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Ahmed A, Kato N, Gautier J. Replication-Independent ICL Repair: From Chemotherapy to Cell Homeostasis. J Mol Biol 2024; 436:168618. [PMID: 38763228 DOI: 10.1016/j.jmb.2024.168618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 05/03/2024] [Accepted: 05/15/2024] [Indexed: 05/21/2024]
Abstract
Interstrand crosslinks (ICLs) are a type of covalent lesion that can prevent transcription and replication by inhibiting DNA strand separation and instead trigger cell death. ICL inducing compounds are commonly used as chemotherapies due to their effectiveness in inhibiting cell proliferation. Naturally occurring crosslinking agents formed from metabolic processes can also pose a challenge to genome stability especially in slowly or non-dividing cells. Cells maintain a variety of ICL repair mechanisms to cope with this stressor within and outside the S phase of the cell cycle. Here, we discuss the mechanisms of various replication-independent ICL repair pathways and how crosslink repair efficiency is tied to aging and disease.
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Affiliation(s)
- Arooba Ahmed
- Institute for Cancer Genetics, Columbia University Vagelos, College of Physicians and Surgeons, New York, NY, USA
| | - Niyo Kato
- Institute for Cancer Genetics, Columbia University Vagelos, College of Physicians and Surgeons, New York, NY, USA
| | - Jean Gautier
- Institute for Cancer Genetics, Columbia University Vagelos, College of Physicians and Surgeons, New York, NY, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Vagelos, College of Physicians and Surgeons, New York, NY, USA; Department of Genetics and Development, Columbia University Vagelos, College of Physicians and Surgeons, New York, NY, USA.
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2
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Somashekara SC, Dhyani KM, Thakur M, Muniyappa K. SUMOylation of yeast Pso2 enhances its translocation and accumulation in the mitochondria and suppresses methyl methanesulfonate-induced mitochondrial DNA damage. Mol Microbiol 2023; 120:587-607. [PMID: 37649278 DOI: 10.1111/mmi.15145] [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: 03/27/2023] [Revised: 08/01/2023] [Accepted: 08/09/2023] [Indexed: 09/01/2023]
Abstract
Saccharomyces cerevisiae Pso2/SNM1 is essential for DNA interstrand crosslink (ICL) repair; however, its mechanism of action remains incompletely understood. While recent work has revealed that Pso2/Snm1 is dual-localized in the nucleus and mitochondria, it remains unclear whether cell-intrinsic and -extrinsic factors regulate its subcellular localization and function. Herein, we show that Pso2 undergoes ubiquitination and phosphorylation, but not SUMOylation, in unstressed cells. Unexpectedly, we found that methyl methanesulfonate (MMS), rather than ICL-forming agents, induced robust SUMOylation of Pso2 on two conserved residues, K97 and K575, and that SUMOylation markedly increased its abundance in the mitochondria. Reciprocally, SUMOylation had no discernible impact on Pso2 translocation to the nucleus, despite the presence of steady-state levels of SUMOylated Pso2 across the cell cycle. Furthermore, substitution of the invariant residues K97 and K575 by arginine in the Pso2 SUMO consensus motifs severely impaired SUMOylation and abolished its translocation to the mitochondria of MMS-treated wild type cells, but not in unstressed cells. We demonstrate that whilst Siz1 and Siz2 SUMO E3 ligases catalyze Pso2 SUMOylation, the former plays a dominant role. Notably, we found that the phenotypic characteristics of the SUMOylation-defective mutant Pso2K97R/K575R closely mirrored those observed in the Pso2Δ petite mutant. Additionally, leveraging next-generation sequencing analysis, we demonstrate that Pso2 mitigates MMS-induced damage to mitochondrial DNA (mtDNA). Viewed together, our work offers previously unknown insights into the link between genotoxic stress-induced SUMOylation of Pso2 and its preferential targeting to the mitochondria, as well as its role in attenuating MMS-induced mtDNA damage.
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Affiliation(s)
| | - Kshitiza M Dhyani
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Manoj Thakur
- Sri Venkateswara College, University of Delhi, New Delhi, India
| | - Kalappa Muniyappa
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
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3
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Martinez MZ, Olmo F, Taylor MC, Caudron F, Wilkinson SR. Dissecting the interstrand crosslink DNA repair system of Trypanosoma cruzi. DNA Repair (Amst) 2023; 125:103485. [PMID: 36989950 DOI: 10.1016/j.dnarep.2023.103485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 03/08/2023] [Accepted: 03/13/2023] [Indexed: 03/18/2023]
Abstract
DNA interstrand crosslinks (ICLs) are toxic lesions that can block essential biological processes. Here we show Trypanosoma cruzi, the causative agent of Chagas disease, is susceptible to ICL-inducing compounds including mechlorethamine and novel nitroreductase-activated prodrugs that have potential in treating this infection. To resolve such lesions, cells co-opt enzymes from "classical" DNA repair pathways that alongside dedicated factors operate in replication-dependent and -independent mechanisms. To assess ICL repair in T. cruzi, orthologues of SNM1, MRE11 and CSB were identified and their function assessed. The T. cruzi enzymes could complement the mechlorethamine susceptibility phenotype displayed by corresponding yeast and/or T. brucei null confirming their role as ICL repair factors while GFP-tagged TcSNM1, TcMRE11 and TcCSB were shown to localise to the nuclei of insect and/or intracellular form parasites. Gene disruption demonstrated that while each activity was non-essential for T. cruzi viability, nulls displayed a growth defect in at least one life cycle stage with TcMRE11-deficient trypomastigotes also compromised in mammalian cell infectivity. Phenotyping revealed all nulls were more susceptible to mechlorethamine than controls, a trait complemented by re-expression of the deleted gene. To assess interplay, the gene disruption approach was extended to generate T. cruzi deficient in TcSNM1/TcMRE11 or in TcSNM1/TcCSB. Analysis demonstrated these activities functioned across two ICL repair pathways with TcSNM1 and TcMRE11 postulated to operate in a replication-dependent system while TcCSB helps resolve transcription-blocking lesions. By unravelling how T. cruzi repairs ICL damage, specific inhibitors targeting repair components could be developed and used to increase the potency of trypanocidal ICL-inducing compounds.
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Affiliation(s)
- Monica Zavala Martinez
- School of Biological & Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Francisco Olmo
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK
| | - Martin C Taylor
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK
| | - Fabrice Caudron
- School of Biological & Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Shane R Wilkinson
- School of Biological & Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK.
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4
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Hrq1/RECQL4 regulation is critical for preventing aberrant recombination during DNA intrastrand crosslink repair and is upregulated in breast cancer. PLoS Genet 2022; 18:e1010122. [PMID: 36126066 PMCID: PMC9488787 DOI: 10.1371/journal.pgen.1010122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 08/18/2022] [Indexed: 11/19/2022] Open
Abstract
Human RECQL4 is a member of the RecQ family of DNA helicases and functions during DNA replication and repair. RECQL4 mutations are associated with developmental defects and cancer. Although RECQL4 mutations lead to disease, RECQL4 overexpression is also observed in cancer, including breast and prostate. Thus, tight regulation of RECQL4 protein levels is crucial for genome stability. Because mammalian RECQL4 is essential, how cells regulate RECQL4 protein levels is largely unknown. Utilizing budding yeast, we investigated the RECQL4 homolog, HRQ1, during DNA crosslink repair. We find that Hrq1 functions in the error-free template switching pathway to mediate DNA intrastrand crosslink repair. Although Hrq1 mediates repair of cisplatin-induced lesions, it is paradoxically degraded by the proteasome following cisplatin treatment. By identifying the targeted lysine residues, we show that preventing Hrq1 degradation results in increased recombination and mutagenesis. Like yeast, human RECQL4 is similarly degraded upon exposure to crosslinking agents. Furthermore, over-expression of RECQL4 results in increased RAD51 foci, which is dependent on its helicase activity. Using bioinformatic analysis, we observe that RECQL4 overexpression correlates with increased recombination and mutations. Overall, our study uncovers a role for Hrq1/RECQL4 in DNA intrastrand crosslink repair and provides further insight how misregulation of RECQL4 can promote genomic instability, a cancer hallmark. RECQL4 is a DNA helicase and functions during DNA replication and repair. While loss-of-function RECQL4 mutations are found in diseases characterized by developmental defects and cancer, such as Rothmund-Thomson syndrome, over-expression of RECQL4 is also observed in cancer, such as breast cancer. Therefore, RECQL4 protein expression must be tightly regulated. Here we used the budding yeast homolog of RECQL4, Hrq1, and discovered that overexpression of Hrq1 protein levels result in increased recombination and mutations, both cancer hallmarks. We find that Hrq1 functions to mediate repair of a specific type of DNA damage, intrastrand crosslinks, which occur when DNA nucleotides on the same strand are chemically linked together. These findings are also conserved in humans suggesting a common mechanism between yeast Hrq1 and human RECQL4. Overall, our study identifies a conserved role for RECQL4 in DNA intrastrand crosslink repair and provides insights into how its misregulation could promote cancer development.
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5
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Somashekara SC, Muniyappa K. Dual targeting of Saccharomyces cerevisiae Pso2 to mitochondria and the nucleus, and its functional relevance in the repair of DNA interstrand crosslinks. G3 (BETHESDA, MD.) 2022; 12:jkac066. [PMID: 35482533 PMCID: PMC9157068 DOI: 10.1093/g3journal/jkac066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 03/15/2022] [Indexed: 11/12/2022]
Abstract
Repair of DNA interstrand crosslinks involves a functional interplay among different DNA surveillance and repair pathways. Previous work has shown that interstrand crosslink-inducing agents cause damage to Saccharomyces cerevisiae nuclear and mitochondrial DNA, and its pso2/snm1 mutants exhibit a petite phenotype followed by loss of mitochondrial DNA integrity and copy number. Complex as it is, the cause and underlying molecular mechanisms remains elusive. Here, by combining a wide range of approaches with in vitro and in vivo analyses, we interrogated the subcellular localization and function of Pso2. We found evidence that the nuclear-encoded Pso2 contains 1 mitochondrial targeting sequence and 2 nuclear localization signals (NLS1 and NLS2), although NLS1 resides within the mitochondrial targeting sequence. Further analysis revealed that Pso2 is a dual-localized interstrand crosslink repair protein; it can be imported into both nucleus and mitochondria and that genotoxic agents enhance its abundance in the latter. While mitochondrial targeting sequence is essential for mitochondrial Pso2 import, either NLS1 or NLS2 is sufficient for its nuclear import; this implies that the 2 nuclear localization signal motifs are functionally redundant. Ablation of mitochondrial targeting sequence abrogated mitochondrial Pso2 import, and concomitantly, raised its levels in the nucleus. Strikingly, mutational disruption of both nuclear localization signal motifs blocked the nuclear Pso2 import; at the same time, they enhanced its translocation into the mitochondria, consistent with the notion that the relationship between mitochondrial targeting sequence and nuclear localization signal motifs is competitive. However, the nuclease activity of import-deficient species of Pso2 was not impaired. The potential relevance of dual targeting of Pso2 into 2 DNA-bearing organelles is discussed.
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Affiliation(s)
| | - Kalappa Muniyappa
- Department of Biochemistry, Indian Institute of Science, Bangalore 560 012, India
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6
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Pérez-Martínez L, Wagner T, Luke B. Telomere Interacting Proteins and TERRA Regulation. Front Genet 2022; 13:872636. [PMID: 35464834 PMCID: PMC9024143 DOI: 10.3389/fgene.2022.872636] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 03/17/2022] [Indexed: 01/10/2023] Open
Abstract
Telomere shortening rates inversely correlate with life expectancy and hence it is critical to understand how telomere shortening is regulated. Recently, the telomeric non-coding RNA, TERRA has been implicated in the regulation of replicative senescence. To better understand how TERRA is regulated we employed a proteomics approach to look for potential RNA regulators that associate with telomeric sequences. Based on the results, we have identified proteins that may regulate TERRA in both a positive and negative manner, depending on the state of the telomere. In this mini-review, we discuss and speculate about these data to expand our understanding of TERRA and telomere interactors with respect to telomere shortening dynamics.
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Affiliation(s)
- Lara Pérez-Martínez
- Institute of Molecular Biology (IMB), Mainz, Germany
- IMDEA Food Institute, Madrid, Spain
| | - Tina Wagner
- Institute of Molecular Biology (IMB), Mainz, Germany
- Institute of Developmental Biology and Neurobiology (IDN), Johannes Gutenberg Universität, Mainz, Germany
| | - Brian Luke
- Institute of Molecular Biology (IMB), Mainz, Germany
- Institute of Developmental Biology and Neurobiology (IDN), Johannes Gutenberg Universität, Mainz, Germany
- *Correspondence: Brian Luke,
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7
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Sakellariou D, Bak ST, Isik E, Barroso SI, Porro A, Aguilera A, Bartek J, Janscak P, Peña-Diaz J. MutSβ regulates G4-associated telomeric R-loops to maintain telomere integrity in ALT cancer cells. Cell Rep 2022; 39:110602. [PMID: 35385755 DOI: 10.1016/j.celrep.2022.110602] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 12/17/2021] [Accepted: 03/10/2022] [Indexed: 12/24/2022] Open
Abstract
Up to 15% of human cancers maintain their telomeres through a telomerase-independent mechanism, termed "alternative lengthening of telomeres" (ALT) that relies on homologous recombination between telomeric sequences. Emerging evidence suggests that the recombinogenic nature of ALT telomeres results from the formation of RNA:DNA hybrids (R-loops) between telomeric DNA and the long-noncoding telomeric repeat-containing RNA (TERRA). Here, we show that the mismatch repair protein MutSβ, a heterodimer of MSH2 and MSH3 subunits, is enriched at telomeres in ALT cancer cells, where it prevents the accumulation of telomeric G-quadruplex (G4) structures and R-loops. Cells depleted of MSH3 display increased incidence of R-loop-dependent telomere fragility and accumulation of telomeric C-circles. We also demonstrate that purified MutSβ recognizes and destabilizes G4 structures in vitro. These data suggest that MutSβ destabilizes G4 structures in ALT telomeres to regulate TERRA R-loops, which is a prerequisite for maintenance of telomere integrity during ALT.
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Affiliation(s)
- Despoina Sakellariou
- Center for Healthy Aging, Department of Neuroscience and Pharmacology, University of Copenhagen, 2200 Copenhagen, Denmark; Danish Cancer Society Research Center, 2100 Copenhagen, Denmark
| | - Sara Thornby Bak
- Center for Healthy Aging, Department of Neuroscience and Pharmacology, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Esin Isik
- Institute of Molecular Cancer Research, University of Zurich, 8057 Zürich, Switzerland
| | - Sonia I Barroso
- Centro Andaluz de Biología Molecular y Medicina Regenerativa CABIMER, University of Seville-CSIC-UPO, Seville, Spain
| | - Antonio Porro
- Institute of Molecular Cancer Research, University of Zurich, 8057 Zürich, Switzerland
| | - Andrés Aguilera
- Centro Andaluz de Biología Molecular y Medicina Regenerativa CABIMER, University of Seville-CSIC-UPO, Seville, Spain
| | - Jiri Bartek
- Danish Cancer Society Research Center, 2100 Copenhagen, Denmark; Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Science for Life Laboratory, Karolinska Institute, 17177 Stockholm, Sweden; Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, 14300 Prague, Czech Republic
| | - Pavel Janscak
- Institute of Molecular Cancer Research, University of Zurich, 8057 Zürich, Switzerland; Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, 14300 Prague, Czech Republic.
| | - Javier Peña-Diaz
- Center for Healthy Aging, Department of Neuroscience and Pharmacology, University of Copenhagen, 2200 Copenhagen, Denmark.
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8
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Acute Exposure to Bisphenol A Causes Oxidative Stress Induction with Mitochondrial Origin in Saccharomyces cerevisiae Cells. J Fungi (Basel) 2021; 7:jof7070543. [PMID: 34356922 PMCID: PMC8303452 DOI: 10.3390/jof7070543] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 07/05/2021] [Indexed: 02/06/2023] Open
Abstract
Bisphenol A (BPA) is a major component of the most commonly used plastic products, such as disposable plastics, Tetra Paks, cans, sport protective equipment, or medical devices. Due to the accumulation of excessive amounts of plastic waste and the subsequent release of BPA into the environment, BPA is classified as a pollutant that is undesirable in the environment. To date, the most interesting finding is the ability of BPA to act as an endocrine disrupting compound due to its binding to estrogen receptors (ERs), and adverse physiological effects on living organisms may result from this action. Since evidence of the potential pro-oxidizing effects of BPA has accumulated over the last years, herein, we focus on the detection of oxidative stress and its origin following BPA exposure using pulsed-field gel electrophoresis, flow cytometry, fluorescent microscopy, and Western blot analysis. Saccharomyces cerevisiae cells served as a model system, as these cells lack ERs allowing us to dissect the ER-dependent and -independent effects of BPA. Our data show that high concentrations of BPA affect cell survival and cause increased intracellular oxidation in yeast, which is primarily generated in the mitochondrion. However, an acute BPA exposure does not lead to significant oxidative damage to DNA or proteins.
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9
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Rogers CM, Simmons Iii RH, Fluhler Thornburg GE, Buehler NJ, Bochman ML. Fanconi anemia-independent DNA inter-strand crosslink repair in eukaryotes. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2020; 158:33-46. [PMID: 32877700 DOI: 10.1016/j.pbiomolbio.2020.08.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 08/21/2020] [Indexed: 02/07/2023]
Abstract
DNA inter-strand crosslinks (ICLs) are dangerous lesions that can be caused by a variety of endogenous and exogenous bifunctional compounds. Because covalently linking both strands of the double helix locally disrupts DNA replication and transcription, failure to remove even a single ICL can be fatal to the cell. Thus, multiple ICL repair pathways have evolved, with the best studied being the canonical Fanconi anemia (FA) pathway. However, recent research demonstrates that different types of ICLs (e.g., backbone distorting vs. non-distorting) can be discriminated by the cell, which then mounts a specific repair response using the FA pathway or one of a variety of FA-independent ICL repair pathways. This review focuses on the latter, covering current work on the transcription-coupled, base excision, acetaldehyde-induced, and SNM1A/RecQ4 ICL repair pathways and highlighting unanswered questions in the field. Answering these questions will provide mechanistic insight into the various pathways of ICL repair and enable ICL-inducing agents to be more effectively used as chemotherapeutics.
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Affiliation(s)
- Cody M Rogers
- Molecular and Cellular Biochemistry Department, Indiana University, 212 S. Hawthorne Dr., Simon Hall MSB1 room 405B, Bloomington, IN, 47405, USA
| | - Robert H Simmons Iii
- Molecular and Cellular Biochemistry Department, Indiana University, 212 S. Hawthorne Dr., Simon Hall MSB1 room 405B, Bloomington, IN, 47405, USA
| | - Gabriella E Fluhler Thornburg
- Molecular and Cellular Biochemistry Department, Indiana University, 212 S. Hawthorne Dr., Simon Hall MSB1 room 405B, Bloomington, IN, 47405, USA
| | - Nicholas J Buehler
- Molecular and Cellular Biochemistry Department, Indiana University, 212 S. Hawthorne Dr., Simon Hall MSB1 room 405B, Bloomington, IN, 47405, USA
| | - Matthew L Bochman
- Molecular and Cellular Biochemistry Department, Indiana University, 212 S. Hawthorne Dr., Simon Hall MSB1 room 405B, Bloomington, IN, 47405, USA.
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10
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Rogers CM, Lee CY, Parkins S, Buehler NJ, Wenzel S, Martínez-Márquez F, Takagi Y, Myong S, Bochman ML. The yeast Hrq1 helicase stimulates Pso2 translesion nuclease activity and thereby promotes DNA interstrand crosslink repair. J Biol Chem 2020; 295:8945-8957. [PMID: 32371399 PMCID: PMC7335788 DOI: 10.1074/jbc.ra120.013626] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 05/05/2020] [Indexed: 12/11/2022] Open
Abstract
DNA interstrand crosslink (ICL) repair requires a complex network of DNA damage response pathways. Removal of the ICL lesions is vital, as they are physical barriers to essential DNA processes that require the separation of duplex DNA, such as replication and transcription. The Fanconi anemia (FA) pathway is the principal mechanism for ICL repair in metazoans and is coupled to DNA replication. In Saccharomyces cerevisiae, a vestigial FA pathway is present, but ICLs are predominantly repaired by a pathway involving the Pso2 nuclease, which is hypothesized to use its exonuclease activity to digest through the lesion to provide access for translesion polymerases. However, Pso2 lacks translesion nuclease activity in vitro, and mechanistic details of this pathway are lacking, especially relative to FA. We recently identified the Hrq1 helicase, a homolog of the disease-linked enzyme RecQ-like helicase 4 (RECQL4), as a component of Pso2-mediated ICL repair. Here, using genetic, biochemical, and biophysical approaches, including single-molecule FRET (smFRET)- and gel-based nuclease assays, we show that Hrq1 stimulates the Pso2 nuclease through a mechanism that requires Hrq1 catalytic activity. Importantly, Hrq1 also stimulated Pso2 translesion nuclease activity through a site-specific ICL in vitro We noted that stimulation of Pso2 nuclease activity is specific to eukaryotic RecQ4 subfamily helicases, and genetic and biochemical data suggest that Hrq1 likely interacts with Pso2 through their N-terminal domains. These results advance our understanding of FA-independent ICL repair and establish a role for the RecQ4 helicases in the repair of these detrimental DNA lesions.
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Affiliation(s)
- Cody M Rogers
- Molecular and Cellular Biochemistry Department, Indiana University, Bloomington, Indiana, USA
| | - Chun-Ying Lee
- Department of Biophysics, Johns Hopkins University, Baltimore, Maryland, USA
| | - Samuel Parkins
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, USA
| | - Nicholas J Buehler
- Molecular and Cellular Biochemistry Department, Indiana University, Bloomington, Indiana, USA
| | - Sabine Wenzel
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Francisco Martínez-Márquez
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Yuichiro Takagi
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Sua Myong
- Department of Biophysics, Johns Hopkins University, Baltimore, Maryland, USA
| | - Matthew L Bochman
- Molecular and Cellular Biochemistry Department, Indiana University, Bloomington, Indiana, USA.
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11
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Bernal M, Yang X, Lisby M, Mazón G. The FANCM family Mph1 helicase localizes to the mitochondria and contributes to mtDNA stability. DNA Repair (Amst) 2019; 82:102684. [DOI: 10.1016/j.dnarep.2019.102684] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 07/31/2019] [Accepted: 08/03/2019] [Indexed: 11/24/2022]
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12
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Dattani A, Wilkinson SR. Deciphering the interstrand crosslink DNA repair network expressed by Trypanosoma brucei. DNA Repair (Amst) 2019; 78:154-166. [DOI: 10.1016/j.dnarep.2019.04.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 03/29/2019] [Accepted: 04/24/2019] [Indexed: 10/26/2022]
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13
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Wilson DM, Rieckher M, Williams AB, Schumacher B. Systematic analysis of DNA crosslink repair pathways during development and aging in Caenorhabditis elegans. Nucleic Acids Res 2017; 45:9467-9480. [PMID: 28934497 PMCID: PMC5766164 DOI: 10.1093/nar/gkx660] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 07/18/2017] [Indexed: 01/12/2023] Open
Abstract
DNA interstrand crosslinks (ICLs) are generated by endogenous sources and chemotherapeutics, and pose a threat to genome stability and cell survival. Using Caenorhabditis elegans mutants, we identify DNA repair factors that protect against the genotoxicity of ICLs generated by trioxsalen/ultraviolet A (TMP/UVA) during development and aging. Mutations in nucleotide excision repair (NER) components (e.g. XPA-1 and XPF-1) imparted extreme sensitivity to TMP/UVA relative to wild-type animals, manifested as developmental arrest, defects in adult tissue morphology and functionality, and shortened lifespan. Compensatory roles for global-genome (XPC-1) and transcription-coupled (CSB-1) NER in ICL sensing were exposed. The analysis also revealed contributions of homologous recombination (BRC-1/BRCA1), the MUS-81, EXO-1, SLX-1 and FAN-1 nucleases, and the DOG-1 (FANCJ) helicase in ICL resolution, influenced by the replicative-status of the cell/tissue. No obvious or critical role in ICL repair was seen for non-homologous end-joining (cku-80) or base excision repair (nth-1, exo-3), the Fanconi-related proteins BRC-2 (BRCA2/FANCD1) and FCD-2 (FANCD2), the WRN-1 or HIM-6 (BLM) helicases, or the GEN-1 or MRT-1 (SNM1) nucleases. Our efforts uncover replication-dependent and -independent ICL repair networks, and establish nematodes as a model for investigating the repair and consequences of DNA crosslinks in metazoan development and in adult post-mitotic and proliferative germ cells.
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Affiliation(s)
- David M Wilson
- Laboratory of Molecular Gerontology, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Matthias Rieckher
- Institute for Genome Stability in Aging and Disease, Medical Faculty, Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), Center for Molecular Medicine Cologne (CMMC) and Systems Biology of Ageing Cologne (Sybacol), University of Cologne, Joseph-Stelzmann-Strasse 26, 50931 Cologne, Germany
| | - Ashley B Williams
- Institute for Genome Stability in Aging and Disease, Medical Faculty, Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), Center for Molecular Medicine Cologne (CMMC) and Systems Biology of Ageing Cologne (Sybacol), University of Cologne, Joseph-Stelzmann-Strasse 26, 50931 Cologne, Germany
| | - Björn Schumacher
- Institute for Genome Stability in Aging and Disease, Medical Faculty, Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), Center for Molecular Medicine Cologne (CMMC) and Systems Biology of Ageing Cologne (Sybacol), University of Cologne, Joseph-Stelzmann-Strasse 26, 50931 Cologne, Germany
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14
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Rogers CM, Wang JCY, Noguchi H, Imasaki T, Takagi Y, Bochman ML. Yeast Hrq1 shares structural and functional homology with the disease-linked human RecQ4 helicase. Nucleic Acids Res 2017; 45:5217-5230. [PMID: 28334827 PMCID: PMC5605238 DOI: 10.1093/nar/gkx151] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 02/22/2017] [Indexed: 12/14/2022] Open
Abstract
The five human RecQ helicases participate in multiple processes required to maintain genome integrity. Of these, the disease-linked RecQ4 is the least studied because it poses many technical challenges. We previously demonstrated that the yeast Hrq1 helicase displays similar functions to RecQ4 in vivo, and here, we report the biochemical and structural characterization of these enzymes. In vitro, Hrq1 and RecQ4 are DNA-stimulated ATPases and robust helicases. Further, these activities were sensitive to DNA sequence and structure, with the helicases preferentially unwinding D-loops. Consistent with their roles at telomeres, telomeric repeat sequence DNA also stimulated binding and unwinding by these enzymes. Finally, electron microscopy revealed that Hrq1 and RecQ4 share similar structural features. These results solidify Hrq1 as a true RecQ4 homolog and position it as the premier model to determine how RecQ4 mutations lead to genomic instability and disease.
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Affiliation(s)
- Cody M Rogers
- Molecular and Cellular Biochemistry Department, Indiana University, Bloomington, IN 47405, USA
| | | | - Hiroki Noguchi
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Tsuyoshi Imasaki
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Yuichiro Takagi
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Matthew L Bochman
- Molecular and Cellular Biochemistry Department, Indiana University, Bloomington, IN 47405, USA
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15
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Ward TA, McHugh PJ, Durant ST. Small molecule inhibitors uncover synthetic genetic interactions of human flap endonuclease 1 (FEN1) with DNA damage response genes. PLoS One 2017. [PMID: 28628639 PMCID: PMC5476263 DOI: 10.1371/journal.pone.0179278] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Flap endonuclease 1 (FEN1) is a structure selective endonuclease required for proficient DNA replication and the repair of DNA damage. Cellularly active inhibitors of this enzyme have previously been shown to induce a DNA damage response and, ultimately, cell death. High-throughput screens of human cancer cell-lines identify colorectal and gastric cell-lines with microsatellite instability (MSI) as enriched for cellular sensitivity to N-hydroxyurea series inhibitors of FEN1, but not the PARP inhibitor olaparib or other inhibitors of the DNA damage response. This sensitivity is due to a synthetic lethal interaction between FEN1 and MRE11A, which is often mutated in MSI cancers through instabilities at a poly(T) microsatellite repeat. Disruption of ATM is similarly synthetic lethal with FEN1 inhibition, suggesting that disruption of FEN1 function leads to the accumulation of DNA double-strand breaks. These are likely a result of the accumulation of aberrant replication forks, that accumulate as a consequence of a failure in Okazaki fragment maturation, as inhibition of FEN1 is toxic in cells disrupted for the Fanconi anemia pathway and post-replication repair. Furthermore, RAD51 foci accumulate as a consequence of FEN1 inhibition and the toxicity of FEN1 inhibitors increases in cells disrupted for the homologous recombination pathway, suggesting a role for homologous recombination in the resolution of damage induced by FEN1 inhibition. Finally, FEN1 appears to be required for the repair of damage induced by olaparib and cisplatin within the Fanconi anemia pathway, and may play a role in the repair of damage associated with its own disruption.
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Affiliation(s)
- Thomas A. Ward
- AstraZeneca, Innovative Medicines and Early Development Biotech Unit, Oncology Bioscience, Alderley Park, Macclesfield, Cheshire, United Kingdom
- Department of Oncology, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
- * E-mail: (TAW); (STD)
| | - Peter J. McHugh
- Department of Oncology, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - Stephen T. Durant
- AstraZeneca, Innovative Medicines and Early Development Biotech Unit, Oncology Bioscience, Alderley Park, Macclesfield, Cheshire, United Kingdom
- AstraZeneca, Innovative Medicines and Early Development Biotech Unit, Oncology Bioscience, Little Chesterford, Cambridge, United Kingdom
- * E-mail: (TAW); (STD)
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16
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MIYAKAWA I. Organization and dynamics of yeast mitochondrial nucleoids. PROCEEDINGS OF THE JAPAN ACADEMY. SERIES B, PHYSICAL AND BIOLOGICAL SCIENCES 2017; 93:339-359. [PMID: 28496055 PMCID: PMC5489437 DOI: 10.2183/pjab.93.021] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Mitochondrial DNA (mtDNA) is packaged by association with specific proteins in compact DNA-protein complexes named mitochondrial nucleoids (mt-nucleoids). The budding yeast Saccharomyces cerevisiae is able to grow either aerobically or anaerobically. Due to this characteristic, S. cerevisiae has been extensively used as a model organism to study genetics, morphology and biochemistry of mitochondria for a long time. Mitochondria of S. cerevisiae frequently fuse and divide, and perform dynamic morphological changes depending on the culture conditions and the stage of life cycle of the yeast cells. The mt-nucleoids also dynamically change their morphology, accompanying morphological changes of mitochondria. The mt-nucleoids have been isolated morphologically intact and functional analyses of mt-nucleoid proteins have been extensively performed. These studies have revealed that the functions of mt-nucleoid proteins are essential for maintenance of mtDNA. The aims of this review are to summarize the history on the research of yeast mt-nucleoids as well as recent findings on the organization of the mt-nucleoids and mitochondrial dynamics.
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Affiliation(s)
- Isamu MIYAKAWA
- Department of Biology, Faculty of Science, Yamaguchi University, Yamaguchi, Japan
- Correspondence should be addressed: I. Miyakawa, Department of Biology, Faculty of Science, Yamaguchi University, 1677-1 Yoshida, Yamaguchi 753-8512, Japan (e-mail: )
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17
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Rendeková J, Ward TA, Šimoničová L, Thomas PH, Nosek J, Tomáška Ľ, McHugh PJ, Chovanec M. Mgm101: A double-duty Rad52-like protein. Cell Cycle 2016; 15:3169-3176. [PMID: 27636878 PMCID: PMC5176325 DOI: 10.1080/15384101.2016.1231288] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Mgm101 has well-characterized activity for the repair and replication of the mitochondrial genome. Recent work has demonstrated a further role for Mgm101 in nuclear DNA metabolism, contributing to an S-phase specific DNA interstrand cross-link repair pathway that acts redundantly with a pathway controlled by Pso2 exonuclease. Due to involvement of FANCM, FANCJ and FANCP homologues (Mph1, Chl1 and Slx4), this pathway has been described as a Fanconi anemia-like pathway. In this pathway, Mgm101 physically interacts with the DNA helicase Mph1 and the MutSα (Msh2/Msh6) heterodimer, but its precise role is yet to be elucidated. Data presented here suggests that Mgm101 functionally overlaps with Rad52, supporting previous suggestions that, based on protein structure and biochemical properties, Mgm101 and Rad52 belong to a family of proteins with similar function. In addition, our data shows that this overlap extends to the function of both proteins at telomeres, where Mgm101 is required for telomere elongation during chromosome replication in rad52 defective cells. We hypothesize that Mgm101 could, in Rad52-like manner, preferentially bind single-stranded DNAs (such as at stalled replication forks, broken chromosomes and natural chromosome ends), stabilize them and mediate single-strand annealing-like homologous recombination event to prevent them from converting into toxic structures.
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Affiliation(s)
- Jana Rendeková
- a Department of Genetics , Cancer Research Institute, Biomedical Research Center, Slovak Academy of Science , Bratislava , Slovak Republic
| | - Thomas A Ward
- b Department of Oncology , Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital , Oxford , UK
| | - Lucia Šimoničová
- c Department of Genetics , Faculty of Natural Sciences, Comenius University , Bratislava , Slovakia
| | - Peter H Thomas
- b Department of Oncology , Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital , Oxford , UK
| | - Jozef Nosek
- d Department of Biochemistry , Faculty of Natural Sciences, Comenius University , Bratislava , Slovakia
| | - Ľubomír Tomáška
- c Department of Genetics , Faculty of Natural Sciences, Comenius University , Bratislava , Slovakia
| | - Peter J McHugh
- b Department of Oncology , Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital , Oxford , UK
| | - Miroslav Chovanec
- a Department of Genetics , Cancer Research Institute, Biomedical Research Center, Slovak Academy of Science , Bratislava , Slovak Republic
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18
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Mte1 interacts with Mph1 and promotes crossover recombination and telomere maintenance. Genes Dev 2016; 30:700-17. [PMID: 26966248 PMCID: PMC4803055 DOI: 10.1101/gad.276204.115] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Accepted: 02/17/2016] [Indexed: 11/25/2022]
Abstract
Silva et al. identify Mte1 as a novel interactor of the Mph1 helicase in Saccharomyces cerevisiae. Their data indicate that Mte1 plays a role in regulation of crossover recombination, response to replication stress, and telomere maintenance. Mph1 is a member of the conserved FANCM family of DNA motor proteins that play key roles in genome maintenance processes underlying Fanconi anemia, a cancer predisposition syndrome in humans. Here, we identify Mte1 as a novel interactor of the Mph1 helicase in Saccharomyces cerevisiae. In vitro, Mte1 (Mph1-associated telomere maintenance protein 1) binds directly to DNA with a preference for branched molecules such as D loops and fork structures. In addition, Mte1 stimulates the helicase and fork regression activities of Mph1 while inhibiting the ability of Mph1 to dissociate recombination intermediates. Deletion of MTE1 reduces crossover recombination and suppresses the sensitivity of mph1Δ mutant cells to replication stress. Mph1 and Mte1 interdependently colocalize at DNA damage-induced foci and dysfunctional telomeres, and MTE1 deletion results in elongated telomeres. Taken together, our data indicate that Mte1 plays a role in regulation of crossover recombination, response to replication stress, and telomere maintenance.
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19
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Pevala V, Truban D, Bauer JA, Košťan J, Kunová N, Bellová J, Brandstetter M, Marini V, Krejčí L, Tomáška Ľ, Nosek J, Kutejová E. The structure and DNA-binding properties of Mgm101 from a yeast with a linear mitochondrial genome. Nucleic Acids Res 2016; 44:2227-39. [PMID: 26743001 PMCID: PMC4797282 DOI: 10.1093/nar/gkv1529] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Accepted: 12/22/2015] [Indexed: 11/14/2022] Open
Abstract
To study the mechanisms involved in the maintenance of a linear mitochondrial genome we investigated the biochemical properties of the recombination protein Mgm101 from Candida parapsilosis. We show that CpMgm101 complements defects associated with the Saccharomyces cerevisiae mgm101-1(ts) mutation and that it is present in both the nucleus and mitochondrial nucleoids of C. parapsilosis. Unlike its S. cerevisiae counterpart, CpMgm101 is associated with the entire nucleoid population and is able to bind to a broad range of DNA substrates in a non-sequence specific manner. CpMgm101 is also able to catalyze strand annealing and D-loop formation. CpMgm101 forms a roughly C-shaped trimer in solution according to SAXS. Electron microscopy of a complex of CpMgm101 with a model mitochondrial telomere revealed homogeneous, ring-shaped structures at the telomeric single-stranded overhangs. The DNA-binding properties of CpMgm101, together with its DNA recombination properties, suggest that it can play a number of possible roles in the replication of the mitochondrial genome and the maintenance of its telomeres.
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Affiliation(s)
- Vladimír Pevala
- Department of Biochemistry and Structural Biology, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, 845 51 Bratislava, Slovakia
| | - Dominika Truban
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University, Mlynská dolina CH-1, Ilkovičova 6, 842 15 Bratislava, Slovakia
| | - Jacob A Bauer
- Department of Biochemistry and Structural Biology, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, 845 51 Bratislava, Slovakia
| | - Július Košťan
- Department for Structural and Computational Biology, Max F. Perutz Laboratories, Dr. Bohr-Gasse 9 (VBC 5), 1030 Vienna, Austria
| | - Nina Kunová
- Department of Biochemistry and Structural Biology, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, 845 51 Bratislava, Slovakia
| | - Jana Bellová
- Department of Biochemistry and Structural Biology, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, 845 51 Bratislava, Slovakia
| | - Marlene Brandstetter
- Electron Microscopy Facility of the Campus Science Support Facilities GmbH, Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Victoria Marini
- Department of Biology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic National Centre for Biomolecular Research, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Lumír Krejčí
- Department of Biology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic National Centre for Biomolecular Research, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Ľubomír Tomáška
- Department of Genetics, Faculty of Natural Sciences, Comenius University, Mlynská dolina B-1, Ilkovičova 6, 842 15 Bratislava, Slovakia
| | - Jozef Nosek
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University, Mlynská dolina CH-1, Ilkovičova 6, 842 15 Bratislava, Slovakia
| | - Eva Kutejová
- Department of Biochemistry and Structural Biology, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, 845 51 Bratislava, Slovakia Institute of Microbiology of the CAS, v. v. i., 142 20 Prague, Czech Republic
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20
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Abstract
Members of the conserved FANCM family of DNA motor proteins play key roles in genome maintenance processes. In this review, Xue et al. provide an integrated view of the functions and regulation of these enzymes in humans and model organisms and how they advance our understanding of genome maintenance processes. Members of the conserved FANCM family of DNA motor proteins play key roles in genome maintenance processes. FANCM supports genome duplication and repair under different circumstances and also functions in the ATR-mediated DNA damage checkpoint. Some of these roles are shared among lower eukaryotic family members. Human FANCM has been linked to Fanconi anemia, a syndrome characterized by cancer predisposition, developmental disorder, and bone marrow failure. Recent studies on human FANCM and its orthologs from other organisms have provided insights into their biological functions, regulation, and collaboration with other genome maintenance factors. This review summarizes the progress made, with the goal of providing an integrated view of the functions and regulation of these enzymes in humans and model organisms and how they advance our understanding of genome maintenance processes.
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Affiliation(s)
- Xiaoyu Xue
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| | - Patrick Sung
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| | - Xiaolan Zhao
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
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21
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Dong H, Nebert DW, Bruford EA, Thompson DC, Joenje H, Vasiliou V. Update of the human and mouse Fanconi anemia genes. Hum Genomics 2015; 9:32. [PMID: 26596371 PMCID: PMC4657327 DOI: 10.1186/s40246-015-0054-y] [Citation(s) in RCA: 108] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2015] [Accepted: 11/10/2015] [Indexed: 12/24/2022] Open
Abstract
Fanconi anemia (FA) is a recessively inherited disease manifesting developmental abnormalities, bone marrow failure, and increased risk of malignancies. Whereas FA has been studied for nearly 90 years, only in the last 20 years have increasing numbers of genes been implicated in the pathogenesis associated with this genetic disease. To date, 19 genes have been identified that encode Fanconi anemia complementation group proteins, all of which are named or aliased, using the root symbol “FANC.” Fanconi anemia subtype (FANC) proteins function in a common DNA repair pathway called “the FA pathway,” which is essential for maintaining genomic integrity. The various FANC mutant proteins contribute to distinct steps associated with FA pathogenesis. Herein, we provide a review update of the 19 human FANC and their mouse orthologs, an evolutionary perspective on the FANC genes, and the functional significance of the FA DNA repair pathway in association with clinical disorders. This is an example of a set of genes––known to exist in vertebrates, invertebrates, plants, and yeast––that are grouped together on the basis of shared biochemical and physiological functions, rather than evolutionary phylogeny, and have been named on this basis by the HUGO Gene Nomenclature Committee (HGNC).
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Affiliation(s)
- Hongbin Dong
- Department of Environmental Health Sciences, Yale School of Public Health, 60 College St, New Haven, CT, 06250, USA
| | - Daniel W Nebert
- Department of Environmental Health and Center for Environmental Genetics, University Cincinnati Medical Center, Cincinnati, OH, 45267-0056, USA
| | - Elspeth A Bruford
- HUGO Gene Nomenclature Committee (HGNC), European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Hinxton, CB10 1SD, UK
| | - David C Thompson
- Department of Clinical Practice, University of Colorado Denver, Aurora, CO, 80045, USA
| | - Hans Joenje
- Department of Clinical Genetics and the Cancer Center Amsterdam/VUmc Institute for Cancer and Immunology, VU University Medical Center, NL-1081 BT, Amsterdam, The Netherlands
| | - Vasilis Vasiliou
- Department of Environmental Health Sciences, Yale School of Public Health, 60 College St, New Haven, CT, 06250, USA.
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22
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Abstract
Figuring out what is wrong in Fanconi anemia (FA) patient cells is critical to understanding the contributions of the FA pathway to DNA repair and tumor suppression. Although FA patients exhibit a wide range of disease manifestation as well as severity (asymptomatic to congenital abnormalities, bone marrow failure, and cancer), cells from FA patients share underlying defects in their ability to process DNA lesions that interfere with DNA replication. In particular, FA cells are very sensitive to agents that induce DNA interstrand crosslinks (ICLs). The cause of this pronounced ICL sensitivity is not fully understood, but has been linked to the aberrant activation of DNA damage repair proteins, checkpoints and pathways. Thus, regulation of these responses through coordination of repair processing at stalled replication forks is an essential function of the FA pathway. Here, we briefly summarize some of the aberrant DNA damage responses contributing to defects in FA cells, and detail the newly-identified relationship between FA and the mismatch repair protein, MSH2. Understanding the contribution of MSH2 and/or other proteins to the replication problem in FA cells will be key to assessing therapeutic options to improve the health of FA patients. Moreover, loss of these factors, if linked to improved replication, could be a key event in the progression of FA cells to cancer cells. Likewise, loss of these factors could synergize to enhance tumorigenesis or confer chemoresistance in tumors defective in FA-BRCA pathway proteins and provide a basis for biomarkers for disease progression and response.
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Affiliation(s)
- Sharon B Cantor
- a Department of Cancer Biology ; University of Massachusetts Medical School; UMASS Memorial Cancer Center ; Worcester , MA USA
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23
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Skoneczna A, Kaniak A, Skoneczny M. Genetic instability in budding and fission yeast-sources and mechanisms. FEMS Microbiol Rev 2015; 39:917-67. [PMID: 26109598 PMCID: PMC4608483 DOI: 10.1093/femsre/fuv028] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/26/2015] [Indexed: 12/17/2022] Open
Abstract
Cells are constantly confronted with endogenous and exogenous factors that affect their genomes. Eons of evolution have allowed the cellular mechanisms responsible for preserving the genome to adjust for achieving contradictory objectives: to maintain the genome unchanged and to acquire mutations that allow adaptation to environmental changes. One evolutionary mechanism that has been refined for survival is genetic variation. In this review, we describe the mechanisms responsible for two biological processes: genome maintenance and mutation tolerance involved in generations of genetic variations in mitotic cells of both Saccharomyces cerevisiae and Schizosaccharomyces pombe. These processes encompass mechanisms that ensure the fidelity of replication, DNA lesion sensing and DNA damage response pathways, as well as mechanisms that ensure precision in chromosome segregation during cell division. We discuss various factors that may influence genome stability, such as cellular ploidy, the phase of the cell cycle, transcriptional activity of a particular region of DNA, the proficiency of DNA quality control systems, the metabolic stage of the cell and its respiratory potential, and finally potential exposure to endogenous or environmental stress. The stability of budding and fission yeast genomes is influenced by two contradictory factors: (1) the need to be fully functional, which is ensured through the replication fidelity pathways of nuclear and mitochondrial genomes through sensing and repairing DNA damage, through precise chromosome segregation during cell division; and (2) the need to acquire changes for adaptation to environmental challenges.
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Affiliation(s)
- Adrianna Skoneczna
- Laboratory of Mutagenesis and DNA Repair, Institute of Biochemistry and Biophysics, Polish Academy of Science, 02-106 Warsaw, Poland
| | - Aneta Kaniak
- Laboratory of Mutagenesis and DNA Repair, Institute of Biochemistry and Biophysics, Polish Academy of Science, 02-106 Warsaw, Poland
| | - Marek Skoneczny
- Department of Genetics, Institute of Biochemistry and Biophysics, Polish Academy of Science, 02-106 Warsaw, Poland
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24
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Kaniak-Golik A, Skoneczna A. Mitochondria-nucleus network for genome stability. Free Radic Biol Med 2015; 82:73-104. [PMID: 25640729 DOI: 10.1016/j.freeradbiomed.2015.01.013] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Revised: 11/25/2014] [Accepted: 01/13/2015] [Indexed: 12/21/2022]
Abstract
The proper functioning of the cell depends on preserving the cellular genome. In yeast cells, a limited number of genes are located on mitochondrial DNA. Although the mechanisms underlying nuclear genome maintenance are well understood, much less is known about the mechanisms that ensure mitochondrial genome stability. Mitochondria influence the stability of the nuclear genome and vice versa. Little is known about the two-way communication and mutual influence of the nuclear and mitochondrial genomes. Although the mitochondrial genome replicates independent of the nuclear genome and is organized by a distinct set of mitochondrial nucleoid proteins, nearly all genome stability mechanisms responsible for maintaining the nuclear genome, such as mismatch repair, base excision repair, and double-strand break repair via homologous recombination or the nonhomologous end-joining pathway, also act to protect mitochondrial DNA. In addition to mitochondria-specific DNA polymerase γ, the polymerases α, η, ζ, and Rev1 have been found in this organelle. A nuclear genome instability phenotype results from a failure of various mitochondrial functions, such as an electron transport chain activity breakdown leading to a decrease in ATP production, a reduction in the mitochondrial membrane potential (ΔΨ), and a block in nucleotide and amino acid biosynthesis. The loss of ΔΨ inhibits the production of iron-sulfur prosthetic groups, which impairs the assembly of Fe-S proteins, including those that mediate DNA transactions; disturbs iron homeostasis; leads to oxidative stress; and perturbs wobble tRNA modification and ribosome assembly, thereby affecting translation and leading to proteotoxic stress. In this review, we present the current knowledge of the mechanisms that govern mitochondrial genome maintenance and demonstrate ways in which the impairment of mitochondrial function can affect nuclear genome stability.
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Affiliation(s)
- Aneta Kaniak-Golik
- Laboratory of Mutagenesis and DNA Repair, Institute of Biochemistry and Biophysics, Polish Academy of Science, 02-106 Warsaw, Poland
| | - Adrianna Skoneczna
- Laboratory of Mutagenesis and DNA Repair, Institute of Biochemistry and Biophysics, Polish Academy of Science, 02-106 Warsaw, Poland.
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25
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Sullivan JA, Tong JL, Wong M, Kumar A, Sarkar H, Ali S, Hussein I, Zaman I, Meredith EL, Helsby NA, Hu L, Wilkinson SR. Unravelling the role of SNM1 in the DNA repair system ofTrypanosoma brucei. Mol Microbiol 2015; 96:827-38. [DOI: 10.1111/mmi.12973] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/16/2015] [Indexed: 12/31/2022]
Affiliation(s)
- James A. Sullivan
- School of Biological & Chemical Sciences; Queen Mary University of London; Mile End Road London E1 4NS UK
| | - Jie Lun Tong
- School of Biological & Chemical Sciences; Queen Mary University of London; Mile End Road London E1 4NS UK
| | - Martin Wong
- School of Biological & Chemical Sciences; Queen Mary University of London; Mile End Road London E1 4NS UK
| | - Ambika Kumar
- School of Biological & Chemical Sciences; Queen Mary University of London; Mile End Road London E1 4NS UK
| | - Hajrah Sarkar
- School of Biological & Chemical Sciences; Queen Mary University of London; Mile End Road London E1 4NS UK
| | - Sarah Ali
- School of Biological & Chemical Sciences; Queen Mary University of London; Mile End Road London E1 4NS UK
| | - Ikran Hussein
- School of Biological & Chemical Sciences; Queen Mary University of London; Mile End Road London E1 4NS UK
| | - Iqra Zaman
- School of Biological & Chemical Sciences; Queen Mary University of London; Mile End Road London E1 4NS UK
| | - Emma Louise Meredith
- School of Biological & Chemical Sciences; Queen Mary University of London; Mile End Road London E1 4NS UK
| | - Nuala A. Helsby
- Department of Molecular Medicine and Pathology; University of Auckland; Private Bag 92019 Auckland New Zealand
| | - Longqin Hu
- Department of Medicinal Chemistry; Ernest Mario School of Pharmacy; Rutgers; The State University of New Jersey; Piscataway NJ 08854 USA
| | - Shane R. Wilkinson
- School of Biological & Chemical Sciences; Queen Mary University of London; Mile End Road London E1 4NS UK
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26
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Peng M, Xie J, Ucher A, Stavnezer J, Cantor SB. Crosstalk between BRCA-Fanconi anemia and mismatch repair pathways prevents MSH2-dependent aberrant DNA damage responses. EMBO J 2014; 33:1698-712. [PMID: 24966277 PMCID: PMC4194102 DOI: 10.15252/embj.201387530] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Several proteins in the BRCA-Fanconi anemia (FA) pathway, such as FANCJ, BRCA1, and FANCD2, interact with mismatch repair (MMR) pathway factors, but the significance of this link remains unknown. Unlike the BRCA-FA pathway, the MMR pathway is not essential for cells to survive toxic DNA interstrand crosslinks (ICLs), although MMR proteins bind ICLs and other DNA structures that form at stalled replication forks. We hypothesized that MMR proteins corrupt ICL repair in cells that lack crosstalk between BRCA-FA and MMR pathways. Here, we show that ICL sensitivity of cells lacking the interaction between FANCJ and the MMR protein MLH1 is suppressed by depletion of the upstream mismatch recognition factor MSH2. MSH2 depletion suppresses an aberrant DNA damage response, restores cell cycle progression, and promotes ICL resistance through a Rad18-dependent mechanism. MSH2 depletion also suppresses ICL sensitivity in cells deficient for BRCA1 or FANCD2, but not FANCA. Rescue by Msh2 loss was confirmed in Fancd2-null primary mouse cells. Thus, we propose that regulation of MSH2-dependent DNA damage response underlies the importance of interactions between BRCA-FA and MMR pathways.
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Affiliation(s)
- Min Peng
- Department of Cancer Biology, University of Massachusetts Medical School, Women's Cancers Program, UMASS Memorial Cancer Center, Worcester, MA, USA
| | - Jenny Xie
- Department of Cancer Biology, University of Massachusetts Medical School, Women's Cancers Program, UMASS Memorial Cancer Center, Worcester, MA, USA
| | - Anna Ucher
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Women's Cancers Program, UMASS Memorial Cancer Center, Worcester, MA, USA
| | - Janet Stavnezer
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Women's Cancers Program, UMASS Memorial Cancer Center, Worcester, MA, USA
| | - Sharon B Cantor
- Department of Cancer Biology, University of Massachusetts Medical School, Women's Cancers Program, UMASS Memorial Cancer Center, Worcester, MA, USA
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Conditional genetic interactions of RTT107, SLX4, and HRQ1 reveal dynamic networks upon DNA damage in S. cerevisiae. G3-GENES GENOMES GENETICS 2014; 4:1059-69. [PMID: 24700328 PMCID: PMC4065249 DOI: 10.1534/g3.114.011205] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The DNA damage response (DDR) is a dynamic process that is crucial for protecting the cell from challenges to genome integrity. Although many genome-wide studies in Saccharomyces cerevisiae have identified genes that contribute to resistance to DNA-damaging agents, more work is needed to elucidate the changes in genetic interaction networks in response to DNA lesions. Here we used conditional epistatic miniarray profiling to analyze the genetic interaction networks of the DDR genes RTT107, SLX4, and HRQ1 under three DNA-damaging conditions: camptothecin, hydroxyurea, and methyl methanesulfonate. Rtt107 and its interaction partner Slx4 are targets of the checkpoint kinase Mec1, which is central to the DDR-signaling cascades. Hrq1 recently was identified as a novel member of the RecQ helicase family in S. cerevisiae but is still poorly characterized. The conditional genetic networks that we generated revealed functional insights into all three genes and showed that there were varied responses to different DNA damaging agents. We observed that RTT107 had more genetic interactions under camptothecin conditions than SLX4 or HRQ1, suggesting that Rtt107 has an important role in response to this type of DNA lesion. Although RTT107 and SLX4 function together, they also had many distinct genetic interactions. In particular, RTT107 and SLX4 showed contrasting genetic interactions for a few genes, which we validated with independently constructed strains. Interestingly, HRQ1 had a genetic interaction profile that correlated with that of SLX4 and both were enriched for very similar gene ontology terms, suggesting that they function together in the DDR.
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Bochman ML, Paeschke K, Chan A, Zakian VA. Hrq1, a homolog of the human RecQ4 helicase, acts catalytically and structurally to promote genome integrity. Cell Rep 2014; 6:346-56. [PMID: 24440721 DOI: 10.1016/j.celrep.2013.12.037] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Revised: 11/27/2013] [Accepted: 12/24/2013] [Indexed: 11/29/2022] Open
Abstract
Human RecQ4 (hRecQ4) affects cancer and aging but is difficult to study because it is a fusion between a helicase and an essential replication factor. Budding yeast Hrq1 is homologous to the disease-linked helicase domain of RecQ4 and, like hRecQ4, is a robust 3'-5' helicase. Additionally, Hrq1 has the unusual property of forming heptameric rings. Cells lacking Hrq1 exhibited two DNA damage phenotypes: hypersensitivity to DNA interstrand crosslinks (ICLs) and telomere addition to DNA breaks. Both activities are rare; their coexistence in a single protein is unprecedented. Resistance to ICLs requires helicase activity, but suppression of telomere addition does not. Hrq1 also affects telomere length by a noncatalytic mechanism, as well as telomerase-independent telomere maintenance. Because Hrq1 binds telomeres in vivo, it probably affects them directly. Thus, the tumor-suppressing activity of RecQ4 could be due to a role in ICL repair and/or suppression of de novo telomere addition.
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Affiliation(s)
- Matthew L Bochman
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA.
| | - Katrin Paeschke
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Angela Chan
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Virginia A Zakian
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
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Munari FM, Revers LF, Cardone JM, Immich BF, Moura DJ, Guecheva TN, Bonatto D, Laurino JP, Saffi J, Brendel M, Henriques JAP. Sak1 kinase interacts with Pso2 nuclease in response to DNA damage induced by interstrand crosslink-inducing agents in Saccharomyces cerevisiae. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2013; 130:241-53. [PMID: 24362320 DOI: 10.1016/j.jphotobiol.2013.11.024] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2012] [Revised: 11/20/2013] [Accepted: 11/27/2013] [Indexed: 11/29/2022]
Abstract
By isolating putative binding partners through the two-hybrid system (THS) we further extended the characterization of the specific interstrand cross-link (ICL) repair gene PSO2 of Saccharomyces cerevisiae. Nine fusion protein products were isolated for Pso2p using THS, among them the Sak1 kinase, which interacted with the C-terminal β-CASP domain of Pso2p. Comparison of mutagen-sensitivity phenotypes of pso2Δ, sak1Δ and pso2Δsak1Δ disruptants revealed that SAK1 is necessary for complete WT-like repair. The epistatic interaction of both mutant alleles suggests that Sak1p and Pso2p act in the same pathway of controlling sensitivity to DNA-damaging agents. We also observed that Pso2p is phosphorylated by Sak1 kinase in vitro and co-immunoprecipitates with Sak1p after 8-MOP+UVA treatment. Survival data after treatment of pso2Δ, yku70Δ and yku70Δpso2Δ with nitrogen mustard, PSO2 and SAK1 with YKU70 or DNL4 single-, double- and triple mutants with 8-MOP+UVA indicated that ICL repair is independent of YKu70p and DNL4p in S. cerevisiae. Furthermore, a non-epistatic interaction was observed between MRE11, PSO2 and SAK1 genes after ICL induction, indicating that their encoded proteins act on the same substrate, but in distinct repair pathways. In contrast, an epistatic interaction was observed for PSO2 and RAD52, PSO2 and RAD50, PSO2 and XRS2 genes in 8-MOP+UVA treated exponentially growing cells.
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Affiliation(s)
- Fernanda M Munari
- Biotechnology Center, Federal University of Rio Grande do Sul (UFRGS), 91507-970 Porto Alegre, RS, Brazil
| | - Luis F Revers
- Biotechnology Center, Federal University of Rio Grande do Sul (UFRGS), 91507-970 Porto Alegre, RS, Brazil
| | - Jacqueline M Cardone
- Biotechnology Center, Federal University of Rio Grande do Sul (UFRGS), 91507-970 Porto Alegre, RS, Brazil
| | - Bruna F Immich
- Biotechnology Center, Federal University of Rio Grande do Sul (UFRGS), 91507-970 Porto Alegre, RS, Brazil; Federal University of Health Sciences of Porto Alegre (UFCSPA), 90050-170 Porto Alegre, RS, Brazil
| | - Dinara J Moura
- Federal University of Health Sciences of Porto Alegre (UFCSPA), 90050-170 Porto Alegre, RS, Brazil
| | - Temenouga N Guecheva
- Biotechnology Center, Federal University of Rio Grande do Sul (UFRGS), 91507-970 Porto Alegre, RS, Brazil; Department of Biophysics, Federal University of Rio Grande do Sul (UFRGS), 91507-970 Porto Alegre, RS, Brazil
| | - Diego Bonatto
- Biotechnology Center, Federal University of Rio Grande do Sul (UFRGS), 91507-970 Porto Alegre, RS, Brazil
| | - Jomar P Laurino
- Biotechnology Institute, University of Caxias do Sul (UCS), 95070-560 Caxias do Sul, RS, Brazil
| | - Jenifer Saffi
- Federal University of Health Sciences of Porto Alegre (UFCSPA), 90050-170 Porto Alegre, RS, Brazil
| | - Martin Brendel
- Department of Biological Sciences, State University of Santa Cruz (UESC), 45662-900 Ilhéus, BA, Brazil
| | - João A P Henriques
- Biotechnology Center, Federal University of Rio Grande do Sul (UFRGS), 91507-970 Porto Alegre, RS, Brazil; Department of Biophysics, Federal University of Rio Grande do Sul (UFRGS), 91507-970 Porto Alegre, RS, Brazil; Biotechnology Institute, University of Caxias do Sul (UCS), 95070-560 Caxias do Sul, RS, Brazil.
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30
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Fontebasso Y, Etheridge T, Oliver A, Murray J, Carr A. The conserved Fanconi anemia nuclease Fan1 and the SUMO E3 ligase Pli1 act in two novel Pso2-independent pathways of DNA interstrand crosslink repair in yeast. DNA Repair (Amst) 2013; 12:1011-23. [PMID: 24192486 PMCID: PMC4045212 DOI: 10.1016/j.dnarep.2013.10.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2013] [Revised: 10/01/2013] [Accepted: 10/07/2013] [Indexed: 10/26/2022]
Abstract
DNA interstrand cross-links (ICLs) represent a physical barrier to the progression of cellular machinery involved in DNA metabolism. Thus, this type of adduct represents a serious threat to genomic stability and as such, several DNA repair pathways have evolved in both higher and lower eukaryotes to identify this type of damage and restore the integrity of the genetic material. Human cells possess a specialized ICL-repair system, the Fanconi anemia (FA) pathway. Conversely yeasts rely on the concerted action of several DNA repair systems. Recent work in higher eukaryotes identified and characterized a novel conserved FA component, FAN1 (Fanconi anemia-associated nuclease 1, or FANCD2/FANCI-associated nuclease 1). In this study, we characterize Fan1 in the yeast Schizosaccharomyces pombe. Using standard genetics, we demonstrate that Fan1 is a key component of a previously unidentified ICL-resolution pathway. Using high-throughput synthetic genetic arrays, we also demonstrate the existence of a third pathway of ICL repair, dependent on the SUMO E3 ligase Pli1. Finally, using sequence-threaded homology models, we predict and validate key residues essential for Fan1 activity in ICL repair.
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Affiliation(s)
- Y. Fontebasso
- Genome Damage and Stability Centre, University of Sussex, Brighton, East Sussex BN1 9RQ, UK
- Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK
| | - T.J. Etheridge
- Genome Damage and Stability Centre, University of Sussex, Brighton, East Sussex BN1 9RQ, UK
| | - A.W. Oliver
- Genome Damage and Stability Centre, University of Sussex, Brighton, East Sussex BN1 9RQ, UK
| | - J.M. Murray
- Genome Damage and Stability Centre, University of Sussex, Brighton, East Sussex BN1 9RQ, UK
| | - A.M. Carr
- Genome Damage and Stability Centre, University of Sussex, Brighton, East Sussex BN1 9RQ, UK
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Rochette S, Gagnon-Arsenault I, Diss G, Landry CR. Modulation of the yeast protein interactome in response to DNA damage. J Proteomics 2013; 100:25-36. [PMID: 24262151 DOI: 10.1016/j.jprot.2013.11.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2013] [Revised: 10/10/2013] [Accepted: 11/05/2013] [Indexed: 01/24/2023]
Abstract
UNLABELLED Cells deploy diverse mechanisms to physiologically adapt to potentially detrimental perturbations. These mechanisms include changes in the organization of protein-protein interaction networks (PINs). Most PINs characterized to date are portrayed in a single environmental condition and are thus likely to miss important connections among biological processes. In this report, we show that the yeast DHFR-PCA on high-density arrays allows to detects modulations of protein-protein interactions (PPIs) in different conditions by testing more than 1000 PPIs in standard and in a drug-inducing DNA damage conditions. We identify 156 PPIs that show significant modulation in response to DNA damage. We provide evidence that modulated PPIs involve essential genes (NOP7, EXO84 and LAS17) playing critical roles in response to DNA damage. Additionally, we show that a significant proportion of PPI changes are likely explained by changes in protein localization and, to a lesser extent, protein abundance. The protein interaction modules affected by changing PPIs support the role of mRNA stability and translation, protein degradation and ubiquitylation and the regulation of the actin cytoskeleton in response to DNA damage. Overall, we provide a valuable tool and dataset for the study of the rewiring of PINs in response to environmental perturbations. BIOLOGICAL SIGNIFICANCE We show that the DHFR-PCA is a high-throughput method that allows the detection of changes in PPIs associated with different environmental conditions using DNA damage response as a testbed. We provide a valuable resource for the study of DNA damage in eukaryotic cells. This article is part of a Special Issue: Can Proteomics Fill the Gap Between Genomics and Phenotypes?
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Affiliation(s)
- Samuel Rochette
- Département de Biologie, PROTEO and Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, Québec G1V 0A6, Canada
| | - Isabelle Gagnon-Arsenault
- Département de Biologie, PROTEO and Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, Québec G1V 0A6, Canada
| | - Guillaume Diss
- Département de Biologie, PROTEO and Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, Québec G1V 0A6, Canada
| | - Christian R Landry
- Département de Biologie, PROTEO and Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, Québec G1V 0A6, Canada.
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Munari FM, Guecheva TN, Bonatto D, Henriques JAP. New features on Pso2 protein family in DNA interstrand cross-link repair and in the maintenance of genomic integrity in Saccharomyces cerevisiae. Fungal Genet Biol 2013; 60:122-32. [PMID: 24076078 DOI: 10.1016/j.fgb.2013.09.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Revised: 09/11/2013] [Accepted: 09/15/2013] [Indexed: 11/27/2022]
Abstract
Pso2 protein, a member of the highly conserved metallo-β-lactamase (MBL) super family of nucleases, plays a central role in interstrand crosslink repair (ICL) in yeast. Pso2 protein is the founder member of a distinct group within the MBL superfamily, called β-CASP family. Three mammalian orthologs of this protein that act on DNA were identified: SNM1A, SNM1B/Apollo and SNM1C/Artemis. Yeast Pso2 and all three mammalian orthologs proteins have been shown to possess nuclease activity. Besides Pso2, ICL repair involves proteins of several DNA repair pathways. Over the last years, new homologs for human proteins have been identified in yeast. In this review, we will focus on studies clarifying the function of Pso2 protein during ICL repair in yeast, emphasizing the contribution of Brazilian research groups in this topic. New sub-pathways in the mechanisms of ICL repair, such as recently identified conserved Fanconi Anemia pathway in yeast as well as a contribution of non-homologous end joining are discussed.
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Affiliation(s)
- Fernanda Mosena Munari
- Biotechnology Center, Federal University of Rio Grande do Sul (UFRGS), 91507-970 Porto Alegre, RS, Brazil
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33
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Williams HL, Gottesman ME, Gautier J. The differences between ICL repair during and outside of S phase. Trends Biochem Sci 2013; 38:386-93. [PMID: 23830640 DOI: 10.1016/j.tibs.2013.05.004] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Revised: 05/14/2013] [Accepted: 05/29/2013] [Indexed: 12/11/2022]
Abstract
DNA interstrand crosslinks (ICLs) are complex lesions that block essential DNA transactions including DNA replication, recombination, and RNA transcription. Naturally occurring ICLs are rare, yet these lesions are the major cause of toxicity following treatment with several classes of crosslinking cancer chemotherapeutic drugs. ICLs are repaired during and outside of S phase by pathways with overlapping as well as distinct features. Here, we discuss some recent insights into the mechanisms of replication-dependent and replication-independent repair of ICLs with special emphasis on the differences between these repair pathways.
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Affiliation(s)
- Hannah L Williams
- Department of Genetics and Development, Institute for Cancer Genetics, Columbia University, New York, NY 10032, USA
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Singh S, Shemesh K, Liefshitz B, Kupiec M. Genetic and physical interactions between the yeast ELG1 gene and orthologs of the Fanconi anemia pathway. Cell Cycle 2013; 12:1625-36. [PMID: 23624835 PMCID: PMC3680542 DOI: 10.4161/cc.24756] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Fanconi anemia (FA) is a human syndrome characterized by genomic instability and increased incidence of cancer. FA is a genetically heterogeneous disease caused by mutations in at least 15 different genes; several of these genes are conserved in the yeast Saccharomyces cerevisiae. Elg1 is also a conserved protein that forms an RFC-like complex, which interacts with SUMOylated PCNA. The mammalian Elg1 protein has been recently found to interact with the FA complex. Here we analyze the genetic interactions between elg1Δand mutants of the yeast FA-like pathway. We show that Elg1 physically contacts the Mhf1/Mhf2 histone-like complex and genetically interacts with MPH1 (ortholog of the FANCM helicase) and CHL1 (ortholog of the FANCJ helicase) genes. We analyze the sensitivity of double, triple, quadruple and quintuple mutants to methylmethane sulfonate (MMS) and to hydroxyurea (HU). Our results show that genetic interactions depend on the type of DNA damaging agent used and show a hierarchy: Chl1 and Elg1 play major roles in the survival to these genotoxins and exhibit synthetic fitness reduction. Mph1 plays a lesser role, and the effect of the Mhf1/2 complex is seen only in the absence of Elg1 on HU-containing medium. Finally, we dissect the relationship between yeast FA-like mutants and the replication clamp, PCNA. Our results point to an intricate network of interactions rather than a single, linear repair pathway.
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Affiliation(s)
- Shivani Singh
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv, Israel
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35
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Abstract
Interstrand crosslinks covalently link complementary DNA strands, block replication and transcription, and can trigger cell death. In eukaryotic systems several pathways, including the Fanconi Anemia pathway, are involved in repairing interstrand crosslinks, but their precise mechanisms remain enigmatic. The lack of functional homologs in simpler model organisms has significantly hampered progress in this field. Two recent studies have finally identified a Fanconi-like interstrand crosslink repair pathway in yeast. Future studies in this simplistic model organism promise to greatly improve our basic understanding of complex interstrand crosslink repair pathways like the Fanconi pathway.
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McHugh PJ, Ward TA, Chovanec M. A prototypical Fanconi anemia pathway in lower eukaryotes? Cell Cycle 2012; 11:3739-44. [PMID: 22895051 DOI: 10.4161/cc.21727] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
DNA interstrand cross-links (ICLs) present a major challenge to cells, preventing separation of the two strands of duplex DNA and blocking major chromosome transactions, including transcription and replication. Due to the complexity of removing this form of DNA damage, no single DNA repair pathway has been shown to be capable of eradicating ICLs. In eukaryotes, ICL repair is a complex process, principally because several repair pathways compete for ICL repair intermediates in a strictly cell cycle-dependent manner. Yeast cells require a combination of nucleotide excision repair, homologous recombination repair and postreplication repair/translesion DNA synthesis to remove ICLs. There are also a number of additional ICL repair factors originally identified in the budding yeast Saccharomyces cerevisiae, called Pso1 though 10, of which Pso2 has an apparently dedicated role in ICL repair. Mammalian cells respond to ICLs by a complex network guided by factors mutated in the inherited cancer-prone disorder Fanconi anemia (FA). Although enormous progress has been made over recent years in identifying and characterizing FA factors as well as in elucidating certain aspects of the biology of FA, the mechanistic details of the ICL repair defects in FA patients remain unknown. Dissection of the FA DNA damage response pathway has, in part, been limited by the absence of FA-like pathways in highly tractable model organisms, such as yeast. Although S. cerevisiae possesses putative homologs of the FA factors FANCM, FANCJ and FANCP (Mph1, Chl1 and Slx4, respectively) as well as of the FANCM-associated proteins MHF1 and MHF2 (Mhf1 and Mhf2), the corresponding mutants display no significant increase in sensitivity to ICLs. Nevertheless, we and others have recently shown that these FA homologs, along with several other factors, control an ICL repair pathway, which has an overlapping or redundant role with a Pso2-controlled pathway. This pathway acts in S-phase and serves to prevent ICL-stalled replication forks from collapsing into DNA double-strand breaks.
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Affiliation(s)
- Peter J McHugh
- Department of Oncology, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
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