA blocks DNA replication more strongly than dG-N2-ABA. dG-N2-ABA allows for a less error-prone bypass than dG-C8-ABA does. Pol η and κ are stronger contributors to TLS over dG-C8-ABA, and Pol κ bypasses dG-C8-ABA in an error-prone manner. TLS efficiency and error-proneness are affected by the sequences surrounding the adduct, as demonstrated in our previous study on an ABP adduct, N-(2′-deoxyguanosine-8-yl)-4-aminobiphenyl (dG-C8-ABP). Elucidation of the general mechanisms determining efficiency, error-proneness, and the polymerases involved in TLS over various adducts is the next step in the research on TLS. These TLS studies will clarify the mechanisms underlying aryl hydrocarbon mutagenesis and carcinogenesis in more detail.
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Affiliation(s)
- Takashi Yagi
- Department of Biology, Graduate School of Science, Osaka Prefecture University, Sakai, Osaka, Japan
| | - Yoshihiro Fujikawa
- Department of Biology, Graduate School of Science, Osaka Prefecture University, Sakai, Osaka, Japan
| | - Tomoko Sawai
- Department of Biology, Graduate School of Science, Osaka Prefecture University, Sakai, Osaka, Japan
| | - Takeji Takamura-Enya
- Department of Applied Chemistry, Kanagawa Institute of Technology, Atsugi, Kanagawa, Japan
| | - Sayoko Ito-Harashima
- Department of Biology, Graduate School of Science, Osaka Prefecture University, Sakai, Osaka, Japan
| | - Masanobu Kawanishi
- Department of Biology, Graduate School of Science, Osaka Prefecture University, Sakai, Osaka, Japan
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Kanemaru Y, Suzuki T, Niimi N, Grúz P, Matsumoto K, Adachi N, Honma M, Nohmi T. Catalytic and non-catalytic roles of DNA polymerase κ in the protection of human cells against genotoxic stresses. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2015; 56:650-62. [PMID: 26031400 DOI: 10.1002/em.21961] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2015] [Revised: 05/13/2015] [Accepted: 05/26/2015] [Indexed: 05/07/2023]
Abstract
DNA polymerase κ (Pol κ) is a specialized DNA polymerase involved in translesion DNA synthesis. Although its bypass activities across lesions are well characterized in biochemistry, its cellular protective roles against genotoxic insults are still elusive. To better understand the in vivo protective roles, we have established a human cell line deficient in the expression of Pol κ (KO) and another expressing catalytically dead Pol κ (CD), to examine the cytotoxic sensitivity to 11 genotoxins including ultraviolet C light (UV). These cell lines were established in a genetic background of Nalm-6-MSH+, a human lymphoblastic cell line that has high efficiency for gene targeting, and functional p53 and mismatch repair activities. We classified the genotoxins into four groups. Group 1 includes benzo[a]pyrene diolepoxide, mitomycin C, and bleomycin, where the sensitivity was equally higher in KO and CD than in the cell line expressing wild-type Pol κ (WT). Group 2 includes hydrogen peroxide and menadione, where hypersensitivity was observed only in KO. Group 3 includes methyl methanesulfonate and ethyl methanesulfonate, where hypersensitivity was observed only in CD. Group 4 includes UV and three chemicals, where the chemicals exhibited similar cytotoxicity to all three cell lines. The results suggest that Pol κ not only protects cells from genotoxic DNA lesions via DNA polymerase activities, but also contributes to genome integrity by acting as a non-catalytic protein against oxidative damage caused by hydrogen peroxide and menadione. The non-catalytic roles of Pol κ in protection against oxidative damage by hydrogen peroxide are discussed.
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Affiliation(s)
- Yuki Kanemaru
- Division of Genetics and Mutagenesis, National Institute of Health Sciences, Setagaya-Ku, Tokyo, 158-8501, Japan
- Division of Toxicology, Department of Pharmacology Toxicology and Therapeutics, Showa University School of Pharmacy, Shinagawa-Ku, Tokyo, 142-0064, Japan
| | - Tetsuya Suzuki
- Division of Genetics and Mutagenesis, National Institute of Health Sciences, Setagaya-Ku, Tokyo, 158-8501, Japan
| | - Naoko Niimi
- Division of Genetics and Mutagenesis, National Institute of Health Sciences, Setagaya-Ku, Tokyo, 158-8501, Japan
| | - Petr Grúz
- Division of Genetics and Mutagenesis, National Institute of Health Sciences, Setagaya-Ku, Tokyo, 158-8501, Japan
| | - Kyomu Matsumoto
- Toxicology Division, The Institute of Environmental Toxicology, Joso-Shi, Ibaraki, 303-0043, Japan
| | - Noritaka Adachi
- Graduate School of Nanobioscience, Yokohama City University, Yokohama, Kanagawa, 236-0027, Japan
| | - Masamitsu Honma
- Division of Genetics and Mutagenesis, National Institute of Health Sciences, Setagaya-Ku, Tokyo, 158-8501, Japan
| | - Takehiko Nohmi
- Division of Genetics and Mutagenesis, National Institute of Health Sciences, Setagaya-Ku, Tokyo, 158-8501, Japan
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Sholder G, Creech A, Loechler EL. How Y-Family DNA polymerase IV is more accurate than Dpo4 at dCTP insertion opposite an N2-dG adduct of benzo[a]pyrene. DNA Repair (Amst) 2015; 35:144-53. [PMID: 26523515 DOI: 10.1016/j.dnarep.2015.09.020] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Revised: 09/11/2015] [Accepted: 09/11/2015] [Indexed: 12/11/2022]
Abstract
To bypass DNA damage, cells have Y-Family DNA polymerases (DNAPs). One Y-Family-class includes DNAP κ and DNAP IV, which accurately insert dCTP opposite N(2)-dG adducts, including from the carcinogen benzo[a]pyrene (BP). Another class includes DNAP η and DNAP V, which insert accurately opposite UV-damage, but inaccurately opposite BP-N(2)-dG. To investigate structural differences between Y-Family-classes, regions are swapped between DNAP IV (a κ/IV-class-member) and Dpo4 (a η/V-class-member); the kinetic consequences are evaluated via primer-extension studies with a BP-N(2)-dG-containing template. Four key structural elements are revealed. (1) Y-Family DNAPs have discreet non-covalent contacts between their little finger-domain (LF-Domain) and their catalytic core-domain (CC-Domain), which we call "non-covalent bridges" (NCBs). Arg37 and Arg38 in DNAP IV's CC-Domain near the active site form a non-covalent bridge (AS-NCB) by interacting with Glu251 and Asp252, respectively, in DNAP IV's LF-Domain. Without these interactions dATP/dGTP/dTTP misinsertions increase. DNAP IV's AS-NCB suppresses misinsertions better than Dpo4's equivalent AS-NCB. (2) DNAP IV also suppresses dATP/dGTP/dTTP misinsertions via a second non-covalent bridge, which is ∼8Å from the active site (Distal-NCB). Dpo4 has no Distal-NCB, rendering it inferior at dATP/dGTP/dTTP suppression. (3) dCTP insertion is facilitated by the larger minor groove opening near the active site in DNAP IV versus Dpo4, which is sensible given that Watson/Crick-like [dCTP:BP-N(2)-dG] pairing requires the BP-moiety to be in the minor groove. (4) Compared to Dpo4, DNAP IV has a smaller major groove opening, which suppresses dGTP misinsertion, implying BP-N(2)-dG bulk in the major groove during Hoogsteen syn-adduct-dG:dGTP pairing. In summary, DNAP IV has a large minor groove opening to enhance dCTP insertion, a plugged major groove opening to suppress dGTP misinsertion, and two non-covalent bridges (near and distal to the active site) to suppress dATP/dGTP/dTTP misinsertions; collectively these four structural features enhance DNAP IV's dNTP insertion fidelity opposite a BP-N(2)-dG adduct compared to Dpo4.
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Affiliation(s)
- Gabriel Sholder
- Biology Department, Boston University, Boston, MA 02215, USA
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Shriber P, Leitner-Dagan Y, Geacintov N, Paz-Elizur T, Livneh Z. DNA sequence context greatly affects the accuracy of bypass across an ultraviolet light 6-4 photoproduct in mammalian cells. Mutat Res 2015; 780:71-6. [PMID: 26302378 DOI: 10.1016/j.mrfmmm.2015.08.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Revised: 07/25/2015] [Accepted: 08/10/2015] [Indexed: 12/18/2022]
Abstract
Translesion DNA synthesis (TLS) is a DNA damage tolerance mechanism carried out by low-fidelity DNA polymerases that bypass DNA lesions, which overcomes replication stalling. Despite the miscoding nature of most common DNA lesions, several of them are bypassed in mammalian cells in a relatively accurate manner, which plays a key role maintaining a low mutation load. Whereas it is generally agreed that TLS across the major UV and sunlight induced DNA lesion, the cyclobutane pyrimidine dimer (CPD), is accurate, there were conflicting reports on whether the same is true for the thymine-thymine pyrimidine-pyrimidone(6-4) ultraviolet light photoproduct (TT6-4PP), which represents the second most common class of UV lesions. Using a TLS assay system based on gapped plasmids carrying site-specific TT6-4PP lesions in defined sequence contexts we show that the DNA sequence context markedly affected both the extent and accuracy of TLS. The sequence exhibiting higher TLS exhibited also higher error-frequency, caused primarily by semi-targeted mutations, at the nearest nucleotides flanking the lesion. Our results resolve the discrepancy reported on TLS across TT6-4PP, and suggest that TLS is more accurate in human cells than in mouse cells.
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Affiliation(s)
- Pola Shriber
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Yael Leitner-Dagan
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, 76100, Israel
| | | | - Tamar Paz-Elizur
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, 76100, Israel.
| | - Zvi Livneh
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, 76100, Israel.
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