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Provasek VE, Kodavati M, Kim B, Mitra J, Hegde ML. TDP43 interacts with MLH1 and MSH6 proteins in a DNA damage-inducible manner. Mol Brain 2024; 17:32. [PMID: 38840222 PMCID: PMC11155029 DOI: 10.1186/s13041-024-01108-3] [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: 05/21/2024] [Accepted: 05/30/2024] [Indexed: 06/07/2024] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease that affects the motor neuron. One aspect of the neuropathology involved in ALS includes increased genomic damage and impaired DNA repair capability. The TAR-DNA binding protein 43 (TDP43) has been associated with both sporadic and familial forms of ALS, and is typically observed as cytosolic mislocalization of protein aggregates, termed TDP43 proteinopathy. TDP43 is a ubiquitous RNA/DNA binding protein with functional implications in a wide range of disease processes, including the repair of DNA double-strand breaks (DSBs). While TDP43 is widely known to regulate RNA metabolism, our lab has reported it also functions directly at the protein level to facilitate DNA repair. Here, we show that the TDP43 protein interacts with DNA mismatch repair (MMR) proteins MLH1 and MSH6 in a DNA damage-inducible manner. We utilized differentiated SH-SY5Y neuronal cultures to identify this inducible relationship using complementary approaches of proximity ligation assay (PLA) and co-immunoprecipitation (CoIP) assay. We observed that signals of TDP43 interaction with MLH1 and MSH6 increased significantly following a 2 h treatment of 10 μM methylmethanesulfonate (MMS), a DNA alkylating agent used to induce MMR repair. Likewise, we observed this effect was abolished in cell lines treated with siRNA directed against TDP43. Finally, we demonstrated these protein interactions were significantly increased in lumbar spinal cord samples of ALS-affected patients compared to age-matched controls. These results will inform our future studies to understand the mechanisms and consequences of this TDP43-MMR interaction in the context of ALS-affected neurons.
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Affiliation(s)
- Vincent E Provasek
- Division of DNA Repair Research within the Center for Neuroregeneration, Department of Neurosurgery, Houston Methodist Research Institute, Houston, TX, 77030, USA.
- School of Medicine, Texas A&M University, College Station, TX, 77843, USA.
| | - Manohar Kodavati
- Division of DNA Repair Research within the Center for Neuroregeneration, Department of Neurosurgery, Houston Methodist Research Institute, Houston, TX, 77030, USA
| | - Brandon Kim
- Department of Neuroscience, Rice University, Houston, TX, 77006, USA
| | - Joy Mitra
- Division of DNA Repair Research within the Center for Neuroregeneration, Department of Neurosurgery, Houston Methodist Research Institute, Houston, TX, 77030, USA
| | - Muralidhar L Hegde
- Division of DNA Repair Research within the Center for Neuroregeneration, Department of Neurosurgery, Houston Methodist Research Institute, Houston, TX, 77030, USA.
- School of Medicine, Texas A&M University, College Station, TX, 77843, USA.
- Department of Neuroscience, Weill Cornell Medical College, New York, NY, 10065, USA.
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2
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Provasek VE, Kodavati M, Kim B, Mitra J, Hegde ML. TDP43 Interacts with MLH1 and MSH6 Proteins in A DNA Damage-Inducible Manner. RESEARCH SQUARE 2024:rs.3.rs-4439430. [PMID: 38826483 PMCID: PMC11142363 DOI: 10.21203/rs.3.rs-4439430/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease that affects the motor neuron. One aspect of the neuropathology involved in ALS includes increased genomic damage and impaired DNA repair capability. The TAR-DNA binding protein 43 (TDP43) has been associated with both sporadic and familial forms of ALS, and is typically observed as cytosolic mislocalization of protein aggregates, termed TDP43 proteinopathy. TDP43 is a ubiquitous RNA/DNA binding protein with functional implications in a wide range of disease processes, including the repair of DNA double strand breaks (DSBs). While TDP43 is widely known to regulate RNA metabolism, our lab has reported it also functions directly at the protein level to facilitate DNA repair. Here, we show that TDP43 protein interacts with DNA mismatch repair (MMR) proteins MLH1 and MSH6 in a DNA damage-inducible manner. We utilized differentiated SH-SY5Y neuronal cultures to identify this inducible relationship using complimentary approaches of proximity ligation assay (PLA) and co-immunoprecipitation (CoIP) assay. We observed that signals of TDP43 interaction with MLH1 and MSH6 increased significantly following a 2 hr treatment of 10μM methylmethanesulfonate (MMS), a DNA alkylating agent used to induce MMR repair. Likewise, we observed this effect was abolished in cell lines treated with siRNA directed against TDP43. Finally, we demonstrated these protein interactions were significantly increased in lumbar spinal cord samples of ALS-affected patients compared to age-matched controls. These results will inform our future studies to understand the mechanisms and consequences of this TDP43-MMR interaction in the context of ALS affected neurons.
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Affiliation(s)
- Vincent E. Provasek
- Division of DNA Repair Research within the Center for Neuroregeneration, Department of Neurosurgery, Houston Methodist Research Institute, Houston, TX 77030, USA
- School of Medicine, Texas A&M University, College Station, TX 77843, USA
| | - Manohar Kodavati
- Division of DNA Repair Research within the Center for Neuroregeneration, Department of Neurosurgery, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Brandon Kim
- Department of Neuroscience, Rice University, Houston, TX 77006
| | - Joy Mitra
- Division of DNA Repair Research within the Center for Neuroregeneration, Department of Neurosurgery, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Muralidhar L. Hegde
- Division of DNA Repair Research within the Center for Neuroregeneration, Department of Neurosurgery, Houston Methodist Research Institute, Houston, TX 77030, USA
- School of Medicine, Texas A&M University, College Station, TX 77843, USA
- Department of Neuroscience, Weill Cornell Medical College, New York, NY 10065, USA
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3
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Huang CH, Chiu SY, Chou YC, Wu KJ. A refined Uni-vector prime editing system improves genome editing outcomes in mammalian cells. Biotechnol J 2024; 19:e2300353. [PMID: 38403398 DOI: 10.1002/biot.202300353] [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: 07/19/2023] [Revised: 01/30/2024] [Accepted: 01/31/2024] [Indexed: 02/27/2024]
Abstract
Prime editing is an advanced technology in CRISPR/Cas research with increasing numbers of improved methodologies. The original multi-vector method hampers the efficiency and precision of prime editing and also has inherent difficulty in generating homozygous mutations in mammalian cells. To overcome these technical issues, we developed a Uni-vector prime editing system, wherein the major components for prime editing were constructed in all-in-one plasmids, pPE3-pPuro and pePEmax-pPuro. The Uni-vector prime editing plasmids enhance the editing efficiency of prime editing and improved the generation of homozygous mutated mammalian cell lines. The editing efficiency is dependent of the transfection efficiency. Remarkably, the Uni-vector ePE5max system achieved an impressive editing rate approximately 79% in average, even in cell lines that are traditionally difficult to transfect, such as FaDu cell line. Furthermore, it resulted in a high frequency of homozygous knocked-in cells, with a rate of 99% in HeLa and 85% in FaDu cells. Together, our Uni-vector approach simplifies the delivery of editing components and improves the editing efficiency, especially in cells with low transfection efficiency. This approach presents an advancement in the field of prime editing.
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Affiliation(s)
- Ching-Hui Huang
- Cancer Genome Research Center, Chang Gung Memorial Hospital, Taoyuan City, Taiwan
| | - Szu-Ying Chiu
- Cancer Genome Research Center, Chang Gung Memorial Hospital, Taoyuan City, Taiwan
| | - Yu-Chi Chou
- Biomedical Translation Research Center, Academia Sinica, Taipei, Taiwan
| | - Kou-Juey Wu
- Cancer Genome Research Center, Chang Gung Memorial Hospital, Taoyuan City, Taiwan
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4
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Gozzi K, Tran NT, Modell JW, Le TBK, Laub MT. Prophage-like gene transfer agents promote Caulobacter crescentus survival and DNA repair during stationary phase. PLoS Biol 2022; 20:e3001790. [PMID: 36327213 PMCID: PMC9632790 DOI: 10.1371/journal.pbio.3001790] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 08/09/2022] [Indexed: 11/05/2022] Open
Abstract
Gene transfer agents (GTAs) are prophage-like entities found in many bacterial genomes that cannot propagate themselves and instead package approximately 5 to 15 kbp fragments of the host genome that can then be transferred to related recipient cells. Although suggested to facilitate horizontal gene transfer (HGT) in the wild, no clear physiological role for GTAs has been elucidated. Here, we demonstrate that the α-proteobacterium Caulobacter crescentus produces bona fide GTAs. The production of Caulobacter GTAs is tightly regulated by a newly identified transcription factor, RogA, that represses gafYZ, the direct activators of GTA synthesis. Cells lacking rogA or expressing gafYZ produce GTAs harboring approximately 8.3 kbp fragment of the genome that can, after cell lysis, be transferred into recipient cells. Notably, we find that GTAs promote the survival of Caulobacter in stationary phase and following DNA damage by providing recipient cells a template for homologous recombination-based repair. This function may be broadly conserved in other GTA-producing organisms and explain the prevalence of this unusual HGT mechanism.
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Affiliation(s)
- Kevin Gozzi
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Ngat T. Tran
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Joshua W. Modell
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Tung B. K. Le
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Michael T. Laub
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
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5
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CNOT6: A Novel Regulator of DNA Mismatch Repair. Cells 2022; 11:cells11030521. [PMID: 35159331 PMCID: PMC8833972 DOI: 10.3390/cells11030521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 01/29/2022] [Accepted: 01/31/2022] [Indexed: 11/16/2022] Open
Abstract
DNA mismatch repair (MMR) is a highly conserved pathway that corrects both base–base mispairs and insertion-deletion loops (IDLs) generated during DNA replication. Defects in MMR have been linked to carcinogenesis and drug resistance. However, the regulation of MMR is poorly understood. Interestingly, CNOT6 is one of four deadenylase subunits in the conserved CCR4-NOT complex and it targets poly(A) tails of mRNAs for degradation. CNOT6 is overexpressed in acute lymphoblastic leukemia (ALL), acute myeloid leukemia (AML) and androgen-independent prostate cancer cells, which suggests that an altered expression of CNOT6 may play a role in tumorigenesis. Here, we report that a depletion of CNOT6 sensitizes human U2OS cells to N-methyl-N′nitro-N-nitrosoguanidine (MNNG) and leads to enhanced apoptosis. We also demonstrate that the depletion of CNOT6 upregulates MMR and decreases the mutation frequency in MMR-proficient cells. Furthermore, the depletion of CNOT6 increases the stability of mRNA transcripts from MMR genes, leading to the increased expression of MMR proteins. Our work provides insight into a novel CNOT6-dependent mechanism for regulating MMR.
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6
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Fuchs RP, Isogawa A, Paulo JA, Onizuka K, Takahashi T, Amunugama R, Duxin JP, Fujii S. Crosstalk between repair pathways elicits double-strand breaks in alkylated DNA and implications for the action of temozolomide. eLife 2021; 10:e69544. [PMID: 34236314 PMCID: PMC8289412 DOI: 10.7554/elife.69544] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 07/07/2021] [Indexed: 12/12/2022] Open
Abstract
Temozolomide (TMZ), a DNA methylating agent, is the primary chemotherapeutic drug used in glioblastoma treatment. TMZ induces mostly N-alkylation adducts (N7-methylguanine and N3-methyladenine) and some O6-methylguanine (O6mG) adducts. Current models propose that during DNA replication, thymine is incorporated across from O6mG, promoting a futile cycle of mismatch repair (MMR) that leads to DNA double-strand breaks (DSBs). To revisit the mechanism of O6mG processing, we reacted plasmid DNA with N-methyl-N-nitrosourea (MNU), a temozolomide mimic, and incubated it in Xenopus egg-derived extracts. We have shown that in this system, MMR proteins are enriched on MNU-treated DNA and we observed robust, MMR-dependent, repair synthesis. Our evidence also suggests that MMR, initiated at O6mG:C sites, is strongly stimulated in cis by repair processing of other lesions, such as N-alkylation adducts. Importantly, MNU-treated plasmids display DSBs in extracts, the frequency of which increases linearly with the square of alkylation dose. We suggest that DSBs result from two independent repair processes, one involving MMR at O6mG:C sites and the other involving base excision repair acting at a nearby N-alkylation adduct. We propose a new, replication-independent mechanism of action of TMZ, which operates in addition to the well-studied cell cycle-dependent mode of action.
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Affiliation(s)
- Robert P Fuchs
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical SchoolBostonUnited States
| | - Asako Isogawa
- Cancer Research Center of Marseille, UMR7258, CNRSMarseilleFrance
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical SchoolBostonUnited States
| | - Kazumitsu Onizuka
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku UniversitySendaiJapan
| | | | - Ravindra Amunugama
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical SchoolBostonUnited States
| | - Julien P Duxin
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical SchoolBostonUnited States
| | - Shingo Fujii
- Cancer Research Center of Marseille, UMR7258, CNRSMarseilleFrance
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7
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Liu Q, Zhu X, Lindström M, Shi Y, Zheng J, Hao X, Gustafsson CM, Liu B. Yeast mismatch repair components are required for stable inheritance of gene silencing. PLoS Genet 2020; 16:e1008798. [PMID: 32469861 PMCID: PMC7286534 DOI: 10.1371/journal.pgen.1008798] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 06/10/2020] [Accepted: 04/26/2020] [Indexed: 11/19/2022] Open
Abstract
Alterations in epigenetic silencing have been associated with ageing and tumour formation. Although substantial efforts have been made towards understanding the mechanisms of gene silencing, novel regulators in this process remain to be identified. To systematically search for components governing epigenetic silencing, we developed a genome-wide silencing screen for yeast (Saccharomyces cerevisiae) silent mating type locus HMR. Unexpectedly, the screen identified the mismatch repair (MMR) components Pms1, Mlh1, and Msh2 as being required for silencing at this locus. We further found that the identified genes were also required for proper silencing in telomeres. More intriguingly, the MMR mutants caused a redistribution of Sir2 deacetylase, from silent mating type loci and telomeres to rDNA regions. As a consequence, acetylation levels at histone positions H3K14, H3K56, and H4K16 were increased at silent mating type loci and telomeres but were decreased in rDNA regions. Moreover, knockdown of MMR components in human HEK293T cells increased subtelomeric DUX4 gene expression. Our work reveals that MMR components are required for stable inheritance of gene silencing patterns and establishes a link between the MMR machinery and the control of epigenetic silencing.
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Affiliation(s)
- Qian Liu
- Department of Chemistry and Molecular Biology, University of Gothenburg, Medicinaregatan, Goteborg, Sweden
| | - Xuefeng Zhu
- Institute of Biomedicine, University of Gothenburg, Goteborg, Sweden
- * E-mail: (XZ); (BL)
| | - Michelle Lindström
- Department of Chemistry and Molecular Biology, University of Gothenburg, Medicinaregatan, Goteborg, Sweden
| | - Yonghong Shi
- Institute of Biomedicine, University of Gothenburg, Goteborg, Sweden
| | - Ju Zheng
- Department of Chemistry and Molecular Biology, University of Gothenburg, Medicinaregatan, Goteborg, Sweden
- Department of Biology, Functional Biology, KU Leuven, Heverlee, Belgium
| | - Xinxin Hao
- Department of Chemistry and Molecular Biology, University of Gothenburg, Medicinaregatan, Goteborg, Sweden
| | | | - Beidong Liu
- Department of Chemistry and Molecular Biology, University of Gothenburg, Medicinaregatan, Goteborg, Sweden
- Center for Large-scale cell-based screening, Faculty of Science, University of Gothenburg, Medicinaregatan, Goteborg, Sweden
- * E-mail: (XZ); (BL)
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8
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Dou Y, Kawaler EA, Cui Zhou D, Gritsenko MA, Huang C, Blumenberg L, Karpova A, Petyuk VA, Savage SR, Satpathy S, Liu W, Wu Y, Tsai CF, Wen B, Li Z, Cao S, Moon J, Shi Z, Cornwell M, Wyczalkowski MA, Chu RK, Vasaikar S, Zhou H, Gao Q, Moore RJ, Li K, Sethuraman S, Monroe ME, Zhao R, Heiman D, Krug K, Clauser K, Kothadia R, Maruvka Y, Pico AR, Oliphant AE, Hoskins EL, Pugh SL, Beecroft SJI, Adams DW, Jarman JC, Kong A, Chang HY, Reva B, Liao Y, Rykunov D, Colaprico A, Chen XS, Czekański A, Jędryka M, Matkowski R, Wiznerowicz M, Hiltke T, Boja E, Kinsinger CR, Mesri M, Robles AI, Rodriguez H, Mutch D, Fuh K, Ellis MJ, DeLair D, Thiagarajan M, Mani DR, Getz G, Noble M, Nesvizhskii AI, Wang P, Anderson ML, Levine DA, Smith RD, Payne SH, Ruggles KV, Rodland KD, Ding L, Zhang B, Liu T, Fenyö D. Proteogenomic Characterization of Endometrial Carcinoma. Cell 2020; 180:729-748.e26. [PMID: 32059776 PMCID: PMC7233456 DOI: 10.1016/j.cell.2020.01.026] [Citation(s) in RCA: 272] [Impact Index Per Article: 68.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 11/11/2019] [Accepted: 01/16/2020] [Indexed: 02/07/2023]
Abstract
We undertook a comprehensive proteogenomic characterization of 95 prospectively collected endometrial carcinomas, comprising 83 endometrioid and 12 serous tumors. This analysis revealed possible new consequences of perturbations to the p53 and Wnt/β-catenin pathways, identified a potential role for circRNAs in the epithelial-mesenchymal transition, and provided new information about proteomic markers of clinical and genomic tumor subgroups, including relationships to known druggable pathways. An extensive genome-wide acetylation survey yielded insights into regulatory mechanisms linking Wnt signaling and histone acetylation. We also characterized aspects of the tumor immune landscape, including immunogenic alterations, neoantigens, common cancer/testis antigens, and the immune microenvironment, all of which can inform immunotherapy decisions. Collectively, our multi-omic analyses provide a valuable resource for researchers and clinicians, identify new molecular associations of potential mechanistic significance in the development of endometrial cancers, and suggest novel approaches for identifying potential therapeutic targets.
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Affiliation(s)
- Yongchao Dou
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Emily A Kawaler
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU School of Medicine, New York, NY 10016, USA
| | - Daniel Cui Zhou
- Department of Medicine and Genetics, Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Marina A Gritsenko
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Chen Huang
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Lili Blumenberg
- Department of Medicine, NYU School of Medicine, New York, NY 10016, USA
| | - Alla Karpova
- Department of Medicine and Genetics, Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Vladislav A Petyuk
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Sara R Savage
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Shankha Satpathy
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Wenke Liu
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU School of Medicine, New York, NY 10016, USA
| | - Yige Wu
- Department of Medicine and Genetics, Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Chia-Feng Tsai
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Bo Wen
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Zhi Li
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU School of Medicine, New York, NY 10016, USA
| | - Song Cao
- Department of Medicine and Genetics, Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Jamie Moon
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Zhiao Shi
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - MacIntosh Cornwell
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU School of Medicine, New York, NY 10016, USA
| | - Matthew A Wyczalkowski
- Department of Medicine and Genetics, Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Rosalie K Chu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Suhas Vasaikar
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Hua Zhou
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU School of Medicine, New York, NY 10016, USA
| | - Qingsong Gao
- Department of Medicine and Genetics, Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Ronald J Moore
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Kai Li
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sunantha Sethuraman
- Department of Medicine and Genetics, Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Matthew E Monroe
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Rui Zhao
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - David Heiman
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Karsten Krug
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Karl Clauser
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ramani Kothadia
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Yosef Maruvka
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Alexander R Pico
- Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA 94158, USA
| | - Amanda E Oliphant
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
| | - Emily L Hoskins
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
| | - Samuel L Pugh
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
| | - Sean J I Beecroft
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
| | - David W Adams
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
| | - Jonathan C Jarman
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
| | - Andy Kong
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Hui-Yin Chang
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Boris Reva
- Department of Genetics and Genomic Sciences, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Yuxing Liao
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Dmitry Rykunov
- Department of Genetics and Genomic Sciences, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Antonio Colaprico
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Division of Biostatistics, Department of Public Health Science, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Xi Steven Chen
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Division of Biostatistics, Department of Public Health Science, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Andrzej Czekański
- Department of Oncology, Wroclaw Medical University, 50-367 Wrocław, Poland; Wroclaw Comprehensive Cancer Center, 53-413 Wrocław, Poland
| | - Marcin Jędryka
- Department of Oncology, Wroclaw Medical University, 50-367 Wrocław, Poland; Wroclaw Comprehensive Cancer Center, 53-413 Wrocław, Poland
| | - Rafał Matkowski
- Department of Oncology, Wroclaw Medical University, 50-367 Wrocław, Poland; Wroclaw Comprehensive Cancer Center, 53-413 Wrocław, Poland
| | - Maciej Wiznerowicz
- Poznan University of Medical Sciences, 61-701 Poznań, Poland; University Hospital of Lord's Transfiguration, 60-569 Poznań, Poland; International Institute for Molecular Oncology, 60-203 Poznań, Poland
| | - Tara Hiltke
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Emily Boja
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Christopher R Kinsinger
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Mehdi Mesri
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Ana I Robles
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Henry Rodriguez
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - David Mutch
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Katherine Fuh
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Matthew J Ellis
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Deborah DeLair
- Department of Pathology, NYU Langone Health, New York, NY 10016, USA
| | - Mathangi Thiagarajan
- Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - D R Mani
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Gad Getz
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Michael Noble
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Alexey I Nesvizhskii
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Pei Wang
- Department of Genetics and Genomic Sciences, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Matthew L Anderson
- College of Medicine Obstetrics & Gynecology, University of South Florida Health, Tampa, FL 33620, USA
| | - Douglas A Levine
- Gynecologic Oncology, Laura and Isaac Perlmutter Cancer Center, NYU Langone Health, New York, NY 10016, USA
| | - Richard D Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Samuel H Payne
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
| | - Kelly V Ruggles
- Department of Medicine, NYU School of Medicine, New York, NY 10016, USA
| | - Karin D Rodland
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA; Department of Cell, Developmental, and Cancer Biology, Oregon Health & Science University, Portland, OR 97221, USA.
| | - Li Ding
- Department of Medicine and Genetics, Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA.
| | - Bing Zhang
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Tao Liu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA.
| | - David Fenyö
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU School of Medicine, New York, NY 10016, USA.
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9
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Maslowska KH, Makiela‐Dzbenska K, Fijalkowska IJ. The SOS system: A complex and tightly regulated response to DNA damage. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2019; 60:368-384. [PMID: 30447030 PMCID: PMC6590174 DOI: 10.1002/em.22267] [Citation(s) in RCA: 221] [Impact Index Per Article: 44.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 10/29/2018] [Accepted: 11/13/2018] [Indexed: 05/10/2023]
Abstract
Genomes of all living organisms are constantly threatened by endogenous and exogenous agents that challenge the chemical integrity of DNA. Most bacteria have evolved a coordinated response to DNA damage. In Escherichia coli, this inducible system is termed the SOS response. The SOS global regulatory network consists of multiple factors promoting the integrity of DNA as well as error-prone factors allowing for survival and continuous replication upon extensive DNA damage at the cost of elevated mutagenesis. Due to its mutagenic potential, the SOS response is subject to elaborate regulatory control involving not only transcriptional derepression, but also post-translational activation, and inhibition. This review summarizes current knowledge about the molecular mechanism of the SOS response induction and progression and its consequences for genome stability. Environ. Mol. Mutagen. 60:368-384, 2019. © 2018 The Authors. Environmental and Molecular Mutagenesis published by Wiley Periodicals, Inc. on behalf of Environmental Mutagen Society.
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Affiliation(s)
- Katarzyna H. Maslowska
- Cancer Research Center of Marseille, CNRS, UMR7258Inserm, U1068; Institut Paoli‐Calmettes, Aix‐Marseille UniversityMarseilleFrance
- Institute of Biochemistry and Biophysics, Polish Academy of SciencesWarsawPoland
| | | | - Iwona J. Fijalkowska
- Institute of Biochemistry and Biophysics, Polish Academy of SciencesWarsawPoland
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10
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Ranawat P, Rawat S. Radiation resistance in thermophiles: mechanisms and applications. World J Microbiol Biotechnol 2017; 33:112. [DOI: 10.1007/s11274-017-2279-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Accepted: 04/26/2017] [Indexed: 12/28/2022]
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11
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Swings T, Van den Bergh B, Wuyts S, Oeyen E, Voordeckers K, Verstrepen KJ, Fauvart M, Verstraeten N, Michiels J. Adaptive tuning of mutation rates allows fast response to lethal stress in Escherichia coli. eLife 2017; 6. [PMID: 28460660 PMCID: PMC5429094 DOI: 10.7554/elife.22939] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 04/18/2017] [Indexed: 12/17/2022] Open
Abstract
While specific mutations allow organisms to adapt to stressful environments, most changes in an organism's DNA negatively impact fitness. The mutation rate is therefore strictly regulated and often considered a slowly-evolving parameter. In contrast, we demonstrate an unexpected flexibility in cellular mutation rates as a response to changes in selective pressure. We show that hypermutation independently evolves when different Escherichia coli cultures adapt to high ethanol stress. Furthermore, hypermutator states are transitory and repeatedly alternate with decreases in mutation rate. Specifically, population mutation rates rise when cells experience higher stress and decline again once cells are adapted. Interestingly, we identified cellular mortality as the major force driving the quick evolution of mutation rates. Together, these findings show how organisms balance robustness and evolvability and help explain the prevalence of hypermutation in various settings, ranging from emergence of antibiotic resistance in microbes to cancer relapses upon chemotherapy.
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Affiliation(s)
- Toon Swings
- Centre of Microbial and Plant Genetics, KU Leuven - University of Leuven, Leuven, Belgium
| | - Bram Van den Bergh
- Centre of Microbial and Plant Genetics, KU Leuven - University of Leuven, Leuven, Belgium
| | - Sander Wuyts
- Centre of Microbial and Plant Genetics, KU Leuven - University of Leuven, Leuven, Belgium
| | - Eline Oeyen
- Centre of Microbial and Plant Genetics, KU Leuven - University of Leuven, Leuven, Belgium
| | - Karin Voordeckers
- Centre of Microbial and Plant Genetics, KU Leuven - University of Leuven, Leuven, Belgium.,VIB Laboratory for Genetics and Genomics, Vlaams Instituut voor Biotechnologie, Leuven, Belgium
| | - Kevin J Verstrepen
- Centre of Microbial and Plant Genetics, KU Leuven - University of Leuven, Leuven, Belgium.,VIB Laboratory for Genetics and Genomics, Vlaams Instituut voor Biotechnologie, Leuven, Belgium
| | - Maarten Fauvart
- Centre of Microbial and Plant Genetics, KU Leuven - University of Leuven, Leuven, Belgium.,Smart Systems and Emerging Technologies Unit, Imec (Interuniversity Micro-Electronics Centre), Leuven, Belgium
| | - Natalie Verstraeten
- Centre of Microbial and Plant Genetics, KU Leuven - University of Leuven, Leuven, Belgium
| | - Jan Michiels
- Centre of Microbial and Plant Genetics, KU Leuven - University of Leuven, Leuven, Belgium
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12
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Grazielle-Silva V, Zeb TF, Bolderson J, Campos PC, Miranda JB, Alves CL, Machado CR, McCulloch R, Teixeira SMR. Distinct Phenotypes Caused by Mutation of MSH2 in Trypanosome Insect and Mammalian Life Cycle Forms Are Associated with Parasite Adaptation to Oxidative Stress. PLoS Negl Trop Dis 2015; 9:e0003870. [PMID: 26083967 PMCID: PMC4470938 DOI: 10.1371/journal.pntd.0003870] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Accepted: 06/02/2015] [Indexed: 11/19/2022] Open
Abstract
Background DNA repair mechanisms are crucial for maintenance of the genome in all organisms, including parasites where successful infection is dependent both on genomic stability and sequence variation. MSH2 is an early acting, central component of the Mismatch Repair (MMR) pathway, which is responsible for the recognition and correction of base mismatches that occur during DNA replication and recombination. In addition, recent evidence suggests that MSH2 might also play an important, but poorly understood, role in responding to oxidative damage in both African and American trypanosomes. Methodology/Principal Findings To investigate the involvement of MMR in the oxidative stress response, null mutants of MSH2 were generated in Trypanosoma brucei procyclic forms and in Trypanosoma cruzi epimastigote forms. Unexpectedly, the MSH2 null mutants showed increased resistance to H2O2 exposure when compared with wild type cells, a phenotype distinct from the previously observed increased sensitivity of T. brucei bloodstream forms MSH2 mutants. Complementation studies indicated that the increased oxidative resistance of procyclic T. brucei was due to adaptation to MSH2 loss. In both parasites, loss of MSH2 was shown to result in increased tolerance to alkylation by MNNG and increased accumulation of 8-oxo-guanine in the nuclear and mitochondrial genomes, indicating impaired MMR. In T. cruzi, loss of MSH2 also increases the parasite capacity to survive within host macrophages. Conclusions/Significance Taken together, these results indicate MSH2 displays conserved, dual roles in MMR and in the response to oxidative stress. Loss of the latter function results in life cycle dependent differences in phenotypic outcomes in T. brucei MSH2 mutants, most likely because of the greater burden of oxidative stress in the insect stage of the parasite. Trypanosoma brucei and Trypanosoma cruzi are protozoa parasites that cause sleeping sickness and Chagas disease, respectively, two neglected tropical diseases endemic in sub-Saharan Africa and Latin America. The high genetic diversity found in the T. cruzi population and the highly diverse repertoire of surface glycoprotein genes found in T. brucei are crucial factors that ensure a successful infection in their hosts. Besides responding to host immune responses, these parasites must deal with various sources of oxidative stress that can cause DNA damage. Thus, by determining the right balance between genomic stability and genetic variation, DNA repair pathways have a big impact in the ability of these parasites to maintain infection. This study is focused on the role of a DNA mismatch repair (MMR) protein named MSH2 in protecting these parasites’ DNA against oxidative assault. Using knock-out mutants, we showed that, besides acting in the MMR pathway as a key protein that recognizes and repairs base mismatches, insertions or deletions that can occur after DNA replication, MSH2 has an additional role in the oxidative stress response. Importantly, this extra role of MSH2 seems to be independent of other MMR components and dependent on the parasite developmental stage.
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Affiliation(s)
- Viviane Grazielle-Silva
- Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
- The Wellcome Trust Center for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, Scotland, United Kingdom
| | - Tehseen Fatima Zeb
- The Wellcome Trust Center for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, Scotland, United Kingdom
| | - Jason Bolderson
- The Wellcome Trust Center for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, Scotland, United Kingdom
| | - Priscila C. Campos
- Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Julia B. Miranda
- Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Ceres L. Alves
- Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Carlos R. Machado
- Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Richard McCulloch
- The Wellcome Trust Center for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, Scotland, United Kingdom
- * E-mail: (RM); (SMRT)
| | - Santuza M. R. Teixeira
- Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
- * E-mail: (RM); (SMRT)
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13
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Charbon G, Bjørn L, Mendoza-Chamizo B, Frimodt-Møller J, Løbner-Olesen A. Oxidative DNA damage is instrumental in hyperreplication stress-induced inviability of Escherichia coli. Nucleic Acids Res 2014; 42:13228-41. [PMID: 25389264 PMCID: PMC4245963 DOI: 10.1093/nar/gku1149] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
In Escherichia coli, an increase in the ATP bound form of the DnaA initiator protein results in hyperinitiation and inviability. Here, we show that such replication stress is tolerated during anaerobic growth. In hyperinitiating cells, a shift from anaerobic to aerobic growth resulted in appearance of fragmented chromosomes and a decrease in terminus concentration, leading to a dramatic increase in ori/ter ratio and cessation of cell growth. Aerobic viability was restored by reducing the level of reactive oxygen species (ROS) or by deleting mutM (Fpg glycosylase). The double-strand breaks observed in hyperinitiating cells therefore results from replication forks encountering single-stranded DNA lesions generated while removing oxidized bases, primarily 8-oxoG, from the DNA. We conclude that there is a delicate balance between chromosome replication and ROS inflicted DNA damage so the number of replication forks can only increase when ROS formation is reduced or when the pertinent repair is compromised.
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Affiliation(s)
- Godefroid Charbon
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK2200 Copenhagen N, Denmark
| | - Louise Bjørn
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK2200 Copenhagen N, Denmark
| | - Belén Mendoza-Chamizo
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK2200 Copenhagen N, Denmark Department of Biochemistry, Molecular Biology and Genetics, University of Extremadura, E06071 Badajoz, Spain
| | - Jakob Frimodt-Møller
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK2200 Copenhagen N, Denmark
| | - Anders Løbner-Olesen
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK2200 Copenhagen N, Denmark
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14
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Ishida M, Ishida T, Tashiro S, Uchida H, Sakai C, Hironobe N, Miura K, Hashimoto Y, Arihiro K, Chayama K, Kihara Y, Yoshizumi M. Smoking cessation reverses DNA double-strand breaks in human mononuclear cells. PLoS One 2014; 9:e103993. [PMID: 25093845 PMCID: PMC4122368 DOI: 10.1371/journal.pone.0103993] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Accepted: 07/04/2014] [Indexed: 12/21/2022] Open
Abstract
OBJECTIVE Cigarette smoking is a major risk factor for atherosclerotic cardiovascular disease, which is responsible for a significant proportion of smoking-related deaths. However, the precise mechanism whereby smoking induces this pathology has not been fully delineated. Based on observation of DNA double-strand breaks (DSBs), the most harmful type of DNA damage, in atherosclerotic lesions, we hypothesized that there is a direct association between smoking and DSBs. The goal of this study was to investigate whether smoking induces DSBs and smoking cessation reverses DSBs in vivo through examination of peripheral mononuclear cells (MNCs). APPROACH AND RESULTS Immunoreactivity of oxidative modification of DNA and DSBs were increased in human atherosclerotic lesions but not in the adjacent normal area. DSBs in human MNCs isolated from the blood of volunteers can be detected as cytologically visible "foci" using an antibody against the phosphorylated form of the histone H2AX (γ-H2AX). Young healthy active smokers (n = 15) showed increased γ-H2AX foci number when compared with non-smokers (n = 12) (foci number/cell: median, 0.37/cell; interquartile range [IQR], 0.31-0.58 vs. 4.36/cell; IQR, 3.09-7.39, p<0.0001). Smoking cessation for 1 month reduced the γ-H2AX foci number (median, 4.44/cell; IQR, 4.36-5.24 to 0.28/cell; IQR, 0.12-0.53, p<0.05). A positive correlation was noted between γ-H2AX foci number and exhaled carbon monoxide levels (r = 0.75, p<0.01). CONCLUSIONS Smoking induces DSBs in human MNCs in vivo, and importantly, smoking cessation for 1 month resulted in a decrease in DSBs to a level comparable to that seen in non-smokers. These data reinforce the notion that the cigarette smoking induces DSBs and highlight the importance of smoking cessation.
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Affiliation(s)
- Mari Ishida
- Department of Cardiovascular Physiology and Medicine, Hiroshima University Graduate School of Biomedical and Health Sciences, Hiroshima, Japan
| | - Takafumi Ishida
- Department of Cardiovascular Medicine, Hiroshima University Graduate School of Biomedical and Health Sciences, Hiroshima, Japan
| | - Satoshi Tashiro
- Department of Cellular Biology, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan
| | - Hitomi Uchida
- Department of Cardiovascular Physiology and Medicine, Hiroshima University Graduate School of Biomedical and Health Sciences, Hiroshima, Japan
| | - Chiemi Sakai
- Department of Cardiovascular Physiology and Medicine, Hiroshima University Graduate School of Biomedical and Health Sciences, Hiroshima, Japan
| | - Naoya Hironobe
- Department of Cardiovascular Medicine, Hiroshima University Graduate School of Biomedical and Health Sciences, Hiroshima, Japan
| | - Katsuya Miura
- Department of Cardiovascular Physiology and Medicine, Hiroshima University Graduate School of Biomedical and Health Sciences, Hiroshima, Japan
| | - Yu Hashimoto
- Department of Cardiovascular Medicine, Hiroshima University Graduate School of Biomedical and Health Sciences, Hiroshima, Japan
| | - Koji Arihiro
- Department of Anatomical Pathology, Hiroshima University Hospital, Hiroshima, Japan
| | - Kazuaki Chayama
- Department of Gastroenterology and Metabolism, Hiroshima University Graduate School of Biomedical and Health Sciences, Hiroshima, Japan
| | - Yasuki Kihara
- Department of Cardiovascular Medicine, Hiroshima University Graduate School of Biomedical and Health Sciences, Hiroshima, Japan
| | - Masao Yoshizumi
- Department of Cardiovascular Physiology and Medicine, Hiroshima University Graduate School of Biomedical and Health Sciences, Hiroshima, Japan
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15
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Egas C, Barroso C, Froufe HJC, Pacheco J, Albuquerque L, da Costa MS. Complete genome sequence of the Radiation-Resistant bacterium Rubrobacter radiotolerans RSPS-4. Stand Genomic Sci 2014; 9:1062-75. [PMID: 25197483 PMCID: PMC4148983 DOI: 10.4056/sigs.5661021] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Rubrobacter radiotolerans strain RSPS-4 is a slightly thermophilic member of the phylum “Actinobacteria” isolated from a hot spring in São Pedro do Sul, Portugal. This aerobic and halotolerant bacterium is also extremely resistant to gamma and UV radiation, which are the main reasons for the interest in sequencing its genome. Here, we present the complete genome sequence of strain RSPS-4 as well as its assembly and annotation. We also compare the gene sequence of this organism with that of the type strain of the species R. radiotolerans isolated from a hot spring in Japan. The genome of strain RSPS-4 comprises one circular chromosome of 2,875,491 bp with a G+C content of 66.91%, and 3 circular plasmids of 190,889 bp, 149,806 bp and 51,047 bp, harboring 3,214 predicted protein coding genes, 46 tRNA genes and a single rRNA operon.
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Affiliation(s)
- C Egas
- Next Generation Sequencing Unit, Biocant, Biotechnology Innovation Center, Cantanhede, Portugal
| | - C Barroso
- Next Generation Sequencing Unit, Biocant, Biotechnology Innovation Center, Cantanhede, Portugal
| | - H J C Froufe
- Next Generation Sequencing Unit, Biocant, Biotechnology Innovation Center, Cantanhede, Portugal
| | - J Pacheco
- Next Generation Sequencing Unit, Biocant, Biotechnology Innovation Center, Cantanhede, Portugal
| | - L Albuquerque
- Center for Neuroscience and Cell Biology, University of Coimbra, 3004-517 Coimbra, Portugal
| | - M S da Costa
- Department of Life Sciences, University of Coimbra, Coimbra, Portugal
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16
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Val ME, Kennedy SP, Soler-Bistué AJ, Barbe V, Bouchier C, Ducos-Galand M, Skovgaard O, Mazel D. Fuse or die: how to survive the loss of Dam inVibrio cholerae. Mol Microbiol 2014; 91:665-78. [DOI: 10.1111/mmi.12483] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/04/2013] [Indexed: 11/26/2022]
Affiliation(s)
- Marie-Eve Val
- Department of Genomes and Genetics; Institut Pasteur; F-75015 Paris France
- CNRS; UMR3525 F-75015 Paris France
| | | | - Alfonso J. Soler-Bistué
- Department of Genomes and Genetics; Institut Pasteur; F-75015 Paris France
- CNRS; UMR3525 F-75015 Paris France
| | | | | | - Magaly Ducos-Galand
- Department of Genomes and Genetics; Institut Pasteur; F-75015 Paris France
- CNRS; UMR3525 F-75015 Paris France
| | - Ole Skovgaard
- Department of Science, Systems and Models; Roskilde University; DK-4000 Roskilde Denmark
| | - Didier Mazel
- Department of Genomes and Genetics; Institut Pasteur; F-75015 Paris France
- CNRS; UMR3525 F-75015 Paris France
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17
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Barclay SS, Tamura T, Ito H, Fujita K, Tagawa K, Shimamura T, Katsuta A, Shiwaku H, Sone M, Imoto S, Miyano S, Okazawa H. Systems biology analysis of Drosophila in vivo screen data elucidates core networks for DNA damage repair in SCA1. Hum Mol Genet 2013; 23:1345-64. [DOI: 10.1093/hmg/ddt524] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
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18
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Abstract
Genetic manipulation in enterohemorrhagic
E. coli O157:H7 is currently restricted to recombineering, a method that utilizes the recombination system of bacteriophage lambda, to introduce gene replacements and base changes
inter alia into the genome. Bacteriophage 933W is a prophage in
E. coli O157:H7 strain EDL933, which encodes the genes (
stx2AB) for the production of Shiga toxin which is the basis for the potentially fatal Hemolytic Uremic Syndrome in infected humans. We replaced the
stx2AB genes with a kanamycin cassette using recombineering. After induction of the prophage by ultra-violet light, we found that bacteriophage lysates were capable of transducing to wildtype, point mutations in the lactose, arabinose and maltose genes. The lysates could also transduce tetracycline resistant cassettes. Bacteriophage 933W is also efficient at transducing markers in
E. coli K-12. Co-transduction experiments indicated that the maximal amount of transferred DNA was likely the size of the bacteriophage genome, 61 kB. All tested transductants, in both
E. coli K-12 and O157:H7, were kanamycin-sensitive indicating that the transducing particles contained host DNA.
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Affiliation(s)
- Martin G Marinus
- Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester MA, 01605, USA
| | - Anthony R Poteete
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA 01605, USA
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19
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Abstract
DNA mismatch repair (MMR) corrects replication errors in newly synthesized DNA. It also has an antirecombination action on heteroduplexes that contain similar but not identical sequences. This review focuses on the genetics and development of MMR and not on the latest biochemical mechanisms. The main focus is on MMR in Escherichia coli, but examples from Streptococcuspneumoniae and Bacillussubtilis have also been included. In most organisms, only MutS (detects mismatches) and MutL (an endonuclease) and a single exonucleaseare present. How this system discriminates between newlysynthesized and parental DNA strands is not clear. In E. coli and its relatives, however, Dam methylation is an integral part of MMR and is the basis for strand discrimination. A dedicated site-specific endonuclease, MutH, is present, andMutL has no endonuclease activity; four exonucleases can participate in MMR. Although it might seem that the accumulated wealth of genetic and biochemical data has given us a detailed picture of the mechanism of MMR in E. coli, the existence of three competing models to explain the initiation phase indicates the complexity of the system. The mechanism of the antirecombination action of MMR is largely unknown, but only MutS and MutL appear to be necessary. A primary site of action appears to be on RecA, although subsequent steps of the recombination process can also be inhibited. In this review, the genetics of Very Short Patch (VSP) repair of T/G mismatches arising from deamination of 5-methylcytosineresidues is also discussed.
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20
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Fenske AE, Glaesener S, Bokemeyer C, Thomale J, Dahm-Daphi J, Honecker F, Dartsch DC. Cisplatin resistance induced in germ cell tumour cells is due to reduced susceptibility towards cell death but not to altered DNA damage induction or repair. Cancer Lett 2012; 324:171-8. [DOI: 10.1016/j.canlet.2012.05.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2012] [Revised: 05/09/2012] [Accepted: 05/11/2012] [Indexed: 11/26/2022]
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21
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Xu T, Brown W, Marinus MG. Bleomycin sensitivity in Escherichia coli is medium-dependent. PLoS One 2012; 7:e33256. [PMID: 22438905 PMCID: PMC3305319 DOI: 10.1371/journal.pone.0033256] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2011] [Accepted: 02/06/2012] [Indexed: 11/19/2022] Open
Abstract
Bleomycin (BLM) is a glycopeptide antibiotic and anti-tumor agent that targets primarily the furanose rings of DNA and in the presence of ferrous ions produces oxidative damage and DNA strand breaks. Escherichia coli cells growing in broth medium and exposed to low concentrations of BLM contain double-strand breaks and require homologous recombination to survive. To a lesser extent, the cells also require the abasic (AP) endonucleases associated with base excision repair, presumably to repair oxidative damage. As expected, there is strong induction of the SOS system in treated cells. In contrast, E. coli cells growing in glucose or glycerol minimal medium are resistant to the lethal action of BLM and do not require either homologous recombination functions or AP-endonucleases for survival. DNA ligase activity, however, is needed for cells growing in minimal medium to resist the lethal effects of BLM. There is weak SOS induction in such treated cells.
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Affiliation(s)
| | | | - Martin G. Marinus
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
- * E-mail:
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22
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Abstract
Mutator strains of Escherichia coli have been used to define mechanisms that account for the high fidelity of chromosome duplication and chromosome stability. Mutant strains defective in post-replicative mismatch repair display a strong mutator phenotype consistent with a role for correction of mismatches arising from replication errors. Inactivation of the gene (dam) encoding DNA adenine methyltransferase results in a mutator phenotype consistent with a role for DNA methylation in strand discrimination during mismatch repair. This review gives a personal perspective on the discovery of dam mutants in E. coli and their relationship to mismatch repair and mutator phenotypes.
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Affiliation(s)
- Martin G Marinus
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655, USA.
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23
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Becket E, Chen F, Tamae C, Miller JH. Determination of hypersensitivity to genotoxic agents among Escherichia coli single gene knockout mutants. DNA Repair (Amst) 2010; 9:949-57. [PMID: 20674514 DOI: 10.1016/j.dnarep.2010.06.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2010] [Revised: 05/19/2010] [Accepted: 06/17/2010] [Indexed: 10/19/2022]
Abstract
We have tested the KEIO collection of 3985 different viable single gene knockouts in Escherichia coli to identify genes whose loss increases sensitivity to one or more of six different chemotherapeutic agents and mutagens: Bleomycin (BLM), Cisplatin (CPT), ICR-191 (ICR), 5-azacytidine (5AZ), Zebularine (ZEB), and 5-bromo-2'-deoxyuridine (5BdU). We discovered a set of 156 strains that display a significant increase in sensitivity to at least one of the agents tested. Each genotoxic agent generates a distinct "sensitivity profile" that is characteristic of the agent. Comparison with an independent study of sensitivity profiles for an extensive set of antibiotics pinpoints those effects that are relatively specific for each agent. In some cases engineered double mutants have greatly increased effects. These results provide insight into the mechanism of action of each agent, and define targets for the design of co-drugs that can potentiate these agents. An example is the finding that mutants lacking one of several genes in the folate biosynthetic pathway are hypersensitive to ZEB, leading to a demonstration of synergy between trimethoprim and ZEB.
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Affiliation(s)
- Elinne Becket
- Department of Microbiology, Immunology, and Molecular Genetics, University of California-Los Angeles, CA 90095, USA
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24
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Abstract
Histone H2AX phosphorylation on a serine four residues from the carboxyl terminus (producing gammaH2AX) is a sensitive marker for DNA double-strand breaks (DSBs). DSBs may lead to cancer but, paradoxically, are also used to kill cancer cells. Using gammaH2AX detection to determine the extent of DSB induction may help to detect precancerous cells, to stage cancers, to monitor the effectiveness of cancer therapies and to develop novel anticancer drugs.
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Affiliation(s)
- William M Bonner
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA.
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25
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Mertens K, Lantsheer L, Ennis DG, Samuel JE. Constitutive SOS expression and damage-inducible AddAB-mediated recombinational repair systems for Coxiella burnetii as potential adaptations for survival within macrophages. Mol Microbiol 2008; 69:1411-26. [PMID: 18647165 DOI: 10.1111/j.1365-2958.2008.06373.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
SUMMARY Coxiella burnetii, a Gram-negative obligate intracellular pathogen, replicates within an parasitophorous vacuole with lysosomal characteristics. To understand how C. burnetii maintains genomic integrity in this environment, a database search for genes involved in DNA repair was performed. Major components of repair, SOS response and recombination were identified, including recA and ruvABC, but lexA and recBCD were absent. Instead, C. burnetii possesses addAB orthologous genes, functional equivalents to recBCD. Survival after treatment with UV, mitomycin C (MC) or methyl methanesulfonate (MMS), as well as homologous recombination in Hfr mating was restored in Escherichia coli deletion strains by C. burnetii recA or addAB. Despite the absence of LexA, co-protease activity for C. burnetii RecA was demonstrated. Dominant-negative inhibition of C. burnetii RecA by recA mutant alleles, modelled after E. coli recA1 and recA56, was observed and more apparent with expression of C. burnetii RecAG159D mutant protein. Expression of a subset of repair genes in C. burnetii was monitored and, in contrast to the non-inducible E. coli recBCD, addAB expression was strongly upregulated under oxidative stress. Constitutive SOS gene expression due to the lack of LexA and induction of AddAB likely reflect a unique repair adaptation of C. burnetii to its hostile niche.
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Affiliation(s)
- Katja Mertens
- Department of Microbial and Molecular Pathogenesis, Texas A&M Health Science Center, College of Medicine, College Station, TX, USA
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26
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Hsieh P, Yamane K. DNA mismatch repair: molecular mechanism, cancer, and ageing. Mech Ageing Dev 2008; 129:391-407. [PMID: 18406444 PMCID: PMC2574955 DOI: 10.1016/j.mad.2008.02.012] [Citation(s) in RCA: 291] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2007] [Revised: 02/22/2008] [Accepted: 02/28/2008] [Indexed: 02/09/2023]
Abstract
DNA mismatch repair (MMR) proteins are ubiquitous players in a diverse array of important cellular functions. In its role in post-replication repair, MMR safeguards the genome correcting base mispairs arising as a result of replication errors. Loss of MMR results in greatly increased rates of spontaneous mutation in organisms ranging from bacteria to humans. Mutations in MMR genes cause hereditary nonpolyposis colorectal cancer, and loss of MMR is associated with a significant fraction of sporadic cancers. Given its prominence in mutation avoidance and its ability to target a range of DNA lesions, MMR has been under investigation in studies of ageing mechanisms. This review summarizes what is known about the molecular details of the MMR pathway and the role of MMR proteins in cancer susceptibility and ageing.
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Affiliation(s)
- Peggy Hsieh
- Genetics & Biochemistry Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
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27
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Feitsma H, Akay A, Cuppen E. Alkylation damage causes MMR-dependent chromosomal instability in vertebrate embryos. Nucleic Acids Res 2008; 36:4047-56. [PMID: 18522974 PMCID: PMC2475609 DOI: 10.1093/nar/gkn341] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
SN1-type alkylating agents, like N-methyl-N-nitrosourea (MNU) and N-ethyl-N-nitrosourea (ENU), are potent mutagens. Exposure to alkylating agents gives rise to O6-alkylguanine, a modified base that is recognized by DNA mismatch repair (MMR) proteins but is not repairable, resulting in replication fork stalling and cell death. We used a somatic mutation detection assay to study the in vivo effects of alkylation damage on lethality and mutation frequency in developing zebrafish embryos. Consistent with the damage-sensing role of the MMR system, mutant embryos lacking the MMR enzyme MSH6 displayed lower lethality than wild-type embryos after exposure to ENU and MNU. In line with this, alkylation-induced somatic mutation frequencies were found to be higher in wild-type embryos than in the msh6 loss-of-function mutants. These mutations were found to be chromosomal aberrations that may be caused by chromosomal breaks that arise from stalled replication forks. As these chromosomal breaks arise at replication, they are not expected to be repaired by non-homologous end joining. Indeed, Ku70 loss-of-function mutants were found to be equally sensitive to ENU as wild-type embryos. Taken together, our results suggest that in vivo alkylation damage results in chromosomal instability and cell death due to aberrantly processed MMR-induced stalled replication forks.
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Affiliation(s)
| | | | - Edwin Cuppen
- *To whom correspondence should be addressed. +31 30 2121969+31 30 2516554
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28
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Schroering AG, Williams KJ. Rapid induction of chromatin-associated DNA mismatch repair proteins after MNNG treatment. DNA Repair (Amst) 2008; 7:951-69. [PMID: 18468964 DOI: 10.1016/j.dnarep.2008.03.023] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2007] [Revised: 03/07/2008] [Accepted: 03/23/2008] [Indexed: 12/18/2022]
Abstract
Treatment with low concentrations of monofunctional alkylating agents induces a G2 arrest only after the second round of DNA synthesis in mammalian cells and requires a proficient mismatch repair (MMR) pathway. Here, we have investigated rapid alkylation-induced recruitment of DNA repair proteins to chromosomal DNA within synchronized populations of MMR proficient cells (HeLa MR) after N-methyl-N'-nitro-N-nitrosoguanidine (MNNG) treatment. Within the first hour, the concentrations of MutS alpha and PCNA increase well beyond their constitutive chromosomally bound levels and MutL alpha is newly recruited to the chromatin-bound MutS alpha. Remarkably, immunoprecipitation experiments demonstrate rapid association of these proteins on the alkylation-damaged chromatin, even when DNA replication is completely blocked. The extent of association of PCNA and MMR proteins on the chromatin is dependent upon the concentration of MNNG and on the specific type of replication block. A subpopulation of the MutS alpha-associated PCNA also becomes monoubiquitinated, a known requirement for PCNA to interact with translesion synthesis (TLS) polymerases. In addition, chromatin-bound SMC1 and NBS1 proteins, associated with DNA double-strand-breaks (DSBs), become phosphorylated within 1-2h of exposure to MNNG. However, these activated proteins are not co-localized on the chromatin with MutS alpha in response to MNNG exposure. PCNA, MutS alpha/MutL alpha and activated SMC1/NBS1 remain chromatin-bound for at least 6-8h after alkylation damage. Thus, cells that are exposed to low levels of alkylation treatment undergo rapid recruitment to and/or activation of key proteins already on the chromatin without the requirement for DNA replication, apparently via different DNA-damage signaling pathways.
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Affiliation(s)
- Allen G Schroering
- University of Toledo College of Medicine, Health Science Campus, Department of Biochemistry & Cancer Biology, Toledo, OH 43614, USA
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29
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Feitsma H, de Bruijn E, van de Belt J, Nijman IJ, Cuppen E. Mismatch repair deficiency does not enhance ENU mutagenesis in the zebrafish germ line. Mutagenesis 2008; 23:325-9. [PMID: 18469325 DOI: 10.1093/mutage/gen019] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
S(N)1-type alkylating agents such as N-ethyl-N-nitrosourea (ENU) are very potent mutagens. They act by transferring their alkyl group to DNA bases, which, upon mispairing during replication, can cause single base pair mutations in the next replication cycle. As DNA mismatch repair (MMR) proteins are involved in the recognition of alkylation damage, we hypothesized that ENU-induced mutation rates could be increased in a MMR-deficient background, which would be beneficial for mutagenesis approaches. We applied a standard ENU mutagenesis protocol to adult zebrafish deficient in the MMR gene msh6 and heterozygous controls to study the effect of MMR on ENU-induced DNA damage. Dose-dependent lethality was found to be similar for homozygous and heterozygous mutants, indicating that there is no difference in ENU resistance. Mutation discovery by high-throughput dideoxy resequencing of genomic targets in outcrossed progeny of the mutagenized fish did also not reveal any differences in germ line mutation frequency. These results may indicate that the maximum mutation load for zebrafish has been reached with the currently used, highly optimized ENU mutagenesis protocol. Alternatively, the MMR system in the zebrafish germ line may be saturated very rapidly, thereby having a limited effect on high-dose ENU mutagenesis.
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Affiliation(s)
- Harma Feitsma
- Hubrecht Institute and Cancer Genomics Center, 3584 CT Utrecht, The Netherlands
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30
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Schrader CE, Guikema JEJ, Linehan EK, Selsing E, Stavnezer J. Activation-Induced Cytidine Deaminase-Dependent DNA Breaks in Class Switch Recombination Occur during G1 Phase of the Cell Cycle and Depend upon Mismatch Repair. THE JOURNAL OF IMMUNOLOGY 2007; 179:6064-71. [DOI: 10.4049/jimmunol.179.9.6064] [Citation(s) in RCA: 110] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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31
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Dwyer DJ, Kohanski MA, Hayete B, Collins JJ. Gyrase inhibitors induce an oxidative damage cellular death pathway in Escherichia coli. Mol Syst Biol 2007; 3:91. [PMID: 17353933 PMCID: PMC1847949 DOI: 10.1038/msb4100135] [Citation(s) in RCA: 345] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2006] [Accepted: 01/26/2007] [Indexed: 01/08/2023] Open
Abstract
Modulation of bacterial chromosomal supercoiling is a function of DNA gyrase-catalyzed strand breakage and rejoining. This reaction is exploited by both antibiotic and proteic gyrase inhibitors, which trap the gyrase molecule at the DNA cleavage stage. Owing to this interaction, double-stranded DNA breaks are introduced and replication machinery is arrested at blocked replication forks. This immediately results in bacteriostasis and ultimately induces cell death. Here we demonstrate, through a series of phenotypic and gene expression analyses, that superoxide and hydroxyl radical oxidative species are generated following gyrase poisoning and play an important role in cell killing by gyrase inhibitors. We show that superoxide-mediated oxidation of iron–sulfur clusters promotes a breakdown of iron regulatory dynamics; in turn, iron misregulation drives the generation of highly destructive hydroxyl radicals via the Fenton reaction. Importantly, our data reveal that blockage of hydroxyl radical formation increases the survival of gyrase-poisoned cells. Together, this series of biochemical reactions appears to compose a maladaptive response, that serves to amplify the primary effect of gyrase inhibition by oxidatively damaging DNA, proteins and lipids.
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Affiliation(s)
- Daniel J Dwyer
- Program in Molecular Biology, Cell Biology and Biochemistry, Boston University, Boston, MA, USA
- Center for BioDynamics and Center for Advanced Biotechnology, Boston University, Boston, MA, USA
| | - Michael A Kohanski
- Center for BioDynamics and Center for Advanced Biotechnology, Boston University, Boston, MA, USA
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
- Boston University School of Medicine, Boston, MA, USA
| | - Boris Hayete
- Center for BioDynamics and Center for Advanced Biotechnology, Boston University, Boston, MA, USA
- Bioinformatics Program, Boston University, Boston, MA, USA
| | - James J Collins
- Program in Molecular Biology, Cell Biology and Biochemistry, Boston University, Boston, MA, USA
- Center for BioDynamics and Center for Advanced Biotechnology, Boston University, Boston, MA, USA
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
- Bioinformatics Program, Boston University, Boston, MA, USA
- Center for BioDynamics and Department of Biomedical Engineering, Boston University, 44 Cummington Street, Boston, MA 02215, USA. Tel.: +617 353 0390; Fax: +617 353 5462;
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32
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Abstract
A number of human genetic diseases have come to be described as being defective in DNA repair. The minimum criterion on which this assignment is based is hypersensitivity to the clastogenic or lethal action of specific DNA damaging agents. In one disease, xeroderma pigmentosum, the molecular evidence for a defect in DNA repair is unequivocal. This condition then acts as a model for dissecting others. For the other diseases the formal evidence for defects in repair is less secure or even lacking. The evidence for repair in each disease is assembled together with any methods that have been used to support the differential diagnosis or for prenatal diagnosis. Attempts to clone human DNA repair genes are in hand and may provide the necessary evidence to decide if all the putative DNA repair defective diseases are genuine. Neoplastic disease and neurological degeneration together with immune defects are frequent clinical features linking this set of diseases, suggesting that effective DNA repair may be important in many aspects of human health.
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