1
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Comstock W, Sanford E, Navarro M, Smolka MB. Profiling Tel1 Signaling Reveals a Non-Canonical Motif Targeting DNA Repair and Telomere Control Machineries. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.03.601872. [PMID: 39005478 PMCID: PMC11244986 DOI: 10.1101/2024.07.03.601872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
The stability of the genome relies on Phosphatidyl Inositol 3-Kinase-related Kinases (PIKKs) that sense DNA damage and trigger elaborate downstream signaling responses. In S. cerevisiae, the Tel1 kinase (ortholog of human ATM) is activated at DNA double strand breaks (DSBs) and short telomeres. Despite the well-established roles of Tel1 in the control of telomere maintenance, suppression of chromosomal rearrangements, activation of cell cycle checkpoints, and repair of DSBs, the substrates through which Tel1 controls these processes remain incompletely understood. Here we performed an in depth phosphoproteomic screen for Tel1-dependent phosphorylation events. To achieve maximal coverage of the phosphoproteome, we developed a scaled-up approach that accommodates large amounts of protein extracts and chromatographic fractions. Compared to previous reports, we expanded the number of detected Tel1-dependent phosphorylation events by over 10-fold. Surprisingly, in addition to the identification of phosphorylation sites featuring the canonical motif for Tel1 phosphorylation (S/T-Q), the results revealed a novel motif (D/E-S/T) highly prevalent and enriched in the set of Tel1-dependent events. This motif is unique to Tel1 signaling and not shared with the Mec1 kinase, providing clues to how Tel1 plays specialized roles in DNA repair and telomere length control. Overall, these findings define a Tel1-signaling network targeting numerous proteins involved in DNA repair, chromatin regulation, and telomere maintenance that represents a framework for dissecting the molecular mechanisms of Tel1 action.
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Affiliation(s)
- Will Comstock
- Weill Institute for Cell and Molecular Biology, Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Ethan Sanford
- Weill Institute for Cell and Molecular Biology, Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Marcos Navarro
- Weill Institute for Cell and Molecular Biology, Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Marcus B Smolka
- Weill Institute for Cell and Molecular Biology, Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
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2
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Xie B, Sanford EJ, Hung SH, Wagner M, Heyer WD, Smolka MB. Multi-step control of homologous recombination via Mec1/ATR suppresses chromosomal rearrangements. EMBO J 2024; 43:3027-3043. [PMID: 38839993 PMCID: PMC11251156 DOI: 10.1038/s44318-024-00139-9] [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: 12/04/2023] [Revised: 05/19/2024] [Accepted: 05/22/2024] [Indexed: 06/07/2024] Open
Abstract
The Mec1/ATR kinase is crucial for genome stability, yet the mechanism by which it prevents gross chromosomal rearrangements (GCRs) remains unknown. Here we find that in cells with deficient Mec1 signaling, GCRs accumulate due to the deregulation of multiple steps in homologous recombination (HR). Mec1 primarily suppresses GCRs through its role in activating the canonical checkpoint kinase Rad53, which ensures the proper control of DNA end resection. Upon loss of Rad53 signaling and resection control, Mec1 becomes hyperactivated and triggers a salvage pathway in which the Sgs1 helicase is recruited to sites of DNA lesions via the 911-Dpb11 scaffolds and phosphorylated by Mec1 to favor heteroduplex rejection and limit HR-driven GCR accumulation. Fusing an ssDNA recognition domain to Sgs1 bypasses the requirement of Mec1 signaling for GCR suppression and nearly eliminates D-loop formation, thus preventing non-allelic recombination events. We propose that Mec1 regulates multiple steps of HR to prevent GCRs while ensuring balanced HR usage when needed for promoting tolerance to replication stress.
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Affiliation(s)
- Bokun Xie
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, USA
| | - Ethan James Sanford
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, USA
| | - Shih-Hsun Hung
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, CA, USA
| | - Mateusz Wagner
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, USA
| | - Wolf-Dietrich Heyer
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, CA, USA
| | - Marcus B Smolka
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, USA.
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3
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Nasheuer HP, Meaney AM. Starting DNA Synthesis: Initiation Processes during the Replication of Chromosomal DNA in Humans. Genes (Basel) 2024; 15:360. [PMID: 38540419 PMCID: PMC10969946 DOI: 10.3390/genes15030360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 03/09/2024] [Accepted: 03/11/2024] [Indexed: 06/14/2024] Open
Abstract
The initiation reactions of DNA synthesis are central processes during human chromosomal DNA replication. They are separated into two main processes: the initiation events at replication origins, the start of the leading strand synthesis for each replicon, and the numerous initiation events taking place during lagging strand DNA synthesis. In addition, a third mechanism is the re-initiation of DNA synthesis after replication fork stalling, which takes place when DNA lesions hinder the progression of DNA synthesis. The initiation of leading strand synthesis at replication origins is regulated at multiple levels, from the origin recognition to the assembly and activation of replicative helicase, the Cdc45-MCM2-7-GINS (CMG) complex. In addition, the multiple interactions of the CMG complex with the eukaryotic replicative DNA polymerases, DNA polymerase α-primase, DNA polymerase δ and ε, at replication forks play pivotal roles in the mechanism of the initiation reactions of leading and lagging strand DNA synthesis. These interactions are also important for the initiation of signalling at unperturbed and stalled replication forks, "replication stress" events, via ATR (ATM-Rad 3-related protein kinase). These processes are essential for the accurate transfer of the cells' genetic information to their daughters. Thus, failures and dysfunctions in these processes give rise to genome instability causing genetic diseases, including cancer. In their influential review "Hallmarks of Cancer: New Dimensions", Hanahan and Weinberg (2022) therefore call genome instability a fundamental function in the development process of cancer cells. In recent years, the understanding of the initiation processes and mechanisms of human DNA replication has made substantial progress at all levels, which will be discussed in the review.
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Affiliation(s)
- Heinz Peter Nasheuer
- Centre for Chromosome Biology, School of Biological and Chemical Sciences, Biochemistry, University of Galway, H91 TK33 Galway, Ireland;
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4
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Ascenção C, Sims JR, Dziubek A, Comstock W, Fogarty EA, Badar J, Freire R, Grimson A, Weiss RS, Cohen PE, Smolka MB. A TOPBP1 allele causing male infertility uncouples XY silencing dynamics from sex body formation. eLife 2024; 12:RP90887. [PMID: 38391183 PMCID: PMC10942628 DOI: 10.7554/elife.90887] [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] [Indexed: 02/24/2024] Open
Abstract
Meiotic sex chromosome inactivation (MSCI) is a critical feature of meiotic prophase I progression in males. While the ATR kinase and its activator TOPBP1 are key drivers of MSCI within the specialized sex body (SB) domain of the nucleus, how they promote silencing remains unclear given their multifaceted meiotic functions that also include DNA repair, chromosome synapsis, and SB formation. Here we report a novel mutant mouse harboring mutations in the TOPBP1-BRCT5 domain. Topbp1B5/B5 males are infertile, with impaired MSCI despite displaying grossly normal events of early prophase I, including synapsis and SB formation. Specific ATR-dependent events are disrupted, including phosphorylation and localization of the RNA:DNA helicase Senataxin. Topbp1B5/B5 spermatocytes initiate, but cannot maintain ongoing, MSCI. These findings reveal a non-canonical role for the ATR-TOPBP1 signaling axis in MSCI dynamics at advanced stages in pachynema and establish the first mouse mutant that separates ATR signaling and MSCI from SB formation.
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Affiliation(s)
- Carolline Ascenção
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell UniversityIthacaUnited States
| | - Jennie R Sims
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell UniversityIthacaUnited States
| | - Alexis Dziubek
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell UniversityIthacaUnited States
| | - William Comstock
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell UniversityIthacaUnited States
| | - Elizabeth A Fogarty
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell UniversityIthacaUnited States
| | - Jumana Badar
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell UniversityIthacaUnited States
| | - Raimundo Freire
- Fundación Canaria del Instituto de Investigación Sanitaria de Canarias (FIISC), Unidad de Investigación, Hospital Universitario de CanariasSanta Cruz de TenerifeSpain
- Instituto de Tecnologías Biomédicas, Universidad de La LagunaLa LagunaSpain
- Universidad Fernando Pessoa CanariasLas Palmas de Gran CanariaSpain
| | - Andrew Grimson
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell UniversityIthacaUnited States
| | - Robert S Weiss
- Department of Biomedical Sciences, Cornell UniversityIthacaUnited States
| | - Paula E Cohen
- Department of Biomedical Sciences, Cornell UniversityIthacaUnited States
| | - Marcus B Smolka
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell UniversityIthacaUnited States
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5
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Ascencao CFR, Sims JR, Dziubek A, Comstock W, Fogarty EA, Badar J, Freire R, Grimson A, Weiss RS, Cohen PE, Smolka M. A TOPBP1 Allele Causing Male Infertility Uncouples XY Silencing Dynamics From Sex Body Formation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.31.543071. [PMID: 37398453 PMCID: PMC10312512 DOI: 10.1101/2023.05.31.543071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Meiotic sex chromosome inactivation (MSCI) is a critical feature of meiotic prophase I progression in males. While the ATR kinase and its activator TOPBP1 are key drivers of MSCI within the specialized sex body (SB) domain of the nucleus, how they promote silencing remains unclear given their multifaceted meiotic functions that also include DNA repair, chromosome synapsis and SB formation. Here we report a novel mutant mouse harboring mutations in the TOPBP1-BRCT5 domain. Topbp1 B5/B5 males are infertile, with impaired MSCI despite displaying grossly normal events of early prophase I, including synapsis and SB formation. Specific ATR-dependent events are disrupted including phosphorylation and localization of the RNA:DNA helicase Senataxin. Topbp1 B5/B5 spermatocytes initiate, but cannot maintain ongoing, MSCI. These findings reveal a non-canonical role for the ATR-TOPBP1 signaling axis in MSCI dynamics at advanced stages in pachynema and establish the first mouse mutant that separates ATR signaling and MSCI from SB formation.
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6
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Xie B, Sanford EJ, Hung SH, Wagner MM, Heyer WD, Smolka MB. Multi-Step Control of Homologous Recombination by Mec1/ATR Ensures Robust Suppression of Gross Chromosomal Rearrangements. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.21.568146. [PMID: 38045423 PMCID: PMC10690203 DOI: 10.1101/2023.11.21.568146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
The Mec1/ATR kinase is crucial for genome stability, yet the mechanism by which it prevents gross chromosomal rearrangements (GCRs) remains unknown. Here we find that in cells with deficient Mec1 signaling, GCRs accumulate due to the deregulation of multiple steps in homologous recombination (HR). Mec1 primarily suppresses GCRs through its role in activating the canonical checkpoint kinase Rad53, which ensures the proper control of DNA end resection. Upon loss of Rad53 signaling and resection control, Mec1 becomes hyperactivated and triggers a salvage pathway in which the Sgs1 helicase is recruited to sites of DNA lesions via the 911-Dpb11 scaffolds to favor heteroduplex rejection and limit HR-driven GCR accumulation. Fusing an ssDNA recognition domain to Sgs1 bypasses the requirement of Mec1 signaling for GCR suppression and nearly eliminates D-loop formation, thus preventing non-allelic recombination events. We propose that Mec1 regulates multiple steps of HR to prevent GCRs while ensuring balanced HR usage when needed for promoting tolerance to replication stress.
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Affiliation(s)
- Bokun Xie
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, USA
| | - Ethan James Sanford
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, USA
| | - Shih-Hsun Hung
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, CA, USA
| | - Mateusz Maciej Wagner
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, USA
| | - Wolf-Dietrich Heyer
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, CA, USA
| | - Marcus B. Smolka
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, USA
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7
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Yates LA, Zhang X. Phosphoregulation of the checkpoint kinase Mec1 ATR. DNA Repair (Amst) 2023; 129:103543. [PMID: 37480741 DOI: 10.1016/j.dnarep.2023.103543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 07/14/2023] [Accepted: 07/15/2023] [Indexed: 07/24/2023]
Abstract
Yeast Mec1, and its mammalian ortholog, Ataxia-Telangiectasia and Rad3-related, are giant protein kinases central to replication stress and double strand DNA break repair. Mec1ATR, in complex with Ddc2ATRIP, is a 'sensor' of single stranded DNA, and phosphorylates numerous cell cycle and DNA repair factors to enforce cell cycle arrest and facilitate repair. Over the last several years, new techniques - particularly in structural biology - have provided molecular mechanisms for Mec1ATR function. It is becoming increasingly clear how post-translational modification of Mec1ATR and its interaction partners modulates the DNA damage checkpoint. In this review, we summarise the most recent work unravelling Mec1ATR function in the DNA damage checkpoint and provide a molecular context for its regulation by phosphorylation.
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Affiliation(s)
- Luke A Yates
- Section of Structural, Department of Infectious Disease, Sir Alexander Fleming Building, Imperial College London, SW7 2AZ, UK; DNA processing machines laboratory, Francis Crick Institute, London NW1 1AT, UK.
| | - Xiaodong Zhang
- Section of Structural, Department of Infectious Disease, Sir Alexander Fleming Building, Imperial College London, SW7 2AZ, UK; DNA processing machines laboratory, Francis Crick Institute, London NW1 1AT, UK.
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8
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Panessa GM, Tassoni-Tsuchida E, Pires MR, Felix RR, Jekabson R, de Souza-Pinto NC, da Cunha FM, Brandman O, Cussiol JRR. Opi1-mediated transcriptional modulation orchestrates genotoxic stress response in budding yeast. Genetics 2023; 225:iyad130. [PMID: 37440469 PMCID: PMC10691878 DOI: 10.1093/genetics/iyad130] [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: 06/05/2023] [Revised: 06/28/2023] [Accepted: 07/03/2023] [Indexed: 07/15/2023] Open
Abstract
In budding yeast, the transcriptional repressor Opi1 regulates phospholipid biosynthesis by repressing expression of genes containing inositol-sensitive upstream activation sequences. Upon genotoxic stress, cells activate the DNA damage response to coordinate a complex network of signaling pathways aimed at preserving genomic integrity. Here, we reveal that Opi1 is important to modulate transcription in response to genotoxic stress. We find that cells lacking Opi1 exhibit hypersensitivity to genotoxins, along with a delayed G1-to-S-phase transition and decreased gamma-H2A levels. Transcriptome analysis using RNA sequencing reveals that Opi1 plays a central role in modulating essential biological processes during methyl methanesulfonate (MMS)-associated stress, including repression of phospholipid biosynthesis and transduction of mating signaling. Moreover, Opi1 induces sulfate assimilation and amino acid metabolic processes, such as arginine and histidine biosynthesis and glycine catabolism. Furthermore, we observe increased mitochondrial DNA instability in opi1Δ cells upon MMS treatment. Notably, we show that constitutive activation of the transcription factor Ino2-Ino4 is responsible for genotoxin sensitivity in Opi1-deficient cells, and the production of inositol pyrophosphates by Kcs1 counteracts Opi1 function specifically during MMS-induced stress. Overall, our findings highlight Opi1 as a critical sensor of genotoxic stress in budding yeast, orchestrating gene expression to facilitate appropriate stress responses.
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Affiliation(s)
- Giovanna Marques Panessa
- Departamento de Bioquímica, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, SP 04023-900, Brazil
| | - Eduardo Tassoni-Tsuchida
- Department of Biology, Stanford University, Stanford, CA 94305, USA
- Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
| | - Marina Rodrigues Pires
- Departamento de Bioquímica, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, SP 04023-900, Brazil
| | - Rodrigo Rodrigues Felix
- Departamento de Bioquímica, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, SP 04023-900, Brazil
| | - Rafaella Jekabson
- Departamento de Bioquímica, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, SP 04023-900, Brazil
| | | | - Fernanda Marques da Cunha
- Departamento de Bioquímica, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, SP 04023-900, Brazil
| | - Onn Brandman
- Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
| | - José Renato Rosa Cussiol
- Departamento de Bioquímica, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, SP 04023-900, Brazil
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9
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Hadjicharalambous A, Whale AJ, Can G, Skehel JM, Houseley JM, Zegerman P. Checkpoint kinase interaction with DNA polymerase alpha regulates replication progression during stress. Wellcome Open Res 2023; 8:327. [PMID: 37766847 PMCID: PMC10521137 DOI: 10.12688/wellcomeopenres.19617.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/06/2023] [Indexed: 09/29/2023] Open
Abstract
Background: In eukaryotes, replication stress activates a checkpoint response, which facilitates genome duplication by stabilising the replisome. How the checkpoint kinases regulate the replisome remains poorly understood. The aim of this study is to identify new targets of checkpoint kinases within the replisome during replication stress. Methods: Here we use an unbiased biotin proximity-ligation approach in Saccharomyces cerevisiae to identify new interactors and substrates of the checkpoint kinase Rad53 in vivo. Results: From this screen, we identified the replication initiation factor Sld7 as a Rad53 substrate, and Pol1, the catalytic subunit of polymerase a, as a Rad53-interactor. We showed that CDK phosphorylation of Pol1 mediates its interaction with Rad53. Combined with other interactions between Rad53 and the replisome, this Rad53-Pol1 interaction is important for viability and replisome progression during replication stress. Conclusions: Together, we explain how the interactions of Rad53 with the replisome are controlled by both replication stress and the cell cycle, and why these interactions might be important for coordinating the stabilisation of both the leading and lagging strand machineries.
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Affiliation(s)
| | - Alex J. Whale
- Epigenetics Programme, Babraham Institute, University of Cambridge, Cambridge, England, CB22 3AT, UK
| | - Geylani Can
- Department of Biochemistry, University of Cambridge, Cambridge, England, CB2 1GA, UK
| | - J. Mark Skehel
- Medical Research Council Laboratory of Molecular Biology, Cambridge Biomedical Campus, London, England, CB2 0QH, UK
| | - Jonathan M. Houseley
- Epigenetics Programme, Babraham Institute, University of Cambridge, Cambridge, England, CB22 3AT, UK
| | - Philip Zegerman
- Department of Biochemistry, University of Cambridge, Cambridge, England, CB2 1GA, UK
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10
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Yates L, Tannous E, Morgan R, Burgers P, Zhang X. A DNA damage-induced phosphorylation circuit enhances Mec1 ATR Ddc2 ATRIP recruitment to Replication Protein A. Proc Natl Acad Sci U S A 2023; 120:e2300150120. [PMID: 36996117 PMCID: PMC10083555 DOI: 10.1073/pnas.2300150120] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 02/24/2023] [Indexed: 03/31/2023] Open
Abstract
The cell cycle checkpoint kinase Mec1ATR and its integral partner Ddc2ATRIP are vital for the DNA damage and replication stress response. Mec1-Ddc2 "senses" single-stranded DNA (ssDNA) by being recruited to the ssDNA binding Replication Protein A (RPA) via Ddc2. In this study, we show that a DNA damage-induced phosphorylation circuit modulates checkpoint recruitment and function. We demonstrate that Ddc2-RPA interactions modulate the association between RPA and ssDNA and that Rfa1-phosphorylation aids in the further recruitment of Mec1-Ddc2. We also uncover an underappreciated role for Ddc2 phosphorylation that enhances its recruitment to RPA-ssDNA that is important for the DNA damage checkpoint in yeast. The crystal structure of a phosphorylated Ddc2 peptide in complex with its RPA interaction domain provides molecular details of how checkpoint recruitment is enhanced, which involves Zn2+. Using electron microscopy and structural modeling approaches, we propose that Mec1-Ddc2 complexes can form higher order assemblies with RPA when Ddc2 is phosphorylated. Together, our results provide insight into Mec1 recruitment and suggest that formation of supramolecular complexes of RPA and Mec1-Ddc2, modulated by phosphorylation, would allow for rapid clustering of damage foci to promote checkpoint signaling.
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Affiliation(s)
- Luke A. Yates
- Section of Structural Biology, Department of Infectious Disease, Imperial College London, South Kensington, LondonSW7 2AZ, United Kingdom
| | - Elias A. Tannous
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Saint Louis, MO63110
| | - R. Marc Morgan
- Department of Life Sciences, Centre for Structural Biology, Imperial College London, South Kensington, LondonSW7 2AZ, United Kingdom
| | - Peter M. Burgers
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Saint Louis, MO63110
| | - Xiaodong Zhang
- Section of Structural Biology, Department of Infectious Disease, Imperial College London, South Kensington, LondonSW7 2AZ, United Kingdom
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11
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Frigerio C, Di Nisio E, Galli M, Colombo CV, Negri R, Clerici M. The Chromatin Landscape around DNA Double-Strand Breaks in Yeast and Its Influence on DNA Repair Pathway Choice. Int J Mol Sci 2023; 24:ijms24043248. [PMID: 36834658 PMCID: PMC9967470 DOI: 10.3390/ijms24043248] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Revised: 01/21/2023] [Accepted: 02/01/2023] [Indexed: 02/09/2023] Open
Abstract
DNA double-strand breaks (DSBs) are harmful DNA lesions, which elicit catastrophic consequences for genome stability if not properly repaired. DSBs can be repaired by either non-homologous end joining (NHEJ) or homologous recombination (HR). The choice between these two pathways depends on which proteins bind to the DSB ends and how their action is regulated. NHEJ initiates with the binding of the Ku complex to the DNA ends, while HR is initiated by the nucleolytic degradation of the 5'-ended DNA strands, which requires several DNA nucleases/helicases and generates single-stranded DNA overhangs. DSB repair occurs within a precisely organized chromatin environment, where the DNA is wrapped around histone octamers to form the nucleosomes. Nucleosomes impose a barrier to the DNA end processing and repair machinery. Chromatin organization around a DSB is modified to allow proper DSB repair either by the removal of entire nucleosomes, thanks to the action of chromatin remodeling factors, or by post-translational modifications of histones, thus increasing chromatin flexibility and the accessibility of repair enzymes to the DNA. Here, we review histone post-translational modifications occurring around a DSB in the yeast Saccharomyces cerevisiae and their role in DSB repair, with particular attention to DSB repair pathway choice.
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Affiliation(s)
- Chiara Frigerio
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, 20126 Milan, Italy
| | - Elena Di Nisio
- Department of Biology and Biotechnologies “C. Darwin”, Sapienza University of Rome, 00185 Rome, Italy
| | - Michela Galli
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, 20126 Milan, Italy
| | - Chiara Vittoria Colombo
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, 20126 Milan, Italy
| | - Rodolfo Negri
- Department of Biology and Biotechnologies “C. Darwin”, Sapienza University of Rome, 00185 Rome, Italy
- Institute of Molecular Biology and Pathology (IBPM), National Research Council (CNR) of Italy, 00185 Rome, Italy
- Correspondence: (R.N.); (M.C.)
| | - Michela Clerici
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, 20126 Milan, Italy
- Correspondence: (R.N.); (M.C.)
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12
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Sheu YJ, Kawaguchi RK, Gillis J, Stillman B. Prevalent and dynamic binding of the cell cycle checkpoint kinase Rad53 to gene promoters. eLife 2022; 11:e84320. [PMID: 36520028 PMCID: PMC9797190 DOI: 10.7554/elife.84320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 11/29/2022] [Indexed: 12/23/2022] Open
Abstract
Replication of the genome must be coordinated with gene transcription and cellular metabolism, especially following replication stress in the presence of limiting deoxyribonucleotides. The Saccharomyces cerevisiae Rad53 (CHEK2 in mammals) checkpoint kinase plays a major role in cellular responses to DNA replication stress. Cell cycle regulated, genome-wide binding of Rad53 to chromatin was examined. Under replication stress, the kinase bound to sites of active DNA replication initiation and fork progression, but unexpectedly to the promoters of about 20% of genes encoding proteins involved in multiple cellular functions. Rad53 promoter binding correlated with changes in expression of a subset of genes. Rad53 promoter binding to certain genes was influenced by sequence-specific transcription factors and less by checkpoint signaling. However, in checkpoint mutants, untimely activation of late-replicating origins reduces the transcription of nearby genes, with concomitant localization of Rad53 to their gene bodies. We suggest that the Rad53 checkpoint kinase coordinates genome-wide replication and transcription under replication stress conditions.
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Affiliation(s)
- Yi-Jun Sheu
- Cold Spring Harbor LaboratoryCold Spring HarborUnited States
| | | | - Jesse Gillis
- Cold Spring Harbor LaboratoryCold Spring HarborUnited States
| | - Bruce Stillman
- Cold Spring Harbor LaboratoryCold Spring HarborUnited States
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13
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Bell ES, Shah P, Zuela-Sopilniak N, Kim D, Varlet AA, Morival JL, McGregor AL, Isermann P, Davidson PM, Elacqua JJ, Lakins JN, Vahdat L, Weaver VM, Smolka MB, Span PN, Lammerding J. Low lamin A levels enhance confined cell migration and metastatic capacity in breast cancer. Oncogene 2022; 41:4211-4230. [PMID: 35896617 PMCID: PMC9925375 DOI: 10.1038/s41388-022-02420-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 07/12/2022] [Accepted: 07/14/2022] [Indexed: 02/07/2023]
Abstract
Aberrations in nuclear size and shape are commonly used to identify cancerous tissue. However, it remains unclear whether the disturbed nuclear structure directly contributes to the cancer pathology or is merely a consequence of other events occurring during tumorigenesis. Here, we show that highly invasive and proliferative breast cancer cells frequently exhibit Akt-driven lower expression of the nuclear envelope proteins lamin A/C, leading to increased nuclear deformability that permits enhanced cell migration through confined environments that mimic interstitial spaces encountered during metastasis. Importantly, increasing lamin A/C expression in highly invasive breast cancer cells reflected gene expression changes characteristic of human breast tumors with higher LMNA expression, and specifically affected pathways related to cell-ECM interactions, cell metabolism, and PI3K/Akt signaling. Further supporting an important role of lamins in breast cancer metastasis, analysis of lamin levels in human breast tumors revealed a significant association between lower lamin A levels, Akt signaling, and decreased disease-free survival. These findings suggest that downregulation of lamin A/C in breast cancer cells may influence both cellular physical properties and biochemical signaling to promote metastatic progression.
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Affiliation(s)
- Emily S. Bell
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY,Current address: Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA
| | - Pragya Shah
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY
| | | | - Dongsung Kim
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY
| | - Alice-Anais Varlet
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY
| | - Julien L.P. Morival
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY
| | - Alexandra L. McGregor
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY,Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY
| | - Philipp Isermann
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY
| | | | - Joshua J. Elacqua
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY
| | - Jonathan N. Lakins
- Center for Bioengineering and Tissue Regeneration, Department of Surgery, University of California, San Francisco, San Francisco, CA
| | - Linda Vahdat
- Department of Medicine, Weill Cornell Medicine, New York, NY
| | - Valerie M. Weaver
- Center for Bioengineering and Tissue Regeneration, Department of Surgery, University of California, San Francisco, San Francisco, CA,Helen Diller Cancer Center, Department of Bioengineering and Therapeutic Sciences, and Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA
| | - Marcus B. Smolka
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY
| | - Paul N. Span
- Department of Radiation Oncology, Radiotherapy & OncoImmunology laboratory, Radboud University Nijmegen Medical Center, Nijmegen, the Netherlands
| | - Jan Lammerding
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, USA. .,Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA.
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14
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James Sanford E, Bustamante Smolka M. A field guide to the proteomics of post-translational modifications in DNA repair. Proteomics 2022; 22:e2200064. [PMID: 35695711 PMCID: PMC9950963 DOI: 10.1002/pmic.202200064] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 05/19/2022] [Accepted: 05/30/2022] [Indexed: 12/15/2022]
Abstract
All cells incur DNA damage from exogenous and endogenous sources and possess pathways to detect and repair DNA damage. Post-translational modifications (PTMs), in the past 20 years, have risen to ineluctable importance in the study of the regulation of DNA repair mechanisms. For example, DNA damage response kinases are critical in both the initial sensing of DNA damage as well as in orchestrating downstream activities of DNA repair factors. Mass spectrometry-based proteomics revolutionized the study of the role of PTMs in the DNA damage response and has canonized PTMs as central modulators of nearly all aspects of DNA damage signaling and repair. This review provides a biologist-friendly guide for the mass spectrometry analysis of PTMs in the context of DNA repair and DNA damage responses. We reflect on the current state of proteomics for exploring new mechanisms of PTM-based regulation and outline a roadmap for designing PTM mapping experiments that focus on the DNA repair and DNA damage responses.
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Key Words
- LC-MS/MS, technology, bottom-up proteomics, technology, signal transduction, cell biology
- phosphoproteomics, technology, post-translational modification analysis, technology, post-translational modifications, cell biology, mass spectrometry
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Affiliation(s)
- Ethan James Sanford
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853
| | - Marcus Bustamante Smolka
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853,Corresponding author:
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15
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A DNA Replication Fork-centric View of the Budding Yeast DNA Damage Response. DNA Repair (Amst) 2022; 119:103393. [DOI: 10.1016/j.dnarep.2022.103393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 08/25/2022] [Accepted: 08/26/2022] [Indexed: 11/23/2022]
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16
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Sims JR, Faça VM, Pereira C, Ascenção C, Comstock W, Badar J, Arroyo-Martinez GA, Freire R, Cohen PE, Weiss RS, Smolka MB. Phosphoproteomics of ATR signaling in mouse testes. eLife 2022; 11:e68648. [PMID: 35133275 PMCID: PMC8824463 DOI: 10.7554/elife.68648] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 12/22/2021] [Indexed: 11/13/2022] Open
Abstract
The phosphatidylinositol 3' kinase (PI3K)-related kinase ATR is crucial for mammalian meiosis. ATR promotes meiotic progression by coordinating key events in DNA repair, meiotic sex chromosome inactivation (MSCI), and checkpoint-dependent quality control during meiotic prophase I. Despite its central roles in meiosis, the ATR-dependent meiotic signaling network remains largely unknown. Here, we used phosphoproteomics to define ATR signaling events in testes from mice following chemical and genetic ablation of ATR signaling. Quantitative analysis of phosphoproteomes obtained after germ cell-specific genetic ablation of the ATR activating 9-1-1 complex or treatment with ATR inhibitor identified over 14,000 phosphorylation sites from testes samples, of which 401 phosphorylation sites were found to be dependent on both the 9-1-1 complex and ATR. Our analyses identified ATR-dependent phosphorylation events in crucial DNA damage signaling and DNA repair proteins including TOPBP1, SMC3, MDC1, RAD50, and SLX4. Importantly, we identified ATR and RAD1-dependent phosphorylation events in proteins involved in mRNA regulatory processes, including SETX and RANBP3, whose localization to the sex body was lost upon ATR inhibition. In addition to identifying the expected ATR-targeted S/T-Q motif, we identified enrichment of an S/T-P-X-K motif in the set of ATR-dependent events, suggesting that ATR promotes signaling via proline-directed kinase(s) during meiosis. Indeed, we found that ATR signaling is important for the proper localization of CDK2 in spermatocytes. Overall, our analysis establishes a map of ATR signaling in mouse testes and highlights potential meiotic-specific actions of ATR during prophase I progression.
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Affiliation(s)
- Jennie R Sims
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell UniversityIthacaUnited States
| | - Vitor M Faça
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell UniversityIthacaUnited States
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São PauloRibeirão PretoBrazil
| | - Catalina Pereira
- Department of Biomedical Sciences, Cornell UniversityIthacaUnited States
| | - Carolline Ascenção
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell UniversityIthacaUnited States
| | - William Comstock
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell UniversityIthacaUnited States
| | - Jumana Badar
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell UniversityIthacaUnited States
| | | | - Raimundo Freire
- Unidad de Investigación, Hospital Universitario de CanariasTenerifeSpain
- Instituto de Tecnologías Biomédicas, Universidad de La LagunaLa LagunaSpain
- Universidad Fernando Pessoa CanariasLas Palmas de Gran CanariaSpain
| | - Paula E Cohen
- Department of Biomedical Sciences, Cornell UniversityIthacaUnited States
| | - Robert S Weiss
- Department of Biomedical Sciences, Cornell UniversityIthacaUnited States
| | - Marcus B Smolka
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell UniversityIthacaUnited States
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17
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DNA Damage-Induced Phosphorylation of Histone H2A at Serine 15 Is Linked to DNA End Resection. Mol Cell Biol 2021; 41:e0005621. [PMID: 34570618 DOI: 10.1128/mcb.00056-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The repair of DNA double-strand breaks (DSBs) occurs in chromatin, and several histone posttranslational modifications have been implicated in the process. Modifications of the histone H2A N-terminal tail have also been linked to DNA damage response, through acetylation or ubiquitination of lysine residues that regulate repair pathway choice. Here, we characterize a new DNA damage-induced phosphorylation on chromatin, at serine 15 of H2A in yeast. We show that this SQ motif functions independently of the classical S129 C-terminal site (γ-H2A) and that mutant-mimicking constitutive phosphorylation increases cell sensitivity to DNA damage. H2AS129ph is induced by Tel1ATM and Mec1ATR, and the loss of Lcd1ATRIP or Mec1 signaling decreases γ-H2A spreading distal to the DSB. In contrast, H2AS15ph is completely dependent on Lcd1ATRIP, indicating that this modification only happens when end resection is engaged. This is supported by an increase in replication protein A (RPA) and a decrease in DNA signal near the DSB in H2A-S15E phosphomimic mutants, indicating higher resection. In mammals, this serine is replaced by a lysine (H2AK15) which undergoes an acetyl-monoubiquityl switch to regulate binding of 53BP1 and resection. This regulation seems functionally conserved with budding yeast H2AS15 and 53BP1-homolog Rad9, using different posttranslational modifications between organisms but achieving the same function.
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18
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Hurst V, Challa K, Jonas F, Forey R, Sack R, Seebacher J, Schmid CD, Barkai N, Shimada K, Gasser SM, Poli J. A regulatory phosphorylation site on Mec1 controls chromatin occupancy of RNA polymerases during replication stress. EMBO J 2021; 40:e108439. [PMID: 34569643 PMCID: PMC8561635 DOI: 10.15252/embj.2021108439] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 09/08/2021] [Accepted: 09/10/2021] [Indexed: 01/16/2023] Open
Abstract
Upon replication stress, budding yeast checkpoint kinase Mec1ATR triggers the downregulation of transcription, thereby reducing the level of RNA polymerase (RNAP) on chromatin to facilitate replication fork progression. Here, we identify a hydroxyurea-induced phosphorylation site on Mec1, Mec1-S1991, that contributes to the eviction of RNAPII and RNAPIII during replication stress. The expression of the non-phosphorylatable mec1-S1991A mutant reduces replication fork progression genome-wide and compromises survival on hydroxyurea. This defect can be suppressed by destabilizing chromatin-bound RNAPII through a TAP fusion to its Rpb3 subunit, suggesting that lethality in mec1-S1991A mutants arises from replication-transcription conflicts. Coincident with a failure to repress gene expression on hydroxyurea in mec1-S1991A cells, highly transcribed genes such as GAL1 remain bound at nuclear pores. Consistently, we find that nuclear pore proteins and factors controlling RNAPII and RNAPIII are phosphorylated in a Mec1-dependent manner on hydroxyurea. Moreover, we show that Mec1 kinase also contributes to reduced RNAPII occupancy on chromatin during an unperturbed S phase by promoting degradation of the Rpb1 subunit.
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Affiliation(s)
- Verena Hurst
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.,Faculty of Natural Sciences, University of Basel, Basel, Switzerland
| | - Kiran Challa
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Felix Jonas
- Departments of Molecular Genetics and Physics of Complex Systems, Weizmann Institute of Science, Rehovot, Israel
| | - Romain Forey
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Equipe labélisée Ligue contre le Cancer, Montpellier, France
| | - Ragna Sack
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Jan Seebacher
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Christoph D Schmid
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Naama Barkai
- Departments of Molecular Genetics and Physics of Complex Systems, Weizmann Institute of Science, Rehovot, Israel
| | - Kenji Shimada
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Susan M Gasser
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.,Faculty of Natural Sciences, University of Basel, Basel, Switzerland
| | - Jérôme Poli
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.,Institut de Génétique Humaine, CNRS, Université de Montpellier, Equipe labélisée Ligue contre le Cancer, Montpellier, France
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19
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Yin Y, Lee WTC, Gupta D, Xue H, Tonzi P, Borowiec JA, Huang TT, Modesti M, Rothenberg E. A basal-level activity of ATR links replication fork surveillance and stress response. Mol Cell 2021; 81:4243-4257.e6. [PMID: 34473946 DOI: 10.1016/j.molcel.2021.08.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 03/03/2021] [Accepted: 08/06/2021] [Indexed: 11/27/2022]
Abstract
Mammalian cells use diverse pathways to prevent deleterious consequences during DNA replication, yet the mechanism by which cells survey individual replisomes to detect spontaneous replication impediments at the basal level, and their accumulation during replication stress, remain undefined. Here, we used single-molecule localization microscopy coupled with high-order-correlation image-mining algorithms to quantify the composition of individual replisomes in single cells during unperturbed replication and under replicative stress. We identified a basal-level activity of ATR that monitors and regulates the amounts of RPA at forks during normal replication. Replication-stress amplifies the basal activity through the increased volume of ATR-RPA interaction and diffusion-driven enrichment of ATR at forks. This localized crowding of ATR enhances its collision probability, stimulating the activation of its replication-stress response. Finally, we provide a computational model describing how the basal activity of ATR is amplified to produce its canonical replication stress response.
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Affiliation(s)
- Yandong Yin
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA.
| | - Wei Ting Chelsea Lee
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
| | - Dipika Gupta
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
| | - Huijun Xue
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
| | - Peter Tonzi
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
| | - James A Borowiec
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
| | - Tony T Huang
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
| | - Mauro Modesti
- Cancer Research Center of Marseille, CNRS UMR 7258, Inserm U1068, Institut Paoli-Calmettes, Aix-Marseille Université UM105, Marseille, France
| | - Eli Rothenberg
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA.
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20
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Arbel M, Liefshitz B, Kupiec M. DNA damage bypass pathways and their effect on mutagenesis in yeast. FEMS Microbiol Rev 2021; 45:5896953. [PMID: 32840566 DOI: 10.1093/femsre/fuaa038] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 08/23/2020] [Indexed: 12/11/2022] Open
Abstract
What is the origin of mutations? In contrast to the naïve notion that mutations are unfortunate accidents, genetic research in microorganisms has demonstrated that most mutations are created by genetically encoded error-prone repair mechanisms. However, error-free repair pathways also exist, and it is still unclear how cells decide when to use one repair method or the other. Here, we summarize what is known about the DNA damage tolerance mechanisms (also known as post-replication repair) for perhaps the best-studied organism, the yeast Saccharomyces cerevisiae. We describe the latest research, which has established the existence of at least two error-free and two error-prone inter-related mechanisms of damage tolerance that compete for the handling of spontaneous DNA damage. We explore what is known about the induction of mutations by DNA damage. We point to potential paradoxes and to open questions that still remain unanswered.
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Affiliation(s)
- Matan Arbel
- The Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Ramat Aviv 69978, Israel
| | - Batia Liefshitz
- The Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Ramat Aviv 69978, Israel
| | - Martin Kupiec
- The Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Ramat Aviv 69978, Israel
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21
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Tannous EA, Burgers PM. Novel insights into the mechanism of cell cycle kinases Mec1(ATR) and Tel1(ATM). Crit Rev Biochem Mol Biol 2021; 56:441-454. [PMID: 34151669 DOI: 10.1080/10409238.2021.1925218] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
DNA replication is a highly precise process which usually functions in a perfect rhythm with cell cycle progression. However, cells are constantly faced with various kinds of obstacles such as blocks in DNA replication, lack of availability of precursors and improper chromosome alignment. When these problems are not addressed, they may lead to chromosome instability and the accumulation of mutations, and even cell death. Therefore, the cell has developed response mechanisms to keep most of these situations under control. Of the many factors that participate in this DNA damage response, members of the family of phosphatidylinositol 3-kinase-related protein kinases (PIKKs) orchestrate the response landscape. Our understanding of two members of the PIKK family, human ATR (yeast Mec1) and ATM (yeast Tel1), and their associated partner proteins, has shown substantial progress through recent biochemical and structural studies. Emerging structural information of these unique kinases show common features that reveal the mechanism of kinase activity.
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Affiliation(s)
- Elias A Tannous
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Saint Louis, MO, USA
| | - Peter M Burgers
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Saint Louis, MO, USA
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22
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Williams RM, Zhang X. Roles of ATM and ATR in DNA double strand breaks and replication stress. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2021; 161:27-38. [DOI: 10.1016/j.pbiomolbio.2020.11.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 11/17/2020] [Accepted: 11/25/2020] [Indexed: 12/22/2022]
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23
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Roles of ATM and ATR in DNA double strand breaks and replication stress. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2021; 163:109-119. [PMID: 33887296 DOI: 10.1016/j.pbiomolbio.2021.03.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 11/17/2020] [Accepted: 11/25/2020] [Indexed: 02/06/2023]
Abstract
The maintenance of genome integrity is critical for the faithful replication of the genome during cell division and for protecting cells from accumulation of DNA damage, which if left unrepaired leads to a loss of genetic information, a breakdown in cell function and ultimately cell death and cancer. ATM and ATR are master kinases that are integral to homologous recombination-mediated repair of double strand breaks and preventing accumulation of dangerous DNA structures and genome instability during replication stress. While the roles of ATM and ATR are heavily intertwined in response to double strand breaks, their roles diverge in the response to replication stress. This review summarises our understanding of the players and their mode of actions in recruitment, activation and activity of ATM and ATR in response to DNA damage and replication stress and discusses how controlling localisation of these kinases and their activators allows them to orchestrate a stress-specific response.
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24
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Spotlight on the Replisome: Aetiology of DNA Replication-Associated Genetic Diseases. Trends Genet 2021; 37:317-336. [DOI: 10.1016/j.tig.2020.09.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 09/07/2020] [Accepted: 09/09/2020] [Indexed: 12/26/2022]
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25
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Sanford EJ, Comstock WJ, Faça VM, Vega SC, Gnügge R, Symington LS, Smolka MB. Phosphoproteomics reveals a distinctive Mec1/ATR signaling response upon DNA end hyper-resection. EMBO J 2021; 40:e104566. [PMID: 33764556 DOI: 10.15252/embj.2020104566] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 02/16/2021] [Accepted: 02/22/2021] [Indexed: 01/27/2023] Open
Abstract
The Mec1/ATR kinase is crucial for genome maintenance in response to a range of genotoxic insults, but it remains unclear how it promotes context-dependent signaling and DNA repair. Using phosphoproteomic analyses, we uncovered a distinctive Mec1/ATR signaling response triggered by extensive nucleolytic processing (resection) of DNA ends. Budding yeast cells lacking Rad9, a checkpoint adaptor and an inhibitor of resection, exhibit a selective increase in Mec1-dependent phosphorylation of proteins associated with single-strand DNA (ssDNA) transactions, including the ssDNA-binding protein Rfa2, the translocase/ubiquitin ligase Uls1, and the Sgs1-Top3-Rmi1 (STR) complex that regulates homologous recombination (HR). Extensive Mec1-dependent phosphorylation of the STR complex, mostly on the Sgs1 helicase subunit, promotes an interaction between STR and the DNA repair scaffolding protein Dpb11. Fusion of Sgs1 to phosphopeptide-binding domains of Dpb11 strongly impairs HR-mediated repair, supporting a model whereby Mec1 signaling regulates STR upon hyper-resection to influence recombination outcomes. Overall, the identification of a distinct Mec1 signaling response triggered by hyper-resection highlights the multi-faceted action of this kinase in the coordination of checkpoint signaling and HR-mediated DNA repair.
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Affiliation(s)
- Ethan J Sanford
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, USA
| | - William J Comstock
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, USA
| | - Vitor M Faça
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, USA.,Department of Biochemistry and Immunology and Cell-Based Therapy Center, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto, Brazil
| | - Stephanie C Vega
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, USA
| | - Robert Gnügge
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - Lorraine S Symington
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - Marcus B Smolka
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, USA
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26
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MTBP phosphorylation controls DNA replication origin firing. Sci Rep 2021; 11:4242. [PMID: 33608586 PMCID: PMC7895959 DOI: 10.1038/s41598-021-83287-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Accepted: 01/28/2021] [Indexed: 12/24/2022] Open
Abstract
Faithful genome duplication requires regulation of origin firing to determine loci, timing and efficiency of replisome generation. Established kinase targets for eukaryotic origin firing regulation are the Mcm2-7 helicase, Sld3/Treslin/TICRR and Sld2/RecQL4. We report that metazoan Sld7, MTBP (Mdm2 binding protein), is targeted by at least three kinase pathways. MTBP was phosphorylated at CDK consensus sites by cell cycle cyclin-dependent kinases (CDK) and Cdk8/19-cyclin C. Phospho-mimetic MTBP CDK site mutants, but not non-phosphorylatable mutants, promoted origin firing in human cells. MTBP was also phosphorylated at DNA damage checkpoint kinase consensus sites. Phospho-mimetic mutations at these sites inhibited MTBP’s origin firing capability. Whilst expressing a non-phospho MTBP mutant was insufficient to relieve the suppression of origin firing upon DNA damage, the mutant induced a genome-wide increase of origin firing in unperturbed cells. Our work establishes MTBP as a regulation platform of metazoan origin firing.
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27
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Lanz MC, Yugandhar K, Gupta S, Sanford EJ, Faça VM, Vega S, Joiner AMN, Fromme JC, Yu H, Smolka MB. In-depth and 3-dimensional exploration of the budding yeast phosphoproteome. EMBO Rep 2021; 22:e51121. [PMID: 33491328 PMCID: PMC7857435 DOI: 10.15252/embr.202051121] [Citation(s) in RCA: 79] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 11/30/2020] [Accepted: 12/03/2020] [Indexed: 01/11/2023] Open
Abstract
Phosphorylation is one of the most dynamic and widespread post-translational modifications regulating virtually every aspect of eukaryotic cell biology. Here, we assemble a dataset from 75 independent phosphoproteomic experiments performed in our laboratory using Saccharomyces cerevisiae. We report 30,902 phosphosites identified from cells cultured in a range of DNA damage conditions and/or arrested in distinct cell cycle stages. To generate a comprehensive resource for the budding yeast community, we aggregate our dataset with the Saccharomyces Genome Database and another recently published study, resulting in over 46,000 budding yeast phosphosites. With the goal of enhancing the identification of functional phosphorylation events, we perform computational positioning of phosphorylation sites on available 3D protein structures and systematically identify events predicted to regulate protein complex architecture. Results reveal hundreds of phosphorylation sites mapping to or near protein interaction interfaces, many of which result in steric or electrostatic "clashes" predicted to disrupt the interaction. With the advancement of Cryo-EM and the increasing number of available structures, our approach should help drive the functional and spatial exploration of the phosphoproteome.
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Affiliation(s)
- Michael C Lanz
- Department of Molecular Biology and GeneticsWeill Institute for Cell and Molecular BiologyCornell UniversityIthacaNYUSA
- Present address:
Department of BiologyStanford UniversityStanfordCAUSA
| | - Kumar Yugandhar
- Department of Computational BiologyWeill Institute for Cell and Molecular BiologyCornell UniversityIthacaNYUSA
| | - Shagun Gupta
- Department of Computational BiologyWeill Institute for Cell and Molecular BiologyCornell UniversityIthacaNYUSA
| | - Ethan J Sanford
- Department of Molecular Biology and GeneticsWeill Institute for Cell and Molecular BiologyCornell UniversityIthacaNYUSA
| | - Vitor M Faça
- Department of Molecular Biology and GeneticsWeill Institute for Cell and Molecular BiologyCornell UniversityIthacaNYUSA
| | - Stephanie Vega
- Department of Molecular Biology and GeneticsWeill Institute for Cell and Molecular BiologyCornell UniversityIthacaNYUSA
| | - Aaron M N Joiner
- Department of Molecular Biology and GeneticsWeill Institute for Cell and Molecular BiologyCornell UniversityIthacaNYUSA
| | - J Christopher Fromme
- Department of Molecular Biology and GeneticsWeill Institute for Cell and Molecular BiologyCornell UniversityIthacaNYUSA
| | - Haiyuan Yu
- Department of Computational BiologyWeill Institute for Cell and Molecular BiologyCornell UniversityIthacaNYUSA
| | - Marcus B Smolka
- Department of Molecular Biology and GeneticsWeill Institute for Cell and Molecular BiologyCornell UniversityIthacaNYUSA
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28
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Westhorpe R, Keszthelyi A, Minchell NE, Jones D, Baxter J. Separable functions of Tof1/Timeless in intra-S-checkpoint signalling, replisome stability and DNA topological stress. Nucleic Acids Res 2020; 48:12169-12187. [PMID: 33166393 PMCID: PMC7708041 DOI: 10.1093/nar/gkaa963] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 10/06/2020] [Accepted: 10/09/2020] [Indexed: 12/16/2022] Open
Abstract
The highly conserved Tof1/Timeless proteins minimise replication stress and promote normal DNA replication. They are required to mediate the DNA replication checkpoint (DRC), the stable pausing of forks at protein fork blocks, the coupling of DNA helicase and polymerase functions during replication stress (RS) and the preferential resolution of DNA topological stress ahead of the fork. Here we demonstrate that the roles of the Saccharomyces cerevisiae Timeless protein Tof1 in DRC signalling and resolution of DNA topological stress require distinct N and C terminal regions of the protein, whereas the other functions of Tof1 are closely linked to the stable interaction between Tof1 and its constitutive binding partner Csm3/Tipin. By separating the role of Tof1 in DRC from fork stabilisation and coupling, we show that Tof1 has distinct activities in checkpoint activation and replisome stability to ensure the viable completion of DNA replication following replication stress.
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Affiliation(s)
- Rose Westhorpe
- Genome Damage and Stability Centre, School of Life Sciences, Science Park Road, University of Sussex, Falmer, Brighton, East Sussex BN1 9RQ, UK
| | - Andrea Keszthelyi
- Genome Damage and Stability Centre, School of Life Sciences, Science Park Road, University of Sussex, Falmer, Brighton, East Sussex BN1 9RQ, UK
| | - Nicola E Minchell
- Genome Damage and Stability Centre, School of Life Sciences, Science Park Road, University of Sussex, Falmer, Brighton, East Sussex BN1 9RQ, UK
| | - David Jones
- Genome Damage and Stability Centre, School of Life Sciences, Science Park Road, University of Sussex, Falmer, Brighton, East Sussex BN1 9RQ, UK
| | - Jonathan Baxter
- Genome Damage and Stability Centre, School of Life Sciences, Science Park Road, University of Sussex, Falmer, Brighton, East Sussex BN1 9RQ, UK
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29
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Faca VM, Sanford EJ, Tieu J, Comstock W, Gupta S, Marshall S, Yu H, Smolka MB. Maximized quantitative phosphoproteomics allows high confidence dissection of the DNA damage signaling network. Sci Rep 2020; 10:18056. [PMID: 33093574 PMCID: PMC7582137 DOI: 10.1038/s41598-020-74939-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 10/08/2020] [Indexed: 02/07/2023] Open
Abstract
The maintenance of genomic stability relies on DNA damage sensor kinases that detect DNA lesions and phosphorylate an extensive network of substrates. The Mec1/ATR kinase is one of the primary sensor kinases responsible for orchestrating DNA damage responses. Despite the importance of Mec1/ATR, the current network of its identified substrates remains incomplete due, in part, to limitations in mass spectrometry-based quantitative phosphoproteomics. Phosphoproteomics suffers from lack of redundancy and statistical power for generating high confidence datasets, since information about phosphopeptide identity, site-localization, and quantitation must often be gleaned from a single peptide-spectrum match (PSM). Here we carefully analyzed the isotope label swapping strategy for phosphoproteomics, using data consistency among reciprocal labeling experiments as a central filtering rule for maximizing phosphopeptide identification and quantitation. We demonstrate that the approach allows drastic reduction of false positive quantitations and identifications even from phosphopeptides with a low number of spectral matches. Application of this approach identifies new Mec1/ATR-dependent signaling events, expanding our understanding of the DNA damage signaling network. Overall, the proposed quantitative phosphoproteomic approach should be generally applicable for investigating kinase signaling networks with high confidence and depth.
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Affiliation(s)
- Vitor Marcel Faca
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, 14853, USA
- Department of Biochemistry and Immunology and Cell-Based Therapy Center, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto, SP, 14049-900, Brazil
| | - Ethan J Sanford
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Jennifer Tieu
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, 14853, USA
| | - William Comstock
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Shagun Gupta
- Department of Computational Biology, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Shannon Marshall
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Haiyuan Yu
- Department of Computational Biology, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Marcus B Smolka
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, 14853, USA.
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30
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Dueva R, Iliakis G. Replication protein A: a multifunctional protein with roles in DNA replication, repair and beyond. NAR Cancer 2020; 2:zcaa022. [PMID: 34316690 PMCID: PMC8210275 DOI: 10.1093/narcan/zcaa022] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 08/23/2020] [Accepted: 08/27/2020] [Indexed: 02/07/2023] Open
Abstract
Single-stranded DNA (ssDNA) forms continuously during DNA replication and is an important intermediate during recombination-mediated repair of damaged DNA. Replication protein A (RPA) is the major eukaryotic ssDNA-binding protein. As such, RPA protects the transiently formed ssDNA from nucleolytic degradation and serves as a physical platform for the recruitment of DNA damage response factors. Prominent and well-studied RPA-interacting partners are the tumor suppressor protein p53, the RAD51 recombinase and the ATR-interacting proteins ATRIP and ETAA1. RPA interactions are also documented with the helicases BLM, WRN and SMARCAL1/HARP, as well as the nucleotide excision repair proteins XPA, XPG and XPF–ERCC1. Besides its well-studied roles in DNA replication (restart) and repair, accumulating evidence shows that RPA is engaged in DNA activities in a broader biological context, including nucleosome assembly on nascent chromatin, regulation of gene expression, telomere maintenance and numerous other aspects of nucleic acid metabolism. In addition, novel RPA inhibitors show promising effects in cancer treatment, as single agents or in combination with chemotherapeutics. Since the biochemical properties of RPA and its roles in DNA repair have been extensively reviewed, here we focus on recent discoveries describing several non-canonical functions.
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Affiliation(s)
- Rositsa Dueva
- Institute of Medical Radiation Biology, University of Duisburg-Essen Medical School, 45122 Essen, Germany
| | - George Iliakis
- Institute of Medical Radiation Biology, University of Duisburg-Essen Medical School, 45122 Essen, Germany
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31
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Memisoglu G, Lanz MC, Eapen VV, Jordan JM, Lee K, Smolka MB, Haber JE. Mec1 ATR Autophosphorylation and Ddc2 ATRIP Phosphorylation Regulates DNA Damage Checkpoint Signaling. Cell Rep 2020; 28:1090-1102.e3. [PMID: 31340146 DOI: 10.1016/j.celrep.2019.06.068] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Revised: 02/21/2019] [Accepted: 06/18/2019] [Indexed: 11/26/2022] Open
Abstract
In budding yeast, a single DNA double-strand break (DSB) triggers the activation of Mec1ATR-dependent DNA damage checkpoint. After about 12 h, cells turn off the checkpoint signaling and adapt despite the persistence of the DSB. We report that the adaptation involves the autophosphorylation of Mec1 at site S1964. A non-phosphorylatable mec1-S1964A mutant causes cells to arrest permanently in response to a single DSB without affecting the initial kinase activity of Mec1. Autophosphorylation of S1964 is dependent on Ddc1Rad9 and Dpb11TopBP1, and it correlates with the timing of adaptation. We also report that Mec1's binding partner, Ddc2ATRIP, is an inherently stable protein that is degraded specifically upon DNA damage. Ddc2 is regulated extensively through phosphorylation, which, in turn, regulates the localization of the Mec1-Ddc2 complex to DNA lesions. Taken together, these results suggest that checkpoint response is regulated through the autophosphorylation of Mec1 kinase and through the changes in Ddc2 abundance and phosphorylation.
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Affiliation(s)
- Gonen Memisoglu
- Department of Biology and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, MA 02454, USA
| | - Michael C Lanz
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - Vinay V Eapen
- Department of Biology and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, MA 02454, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Jacqueline M Jordan
- Department of Biology and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, MA 02454, USA
| | - Kihoon Lee
- Department of Biology and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, MA 02454, USA; Seegene, Inc., Ogeum-ro, Songpa-gu, Seoul 05548, Korea
| | - Marcus B Smolka
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - James E Haber
- Department of Biology and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, MA 02454, USA.
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32
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Bruhn C, Ajazi A, Ferrari E, Lanz MC, Batrin R, Choudhary R, Walvekar A, Laxman S, Longhese MP, Fabre E, Smolka MB, Foiani M. The Rad53 CHK1/CHK2-Spt21 NPAT and Tel1 ATM axes couple glucose tolerance to histone dosage and subtelomeric silencing. Nat Commun 2020; 11:4154. [PMID: 32814778 PMCID: PMC7438486 DOI: 10.1038/s41467-020-17961-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 07/23/2020] [Indexed: 12/14/2022] Open
Abstract
The DNA damage response (DDR) coordinates DNA metabolism with nuclear and non-nuclear processes. The DDR kinase Rad53CHK1/CHK2 controls histone degradation to assist DNA repair. However, Rad53 deficiency causes histone-dependent growth defects in the absence of DNA damage, pointing out unknown physiological functions of the Rad53-histone axis. Here we show that histone dosage control by Rad53 ensures metabolic homeostasis. Under physiological conditions, Rad53 regulates histone levels through inhibitory phosphorylation of the transcription factor Spt21NPAT on Ser276. Rad53-Spt21 mutants display severe glucose dependence, caused by excess histones through two separable mechanisms: dampening of acetyl-coenzyme A-dependent carbon metabolism through histone hyper-acetylation, and Sirtuin-mediated silencing of starvation-induced subtelomeric domains. We further demonstrate that repression of subtelomere silencing by physiological Tel1ATM and Rpd3HDAC activities coveys tolerance to glucose restriction. Our findings identify DDR mutations, histone imbalances and aberrant subtelomeric chromatin as interconnected causes of glucose dependence, implying that DDR kinases coordinate metabolism and epigenetic changes.
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Affiliation(s)
- Christopher Bruhn
- The FIRC Institute of Molecular Oncology (IFOM), Via Adamello 16, 20139, Milan, Italy.
| | - Arta Ajazi
- The FIRC Institute of Molecular Oncology (IFOM), Via Adamello 16, 20139, Milan, Italy
| | - Elisa Ferrari
- The FIRC Institute of Molecular Oncology (IFOM), Via Adamello 16, 20139, Milan, Italy
| | - Michael Charles Lanz
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Renaud Batrin
- Université de Paris, Laboratoire Génomes, Biologie Cellulaire et Thérapeutiques, CNRS UMR7212, INSERM U944, Centre de Recherche St Louis, F-75010, Paris, France
| | - Ramveer Choudhary
- The FIRC Institute of Molecular Oncology (IFOM), Via Adamello 16, 20139, Milan, Italy
| | - Adhish Walvekar
- Institute for Stem Cell Science and Regenerative Medicine (inStem), Bangalore, Karnataka, 560065, India
| | - Sunil Laxman
- Institute for Stem Cell Science and Regenerative Medicine (inStem), Bangalore, Karnataka, 560065, India
| | - Maria Pia Longhese
- Dipartimento di Biotecnologie e Bioscienze, Università degli Studi di Milano-Bicocca, Edificio U3, Piazza della Scienza 2, 20126, Milan, Italy
| | - Emmanuelle Fabre
- Université de Paris, Laboratoire Génomes, Biologie Cellulaire et Thérapeutiques, CNRS UMR7212, INSERM U944, Centre de Recherche St Louis, F-75010, Paris, France
| | - Marcus Bustamente Smolka
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Marco Foiani
- The FIRC Institute of Molecular Oncology (IFOM), Via Adamello 16, 20139, Milan, Italy.
- Università degli Studi di Milano, Via Festa del Perdono 7, 20122, Milan, Italy.
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33
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Protective Mechanisms Against DNA Replication Stress in the Nervous System. Genes (Basel) 2020; 11:genes11070730. [PMID: 32630049 PMCID: PMC7397197 DOI: 10.3390/genes11070730] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 06/25/2020] [Accepted: 06/25/2020] [Indexed: 02/06/2023] Open
Abstract
The precise replication of DNA and the successful segregation of chromosomes are essential for the faithful transmission of genetic information during the cell cycle. Alterations in the dynamics of genome replication, also referred to as DNA replication stress, may lead to DNA damage and, consequently, mutations and chromosomal rearrangements. Extensive research has revealed that DNA replication stress drives genome instability during tumorigenesis. Over decades, genetic studies of inherited syndromes have established a connection between the mutations in genes required for proper DNA repair/DNA damage responses and neurological diseases. It is becoming clear that both the prevention and the responses to replication stress are particularly important for nervous system development and function. The accurate regulation of cell proliferation is key for the expansion of progenitor pools during central nervous system (CNS) development, adult neurogenesis, and regeneration. Moreover, DNA replication stress in glial cells regulates CNS tumorigenesis and plays a role in neurodegenerative diseases such as ataxia telangiectasia (A-T). Here, we review how replication stress generation and replication stress response (RSR) contribute to the CNS development, homeostasis, and disease. Both cell-autonomous mechanisms, as well as the evidence of RSR-mediated alterations of the cellular microenvironment in the nervous system, were discussed.
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34
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Abstract
Cells confront DNA damage in every cell cycle. Among the most deleterious types of DNA damage are DNA double-strand breaks (DSBs), which can cause cell lethality if unrepaired or cancers if improperly repaired. In response to DNA DSBs, cells activate a complex DNA damage checkpoint (DDC) response that arrests the cell cycle, reprograms gene expression, and mobilizes DNA repair factors to prevent the inheritance of unrepaired and broken chromosomes. Here we examine the DDC, induced by DNA DSBs, in the budding yeast model system and in mammals.
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Affiliation(s)
- David P Waterman
- Department of Biology and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts 02454, USA;
| | - James E Haber
- Department of Biology and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts 02454, USA;
| | - Marcus B Smolka
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York 14853, USA;
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35
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Forey R, Poveda A, Sharma S, Barthe A, Padioleau I, Renard C, Lambert R, Skrzypczak M, Ginalski K, Lengronne A, Chabes A, Pardo B, Pasero P. Mec1 Is Activated at the Onset of Normal S Phase by Low-dNTP Pools Impeding DNA Replication. Mol Cell 2020; 78:396-410.e4. [PMID: 32169162 DOI: 10.1016/j.molcel.2020.02.021] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 01/09/2020] [Accepted: 02/24/2020] [Indexed: 10/24/2022]
Abstract
The Mec1 and Rad53 kinases play a central role during acute replication stress in budding yeast. They are also essential for viability in normal growth conditions, but the signal that activates the Mec1-Rad53 pathway in the absence of exogenous insults is currently unknown. Here, we show that this pathway is active at the onset of normal S phase because deoxyribonucleotide triphosphate (dNTP) levels present in G1 phase may not be sufficient to support processive DNA synthesis and impede DNA replication. This activation can be suppressed experimentally by increasing dNTP levels in G1 phase. Moreover, we show that unchallenged cells entering S phase in the absence of Rad53 undergo irreversible fork collapse and mitotic catastrophe. Together, these data indicate that cells use suboptimal dNTP pools to detect the onset of DNA replication and activate the Mec1-Rad53 pathway, which in turn maintains functional forks and triggers dNTP synthesis, allowing the completion of DNA replication.
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Affiliation(s)
- Romain Forey
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Montpellier, France
| | - Ana Poveda
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Montpellier, France; Instituto de Investigación en Salud Pública y Zoonosis, Facultad de Ciencias Químicas, Universidad Central del Ecuador, Quito, Ecuador
| | - Sushma Sharma
- Department of Medical Biochemistry and Biophysics and Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden
| | - Antoine Barthe
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Montpellier, France
| | - Ismael Padioleau
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Montpellier, France
| | - Claire Renard
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Montpellier, France
| | - Robin Lambert
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Montpellier, France
| | - Magdalena Skrzypczak
- Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, Zwirki i Wigury 93, 02-089 Warsaw, Poland
| | - Krzysztof Ginalski
- Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, Zwirki i Wigury 93, 02-089 Warsaw, Poland
| | - Armelle Lengronne
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Montpellier, France
| | - Andrei Chabes
- Department of Medical Biochemistry and Biophysics and Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden
| | - Benjamin Pardo
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Montpellier, France.
| | - Philippe Pasero
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Montpellier, France.
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36
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Yugandhar K, Wang TY, Leung AKY, Lanz MC, Motorykin I, Liang J, Shayhidin EE, Smolka MB, Zhang S, Yu H. MaXLinker: Proteome-wide Cross-link Identifications with High Specificity and Sensitivity. Mol Cell Proteomics 2020; 19:554-568. [PMID: 31839598 PMCID: PMC7050104 DOI: 10.1074/mcp.tir119.001847] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Indexed: 11/06/2022] Open
Abstract
Protein-protein interactions play a vital role in nearly all cellular functions. Hence, understanding their interaction patterns and three-dimensional structural conformations can provide crucial insights about various biological processes and underlying molecular mechanisms for many disease phenotypes. Cross-linking mass spectrometry (XL-MS) has the unique capability to detect protein-protein interactions at a large scale along with spatial constraints between interaction partners. The inception of MS-cleavable cross-linkers enabled the MS2-MS3 XL-MS acquisition strategy that provides cross-link information from both MS2 and MS3 level. However, the current cross-link search algorithm available for MS2-MS3 strategy follows a "MS2-centric" approach and suffers from a high rate of mis-identified cross-links. We demonstrate the problem using two new quality assessment metrics ["fraction of mis-identifications" (FMI) and "fraction of interprotein cross-links from known interactions" (FKI)]. We then address this problem, by designing a novel "MS3-centric" approach for cross-link identification and implementing it as a search engine named MaXLinker. MaXLinker outperforms the currently popular search engine with a lower mis-identification rate, and higher sensitivity and specificity. Moreover, we performed human proteome-wide cross-linking mass spectrometry using K562 cells. Employing MaXLinker, we identified a comprehensive set of 9319 unique cross-links at 1% false discovery rate, comprising 8051 intraprotein and 1268 interprotein cross-links. Finally, we experimentally validated the quality of a large number of novel interactions identified in our study, providing a conclusive evidence for MaXLinker's robust performance.
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Affiliation(s)
- Kumar Yugandhar
- Department of Computational Biology, Cornell University, Ithaca, New York,14853; Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York, 14853
| | - Ting-Yi Wang
- Department of Computational Biology, Cornell University, Ithaca, New York,14853; Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York, 14853
| | - Alden King-Yung Leung
- Department of Computational Biology, Cornell University, Ithaca, New York,14853; Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York, 14853
| | - Michael Charles Lanz
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York, 14853; Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853
| | - Ievgen Motorykin
- Mass Spectrometry and Proteomics Facility, Institute of Biotechnology, Cornell University, Ithaca, New York,14853
| | - Jin Liang
- Department of Computational Biology, Cornell University, Ithaca, New York,14853; Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York, 14853
| | - Elnur Elyar Shayhidin
- Department of Computational Biology, Cornell University, Ithaca, New York,14853; Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York, 14853
| | - Marcus Bustamante Smolka
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York, 14853; Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853
| | - Sheng Zhang
- Mass Spectrometry and Proteomics Facility, Institute of Biotechnology, Cornell University, Ithaca, New York,14853
| | - Haiyuan Yu
- Department of Computational Biology, Cornell University, Ithaca, New York,14853; Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York, 14853.
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37
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Cussiol JRR, Soares BL, Oliveira FMBD. From yeast to humans: Understanding the biology of DNA Damage Response (DDR) kinases. Genet Mol Biol 2019; 43:e20190071. [PMID: 31930279 PMCID: PMC7198005 DOI: 10.1590/1678-4685-gmb-2019-0071] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 07/19/2019] [Indexed: 12/20/2022] Open
Abstract
The DNA Damage Response (DDR) is a complex network of biological processes that protect cells from accumulating aberrant DNA structures, thereby maintaining genomic stability and, as a consequence, preventing the development of cancer and other diseases. The DDR pathway is coordinated by a signaling cascade mediated by the PI3K-like kinases (PIKK) ATM and ATR and by their downstream kinases CHK2 and CHK1, respectively. Together, these kinases regulate several aspects of the cellular program in response to genomic stress. Much of our understanding of these kinases came from studies performed in the 1990s using yeast as a model organism. The purpose of this review is to present a historical perspective on the discovery of the DDR kinases in yeast and the importance of this model for the identification and functional understanding of their mammalian orthologues.
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Affiliation(s)
| | - Bárbara Luísa Soares
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
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38
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House NC, Polleys EJ, Quasem I, De la Rosa Mejia M, Joyce CE, Takacsi-Nagy O, Krebs JE, Fuchs SM, Freudenreich CH. Distinct roles for S. cerevisiae H2A copies in recombination and repeat stability, with a role for H2A.1 threonine 126. eLife 2019; 8:53362. [PMID: 31804179 PMCID: PMC6927750 DOI: 10.7554/elife.53362] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 11/26/2019] [Indexed: 01/14/2023] Open
Abstract
CAG/CTG trinuncleotide repeats are fragile sequences that when expanded form DNA secondary structures and cause human disease. We evaluated CAG/CTG repeat stability and repair outcomes in histone H2 mutants in S. cerevisiae. Although the two copies of H2A are nearly identical in amino acid sequence, CAG repeat stability depends on H2A copy 1 (H2A.1) but not copy 2 (H2A.2). H2A.1 promotes high-fidelity homologous recombination, sister chromatid recombination (SCR), and break-induced replication whereas H2A.2 does not share these functions. Both decreased SCR and the increase in CAG expansions were due to the unique Thr126 residue in H2A.1 and hta1Δ or hta1-T126A mutants were epistatic to deletion of the Polδ subunit Pol32, suggesting a role for H2A.1 in D-loop extension. We conclude that H2A.1 plays a greater repair-specific role compared to H2A.2 and may be a first step towards evolution of a repair-specific function for H2AX compared to H2A in mammalian cells.
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Affiliation(s)
- Nealia Cm House
- Department of Biology, Tufts University, Medford, United States
| | - Erica J Polleys
- Department of Biology, Tufts University, Medford, United States
| | | | | | - Cailin E Joyce
- Department of Biology, Tufts University, Medford, United States
| | | | - Jocelyn E Krebs
- Department of Biological Sciences, University of Alaska Anchorage, Anchorage, United States
| | - Stephen M Fuchs
- Department of Biology, Tufts University, Medford, United States
| | - Catherine H Freudenreich
- Department of Biology, Tufts University, Medford, United States.,Program in Genetics, Graduate School of Biomedical Sciences, Tufts University, Boston, United States
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Keener R, Connelly CJ, Greider CW. Tel1 Activation by the MRX Complex Is Sufficient for Telomere Length Regulation but Not for the DNA Damage Response in Saccharomyces cerevisiae. Genetics 2019; 213:1271-1288. [PMID: 31645360 PMCID: PMC6893380 DOI: 10.1534/genetics.119.302713] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 10/17/2019] [Indexed: 12/26/2022] Open
Abstract
Previous models suggested that regulation of telomere length in Saccharomyces cerevisiae by Tel1(ATM) and Mec1(ATR) would parallel the established pathways regulating the DNA damage response. Here, we provide evidence that telomere length regulation differs from the DNA damage response in both the Tel1 and Mec1 pathways. We found that Rad53 mediates a Mec1 telomere length regulation pathway but is dispensable for Tel1 telomere length regulation, whereas in the DNA damage response, Rad53 is regulated by both Mec1 and Tel1 Using epistasis analysis with a Tel1 hypermorphic allele, Tel1-hy909, we found that the MRX complex is not required downstream of Tel1 for telomere elongation but is required downstream of Tel1 for the DNA damage response. Our data suggest that nucleolytic telomere end processing is not a required step for telomerase to elongate telomeres.
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Affiliation(s)
- Rebecca Keener
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
- Biochemistry, Cellular and Molecular Biology Graduate Program, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
| | - Carla J Connelly
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
| | - Carol W Greider
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
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Distinct associations of the Saccharomyces cerevisiae Rad9 protein link Mac1-regulated transcription to DNA repair. Curr Genet 2019; 66:531-548. [PMID: 31784768 DOI: 10.1007/s00294-019-01047-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 11/06/2019] [Accepted: 11/18/2019] [Indexed: 12/12/2022]
Abstract
While it is known that ScRad9 DNA damage checkpoint protein is recruited to damaged DNA by recognizing specific histone modifications, here we report a different way of Rad9 recruitment on chromatin under non DNA damaging conditions. We found Rad9 to bind directly with the copper-modulated transcriptional activator Mac1, suppressing both its DNA binding and transactivation functions. Rad9 was recruited to active Mac1-target promoters (CTR1, FRE1) and along CTR1 coding region following the association pattern of RNA polymerase (Pol) II. Hir1 histone chaperone also interacted directly with Rad9 and was partly required for its localization throughout CTR1 gene. Moreover, Mac1-dependent transcriptional initiation was necessary and sufficient for Rad9 recruitment to the heterologous ACT1 coding region. In addition to Rad9, Rad53 kinase also localized to CTR1 coding region in a Rad9-dependent manner. Our data provide an example of a yeast DNA-binding transcriptional activator that interacts directly with a DNA damage checkpoint protein in vivo and is functionally restrained by this protein, suggesting a new role for Rad9 in connecting factors of the transcription machinery with the DNA repair pathway under unchallenged conditions.
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41
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Achuthankutty D, Thakur RS, Haahr P, Hoffmann S, Drainas AP, Bizard AH, Weischenfeldt J, Hickson ID, Mailand N. Regulation of ETAA1-mediated ATR activation couples DNA replication fidelity and genome stability. J Cell Biol 2019; 218:3943-3953. [PMID: 31615875 PMCID: PMC6891097 DOI: 10.1083/jcb.201905064] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 08/28/2019] [Accepted: 09/10/2019] [Indexed: 12/23/2022] Open
Abstract
Achuthankutty et al. show that the recently identified ATR kinase activator ETAA1 has an important role in protecting against chromosomal instability arising from incompletely replicated DNA, driven by cell cycle– and replication stress–regulated, phosphorylation-dependent control of its ATR-activating domain. The ATR kinase is a master regulator of the cellular response to DNA replication stress. Activation of ATR relies on dual pathways involving the TopBP1 and ETAA1 proteins, both of which harbor ATR-activating domains (AADs). However, the exact contribution of the recently discovered ETAA1 pathway to ATR signaling in different contexts remains poorly understood. Here, using an unbiased CRISPR-Cas9–based genome-scale screen, we show that the ATR-stimulating function of ETAA1 becomes indispensable for cell fitness and chromosome stability when the fidelity of DNA replication is compromised. We demonstrate that the ATR-activating potential of ETAA1 is controlled by cell cycle– and replication stress–dependent phosphorylation of highly conserved residues within its AAD, and that the stimulatory impact of these modifications is required for the ability of ETAA1 to prevent mitotic chromosome abnormalities following replicative stress. Our findings suggest an important role of ETAA1 in protecting against genome instability arising from incompletely duplicated DNA via regulatory control of its ATR-stimulating potential.
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Affiliation(s)
- Divya Achuthankutty
- Protein Signaling Program, Novo Nordisk Foundation Center for Protein Research, Copenhagen, Denmark.,Center for Chromosome Stability, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Roshan Singh Thakur
- Center for Chromosome Stability, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Peter Haahr
- Protein Signaling Program, Novo Nordisk Foundation Center for Protein Research, Copenhagen, Denmark
| | - Saskia Hoffmann
- Protein Signaling Program, Novo Nordisk Foundation Center for Protein Research, Copenhagen, Denmark
| | | | - Anna H Bizard
- Center for Chromosome Stability, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Joachim Weischenfeldt
- Biotech Research and Innovation Center, University of Copenhagen and Finsen Laboratory, Copenhagen, Denmark
| | - Ian D Hickson
- Center for Chromosome Stability, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Niels Mailand
- Protein Signaling Program, Novo Nordisk Foundation Center for Protein Research, Copenhagen, Denmark .,Center for Chromosome Stability, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
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42
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Lanz MC, Dibitetto D, Smolka MB. DNA damage kinase signaling: checkpoint and repair at 30 years. EMBO J 2019; 38:e101801. [PMID: 31393028 PMCID: PMC6745504 DOI: 10.15252/embj.2019101801] [Citation(s) in RCA: 151] [Impact Index Per Article: 30.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 07/03/2019] [Accepted: 07/24/2019] [Indexed: 12/27/2022] Open
Abstract
From bacteria to mammalian cells, damaged DNA is sensed and targeted by DNA repair pathways. In eukaryotes, kinases play a central role in coordinating the DNA damage response. DNA damage signaling kinases were identified over two decades ago and linked to the cell cycle checkpoint concept proposed by Weinert and Hartwell in 1988. Connections between the DNA damage signaling kinases and DNA repair were scant at first, and the initial perception was that the importance of these kinases for genome integrity was largely an indirect effect of their roles in checkpoints, DNA replication, and transcription. As more substrates of DNA damage signaling kinases were identified, it became clear that they directly regulate a wide range of DNA repair factors. Here, we review our current understanding of DNA damage signaling kinases, delineating the key substrates in budding yeast and humans. We trace the progress of the field in the last 30 years and discuss our current understanding of the major substrate regulatory mechanisms involved in checkpoint responses and DNA repair.
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Affiliation(s)
- Michael Charles Lanz
- Department of Molecular Biology and GeneticsWeill Institute for Cell and Molecular BiologyCornell UniversityIthacaNYUSA
| | - Diego Dibitetto
- Department of Molecular Biology and GeneticsWeill Institute for Cell and Molecular BiologyCornell UniversityIthacaNYUSA
| | - Marcus Bustamante Smolka
- Department of Molecular Biology and GeneticsWeill Institute for Cell and Molecular BiologyCornell UniversityIthacaNYUSA
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43
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Biswas H, Goto G, Wang W, Sung P, Sugimoto K. Ddc2ATRIP promotes Mec1ATR activation at RPA-ssDNA tracts. PLoS Genet 2019; 15:e1008294. [PMID: 31369547 PMCID: PMC6692047 DOI: 10.1371/journal.pgen.1008294] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 08/13/2019] [Accepted: 07/07/2019] [Indexed: 11/19/2022] Open
Abstract
The DNA damage checkpoint response is controlled by the phosphatidylinositol 3-kinase-related kinases (PIKK), including ataxia telangiectasia-mutated (ATM) and ATM and Rad3-related (ATR). ATR forms a complex with its partner ATRIP. In budding yeast, ATR and ATRIP correspond to Mec1 and Ddc2, respectively. ATRIP/Ddc2 interacts with replication protein A-bound single-stranded DNA (RPA-ssDNA) and recruits ATR/Mec1 to sites of DNA damage. Mec1 is stimulated by the canonical activators including Ddc1, Dpb11 and Dna2. We have characterized the ddc2-S4 mutation and shown that Ddc2 not only recruits Mec1 to sites of DNA damage but also stimulates Mec1 kinase activity. However, the underlying mechanism of Ddc2-dependent Mec1 activation remains to be elucidated. Here we show that Ddc2 promotes Mec1 activation independently of Ddc1/Dpb11/Dna2 function in vivo and through ssDNA recognition in vitro. The ddc2-S4 mutation diminishes damage-induced phosphorylation of the checkpoint mediators, Rad9 and Mrc1. Rad9 controls checkpoint throughout the cell-cycle whereas Mrc1 is specifically required for the S-phase checkpoint. Notably, S-phase checkpoint signaling is more defective in ddc2-S4 mutants than in cells where the Mec1 activators (Ddc1/Dpb11 and Dna2) are dysfunctional. To understand a role of Ddc2 in Mec1 activation, we reconstituted an in vitro assay using purified Mec1-Ddc2 complex, RPA and ssDNA. Whereas ssDNA stimulates kinase activity of the Mec1-Ddc2 complex, RPA does not. However, RPA can promote ssDNA-dependent Mec1 activation. Neither ssDNA nor RPA-ssDNA efficiently stimulates the Mec1-Ddc2 complex containing Ddc2-S4 mutant. Together, our data support a model in which Ddc2 promotes Mec1 activation at RPA-ssDNA tracts.
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Affiliation(s)
- Himadri Biswas
- Department of Microbiology, Biochemistry and Molecular Genetics, International Center for Public Health, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, New Jersey, United States of America
| | - Greicy Goto
- Department of Microbiology, Biochemistry and Molecular Genetics, International Center for Public Health, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, New Jersey, United States of America
| | - Weibin Wang
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Patrick Sung
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut, United States of America
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, Texas, United States of America
| | - Katsunori Sugimoto
- Department of Microbiology, Biochemistry and Molecular Genetics, International Center for Public Health, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, New Jersey, United States of America
- * E-mail:
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44
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A role for the yeast PCNA unloader Elg1 in eliciting the DNA damage checkpoint. Curr Genet 2019; 66:79-84. [PMID: 31332476 DOI: 10.1007/s00294-019-01020-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2019] [Revised: 07/16/2019] [Accepted: 07/17/2019] [Indexed: 12/28/2022]
Abstract
During cell proliferation, the genome is constantly threatened by cellular and external factors. When the DNA is damaged, or when its faithful duplication is delayed by DNA polymerase stalling, the cells induce a coordinated response termed the DNA damage response (DDR) or checkpoint. Elg1 forms an RFC-like complex in charge of unloading the DNA polymerase processively factor PCNA during DNA replication and DNA repair. Using checkpoint-inducible strains, a recently published paper (Sau et al. in mBio 10(3):e01159-19. https://doi.org/10.1128/mbio.01159-19, 2019) uncovered a role for Elg1 in eliciting the DNA damage checkpoint (DC), one of the branches of the DDR. The apical kinase Mec1/ATR phosphorylates Elg1, as well as the adaptor proteins Rad9/53BP1 and Dpb11/TopBP1, which are recruited to the site of DNA damage to amplify the checkpoint signal. In the absence of Elg1, Rad9 and Dpb11 are recruited but fail to be phosphorylated and the signal is therefore not amplified. Thus, Elg1 appears to coordinate DNA repair and the induction of the DNA damage checkpoint.
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45
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Quantitative mechanisms of DNA damage sensing and signaling. Curr Genet 2019; 66:59-62. [PMID: 31227863 PMCID: PMC7021746 DOI: 10.1007/s00294-019-01007-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 06/13/2019] [Accepted: 06/14/2019] [Indexed: 11/13/2022]
Abstract
DNA damage occurs abundantly during normal cellular proliferation. This necessitates that cellular DNA damage response and checkpoint pathways monitor the cellular DNA damage load and that DNA damage signaling is quantitative. Yet, how DNA lesions are counted and converted into a quantitative response remains poorly understood. We have recently obtained insights into this question investigating DNA damage signaling elicited by single-stranded DNA (ssDNA). Intriguingly, our findings suggest that local and global DNA damage signaling react differentially to increasing amounts of DNA damage. In this mini-review, we will discuss these findings and put them into perspective of current knowledge on the DNA damage response.
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46
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Abstract
The Elg1protein forms an RFC-like complex in charge of unloading PCNA from chromatin during DNA replication and repair. Mutations in the ELG1 gene caused genomic instability in all organisms tested and cancer in mammals. Here we show that Elg1 plays a role in the induction of the DNA damage checkpoint, a cellular response to DNA damage. We show that this defect is due to a defect in the signal amplification process during induction. Thus, cells coordinate the cell's response and the PCNA unloading through the activity of Elg1. The PCNA (proliferating cell nuclear antigen) ring plays central roles during DNA replication and repair. The yeast Elg1 RFC-like complex (RLC) is the principal unloader of chromatin-bound PCNA and thus plays a central role in maintaining genome stability. Here we identify a role for Elg1 in the unloading of PCNA during DNA damage. Using DNA damage checkpoint (DC)-inducible and replication checkpoint (RC)-inducible strains, we show that Elg1 is essential for eliciting the signal in the DC branch. In the absence of Elg1 activity, the Rad9 (53BP1) and Dpb11 (TopBP1) adaptor proteins are recruited but fail to be phosphorylated by Mec1 (ATR), resulting in a lack of checkpoint activation. The chromatin immunoprecipitation of PCNA at the Lac operator sites reveals that accumulated local PCNA influences the checkpoint activation process in elg1 mutants. Our data suggest that Elg1 participates in a mechanism that may coordinate PCNA unloading during DNA repair with DNA damage checkpoint induction.
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47
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Shami Shah A, Batrouni AG, Kim D, Punyala A, Cao W, Han C, Goldberg ML, Smolka MB, Baskin JM. PLEKHA4/kramer Attenuates Dishevelled Ubiquitination to Modulate Wnt and Planar Cell Polarity Signaling. Cell Rep 2019; 27:2157-2170.e8. [PMID: 31091453 PMCID: PMC6594551 DOI: 10.1016/j.celrep.2019.04.060] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 02/26/2019] [Accepted: 04/11/2019] [Indexed: 12/13/2022] Open
Abstract
Wnt signaling pathways direct key physiological decisions in development. Here, we establish a role for a pleckstrin homology domain-containing protein, PLEKHA4, as a modulator of signaling strength in Wnt-receiving cells. PLEKHA4 oligomerizes into clusters at PI(4,5)P2-rich regions of the plasma membrane and recruits the Cullin-3 (CUL3) E3 ubiquitin ligase substrate adaptor Kelch-like protein 12 (KLHL12) to these assemblies. This recruitment decreases CUL3-KLHL12-mediated polyubiquitination of Dishevelled, a central intermediate in canonical and non-canonical Wnt signaling. Knockdown of PLEKHA4 in mammalian cells demonstrates that PLEKHA4 positively regulates canonical and non-canonical Wnt signaling via these effects on the Dishevelled polyubiquitination machinery. In vivo knockout of the Drosophila melanogaster PLEKHA4 homolog, kramer, selectively affects the non-canonical, planar cell polarity (PCP) signaling pathway. We propose that PLEKHA4 tunes the sensitivities of cells toward the stimulation of Wnt or PCP signaling by sequestering a key E3 ligase adaptor controlling Dishevelled polyubiquitination within PI(4,5)P2-rich plasma membrane clusters.
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Affiliation(s)
- Adnan Shami Shah
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA; Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - Alex G Batrouni
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA; Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - Dongsung Kim
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA; Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Amith Punyala
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA; Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - Wendy Cao
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA; Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - Chun Han
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA; Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Michael L Goldberg
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Marcus B Smolka
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA; Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Jeremy M Baskin
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA; Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA.
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48
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Falquet B, Rass U. Structure-Specific Endonucleases and the Resolution of Chromosome Underreplication. Genes (Basel) 2019; 10:E232. [PMID: 30893921 PMCID: PMC6470701 DOI: 10.3390/genes10030232] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 03/11/2019] [Accepted: 03/13/2019] [Indexed: 12/11/2022] Open
Abstract
Complete genome duplication in every cell cycle is fundamental for genome stability and cell survival. However, chromosome replication is frequently challenged by obstacles that impede DNA replication fork (RF) progression, which subsequently causes replication stress (RS). Cells have evolved pathways of RF protection and restart that mitigate the consequences of RS and promote the completion of DNA synthesis prior to mitotic chromosome segregation. If there is entry into mitosis with underreplicated chromosomes, this results in sister-chromatid entanglements, chromosome breakage and rearrangements and aneuploidy in daughter cells. Here, we focus on the resolution of persistent replication intermediates by the structure-specific endonucleases (SSEs) MUS81, SLX1-SLX4 and GEN1. Their actions and a recently discovered pathway of mitotic DNA repair synthesis have emerged as important facilitators of replication completion and sister chromatid detachment in mitosis. As RS is induced by oncogene activation and is a common feature of cancer cells, any advances in our understanding of the molecular mechanisms related to chromosome underreplication have important biomedical implications.
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Affiliation(s)
- Benoît Falquet
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, CH-4058 Basel, Switzerland.
- Faculty of Natural Sciences, University of Basel, Petersplatz 10, CH-4003 Basel, Switzerland.
| | - Ulrich Rass
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9RQ, UK.
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49
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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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50
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Bass TE, Cortez D. Quantitative phosphoproteomics reveals mitotic function of the ATR activator ETAA1. J Cell Biol 2019; 218:1235-1249. [PMID: 30755469 PMCID: PMC6446857 DOI: 10.1083/jcb.201810058] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 01/04/2019] [Accepted: 01/23/2019] [Indexed: 01/01/2023] Open
Abstract
Bass and Cortez use comparative quantitative mass spectrometry analyses of cells lacking either ATR activator, ETAA1 or TOPBP1. They identify a role for ETAA1 and ATR activation in the regulation of chromosome alignment and segregation in mitosis through Aurora B activity. The ATR kinase controls cell cycle transitions and the DNA damage response. ATR activity is regulated through two ATR-activating proteins, ETAA1 and TOPBP1. To examine how each activator contributes to ATR signaling, we used quantitative mass spectrometry to identify changes in protein phosphorylation in ETAA1- or TOPBP1-deficient cells. We identified 724, 285, and 118 phosphosites to be regulated by TOPBP1, ETAA1, or both ATR activators, respectively. Gene ontology analysis of TOPBP1- and ETAA1-dependent phosphoproteins revealed TOPBP1 to be a primary ATR activator for replication stress, while ETAA1 regulates mitotic ATR signaling. Inactivation of ATR or ETAA1, but not TOPBP1, results in decreased Aurora B kinase activity during mitosis. Additionally, ATR activation by ETAA1 is required for proper chromosome alignment during metaphase and for a fully functional spindle assembly checkpoint response. Thus, we conclude that ETAA1 and TOPBP1 regulate distinct aspects of ATR signaling with ETAA1 having a dominant function in mitotic cells.
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Affiliation(s)
- Thomas E Bass
- Department of Biochemistry, Vanderbilt University School of Medicine, Vanderbilt University, Nashville, TN
| | - David Cortez
- Department of Biochemistry, Vanderbilt University School of Medicine, Vanderbilt University, Nashville, TN
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