1
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Siler J, Guo N, Liu Z, Qin Y, Bi X. γH2A/γH2AX Mediates DNA Damage-Specific Control of Checkpoint Signaling in Saccharomyces cerevisiae. Int J Mol Sci 2024; 25:2462. [PMID: 38473708 DOI: 10.3390/ijms25052462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Revised: 02/13/2024] [Accepted: 02/16/2024] [Indexed: 03/14/2024] Open
Abstract
DNA lesions trigger DNA damage checkpoint (DDC) signaling which arrests cell cycle progression and promotes DNA damage repair. In Saccharomyces cerevisiae, phosphorylation of histone H2A (γH2A, equivalent to γH2AX in mammals) is an early chromatin mark induced by DNA damage that is recognized by a group of DDC and DNA repair factors. We find that γH2A negatively regulates the G2/M checkpoint in response to the genotoxin camptothecin, which is a DNA topoisomerase I poison. γH2A also suppresses DDC signaling induced by the DNA alkylating agent methyl methanesulfonate. These results differ from prior findings, which demonstrate positive or no roles of γH2A in DDC in response to other DNA damaging agents such as phleomycin and ionizing radiation, which suggest that γH2A has DNA damage-specific effects on DDC signaling. We also find evidence supporting the notion that γH2A regulates DDC signaling by mediating the competitive recruitment of the DDC mediator Rad9 and the DNA repair factor Rtt107 to DNA lesions. We propose that γH2A/γH2AX serves to create a dynamic balance between DDC and DNA repair that is influenced by the nature of DNA damage.
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Affiliation(s)
- Jasmine Siler
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Na Guo
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
- College of Food Science and Engineering, Jilin University, Changchun 130012, China
| | - Zhengfeng Liu
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Yuhua Qin
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Xin Bi
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
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2
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Rinaldi C, Pizzul P, Casari E, Mangiagalli M, Tisi R, Longhese MP. The Ku complex promotes DNA end-bridging and this function is antagonized by Tel1/ATM kinase. Nucleic Acids Res 2023; 51:1783-1802. [PMID: 36762474 PMCID: PMC9976877 DOI: 10.1093/nar/gkad062] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 01/18/2023] [Accepted: 01/20/2023] [Indexed: 02/11/2023] Open
Abstract
DNA double-strand breaks (DSBs) can be repaired by either homologous recombination (HR) or non-homologous end-joining (NHEJ). NHEJ is induced by the binding to DSBs of the Ku70-Ku80 heterodimer, which acts as a hub for the recruitment of downstream NHEJ components. An important issue in DSB repair is the maintenance of the DSB ends in close proximity, a function that in yeast involves the MRX complex and Sae2. Here, we provide evidence that Ku contributes to keep the DNA ends tethered to each other. The ku70-C85Y mutation, which increases Ku affinity for DNA and its persistence very close to the DSB ends, enhances DSB end-tethering and suppresses the end-tethering defect of sae2Δ cells. Impairing histone removal around DSBs either by eliminating Tel1 kinase activity or nucleosome remodelers enhances Ku persistence at DSBs and DSB bridging, suggesting that Tel1 antagonizes the Ku function in supporting end-tethering by promoting nucleosome removal and possibly Ku sliding inwards. As Ku provides a block to DSB resection, this Tel1 function can be important to regulate the mode by which DSBs are repaired.
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Affiliation(s)
- Carlo Rinaldi
- Dipartimento di Biotecnologie e Bioscienze, Università degli Studi di Milano-Bicocca, 20126 Milano, Italy
| | - Paolo Pizzul
- Dipartimento di Biotecnologie e Bioscienze, Università degli Studi di Milano-Bicocca, 20126 Milano, Italy
| | - Erika Casari
- Dipartimento di Biotecnologie e Bioscienze, Università degli Studi di Milano-Bicocca, 20126 Milano, Italy
| | - Marco Mangiagalli
- Dipartimento di Biotecnologie e Bioscienze, Università degli Studi di Milano-Bicocca, 20126 Milano, Italy
| | - Renata Tisi
- Dipartimento di Biotecnologie e Bioscienze, Università degli Studi di Milano-Bicocca, 20126 Milano, Italy
| | - Maria Pia Longhese
- Dipartimento di Biotecnologie e Bioscienze, Università degli Studi di Milano-Bicocca, 20126 Milano, Italy
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3
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Sharma AK, Fitieh AM, Hafez Ali JY, Ismail IH. Protocol to measure end resection intermediates at sequence-specific DNA double-strand breaks by quantitative polymerase chain reaction using ER-AsiSI U2OS cells. STAR Protoc 2022; 3:101861. [PMID: 36595899 PMCID: PMC9678777 DOI: 10.1016/j.xpro.2022.101861] [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: 06/06/2022] [Revised: 08/23/2022] [Accepted: 10/25/2022] [Indexed: 11/19/2022] Open
Abstract
DNA end resection is a critical step in the homologous recombination pathway of repairing DNA double-strand breaks (DSBs) that can be visualized in cells by detecting the generation of single-stranded DNA (ssDNA) intermediates formed during the resection of the DSBs. Here, we describe quantitative polymerase-chain-reaction-based procedures to quantitatively measure ssDNA intermediates formed during the DNA end resection. Using the ER-AsiSI system, we use differential digestion patterns by restriction endonucleases that digest unresected double-stranded DNA at DSB sites. For complete details on the use and execution of this protocol, please refer to Fitieh et al. (2022).1.
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Affiliation(s)
- Ajit K. Sharma
- Department of Oncology, Faculty of Medicine & Dentistry, University of Alberta, Cross Cancer Institute, 11560 University Avenue, Edmonton, AB T6G 1Z2, Canada
| | - Amira Mohammed Fitieh
- Department of Oncology, Faculty of Medicine & Dentistry, University of Alberta, Cross Cancer Institute, 11560 University Avenue, Edmonton, AB T6G 1Z2, Canada,Biophysics Department, Faculty of Science, Cairo University, Giza 12613, Egypt
| | - Jana Yasser Hafez Ali
- Department of Oncology, Faculty of Medicine & Dentistry, University of Alberta, Cross Cancer Institute, 11560 University Avenue, Edmonton, AB T6G 1Z2, Canada
| | - Ismail Hassan Ismail
- Department of Oncology, Faculty of Medicine & Dentistry, University of Alberta, Cross Cancer Institute, 11560 University Avenue, Edmonton, AB T6G 1Z2, Canada,Biophysics Department, Faculty of Science, Cairo University, Giza 12613, Egypt,Corresponding author
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4
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Yam CQX, Lim HH, Surana U. DNA damage checkpoint execution and the rules of its disengagement. Front Cell Dev Biol 2022; 10:1020643. [PMID: 36274841 PMCID: PMC9582513 DOI: 10.3389/fcell.2022.1020643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 09/21/2022] [Indexed: 11/13/2022] Open
Abstract
Chromosomes are susceptible to damage during their duplication and segregation or when exposed to genotoxic stresses. Left uncorrected, these lesions can result in genomic instability, leading to cells’ diminished fitness, unbridled proliferation or death. To prevent such fates, checkpoint controls transiently halt cell cycle progression to allow time for the implementation of corrective measures. Prominent among these is the DNA damage checkpoint which operates at G2/M transition to ensure that cells with damaged chromosomes do not enter the mitotic phase. The execution and maintenance of cell cycle arrest are essential aspects of G2/M checkpoint and have been studied in detail. Equally critical is cells’ ability to switch-off the checkpoint controls after a successful completion of corrective actions and to recommence cell cycle progression. Interestingly, when corrective measures fail, cells can mount an unusual cellular response, termed adaptation, where they escape checkpoint arrest and resume cell cycle progression with damaged chromosomes at the cost of genome instability or even death. Here, we discuss the DNA damage checkpoint, the mitotic networks it inhibits to prevent segregation of damaged chromosomes and the strategies cells employ to quench the checkpoint controls to override the G2/M arrest.
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Affiliation(s)
| | - Hong Hwa Lim
- A*STAR Singapore Immunology Network, Singapore, Singapore
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Uttam Surana
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Department of Pharmacology, National University of Singapore, Singapore, Singapore
- *Correspondence: Uttam Surana,
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5
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Schilke BA, Craig EA. Essentiality of Sis1, a J-domain protein Hsp70 cochaperone, can be overcome by Tti1, a specialized PIKK chaperone. Mol Biol Cell 2021; 33:br3. [PMID: 34935410 PMCID: PMC9250385 DOI: 10.1091/mbc.e21-10-0493] [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] [Indexed: 11/11/2022] Open
Abstract
J-domain protein cochaperones drive much of the functional diversity of Hsp70-based chaperone systems. Sis1 is the only essential J-domain protein of the cytosol/nucleus of Saccharomyces cerevisiae. Why it is required for cell growth is not understood, nor how critical its role is in regulation of heat shock transcription factor 1 (Hsf1). We report that single-residue substitutions in Tti1, a component of the heterotrimeric TTT complex, a specialized chaperone system for phosphatidylinositol 3-kinase-related kinase (PIKK) proteins, allow growth of cells lacking Sis1. Upon depletion of Sis1, cells become hypersensitive to rapamycin, a specific inhibitor of TORC1 kinase. In addition, levels of the three essential PIKKs (Mec1, Tra1, and Tor2), as well as Tor1, decrease upon Sis1 depletion. Overexpression of Tti1 allows growth without an increase in the other subunits of the TTT complex, Tel2 and Tti2, suggesting that it can function independent of the complex. Cells lacking Sis1, with viability supported by Tti1 suppressor, substantially up-regulate some, but not all, heat shock elements activated by Hsf1. Together, our results suggest that Sis1 is required as a cochaperone of Hsp70 for the folding/maintenance of PIKKs, making Sis1 an essential gene, and its requirement for Hsf1 regulation is more nuanced than generally appreciated.
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Affiliation(s)
- Brenda A Schilke
- Department of Biochemistry, 433 Babcock Drive, University of Wisconsin - Madison, Madison, Wisconsin 53706
| | - Elizabeth A Craig
- Department of Biochemistry, 433 Babcock Drive, University of Wisconsin - Madison, Madison, Wisconsin 53706
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6
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Casari E, Gobbini E, Gnugnoli M, Mangiagalli M, Clerici M, Longhese MP. Dpb4 promotes resection of DNA double-strand breaks and checkpoint activation by acting in two different protein complexes. Nat Commun 2021; 12:4750. [PMID: 34362907 PMCID: PMC8346560 DOI: 10.1038/s41467-021-25090-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Accepted: 07/20/2021] [Indexed: 12/24/2022] Open
Abstract
Budding yeast Dpb4 (POLE3/CHRAC17 in mammals) is a highly conserved histone fold protein that is shared by two protein complexes: the chromatin remodeler ISW2/hCHRAC and the DNA polymerase ε (Pol ε) holoenzyme. In Saccharomyces cerevisiae, Dpb4 forms histone-like dimers with Dls1 in the ISW2 complex and with Dpb3 in the Pol ε complex. Here, we show that Dpb4 plays two functions in sensing and processing DNA double-strand breaks (DSBs). Dpb4 promotes histone removal and DSB resection by interacting with Dls1 to facilitate the association of the Isw2 ATPase to DSBs. Furthermore, it promotes checkpoint activation by interacting with Dpb3 to facilitate the association of the checkpoint protein Rad9 to DSBs. Persistence of both Isw2 and Rad9 at DSBs is enhanced by the A62S mutation that is located in the Dpb4 histone fold domain and increases Dpb4 association at DSBs. Thus, Dpb4 exerts two distinct functions at DSBs depending on its interactors. The histone folding protein Dpb4 forms histone-like dimers within the ISW2 complex and the Pol ε complex in S. cerevisiae. Here the authors reveal insights into two distinct functions that Dpb4 exerts at DSBs depending on its interactors.
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Affiliation(s)
- Erika Casari
- Dipartimento di Biotecnologie e Bioscienze, Università degli Studi di Milano-Bicocca, Milano, Italy
| | - Elisa Gobbini
- Dipartimento di Biotecnologie e Bioscienze, Università degli Studi di Milano-Bicocca, Milano, Italy
| | - Marco Gnugnoli
- Dipartimento di Biotecnologie e Bioscienze, Università degli Studi di Milano-Bicocca, Milano, Italy
| | - Marco Mangiagalli
- Dipartimento di Biotecnologie e Bioscienze, Università degli Studi di Milano-Bicocca, Milano, Italy
| | - Michela Clerici
- Dipartimento di Biotecnologie e Bioscienze, Università degli Studi di Milano-Bicocca, Milano, Italy
| | - Maria Pia Longhese
- Dipartimento di Biotecnologie e Bioscienze, Università degli Studi di Milano-Bicocca, Milano, Italy.
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7
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Hoerr RE, Ngo K, Friedman KL. When the Ends Justify the Means: Regulation of Telomere Addition at Double-Strand Breaks in Yeast. Front Cell Dev Biol 2021; 9:655377. [PMID: 33816507 PMCID: PMC8012806 DOI: 10.3389/fcell.2021.655377] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 02/15/2021] [Indexed: 11/23/2022] Open
Abstract
Telomeres, repetitive sequences located at the ends of most eukaryotic chromosomes, provide a mechanism to replenish terminal sequences lost during DNA replication, limit nucleolytic resection, and protect chromosome ends from engaging in double-strand break (DSB) repair. The ribonucleoprotein telomerase contains an RNA subunit that serves as the template for the synthesis of telomeric DNA. While telomere elongation is typically primed by a 3′ overhang at existing chromosome ends, telomerase can act upon internal non-telomeric sequences. Such de novo telomere addition can be programmed (for example, during chromosome fragmentation in ciliated protozoa) or can occur spontaneously in response to a chromosome break. Telomerase action at a DSB can interfere with conservative mechanisms of DNA repair and results in loss of distal sequences but may prevent additional nucleolytic resection and/or chromosome rearrangement through formation of a functional telomere (termed “chromosome healing”). Here, we review studies of spontaneous and induced DSBs in the yeast Saccharomyces cerevisiae that shed light on mechanisms that negatively regulate de novo telomere addition, in particular how the cell prevents telomerase action at DSBs while facilitating elongation of critically short telomeres. Much of our understanding comes from the use of perfect artificial telomeric tracts to “seed” de novo telomere addition. However, endogenous sequences that are enriched in thymine and guanine nucleotides on one strand (TG-rich) but do not perfectly match the telomere consensus sequence can also stimulate unusually high frequencies of telomere formation following a DSB. These observations suggest that some internal sites may fully or partially escape mechanisms that normally negatively regulate de novo telomere addition.
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Affiliation(s)
- Remington E Hoerr
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, United States
| | - Katrina Ngo
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, United States
| | - Katherine L Friedman
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, United States
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8
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Marsella A, Gobbini E, Cassani C, Tisi R, Cannavo E, Reginato G, Cejka P, Longhese MP. Sae2 and Rif2 regulate MRX endonuclease activity at DNA double-strand breaks in opposite manners. Cell Rep 2021; 34:108906. [PMID: 33789097 PMCID: PMC8028314 DOI: 10.1016/j.celrep.2021.108906] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 01/29/2021] [Accepted: 03/04/2021] [Indexed: 11/17/2022] Open
Abstract
The Mre11-Rad50-Xrs2 (MRX) complex detects and processes DNA double-strand breaks (DSBs). Its DNA binding and processing activities are regulated by transitions between an ATP-bound state and a post-hydrolysis cutting state that is nucleolytically active. Mre11 endonuclease activity is stimulated by Sae2, whose lack increases MRX persistence at DSBs and checkpoint activation. Here we show that the Rif2 protein inhibits Mre11 endonuclease activity and is responsible for the increased MRX retention at DSBs in sae2Δ cells. We identify a Rad50 residue that is important for Rad50-Rif2 interaction and Rif2 inhibition of Mre11 nuclease. This residue is located near a Rad50 surface that binds Sae2 and is important in stabilizing the Mre11-Rad50 (MR) interaction in the cutting state. We propose that Sae2 stimulates Mre11 endonuclease activity by stabilizing a post-hydrolysis MR conformation that is competent for DNA cleavage, whereas Rif2 antagonizes this Sae2 function and stabilizes an endonuclease inactive MR conformation. Sae2 stimulates Mre11 endonuclease activity by stabilizing the MRX cutting state Rif2 inhibits Sae2-mediated stimulation of Mre11 endonuclease activity The rad50-N18S mutation escapes Rif2-mediated inhibition of Mre11 nuclease Rif2 stabilizes an endonuclease inactive MR conformation that persistently binds DSBs
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Affiliation(s)
- Antonio Marsella
- Dipartimento di Biotecnologie e Bioscienze, Università degli Studi di Milano-Bicocca, Milano 20126, Italy
| | - Elisa Gobbini
- Dipartimento di Biotecnologie e Bioscienze, Università degli Studi di Milano-Bicocca, Milano 20126, Italy
| | - Corinne Cassani
- Dipartimento di Biotecnologie e Bioscienze, Università degli Studi di Milano-Bicocca, Milano 20126, Italy
| | - Renata Tisi
- Dipartimento di Biotecnologie e Bioscienze, Università degli Studi di Milano-Bicocca, Milano 20126, Italy
| | - Elda Cannavo
- Institute for Research in Biomedicine, Faculty of Biomedical Sciences, Università della Svizzera italiana (USI), Bellinzona, Switzerland
| | - Giordano Reginato
- Institute for Research in Biomedicine, Faculty of Biomedical Sciences, Università della Svizzera italiana (USI), Bellinzona, Switzerland; Department of Biology, Institute of Biochemistry, Eidgenössische Technische Hochschule (ETH), Zürich, Switzerland
| | - Petr Cejka
- Institute for Research in Biomedicine, Faculty of Biomedical Sciences, Università della Svizzera italiana (USI), Bellinzona, Switzerland; Department of Biology, Institute of Biochemistry, Eidgenössische Technische Hochschule (ETH), Zürich, Switzerland
| | - Maria Pia Longhese
- Dipartimento di Biotecnologie e Bioscienze, Università degli Studi di Milano-Bicocca, Milano 20126, Italy.
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9
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Gobbini E, Casari E, Colombo CV, Bonetti D, Longhese MP. The 9-1-1 Complex Controls Mre11 Nuclease and Checkpoint Activation during Short-Range Resection of DNA Double-Strand Breaks. Cell Rep 2020; 33:108287. [DOI: 10.1016/j.celrep.2020.108287] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Revised: 09/08/2020] [Accepted: 09/28/2020] [Indexed: 12/17/2022] Open
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10
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Tisi R, Vertemara J, Zampella G, Longhese MP. Functional and structural insights into the MRX/MRN complex, a key player in recognition and repair of DNA double-strand breaks. Comput Struct Biotechnol J 2020; 18:1137-1152. [PMID: 32489527 PMCID: PMC7260605 DOI: 10.1016/j.csbj.2020.05.013] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Revised: 05/07/2020] [Accepted: 05/09/2020] [Indexed: 01/20/2023] Open
Abstract
Chromosomal DNA double-strand breaks (DSBs) are potentially lethal DNA lesions that pose a significant threat to genome stability and therefore need to be repaired to preserve genome integrity. Eukaryotic cells possess two main mechanisms for repairing DSBs: non-homologous end-joining (NHEJ) and homologous recombination (HR). HR requires that the 5' terminated strands at both DNA ends are nucleolytically degraded by a concerted action of nucleases in a process termed DNA-end resection. This degradation leads to the formation of 3'-ended single-stranded DNA (ssDNA) ends that are essential to use homologous DNA sequences for repair. The evolutionarily conserved Mre11-Rad50-Xrs2/NBS1 complex (MRX/MRN) has enzymatic and structural activities to initiate DSB resection and to maintain the DSB ends tethered to each other for their repair. Furthermore, it is required to recruit and activate the protein kinase Tel1/ATM, which plays a key role in DSB signaling. All these functions depend on ATP-regulated DNA binding and nucleolytic activities of the complex. Several structures have been obtained in recent years for Mre11 and Rad50 subunits from archaea, and a few from the bacterial and eukaryotic orthologs. Nevertheless, the mechanism of activation of this protein complex is yet to be fully elucidated. In this review, we focused on recent biophysical and structural insights on the MRX complex and their interplay.
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Affiliation(s)
- Renata Tisi
- Dipartimento di Biotecnologie and Bioscienze, Università degli Studi di Milano-Bicocca, Milan, Italy
| | - Jacopo Vertemara
- Dipartimento di Biotecnologie and Bioscienze, Università degli Studi di Milano-Bicocca, Milan, Italy
| | - Giuseppe Zampella
- Dipartimento di Biotecnologie and Bioscienze, Università degli Studi di Milano-Bicocca, Milan, Italy
| | - Maria Pia Longhese
- Dipartimento di Biotecnologie and Bioscienze, Università degli Studi di Milano-Bicocca, Milan, Italy
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11
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Cassani C, Vertemara J, Bassani M, Marsella A, Tisi R, Zampella G, Longhese MP. The ATP-bound conformation of the Mre11-Rad50 complex is essential for Tel1/ATM activation. Nucleic Acids Res 2019; 47:3550-3567. [PMID: 30698745 PMCID: PMC6468247 DOI: 10.1093/nar/gkz038] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 12/17/2018] [Accepted: 01/15/2019] [Indexed: 01/01/2023] Open
Abstract
Activation of the checkpoint protein Tel1 requires the Mre11–Rad50–Xrs2 (MRX) complex, which recruits Tel1 at DNA double-strand breaks (DSBs) through direct interaction between Tel1 and Xrs2. However, in vitro Tel1 activation by MRX requires ATP binding to Rad50, suggesting a role also for the MR subcomplex in Tel1 activation. Here we describe two separation-of-functions alleles, mre11-S499P and rad50-A78T, which we show to specifically affect Tel1 activation without impairing MRX functions in DSB repair. Both Mre11-S499P and Rad50-A78T reduce Tel1–MRX interaction leading to poor Tel1 association at DSBs and consequent loss of Tel1 activation. The Mre11-S499P variant reduces Mre11–Rad50 interaction, suggesting an important role for MR complex formation in Tel1 activation. Molecular dynamics simulations show that the wild type MR subcomplex bound to ATP lingers in a tightly ‘closed’ conformation, while ADP presence leads to the destabilization of Rad50 dimer and of Mre11–Rad50 association, both events being required for MR conformational transition to an open state. By contrast, MRA78T undertakes complex opening even if Rad50 is bound to ATP, indicating that defective Tel1 activation caused by MRA78T results from destabilization of the ATP-bound conformational state.
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Affiliation(s)
- Corinne Cassani
- Dipartimento di Biotecnologie e Bioscienze, Università degli Studi di Milano - Bicocca, 20126 Milano, Italy
| | - Jacopo Vertemara
- Dipartimento di Biotecnologie e Bioscienze, Università degli Studi di Milano - Bicocca, 20126 Milano, Italy
| | - Matteo Bassani
- Dipartimento di Biotecnologie e Bioscienze, Università degli Studi di Milano - Bicocca, 20126 Milano, Italy
| | - Antonio Marsella
- Dipartimento di Biotecnologie e Bioscienze, Università degli Studi di Milano - Bicocca, 20126 Milano, Italy
| | - Renata Tisi
- Dipartimento di Biotecnologie e Bioscienze, Università degli Studi di Milano - Bicocca, 20126 Milano, Italy
| | - Giuseppe Zampella
- Dipartimento di Biotecnologie e Bioscienze, Università degli Studi di Milano - Bicocca, 20126 Milano, Italy
| | - Maria Pia Longhese
- Dipartimento di Biotecnologie e Bioscienze, Università degli Studi di Milano - Bicocca, 20126 Milano, Italy
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12
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Menin L, Colombo CV, Maestrini G, Longhese MP, Clerici M. Tel1/ATM Signaling to the Checkpoint Contributes to Replicative Senescence in the Absence of Telomerase. Genetics 2019; 213:411-429. [PMID: 31391264 PMCID: PMC6781906 DOI: 10.1534/genetics.119.302391] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 07/27/2019] [Indexed: 11/18/2022] Open
Abstract
Telomeres progressively shorten at every round of DNA replication in the absence of telomerase. When they become critically short, telomeres trigger replicative senescence by activating a DNA damage response that is governed by the Mec1/ATR and Tel1/ATM protein kinases. While Mec1/ATR is known to block cell division when extended single-stranded DNA (ssDNA) accumulates at eroded telomeres, the molecular mechanism by which Tel1/ATM promotes senescence is still unclear. By characterizing a Tel1-hy184 mutant variant that compensates for the lack of Mec1 functions, we provide evidence that Tel1 promotes senescence by signaling to a Rad9-dependent checkpoint. Tel1-hy184 anticipates senescence onset in telomerase-negative cells, while the lack of Tel1 or the expression of a kinase-defective (kd) Tel1 variant delays it. Both Tel1-hy184 and Tel1-kd do not alter ssDNA generation at telomeric DNA ends. Furthermore, Rad9 and (only partially) Mec1 are responsible for the precocious senescence promoted by Tel1-hy184. This precocious senescence is mainly caused by the F1751I, D1985N, and E2133K amino acid substitutions, which are located in the FRAP-ATM-TRAPP domain of Tel1 and also increase Tel1 binding to DNA ends. Altogether, these results indicate that Tel1 induces replicative senescence by directly signaling dysfunctional telomeres to the checkpoint machinery.
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Affiliation(s)
- Luca Menin
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Milano 20126, Italy
| | - Chiara Vittoria Colombo
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Milano 20126, Italy
| | - Giorgia Maestrini
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Milano 20126, Italy
| | - Maria Pia Longhese
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Milano 20126, Italy
| | - Michela Clerici
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Milano 20126, Italy
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13
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Cassani C, Gobbini E, Vertemara J, Wang W, Marsella A, Sung P, Tisi R, Zampella G, Longhese MP. Structurally distinct Mre11 domains mediate MRX functions in resection, end-tethering and DNA damage resistance. Nucleic Acids Res 2019; 46:2990-3008. [PMID: 29420790 PMCID: PMC5888019 DOI: 10.1093/nar/gky086] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 01/31/2018] [Indexed: 11/27/2022] Open
Abstract
Sae2 cooperates with the Mre11–Rad50-Xrs2 (MRX) complex to initiate resection of DNA double-strand breaks (DSBs) and to maintain the DSB ends in close proximity to allow their repair. How these diverse MRX-Sae2 functions contribute to DNA damage resistance is not known. Here, we describe mre11 alleles that suppress the hypersensitivity of sae2Δ cells to genotoxic agents. By assessing the impact of these mutations at the cellular and structural levels, we found that all the mre11 alleles that restore sae2Δ resistance to both camptothecin and phleomycin affect the Mre11 N-terminus and suppress the resection defect of sae2Δ cells by lowering MRX and Tel1 association to DSBs. As a consequence, the diminished Tel1 persistence potentiates Sgs1-Dna2 resection activity by decreasing Rad9 association to DSBs. By contrast, the mre11 mutations restoring sae2Δ resistance only to phleomycin are located in Mre11 C-terminus and bypass Sae2 function in end-tethering but not in DSB resection, possibly by destabilizing the Mre11–Rad50 open conformation. These findings unmask the existence of structurally distinct Mre11 domains that support resistance to genotoxic agents by mediating different processes.
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Affiliation(s)
- Corinne Cassani
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Milano, Italy
| | - Elisa Gobbini
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Milano, Italy
| | - Jacopo Vertemara
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Milano, Italy
| | - Weibin Wang
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Antonio Marsella
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Milano, Italy
| | - Patrick Sung
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Renata Tisi
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Milano, Italy
| | - Giuseppe Zampella
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Milano, Italy
| | - Maria Pia Longhese
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Milano, Italy
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14
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Casari E, Rinaldi C, Marsella A, Gnugnoli M, Colombo CV, Bonetti D, Longhese MP. Processing of DNA Double-Strand Breaks by the MRX Complex in a Chromatin Context. Front Mol Biosci 2019; 6:43. [PMID: 31231660 PMCID: PMC6567933 DOI: 10.3389/fmolb.2019.00043] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 05/21/2019] [Indexed: 12/24/2022] Open
Abstract
DNA double-strand breaks (DSBs) are highly cytotoxic lesions that must be repaired to ensure genomic stability and avoid cell death. The cellular response to DSBs is initiated by the evolutionarily conserved Mre11-Rad50-Xrs2/NBS1 (MRX/MRN) complex that has structural and catalytic functions. Furthermore, it is responsible for DSB signaling through the activation of the checkpoint kinase Tel1/ATM. Here, we review functions and regulation of the MRX/MRN complex in DSB processing in a chromatin context, as well as its interplay with Tel1/ATM.
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Affiliation(s)
- Erika Casari
- Dipartimento di Biotecnologie e Bioscienze, Università degli Studi di Milano-Bicocca, Milan, Italy
| | - Carlo Rinaldi
- Dipartimento di Biotecnologie e Bioscienze, Università degli Studi di Milano-Bicocca, Milan, Italy
| | - Antonio Marsella
- Dipartimento di Biotecnologie e Bioscienze, Università degli Studi di Milano-Bicocca, Milan, Italy
| | - Marco Gnugnoli
- Dipartimento di Biotecnologie e Bioscienze, Università degli Studi di Milano-Bicocca, Milan, Italy
| | - Chiara Vittoria Colombo
- Dipartimento di Biotecnologie e Bioscienze, Università degli Studi di Milano-Bicocca, Milan, Italy
| | - Diego Bonetti
- Dipartimento di Biotecnologie e Bioscienze, Università degli Studi di Milano-Bicocca, Milan, Italy
| | - Maria Pia Longhese
- Dipartimento di Biotecnologie e Bioscienze, Università degli Studi di Milano-Bicocca, Milan, Italy
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15
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Quantitative sensing and signalling of single-stranded DNA during the DNA damage response. Nat Commun 2019; 10:944. [PMID: 30808869 PMCID: PMC6391461 DOI: 10.1038/s41467-019-08889-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 02/05/2019] [Indexed: 12/11/2022] Open
Abstract
The DNA damage checkpoint senses the presence of DNA lesions and controls the cellular response thereto. A crucial DNA damage signal is single-stranded DNA (ssDNA), which is frequently found at sites of DNA damage and recruits the sensor checkpoint kinase Mec1-Ddc2. However, how this signal – and therefore the cell's DNA damage load – is quantified, is poorly understood. Here, we use genetic manipulation of DNA end resection to induce quantitatively different ssDNA signals at a site-specific double strand break in budding yeast and identify two distinct signalling circuits within the checkpoint. The local checkpoint signalling circuit leading to γH2A phosphorylation is unresponsive to increased amounts of ssDNA, while the global checkpoint signalling circuit, which triggers Rad53 activation, integrates the ssDNA signal quantitatively. The global checkpoint signal critically depends on the 9-1-1 and its downstream acting signalling axis, suggesting that ssDNA quantification depends on at least two sensor complexes. DNA damage triggers checkpoint signalling mechanisms. Here the authors reveal differential phosphorylation of targets of the Mec1-Ddc2 checkpoint kinase by analyzing the effect of quantitatively different ssDNA signals.
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16
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Uncoupling Sae2 Functions in Downregulation of Tel1 and Rad53 Signaling Activities. Genetics 2018; 211:515-530. [PMID: 30538107 DOI: 10.1534/genetics.118.301830] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 12/09/2018] [Indexed: 11/18/2022] Open
Abstract
The Mre11-Rad50-Xrs2 (MRX) complex acts together with the Sae2 protein to initiate resection of DNA double-strand breaks (DSBs) and to regulate a checkpoint response that couples cell cycle progression with DSB repair. Sae2 supports resistance to DNA damage and downregulates the signaling activities of MRX, Tel1, and Rad53 checkpoint proteins at the sites of damage. How these functions are connected to each other is not known. Here, we describe the separation-of-function sae2-ms mutant that, similar to SAE2 deletion, upregulates MRX and Tel1 signaling activities at DSBs by reducing Mre11 endonuclease activity. However, unlike SAE2 deletion, Sae2-ms causes neither DNA damage sensitivity nor enhanced Rad53 activation, indicating that DNA damage resistance depends mainly on Sae2-mediated Rad53 inhibition. The lack of Sae2, but not the presence of Sae2-ms, impairs long-range resection and increases both Rad9 accumulation at DSBs and Rad53-Rad9 interaction independently of Mre11 nuclease activity. Altogether, these data lead to a model whereby Sae2 plays distinct functions in limiting MRX-Tel1 and Rad9 abundance at DSBs, with the control on Rad9 association playing the major role in supporting DNA damage resistance and in regulating long-range resection and checkpoint activation.
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17
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Bonetti D, Colombo CV, Clerici M, Longhese MP. Processing of DNA Ends in the Maintenance of Genome Stability. Front Genet 2018; 9:390. [PMID: 30258457 PMCID: PMC6143663 DOI: 10.3389/fgene.2018.00390] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 08/29/2018] [Indexed: 12/17/2022] Open
Abstract
DNA double-strand breaks (DSBs) are particularly hazardous lesions as their inappropriate repair can result in chromosome rearrangements, an important driving force of tumorigenesis. DSBs can be repaired by end joining mechanisms or by homologous recombination (HR). HR requires the action of several nucleases that preferentially remove the 5′-terminated strands at both DSB ends in a process called DNA end resection. The same nucleases are also involved in the processing of replication fork structures. Much of our understanding of these pathways has come from studies in the model organism Saccharomyces cerevisiae. Here, we review the current knowledge of the mechanism of resection at DNA DSBs and replication forks.
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Affiliation(s)
- Diego Bonetti
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Milan, Italy
| | | | - Michela Clerici
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Milan, Italy
| | - Maria Pia Longhese
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Milan, Italy
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18
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Audry J, Wang J, Eisenstatt JR, Berkner KL, Runge KW. The inhibition of checkpoint activation by telomeres does not involve exclusion of dimethylation of histone H4 lysine 20 (H4K20me2). F1000Res 2018; 7:1027. [PMID: 30498568 PMCID: PMC6240467 DOI: 10.12688/f1000research.15166.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/28/2018] [Indexed: 10/05/2023] Open
Abstract
DNA double-strand (DSBs) breaks activate the DNA damage checkpoint machinery to pause or halt the cell cycle. Telomeres, the specific DNA-protein complexes at linear eukaryotic chromosome ends, are capped DSBs that do not activate DNA damage checkpoints. This "checkpoint privileged" status of telomeres was previously investigated in the yeast Schizosaccharomyces pombe lacking the major double-stranded telomere DNA binding protein Taz1. Telomeric DNA repeats in cells lacking Taz1 are 10 times longer than normal and contain single-stranded DNA regions. DNA damage checkpoint proteins associate with these damaged telomeres, but the DNA damage checkpoint is not activated. This severing of the DNA damage checkpoint signaling pathway was reported to stem from exclusion of histone H4 lysine 20 dimethylation (H4K20me2) from telomeric nucleosomes in both wild type cells and cells lacking Taz1. However, experiments to identify the mechanism of this exclusion failed, prompting our re-evaluation of H4K20me2 levels at telomeric chromatin. In this short report, we used an extensive series of controls to identify an antibody specific for the H4K20me2 modification and show that the level of this modification is the same at telomeres and internal loci in both wild type cells and those lacking Taz1. Consequently, telomeres must block activation of the DNA Damage Response by another mechanism that remains to be determined.
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Affiliation(s)
- Julien Audry
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Lerner College of Medicine, Case Western Reserve University, Cleveland, OH, 44195, USA
| | - Jinyu Wang
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Lerner College of Medicine, Case Western Reserve University, Cleveland, OH, 44195, USA
- Department of Genetics and Genomic Sciences, School of Medicine, Case Western Reserve University, Cleveland, Ohio, 44106, USA
| | - Jessica R. Eisenstatt
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Lerner College of Medicine, Case Western Reserve University, Cleveland, OH, 44195, USA
- Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Kathleen L. Berkner
- Department of Molecular Cardiology, Lerner Research Institute, Cleveland Clinic, Lerner College of Medicine, Case Western Reserve University, Cleveland, OH, 44195, USA
| | - Kurt W. Runge
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Lerner College of Medicine, Case Western Reserve University, Cleveland, OH, 44195, USA
- Department of Genetics and Genomic Sciences, School of Medicine, Case Western Reserve University, Cleveland, Ohio, 44106, USA
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19
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Audry J, Wang J, Eisenstatt JR, Berkner KL, Runge KW. The inhibition of checkpoint activation by telomeres does not involve exclusion of dimethylation of histone H4 lysine 20 (H4K20me2). F1000Res 2018; 7:1027. [PMID: 30498568 PMCID: PMC6240467 DOI: 10.12688/f1000research.15166.2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/27/2018] [Indexed: 12/15/2022] Open
Abstract
DNA double-strand breaks (DSBs) activate the DNA damage checkpoint machinery to pause or halt the cell cycle. Telomeres, the specific DNA-protein complexes at linear eukaryotic chromosome ends, are capped DSBs that do not activate DNA damage checkpoints. This "checkpoint privileged" status of telomeres was previously investigated in the yeast Schizosaccharomyces pombelacking the major double-stranded telomere DNA binding protein Taz1. Telomeric DNA repeats in cells lacking Taz1 are 10 times longer than normal and contain single-stranded DNA regions. DNA damage checkpoint proteins associate with these damaged telomeres, but the DNA damage checkpoint is not activated. This severing of the DNA damage checkpoint signaling pathway was reported to stem from exclusion of histone H4 lysine 20 dimethylation (H4K20me2) from telomeric nucleosomes in both wild type cells and cells lacking Taz1. However, experiments to identify the mechanism of this exclusion failed, prompting our re-evaluation of H4K20me2 levels at telomeric chromatin. In this short report, we used an extensive series of controls to identify an antibody specific for the H4K20me2 modification and show that the level of this modification is the same at telomeres and internal loci in both wild type cells and those lacking Taz1. Consequently, telomeres must block activation of the DNA Damage Response by another mechanism that remains to be determined.
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Affiliation(s)
- Julien Audry
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Lerner College of Medicine, Case Western Reserve University, Cleveland, OH, 44195, USA
| | - Jinyu Wang
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Lerner College of Medicine, Case Western Reserve University, Cleveland, OH, 44195, USA
- Department of Genetics and Genomic Sciences, School of Medicine, Case Western Reserve University, Cleveland, Ohio, 44106, USA
| | - Jessica R. Eisenstatt
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Lerner College of Medicine, Case Western Reserve University, Cleveland, OH, 44195, USA
- Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Kathleen L. Berkner
- Department of Molecular Cardiology, Lerner Research Institute, Cleveland Clinic, Lerner College of Medicine, Case Western Reserve University, Cleveland, OH, 44195, USA
| | - Kurt W. Runge
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Lerner College of Medicine, Case Western Reserve University, Cleveland, OH, 44195, USA
- Department of Genetics and Genomic Sciences, School of Medicine, Case Western Reserve University, Cleveland, Ohio, 44106, USA
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20
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Menin L, Ursich S, Trovesi C, Zellweger R, Lopes M, Longhese MP, Clerici M. Tel1/ATM prevents degradation of replication forks that reverse after topoisomerase poisoning. EMBO Rep 2018; 19:e45535. [PMID: 29739811 PMCID: PMC6030699 DOI: 10.15252/embr.201745535] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Revised: 04/12/2018] [Accepted: 04/19/2018] [Indexed: 01/01/2023] Open
Abstract
In both yeast and mammals, the topoisomerase poison camptothecin (CPT) induces fork reversal, which has been proposed to stabilize replication forks, thus providing time for the repair of CPT-induced lesions and supporting replication restart. We show that Tel1, the Saccharomyces cerevisiae orthologue of human ATM kinase, stabilizes CPT-induced reversed forks by counteracting their nucleolytic degradation by the MRX complex. Tel1-lacking cells are hypersensitive to CPT specifically and show less reversed forks in the presence of CPT The lack of Mre11 nuclease activity restores wild-type levels of reversed forks in CPT-treated tel1Δ cells without affecting fork reversal in wild-type cells. Moreover, Mrc1 inactivation prevents fork reversal in wild-type, tel1Δ, and mre11 nuclease-deficient cells and relieves the hypersensitivity of tel1Δ cells to CPT Altogether, our data indicate that Tel1 counteracts Mre11 nucleolytic activity at replication forks that undergo Mrc1-mediated reversal in the presence of CPT.
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Affiliation(s)
- Luca Menin
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Milano, Italy
| | - Sebastian Ursich
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Camilla Trovesi
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Milano, Italy
| | - Ralph Zellweger
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Massimo Lopes
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Maria Pia Longhese
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Milano, Italy
| | - Michela Clerici
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Milano, Italy
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21
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Gobbini E, Cassani C, Vertemara J, Wang W, Mambretti F, Casari E, Sung P, Tisi R, Zampella G, Longhese MP. The MRX complex regulates Exo1 resection activity by altering DNA end structure. EMBO J 2018; 37:embj.201798588. [PMID: 29925516 DOI: 10.15252/embj.201798588] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 05/24/2018] [Accepted: 05/30/2018] [Indexed: 01/19/2023] Open
Abstract
Homologous recombination is triggered by nucleolytic degradation (resection) of DNA double-strand breaks (DSBs). DSB resection requires the Mre11-Rad50-Xrs2 (MRX) complex, which promotes the activity of Exo1 nuclease through a poorly understood mechanism. Here, we describe the Mre11-R10T mutant variant that accelerates DSB resection compared to wild-type Mre11 by potentiating Exo1-mediated processing. This increased Exo1 resection activity leads to a decreased association of the Ku complex to DSBs and an enhanced DSB resection in G1, indicating that Exo1 has a direct function in preventing Ku association with DSBs. Molecular dynamics simulations show that rotation of the Mre11 capping domains is able to induce unwinding of double-strand DNA (dsDNA). The R10T substitution causes altered orientation of the Mre11 capping domain that leads to persistent melting of the dsDNA end. We propose that MRX creates a specific DNA end structure that promotes Exo1 resection activity by facilitating the persistence of this nuclease on the DSB ends, uncovering a novel MRX function in DSB resection.
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Affiliation(s)
- Elisa Gobbini
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Milan, Italy
| | - Corinne Cassani
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Milan, Italy
| | - Jacopo Vertemara
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Milan, Italy
| | - Weibin Wang
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT, USA
| | - Fabiana Mambretti
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Milan, Italy
| | - Erika Casari
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Milan, Italy
| | - Patrick Sung
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT, USA
| | - Renata Tisi
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Milan, Italy
| | - Giuseppe Zampella
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Milan, Italy
| | - Maria Pia Longhese
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Milan, Italy
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22
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Marsella A, Cassani C, Casari E, Tisi R, Longhese MP. Structure–function relationships of the Mre11 protein in the control of DNA end bridging and processing. Curr Genet 2018; 65:11-16. [PMID: 29922906 DOI: 10.1007/s00294-018-0861-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 06/15/2018] [Accepted: 06/15/2018] [Indexed: 12/18/2022]
Affiliation(s)
- Antonio Marsella
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Milan, Italy
| | - Corinne Cassani
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Milan, Italy
| | - Erika Casari
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Milan, Italy
| | - Renata Tisi
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Milan, Italy.
| | - Maria Pia Longhese
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Milan, Italy.
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23
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Barrientos-Moreno M, Murillo-Pineda M, Muñoz-Cabello AM, Prado F. Histone depletion prevents telomere fusions in pre-senescent cells. PLoS Genet 2018; 14:e1007407. [PMID: 29879139 PMCID: PMC5991667 DOI: 10.1371/journal.pgen.1007407] [Citation(s) in RCA: 5] [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: 11/08/2017] [Accepted: 05/09/2018] [Indexed: 12/20/2022] Open
Abstract
Upon telomerase inactivation, telomeres gradually shorten with each cell division until cells enter replicative senescence. In Saccharomyces cerevisiae, the kinases Mec1/ATR and Tel1/ATM protect the genome during pre-senescence by preventing telomere-telomere fusions (T-TFs) and the subsequent genetic instability associated with fusion-bridge-breakage cycles. Here we report that T-TFs in mec1Δ tel1Δ cells can be suppressed by reducing the pool of available histones. This protection associates neither with changes in bulk telomere length nor with major changes in the structure of subtelomeric chromatin. We show that the absence of Mec1 and Tel1 strongly augments double-strand break (DSB) repair by non-homologous end joining (NHEJ), which might contribute to the high frequency of T-TFs in mec1Δ tel1Δ cells. However, histone depletion does not prevent telomere fusions by inhibiting NHEJ, which is actually increased in histone-depleted cells. Rather, histone depletion protects telomeres from fusions by homologous recombination (HR), even though HR is proficient in maintaining the proliferative state of pre-senescent mec1Δ tel1Δ cells. Therefore, HR during pre-senescence not only helps stalled replication forks but also prevents T-TFs by a mechanism that, in contrast to the previous one, is promoted by a reduction in the histone pool and can occur in the absence of Rad51. Our results further suggest that the Mec1-dependent depletion of histones that occurs during pre-senescence in cells without telomerase (tlc1Δ) prevents T-TFs by favoring the processing of unprotected telomeres by Rad51-independent HR. Telomere shortening upon telomerase inactivation leads to an irreversible cell division arrest known as replicative senescence, which is considered as a tumor suppressor mechanism. Since pre-senescence is critical for tissue homeostasis, cells are endowed with recombination mechanisms that facilitate the replication of short telomeres and prevent premature entry into senescence. Consequently, pre-senescent cells divide with critically short telomeres, which have lost most of their shelterin proteins. The tumor suppressor genes ATR and ATM, as well as their yeast homologs Mec1 and Tel1, prevent telomere fusions during pre-senescence by unknown mechanisms. Here we show that the absence of Mec1 and Tel1 strongly augments DSB repair by non-homologous end joining, which might explain the high rate of telomere fusions in mec1Δ tel1Δ cells. Moreover, we show that a reduction in the pool of available histones prevents telomere fusions in mec1Δ tel1Δ cells by stimulating Rad51-independent homologous recombination. Our results suggest that the Mec1-dependent process of histone depletion that accompanies pre-senescence in cells lacking telomerase activity is required to prevent telomere fusions by promoting the processing of unprotected telomeres by recombination instead of non-homologous end joining.
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Affiliation(s)
- Marta Barrientos-Moreno
- Department of Genome Biology, Andalusian Molecular Biology and Regenerative Medicine Center (CABIMER), CSIC-University of Seville-University Pablo de Olavide, Seville, Spain
| | - Marina Murillo-Pineda
- Department of Genome Biology, Andalusian Molecular Biology and Regenerative Medicine Center (CABIMER), CSIC-University of Seville-University Pablo de Olavide, Seville, Spain
| | - Ana M. Muñoz-Cabello
- Department of Genome Biology, Andalusian Molecular Biology and Regenerative Medicine Center (CABIMER), CSIC-University of Seville-University Pablo de Olavide, Seville, Spain
| | - Félix Prado
- Department of Genome Biology, Andalusian Molecular Biology and Regenerative Medicine Center (CABIMER), CSIC-University of Seville-University Pablo de Olavide, Seville, Spain
- * E-mail:
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24
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Colombo CV, Menin L, Clerici M. Alkaline Denaturing Southern Blot Analysis to Monitor Double-Strand Break Processing. Methods Mol Biol 2018; 1672:131-145. [PMID: 29043622 DOI: 10.1007/978-1-4939-7306-4_11] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Generation of 3' single-stranded DNA (ssDNA) tails at the ends of a double-strand break (DSB) is essential to repair the break through accurate homology-mediated repair pathways. Several methods have been developed to measure ssDNA accumulation at a DSB in the budding yeast Saccharomyces cerevisiae. Here, we describe one of these assays, which is based on the inability of restriction enzymes to cleave ssDNA. Digestion of genomic DNA prepared at different time points after DSB generation leads to the formation of ssDNA fragments whose length increases as the 5' strand degradation proceeds beyond restriction sites. After the separation by electrophoresis on alkaline denaturing agarose gel, these ssDNA fragments can be visualized by hybridization with an RNA probe that anneals with the 3'-undegraded DSB strand. This assay allows a direct and comprehensive visualization of DSB end processing.
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Affiliation(s)
| | - Luca Menin
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Milano, Italy
| | - Michela Clerici
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Milano, Italy.
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25
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Colombo CV, Trovesi C, Menin L, Longhese MP, Clerici M. The RNA binding protein Npl3 promotes resection of DNA double-strand breaks by regulating the levels of Exo1. Nucleic Acids Res 2017; 45:6530-6545. [PMID: 28472517 PMCID: PMC5499764 DOI: 10.1093/nar/gkx347] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 04/21/2017] [Indexed: 12/29/2022] Open
Abstract
Eukaryotic cells preserve genome integrity upon DNA damage by activating a signaling network that promotes DNA repair and controls cell cycle progression. One of the most severe DNA damage is the DNA double-strand break (DSB), whose 5΄ ends can be nucleolitically resected by multiple nucleases to create 3΄-ended single-stranded DNA tails that trigger DSB repair by homologous recombination. Here, we identify the Saccharomyces cerevisiae RNA binding protein Npl3 as a new player in DSB resection. Npl3 is related to both the metazoan serine-arginine-rich and the heterogeneous nuclear ribonucleo-proteins. NPL3 deletion impairs the generation of long ssDNA tails at the DSB ends, whereas it does not exacerbate the resection defect of exo1Δ cells. Furthermore, either the lack of Npl3 or the inactivation of its RNA-binding domains causes decrease of the exonuclease Exo1 protein levels as well as generation of unusual and extended EXO1 RNA species. These findings, together with the observation that EXO1 overexpression partially suppresses the resection defect of npl3Δ cells, indicate that Npl3 participates in DSB resection by promoting the proper biogenesis of EXO1 mRNA.
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Affiliation(s)
- Chiara Vittoria Colombo
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, 20126 Milano, Italy
| | - Camilla Trovesi
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, 20126 Milano, Italy
| | - Luca Menin
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, 20126 Milano, Italy
| | - Maria Pia Longhese
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, 20126 Milano, Italy
| | - Michela Clerici
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, 20126 Milano, Italy
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Pawłowska E, Szczepanska J, Blasiak J. DNA2-An Important Player in DNA Damage Response or Just Another DNA Maintenance Protein? Int J Mol Sci 2017; 18:ijms18071562. [PMID: 28718810 PMCID: PMC5536050 DOI: 10.3390/ijms18071562] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Revised: 07/13/2017] [Accepted: 07/17/2017] [Indexed: 02/01/2023] Open
Abstract
The human DNA2 (DNA replication helicase/nuclease 2) protein is expressed in both the nucleus and mitochondria, where it displays ATPase-dependent nuclease and helicase activities. DNA2 plays an important role in the removing of long flaps in DNA replication and long-patch base excision repair (LP-BER), interacting with the replication protein A (RPA) and the flap endonuclease 1 (FEN1). DNA2 can promote the restart of arrested replication fork along with Werner syndrome ATP-dependent helicase (WRN) and Bloom syndrome protein (BLM). In mitochondria, DNA2 can facilitate primer removal during strand-displacement replication. DNA2 is involved in DNA double strand (DSB) repair, in which it is complexed with BLM, RPA and MRN for DNA strand resection required for homologous recombination repair. DNA2 can be a major protein involved in the repair of complex DNA damage containing a DSB and a 5' adduct resulting from a chemical group bound to DNA 5' ends, created by ionizing radiation and several anticancer drugs, including etoposide, mitoxantrone and some anthracyclines. The role of DNA2 in telomere end maintenance and cell cycle regulation suggests its more general role in keeping genomic stability, which is impaired in cancer. Therefore DNA2 can be an attractive target in cancer therapy. This is supported by enhanced expression of DNA2 in many cancer cell lines with oncogene activation and premalignant cells. Therefore, DNA2 can be considered as a potential marker, useful in cancer therapy. DNA2, along with PARP1 inhibition, may be considered as a potential target for inducing synthetic lethality, a concept of killing tumor cells by targeting two essential genes.
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Affiliation(s)
- Elzbieta Pawłowska
- Department of Orthodontics, Medical University of Lodz, 92-216 Lodz, Poland.
| | - Joanna Szczepanska
- Department of Pediatric Dentistry, Medical University of Lodz, 92-216 Lodz, Poland.
| | - Janusz Blasiak
- Department of Molecular Genetics, Faculty of Biology and Environmental Protection, University of Lodz, 90-236 Lodz, Poland.
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Siler J, Xia B, Wong C, Kath M, Bi X. Cell cycle-dependent positive and negative functions of Fun30 chromatin remodeler in DNA damage response. DNA Repair (Amst) 2017; 50:61-70. [PMID: 28089177 DOI: 10.1016/j.dnarep.2016.12.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Revised: 12/03/2016] [Accepted: 12/31/2016] [Indexed: 11/17/2022]
Abstract
The evolutionally conserved Fun30 chromatin remodeler in Saccharomyces cerevisiae has been shown to contribute to cellular resistance to genotoxic stress inflicted by camptothecin (CPT), methyl methanesulfonate (MMS) and hydroxyurea (HU). Fun30 aids in extensive DNA resection of DNA double stranded break (DSB) ends, which is thought to underlie its role in CPT-resistance. How Fun30 promotes MMS- or HU-resistance has not been resolved. Interestingly, we have recently found Fun30 to also play a negative role in cellular tolerance to MMS and HU in the absence of the Rad5-dependent DNA damage tolerance pathway. In this report, we show that Fun30 acts to down regulate Rad9-dependent DNA damage checkpoint triggered by CPT or MMS, but does not affect Rad9-independent intra-S phase replication checkpoint induced by MMS or HU. These results support the notion that Fun30 contributes to cellular response to DSBs by preventing excessive DNA damage checkpoint activation in addition to its role in facilitating DNA end resection. On the other hand, we present evidence suggesting that Fun30's negative function in MMS- and HU-tolerance in the absence of Rad5 is not related to its regulation of checkpoint activity. Moreover, we find Fun30 to be cell cycle regulated with its abundance peaking in G2/M phase of the cell cycle. Importantly, we demonstrate that artificially restricting Fun30 expression to G2/M does not affect its positive or negative function in genotoxin-resistance, but confining Fun30 to S phase abolishes its functions. These results indicate that both positive and negative functions of Fun30 in DNA damage response occur mainly in G2/M phase.
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Affiliation(s)
- Jasmine Siler
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Bowen Xia
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Carina Wong
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Morgan Kath
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Xin Bi
- Department of Biology, University of Rochester, Rochester, NY 14627, USA.
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28
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Vasianovich Y, Altmannova V, Kotenko O, Newton MD, Krejci L, Makovets S. Unloading of homologous recombination factors is required for restoring double-stranded DNA at damage repair loci. EMBO J 2016; 36:213-231. [PMID: 27932447 PMCID: PMC5239998 DOI: 10.15252/embj.201694628] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2016] [Revised: 11/06/2016] [Accepted: 11/08/2016] [Indexed: 11/22/2022] Open
Abstract
Cells use homology‐dependent DNA repair to mend chromosome breaks and restore broken replication forks, thereby ensuring genome stability and cell survival. DNA break repair via homology‐based mechanisms involves nuclease‐dependent DNA end resection, which generates long tracts of single‐stranded DNA required for checkpoint activation and loading of homologous recombination proteins Rad52/51/55/57. While recruitment of the homologous recombination machinery is well characterized, it is not known how its presence at repair loci is coordinated with downstream re‐synthesis of resected DNA. We show that Rad51 inhibits recruitment of proliferating cell nuclear antigen (PCNA), the platform for assembly of the DNA replication machinery, and that unloading of Rad51 by Srs2 helicase is required for efficient PCNA loading and restoration of resected DNA. As a result, srs2Δ mutants are deficient in DNA repair correlating with extensive DNA processing, but this defect in srs2Δ mutants can be suppressed by inactivation of the resection nuclease Exo1. We propose a model in which during re‐synthesis of resected DNA, the replication machinery must catch up with the preceding processing nucleases, in order to close the single‐stranded gap and terminate further resection.
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Affiliation(s)
- Yulia Vasianovich
- Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Veronika Altmannova
- Department of Biology, Masaryk University, Brno, Czech Republic.,International Clinical Research Center, St. Anne's University Hospital in Brno, Brno, Czech Republic
| | - Oleksii Kotenko
- Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Matthew D Newton
- Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Lumir Krejci
- Department of Biology, Masaryk University, Brno, Czech Republic.,International Clinical Research Center, St. Anne's University Hospital in Brno, Brno, Czech Republic.,National Centre for Biomolecular Research, Masaryk University, Brno, Czech Republic
| | - Svetlana Makovets
- Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
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