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Marple T, Son MY, Cheng X, Ko JH, Sung P, Hasty P. TREX2 deficiency suppresses spontaneous and genotoxin-associated mutagenesis. Cell Rep 2024; 43:113637. [PMID: 38175749 PMCID: PMC10883656 DOI: 10.1016/j.celrep.2023.113637] [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: 07/25/2023] [Revised: 09/15/2023] [Accepted: 12/15/2023] [Indexed: 01/06/2024] Open
Abstract
TREX2, a 3'-5' exonuclease, is a part of the DNA damage tolerance (DDT) pathway that stabilizes replication forks (RFs) by ubiquitinating PCNA along with the ubiquitin E3 ligase RAD18 and other DDT factors. Mismatch repair (MMR) corrects DNA polymerase errors, including base mismatches and slippage. Here we demonstrate that TREX2 deletion reduces mutations in cells upon exposure to genotoxins, including those that cause base lesions and DNA polymerase slippage. Importantly, we show that TREX2 generates most of the spontaneous mutations in MMR-mutant cells derived from mice and people. TREX2-induced mutagenesis is dependent on the nuclease and DNA-binding attributes of TREX2. RAD18 deletion also reduces spontaneous mutations in MMR-mutant cells, albeit to a lesser degree. Inactivation of both MMR and TREX2 additively increases RF stalls, while it decreases DNA breaks, consistent with a synthetic phenotype.
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Affiliation(s)
- Teresa Marple
- Department of Molecular Medicine and Institute of Biotechnology, University of Texas Health San Antonio, San Antonio, TX 78229, USA; Greehey Children's Cancer Research Institute, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Mi Young Son
- Department of Molecular Medicine and Institute of Biotechnology, University of Texas Health San Antonio, San Antonio, TX 78229, USA; Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX 78229, USA; Sam and Ann Barshop Institute for Longevity and Aging Studies, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Xiaodong Cheng
- Department of Molecular Medicine and Institute of Biotechnology, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Jun Ho Ko
- Department of Molecular Medicine and Institute of Biotechnology, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Patrick Sung
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX 78229, USA; The Mays Cancer Center, University of Texas Health San Antonio MD Anderson Cancer Center, San Antonio, TX 78229, USA; Greehey Children's Cancer Research Institute, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Paul Hasty
- Department of Molecular Medicine and Institute of Biotechnology, University of Texas Health San Antonio, San Antonio, TX 78229, USA; The Mays Cancer Center, University of Texas Health San Antonio MD Anderson Cancer Center, San Antonio, TX 78229, USA; Sam and Ann Barshop Institute for Longevity and Aging Studies, University of Texas Health San Antonio, San Antonio, TX 78229, USA.
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Nakano K, Yamada Y, Takahashi E, Arimoto S, Okamoto K, Negishi K, Negishi T. E. coli mismatch repair enhances AT-to-GC mutagenesis caused by alkylating agents. MUTATION RESEARCH-GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2017; 815:22-27. [PMID: 28283089 DOI: 10.1016/j.mrgentox.2017.02.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Revised: 01/16/2017] [Accepted: 02/13/2017] [Indexed: 01/18/2023]
Abstract
Alkylating agents are known to induce the formation of O6-alkylguanine (O6-alkG) and O4-alkylthymine (O4-alkT) in DNA. These lesions have been widely investigated as major sources of mutations. We previously showed that mismatch repair (MMR) facilitates the suppression of GC-to-AT mutations caused by O6-methylguanine more efficiently than the suppression of GC-to-AT mutations caused by O6-ethylguanine. However, the manner by which O4-alkyT lesions are repaired remains unclear. In the present study, we investigated the repair pathway involved in the repair of O4-alkT. The E. coli CC106 strain, which harbors Δprolac in its genomic DNA and carries the F'CC106 episome, can be used to detect AT-to-GC reverse-mutation of the gene encoding β-galactosidase. Such AT-to-GC mutations should be induced through the formation of O4-alkT at AT base pairs. As expected, an O6-alkylguanine-DNA alkyltransferase (AGT) -deficient CC106 strain, which is defective in both ada and agt genes, exhibited elevated mutant frequencies in the presence of methylating agents and ethylating agents. However, in the UvrA-deficient strain, the methylating agents were less mutagenic than in wild-type, while ethylating agents were more mutagenic than in wild-type, as observed with agents that induce O6-alkylguanine modifications. Unexpectedly, the mutant frequencies decreased in a MutS-deficient strain, and a similar tendency was observed in MutL- or MutH-deficient strains. Thus, MMR appears to promote mutation at AT base pairs. Similar results were obtained in experiments employing double-mutant strains harboring defects in both MMR and AGT, or MMR and NER. E. coli MMR enhances AT-to-GC mutagenesis, such as that caused by O4-alkylthymine. We hypothesize that the MutS protein recognizes the O4-alkT:A base pair more efficiently than O4-alkT:G. Such a distinction would result in misincorporation of G at the O4-alkT site, followed by higher mutation frequencies in wild-type cells, which have MutS protein, compared to MMR-deficient strains.
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Affiliation(s)
- Kota Nakano
- Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Tsushima-naka, Kita-ku, Okayama, 700-8530, Japan
| | - Yoko Yamada
- Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Tsushima-naka, Kita-ku, Okayama, 700-8530, Japan
| | - Eizo Takahashi
- Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Tsushima-naka, Kita-ku, Okayama, 700-8530, Japan; Nihon Pharmaceutical University, Ina, Kita-Adachi-Gun, Saitama, 362-0806, Japan
| | - Sakae Arimoto
- Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Tsushima-naka, Kita-ku, Okayama, 700-8530, Japan
| | - Keinosuke Okamoto
- Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Tsushima-naka, Kita-ku, Okayama, 700-8530, Japan
| | - Kazuo Negishi
- Nihon Pharmaceutical University, Ina, Kita-Adachi-Gun, Saitama, 362-0806, Japan
| | - Tomoe Negishi
- Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Tsushima-naka, Kita-ku, Okayama, 700-8530, Japan; Nihon Pharmaceutical University, Ina, Kita-Adachi-Gun, Saitama, 362-0806, Japan.
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Gallego-Llamas J, Timms AE, Pitstick R, Peters J, Carlson GA, Beier DR. Improvement of ENU Mutagenesis Efficiency Using Serial Injection and Mismatch Repair Deficiency Mice. PLoS One 2016; 11:e0159377. [PMID: 27441645 PMCID: PMC4956170 DOI: 10.1371/journal.pone.0159377] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 07/03/2016] [Indexed: 12/05/2022] Open
Abstract
ENU mutagenesis is a powerful method for generating novel lines of mice that are informative with respect to both fundamental biological processes and human disease. Rapid developments in genomic technology have made the task of identifying causal mutations by positional cloning remarkably efficient. One limitation of this approach remains the mutation frequency achievable using standard treatment protocols, which currently generate approximately 1–2 sequence changes per megabase when optimized. In this study we used two strategies to attempt to increase the number of mutations induced by ENU treatment. One approach employed mice carrying a mutation in the DNA repair enzyme Msh6. The second strategy involved injection of ENU to successive generations of mice. To evaluate the number of ENU-induced mutations, single mice or pooled samples were analyzed using whole exome sequencing. The results showed that there is considerable variability in the induced mutation frequency using these approaches, but an overall increase in ENU-induced variants from one generation to another was observed. The analysis of the mice deficient for Msh6 also showed an increase in the ENU-induced variants compared to the wild-type ENU-treated mice. However, in both cases the increase in ENU-induced mutation frequency was modest.
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Affiliation(s)
- Jabier Gallego-Llamas
- Center for Developmental Biology and Regenerative Medicine, Seattle Children’s Research Institute, Seattle, WA, United States of America
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, United States of America
| | - Andrew E. Timms
- Center for Developmental Biology and Regenerative Medicine, Seattle Children’s Research Institute, Seattle, WA, United States of America
| | - Rose Pitstick
- McLaughlin Research Institute, Great Falls, MT, United States of America
| | - Janet Peters
- McLaughlin Research Institute, Great Falls, MT, United States of America
| | - George A. Carlson
- McLaughlin Research Institute, Great Falls, MT, United States of America
| | - David R. Beier
- Center for Developmental Biology and Regenerative Medicine, Seattle Children’s Research Institute, Seattle, WA, United States of America
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, United States of America
- * E-mail:
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Malignant Peripheral Nerve Sheath Tumors. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 916:495-530. [DOI: 10.1007/978-3-319-30654-4_22] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Taira K, Kaneto S, Nakano K, Watanabe S, Takahashi E, Arimoto S, Okamoto K, Schaaper RM, Negishi K, Negishi T. Distinct pathways for repairing mutagenic lesions induced by methylating and ethylating agents. Mutagenesis 2013; 28:341-50. [PMID: 23446177 PMCID: PMC3630523 DOI: 10.1093/mutage/get010] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
DNA alkylation damage can be repaired by nucleotide excision repair (NER), base excision repair (BER) or by direct removal of alkyl groups from modified bases by O(6)-alkylguanine DNA alkyltransferase (AGT; E.C. 2.1.1.63). DNA mismatch repair (MMR) is also likely involved in this repair. We have investigated alkylation-induced mutagenesis in a series of NER- or AGT-deficient Escherichia coli strains, alone or in combination with defects in the MutS, MutL or MutH components of MMR. All strains used contained the F'prolac from strain CC102 (F'CC102) episome capable of detecting specifically lac GC to AT reverse mutations resulting from O(6)-alkylguanine. The results showed the repair of O(6)-methylguanine to be performed by AGT ≫ MMR > NER in order of importance, whereas the repair of O(6)-ethylguanine followed the order NER > AGT > MMR. Studies with double mutants showed that in the absence of AGT or NER repair pathways, the lack of MutS protein generally increased mutant frequencies for both methylating and ethylating agents, suggesting a repair or mutation avoidance role for this protein. However, lack of MutL or MutH protein did not increase alkylation-induced mutagenesis under these conditions and, in fact, reduced mutagenesis by the N-alkyl-N-nitrosoureas MNU and ENU. The combined results suggest that little or no alkylation damage is actually corrected by the mutHLS MMR system; instead, an as yet unspecified interaction of MutS protein with alkylated DNA may promote the involvement of a repair system other than MMR to avoid a mutagenic outcome. Furthermore, both mutagenic and antimutagenic effects of MMR were detected, revealing a dual function of the MMR system in alkylation-exposed cells.
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Affiliation(s)
- Kentaro Taira
- Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Tsushima, Okayama 700-8530, Japan
- NIEHS, Research Triangle Park, NC 27709, USA and
- Nihon Pharmaceutical University, Ina, Kita-Adachi-Gun, Saitama 362-0806, Japan
| | - Satomi Kaneto
- Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Tsushima, Okayama 700-8530, Japan
- NIEHS, Research Triangle Park, NC 27709, USA and
- Nihon Pharmaceutical University, Ina, Kita-Adachi-Gun, Saitama 362-0806, Japan
| | - Kota Nakano
- Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Tsushima, Okayama 700-8530, Japan
- NIEHS, Research Triangle Park, NC 27709, USA and
- Nihon Pharmaceutical University, Ina, Kita-Adachi-Gun, Saitama 362-0806, Japan
| | - Shinji Watanabe
- Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Tsushima, Okayama 700-8530, Japan
- NIEHS, Research Triangle Park, NC 27709, USA and
- Nihon Pharmaceutical University, Ina, Kita-Adachi-Gun, Saitama 362-0806, Japan
| | - Eizo Takahashi
- Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Tsushima, Okayama 700-8530, Japan
- NIEHS, Research Triangle Park, NC 27709, USA and
- Nihon Pharmaceutical University, Ina, Kita-Adachi-Gun, Saitama 362-0806, Japan
| | - Sakae Arimoto
- Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Tsushima, Okayama 700-8530, Japan
- NIEHS, Research Triangle Park, NC 27709, USA and
- Nihon Pharmaceutical University, Ina, Kita-Adachi-Gun, Saitama 362-0806, Japan
| | - Keinosuke Okamoto
- Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Tsushima, Okayama 700-8530, Japan
- NIEHS, Research Triangle Park, NC 27709, USA and
- Nihon Pharmaceutical University, Ina, Kita-Adachi-Gun, Saitama 362-0806, Japan
| | | | - Kazuo Negishi
- Nihon Pharmaceutical University, Ina, Kita-Adachi-Gun, Saitama 362-0806, Japan
| | - Tomoe Negishi
- *To whom correspondence should be addressed. Tel: +81 86 251 7946; Fax: +81 86 251 7926; E-mail:
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Pei DS, Strauss PR. Zebrafish as a model system to study DNA damage and repair. Mutat Res 2013; 743-744:151-159. [PMID: 23211879 DOI: 10.1016/j.mrfmmm.2012.10.003] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2012] [Revised: 10/19/2012] [Accepted: 10/23/2012] [Indexed: 05/20/2023]
Abstract
Zebrafish (Danio rerio) have become a popular vertebrate model to study embryological development, because of unique advantages not found in other model systems. Zebrafish share many gene functions with other vertebrates including humans, making zebrafish a useful system for studying cancer etiology. However, systematic studies of DNA damage and repair pathways using adult or embryonic zebrafish have not been extensively reported. The zebrafish genome contains nearly all the genes involved in different DNA repair pathways in eukaryotes, including direct reversal (DR), mismatch repair (MMR) nucleotide excision repair (NER), base excision repair (BER), homologous recombination (HR), non-homologous end joining (NHEJ) and translesion synthesis (TLS). It also includes the genes of the p53-mediated damage recognition pathway. Therefore, zebrafish provide an ideal model for gaining fundamental insights into mechanisms of DNA damage and repair, especially during embryological development. This review introduces recent work on different DNA damage and repair studies in zebrafish, with special emphasis on the role of BER in zebrafish early embryological development. AP endonuclease 1 (Apex1), a critical protein in the BER pathway, not only regulates BER but also controls cyclic AMP response binding protein (Creb1), which itself regulates ∼25% of eukaryotic coding sequences. In addition, Apex1 indirectly regulates levels of p53. As these findings also occur in murine B cells, they illustrate the usefulness of the zebrafish system in elucidating fundamental mechanisms.
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Affiliation(s)
- De-Sheng Pei
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 401122, China; Department of Biology, Northeastern University, Boston, MA 02115, USA.
| | - Phyllis R Strauss
- Department of Biology, Northeastern University, Boston, MA 02115, USA.
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Valentine CR, Delongchamp RR, Pearce MG, Rainey HF, Dobrovolsky VN, Malling HV, Heflich RH. In vivo mutation analysis using the ΦX174 transgenic mouse and comparisons with other transgenes and endogenous genes. Mutat Res 2010; 705:205-16. [PMID: 20637298 DOI: 10.1016/j.mrrev.2010.07.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2010] [Revised: 06/24/2010] [Accepted: 07/02/2010] [Indexed: 01/01/2023]
Abstract
The ΦX174 transgenic mouse was first developed as an in vivo Ames test, detecting base pair substitution (bps) at a single bp in a reversion assay. A forward mutational assay was also developed, which is a gain of function assay that also detects bps exclusively. Later work with both assays focused on establishing that a mutation was fixed in vivo using single-burst analysis: determining the number of mutant progeny virus from an electroporated cell by dividing the culture into aliquots before scoring mutants. We review results obtained from single-burst analysis, including testing the hypothesis that high mutant frequencies (MFs) of G:C to A:T mutation recovered by transgenic targets include significant numbers of unrepaired G:T mismatches. Comparison between the ΦX174 and lacI transgenes in mouse spleen indicates that the spontaneous bps mutation frequency per nucleotide (mf(n)) is not significantly lower for ΦX174 than for lacI; the response to ENU is also comparable. For the lacI transgene, the spontaneous bps mf(n) is highly age-dependent up to 12 weeks of age and the linear trend extrapolates at conception to a frequency close to the human bps mf(n) per generation of 1.7 × 10(-8). Unexpectedly, we found that the lacI somatic (spleen) bps mf(n) per cell division at early ages was estimated to be the same as for the human germ-line. The bps mf(n) in bone marrow for the gpt transgene is comparable to spleen for the lacI and ΦX174 transgenes. We conclude that the G:C to A:T transition is characteristic of spontaneous in vivo mutation and that the MFs measured in these transgenes at early ages reflect the expected accumulation of in vivo mutation typical of endogenous mammalian mutation rates. However, spontaneous and induced mf(n)s per nucleotide for the cII gene in spleen are 5-10 times higher than for these other transgenes.
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Affiliation(s)
- Carrie R Valentine
- Division of Genetic and Reproductive Toxicology, National Center for Toxicological Research, 3900 NCTR Road, HFT-120, Jefferson, AR 72079, USA
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van Boxtel R, Toonen PW, Verheul M, van Roekel HS, Nijman IJ, Guryev V, Cuppen E. Improved generation of rat gene knockouts by target-selected mutagenesis in mismatch repair-deficient animals. BMC Genomics 2008; 9:460. [PMID: 18840264 PMCID: PMC2567347 DOI: 10.1186/1471-2164-9-460] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2008] [Accepted: 10/07/2008] [Indexed: 01/15/2023] Open
Abstract
Background The laboratory rat (Rattus norvegicus) is one of the preferred model organisms in physiological and pharmacological research, although the availability of specific genetic models, especially gene knockouts, is limited. N-ethyl-N-nitrosourea (ENU)-driven target-selected mutagenesis is currently the most successful method in rats, although it is still very laborious and expensive. Results As ENU-induced DNA damage is normally recognized by the mismatch repair (MMR) system, we hypothesized that the effectiveness of the target-selected mutagenesis approach could be improved by using a MMR-deficient genetic background. Indeed, Msh6 knockout rats were found to be more sensitive to ENU treatment and the germ line mutation rate was boosted more than two-fold to 1 mutation per 585 kb. In addition, the molecular mutation spectrum was found to be changed in favor of generating knockout-type alleles by ~20%, resulting in an overall increase in efficiency of ~2.5 fold. The improved effectiveness was demonstrated by high throughput mutation discovery in 70 Mb of sequence in a set of only 310 mutant F1 rats. This resulted in the identification of 89 mutations of which four introduced a premature stopcodon and 64 resulted in amino acid changes. Conclusion Taken together, we show that the use of a MMR-deficient background considerably improves ENU-driven target-selected mutagenesis in the rat, thereby reducing animal use as well as screening costs. The use of a mismatch repair-deficient genetic background for improving mutagenesis and target-selected knockout efficiency is in principle applicable to any organism of interest.
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Affiliation(s)
- Ruben van Boxtel
- Hubrecht Institute for Developmental Biology and Stem Cell Research, Cancer Genomics Center, Royal Netherlands Academy of Sciences, Utrecht, The Netherlands.
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Recent Papers on Zebrafish and Other Aquarium Fish Models. Zebrafish 2008. [DOI: 10.1089/zeb.2008.9987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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