1
|
Prorok P, Wolf E, Cardoso MC. Timeless-Tipin interactions with MCM and RPA mediate DNA replication stress response. Front Cell Dev Biol 2024; 12:1346534. [PMID: 38487270 PMCID: PMC10939015 DOI: 10.3389/fcell.2024.1346534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 02/12/2024] [Indexed: 03/17/2024] Open
Abstract
The accuracy of replication is one of the most important mechanisms ensuring the stability of the genome. The fork protection complex prevents premature replisome stalling and/or premature disassembly upon stress. Here, we characterize the Timeless-Tipin complex, a component of the fork protection complex. We used microscopy approaches, including colocalization analysis and proximity ligation assay, to investigate the spatial localization of the complex during ongoing replication in human cells. Taking advantage of the replication stress induction and the ensuing polymerase-helicase uncoupling, we characterized the Timeless-Tipin localization within the replisome. Replication stress was induced using hydroxyurea (HU) and aphidicolin (APH). While HU depletes the substrate for DNA synthesis, APH binds directly inside the catalytic pocket of DNA polymerase and inhibits its activity. Our data revealed that the Timeless-Tipin complex, independent of the stress, remains bound on chromatin upon stress induction and progresses together with the replicative helicase. This is accompanied by the spatial dissociation of the complex from the blocked replication machinery. Additionally, after stress induction, Timeless interaction with RPA, which continuously accumulates on ssDNA, was increased. Taken together, the Timeless-Tipin complex acts as a universal guardian of the mammalian replisome in an unperturbed S-phase progression as well as during replication stress.
Collapse
Affiliation(s)
- Paulina Prorok
- Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, Darmstadt, Germany
| | - Eva Wolf
- Institute of Molecular Physiology (IMP), Johannes Gutenberg-University Mainz, Mainz, Germany
| | - M. Cristina Cardoso
- Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, Darmstadt, Germany
| |
Collapse
|
2
|
Vipat S, Moiseeva TN. The TIMELESS Roles in Genome Stability and Beyond. J Mol Biol 2024; 436:168206. [PMID: 37481157 DOI: 10.1016/j.jmb.2023.168206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 06/20/2023] [Accepted: 07/12/2023] [Indexed: 07/24/2023]
Abstract
TIMELESS protein (TIM) protects replication forks from stalling at difficult-to-replicate regions and plays an important role in DNA damage response, including checkpoint signaling, protection of stalled replication forks and DNA repair. Loss of TIM causes severe replication stress, while its overexpression is common in various types of cancer, providing protection from DNA damage and resistance to chemotherapy. Although TIM has mostly been studied for its part in replication stress response, its additional roles in supporting genome stability and a wide variety of other cellular pathways are gradually coming to light. This review discusses the diverse functions of TIM and its orthologs in healthy and cancer cells, open questions, and potential future directions.
Collapse
Affiliation(s)
- Sameera Vipat
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn 12618, Estonia
| | - Tatiana N Moiseeva
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn 12618, Estonia.
| |
Collapse
|
3
|
Pellegrini L. The CMG DNA helicase and the core replisome. Curr Opin Struct Biol 2023; 81:102612. [PMID: 37244171 DOI: 10.1016/j.sbi.2023.102612] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Revised: 04/19/2023] [Accepted: 04/25/2023] [Indexed: 05/29/2023]
Abstract
Eukaryotic DNA replication is performed by the replisome, a large and dynamic multi-protein machine endowed with the required enzymatic components for the synthesis of new DNA. Recent cryo-electron microscopy (cryoEM) analyses have revealed the conserved architecture of the core eukaryotic replisome, comprising the CMG (Cdc45-MCM-GINS) DNA helicase, the leading-strand DNA polymerase epsilon, the Timeless-Tipin heterodimer, the hub protein AND-1 and the checkpoint protein Claspin. These results bid well for arriving soon at an integrated understanding of the structural basis of semi-discontinuous DNA replication. They further set the scene for the characterisation of the mechanisms that interface DNA synthesis with concurrent processes such as DNA repair, propagation of chromatin structure and establishment of sister chromatid cohesion.
Collapse
|
4
|
Patel JA, Zezelic C, Rageul J, Saldanha J, Khan A, Kim H. Replisome dysfunction upon inducible TIMELESS degradation synergizes with ATR inhibition to trigger replication catastrophe. Nucleic Acids Res 2023; 51:6246-6263. [PMID: 37144518 PMCID: PMC10325925 DOI: 10.1093/nar/gkad363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 03/29/2023] [Accepted: 04/26/2023] [Indexed: 05/06/2023] Open
Abstract
The structure of DNA replication forks is preserved by TIMELESS (TIM) in the fork protection complex (FPC) to support seamless fork progression. While the scaffolding role of the FPC to couple the replisome activity is much appreciated, the detailed mechanism whereby inherent replication fork damage is sensed and counteracted during DNA replication remains largely elusive. Here, we implemented an auxin-based degron system that rapidly triggers inducible proteolysis of TIM as a source of endogenous DNA replication stress and replisome dysfunction to dissect the signaling events that unfold at stalled forks. We demonstrate that acute TIM degradation activates the ATR-CHK1 checkpoint, whose inhibition culminates in replication catastrophe by single-stranded DNA accumulation and RPA exhaustion. Mechanistically, unrestrained replisome uncoupling, excessive origin firing, and aberrant reversed fork processing account for the synergistic fork instability. Simultaneous TIM loss and ATR inactivation triggers DNA-PK-dependent CHK1 activation, which is unexpectedly necessary for promoting fork breakage by MRE11 and catastrophic cell death. We propose that acute replisome dysfunction results in a hyper-dependency on ATR to activate local and global fork stabilization mechanisms to counteract irreversible fork collapse. Our study identifies TIM as a point of replication vulnerability in cancer that can be exploited with ATR inhibitors.
Collapse
Affiliation(s)
- Jinal A Patel
- Department of Pharmacological Sciences, State University of New York at Stony Brook, Stony Brook, NY 11794, USA
| | - Camryn Zezelic
- Department of Pharmacological Sciences, State University of New York at Stony Brook, Stony Brook, NY 11794, USA
| | - Julie Rageul
- Department of Pharmacological Sciences, State University of New York at Stony Brook, Stony Brook, NY 11794, USA
| | - Joanne Saldanha
- The Graduate program in Genetics, State University of New York at Stony Brook, Stony Brook, NY 11794, USA
| | - Arafat Khan
- Department of Pharmacological Sciences, State University of New York at Stony Brook, Stony Brook, NY 11794, USA
| | - Hyungjin Kim
- Department of Pharmacological Sciences, State University of New York at Stony Brook, Stony Brook, NY 11794, USA
- Stony Brook Cancer Center, Renaissance School of Medicine at Stony Brook University, Stony Brook, NY 11794, USA
| |
Collapse
|
5
|
Nemeth T, Yoshizawa-Sugata N, Pallier A, Tajima Y, Ma Y, Tóth É, Masai H, Yamakoshi Y. Water-Soluble Gd(III)-Porphyrin Complexes Capable of Both Photosensitization and Relaxation Enhancement. CHEMICAL & BIOMEDICAL IMAGING 2023; 1:157-167. [PMID: 37235189 PMCID: PMC10207321 DOI: 10.1021/cbmi.3c00007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 04/26/2023] [Accepted: 04/28/2023] [Indexed: 05/28/2023]
Abstract
With the aim of developing more stable Gd(III)-porphyrin complexes, two types of ligands 1 and 2 with carboxylic acid anchors were synthesized. Due to the N-substituted pyridyl cation attached to the porphyrin core, these porphyrin ligands were highly water-soluble and formed the corresponding Gd(III) chelates, Gd-1 and Gd-2. Gd-1 was sufficiently stable in neutral buffer, presumably due to the preferred conformation of the carboxylate-terminated anchors connected to nitrogen in the meta position of the pyridyl group helping to stabilize Gd(III) complexation by the porphyrin center. 1H NMRD (nuclear magnetic relaxation dispersion) measurements on Gd-1 revealed high longitudinal water proton relaxivity (r1 = 21.2 mM-1 s-1 at 60 MHz and 25 °C), which originates from slow rotational motion resulting from aggregation in aqueous solution. Under visible light irradiation, Gd-1 showed extensive photoinduced DNA cleavage in line with efficient photoinduced singlet oxygen generation. Cell-based assays revealed no significant dark cytotoxicity of Gd-1, while it showed sufficient photocytotoxicity on cancer cell lines under visible light irradiation. These results indicate the potential of this Gd(III)-porphyrin complex (Gd-1) as a core for the development of bifunctional systems acting as an efficient photodynamic therapy photosensitizer (PDT-PS) with magnetic resonance imaging (MRI) detection capabilities.
Collapse
Affiliation(s)
- Tamas Nemeth
- Department
of Chemistry and Applied Biosciences, ETH
Zürich, Vladimir-Prelog-Weg 3, CH8093 Zürich, Switzerland
| | - Naoko Yoshizawa-Sugata
- Research
Center for Genome & Medical Sciences, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya, Tokyo 156-8506, Japan
| | - Agnes Pallier
- Centre
de Biophysique Moléculaire, CNRS UPR 4301, University of Orléans, Rue Charles Sadron, 45071 Cedex 2 Orléans, France
| | - Youichi Tajima
- Department
of Basic Medical Sciences, Tokyo Metropolitan
Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya, Tokyo 156-8506, Japan
| | - Yue Ma
- Department
of Chemistry and Applied Biosciences, ETH
Zürich, Vladimir-Prelog-Weg 3, CH8093 Zürich, Switzerland
| | - Éva Tóth
- Centre
de Biophysique Moléculaire, CNRS UPR 4301, University of Orléans, Rue Charles Sadron, 45071 Cedex 2 Orléans, France
| | - Hisao Masai
- Department
of Basic Medical Sciences, Tokyo Metropolitan
Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya, Tokyo 156-8506, Japan
| | - Yoko Yamakoshi
- Department
of Chemistry and Applied Biosciences, ETH
Zürich, Vladimir-Prelog-Weg 3, CH8093 Zürich, Switzerland
| |
Collapse
|
6
|
Carney SV, Banerjee K, Mujeeb A, Zhu B, Haase S, Varela ML, Kadiyala P, Tronrud CE, Zhu Z, Mukherji D, Gorla P, Sun Y, Tagett R, Núñez FJ, Luo M, Luo W, Ljungman M, Liu Y, Xia Z, Schwendeman A, Qin T, Sartor MA, Costello JF, Cahill DP, Lowenstein PR, Castro MG. Zinc Finger MYND-Type Containing 8 (ZMYND8) Is Epigenetically Regulated in Mutant Isocitrate Dehydrogenase 1 (IDH1) Glioma to Promote Radioresistance. Clin Cancer Res 2023; 29:1763-1782. [PMID: 36692427 PMCID: PMC10159884 DOI: 10.1158/1078-0432.ccr-22-1896] [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: 06/15/2022] [Revised: 10/27/2022] [Accepted: 12/22/2022] [Indexed: 01/25/2023]
Abstract
PURPOSE Mutant isocitrate dehydrogenase 1 (mIDH1) alters the epigenetic regulation of chromatin, leading to a hypermethylation phenotype in adult glioma. This work focuses on identifying gene targets epigenetically dysregulated by mIDH1 to confer therapeutic resistance to ionizing radiation (IR). EXPERIMENTAL DESIGN We evaluated changes in the transcriptome and epigenome in a radioresistant mIDH1 patient-derived glioma cell culture (GCC) following treatment with an mIDH1-specific inhibitor, AGI-5198. We identified Zinc Finger MYND-Type Containing 8 (ZMYND8) as a potential target of mIDH1 reprogramming. We suppressed ZMYND8 expression by shRNA knockdown and genetic knockout (KO) in mIDH1 glioma cells and then assessed cellular viability to IR. We assessed the sensitivity of mIDH1 GCCS to pharmacologic inhibition of ZMYND8-interacting partners: HDAC, BRD4, and PARP. RESULTS Inhibition of mIDH1 leads to an upregulation of gene networks involved in replication stress. We found that the expression of ZMYND8, a regulator of DNA damage response, was decreased in three patient-derived mIDH1 GCCs after treatment with AGI-5198. Knockdown of ZMYND8 expression sensitized mIDH1 GCCs to radiotherapy marked by decreased cellular viability. Following IR, mIDH1 glioma cells with ZMYND8 KO exhibit significant phosphorylation of ATM and sustained γH2AX activation. ZMYND8 KO mIDH1 GCCs were further responsive to IR when treated with either BRD4 or HDAC inhibitors. PARP inhibition further enhanced the efficacy of radiotherapy in ZMYND8 KO mIDH1 glioma cells. CONCLUSIONS These findings indicate the impact of ZMYND8 in the maintenance of genomic integrity and repair of IR-induced DNA damage in mIDH1 glioma. See related commentary by Sachdev et al., p. 1648.
Collapse
Affiliation(s)
- Stephen V. Carney
- Cancer Biology Training Program, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Kaushik Banerjee
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Anzar Mujeeb
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Brandon Zhu
- Graduate Program in Biomedical Engineering, University of Michigan College of Engineering, Ann Arbor, MI, USA
| | - Santiago Haase
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Maria L. Varela
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Padma Kadiyala
- Graduate Program in Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Claire E. Tronrud
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Ziwen Zhu
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Devarshi Mukherji
- Neuroscience, University of Michigan College of Literature, Science, the Arts (LSA), Ann Arbor, MI 48109, USA
| | - Preethi Gorla
- Neuroscience, University of Michigan College of Literature, Science, the Arts (LSA), Ann Arbor, MI 48109, USA
| | - Yilun Sun
- Department of Radiation Oncology, University Hospitals/Case Western Reserve University, Cleveland, OH, USA
| | - Rebecca Tagett
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Felipe J. Núñez
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Maowu Luo
- Department of Pathology, UT Southwestern Medical Center, Dallas TX 75390, USA
| | - Weibo Luo
- Department of Pathology, UT Southwestern Medical Center, Dallas TX 75390, USA
- Department of Pharmacology, UT Southwestern Medical Center, Dallas TX 75390, USA
| | - Mats Ljungman
- Department of Radiation Oncology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Environmental Health Science, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yayuan Liu
- Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, MI 48109, USA
| | - Ziyun Xia
- Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, MI 48109, USA
| | - Anna Schwendeman
- Department of Radiation Oncology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Tingting Qin
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Maureen A. Sartor
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Joseph F. Costello
- Department of Neurological Surgery, University of California, San Francisco, California, 94143 USA
| | - Daniel P. Cahill
- Department of Neurosurgery, Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston Massachusetts, 02114, USA
| | - Pedro R. Lowenstein
- Cancer Biology Training Program, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Graduate Program in Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Biosciences Initiative in Brain Cancer, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Maria G. Castro
- Cancer Biology Training Program, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Graduate Program in Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Biosciences Initiative in Brain Cancer, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| |
Collapse
|
7
|
Clyne CD, Kusnadi KP, Cowcher A, Morgan J, Yang J, Fuller PJ, Young MJ. Regulation of mineralocorticoid receptor activation by circadian protein TIMELESS. J Mol Endocrinol 2023; 70:JME-21-0279. [PMID: 36099062 DOI: 10.1530/jme-21-0279] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 09/13/2022] [Indexed: 01/19/2023]
Abstract
The mineralocorticoid receptor (MR) is a ligand-activated transcription factor that regulates cardiorenal physiology and disease. Ligand-dependent MR transactivation involves a conformational change in the MR and recruitment of coregulatory proteins to form a unique DNA-binding complex at the hormone response element in target gene promoters. Differences in the recruitment of coregulatory proteins can promote tissue-, ligand- or gene-specific transcriptional outputs. The goal of this study was to evaluate the circadian protein TIMELESS as a selective regulator of MR transactivation. TIMELESS has an established role in cell cycle regulation and DNA repair. TIMELESS may not be central to mammalian clock function and does not bind DNA; however, RNA and protein levels oscillate over 24 h. Co-expression of TIMELESS down-regulated MR transactivation of an MR-responsive reporter in HEK293 cells, yet enhanced transactivation mediated by other steroid receptors. TIMELESS markedly inhibited MR transactivation of synthetic and native gene promoters and expression of MR target genes in H9c2 cardiac myoblasts. Immunofluorescence showed aldosterone induces colocalisation of TIMELESS and MR, although a direct interaction was not confirmed by coimmunoprecipitation. Potential regulation of circadian clock targets cryptochrome 1 and 2 by TIMELESS was not detected. However, our data suggest that these effects may involve TIMELESS coactivation of oestrogen receptor alpha (ERα). Taken together, these data suggest that TIMELESS may contribute to MR transcriptional outputs via enhancing ERα inhibitory actions on MR transactivation. Given the variable expression of TIMELESS in different cell types, these data offer new opportunities for the development of MR modulators with selective actions.
Collapse
Affiliation(s)
- Colin D Clyne
- Centre for Endocrinology and Metabolism, Hudson Institute of Medical Research, Clayton, Australia
| | - Kevin P Kusnadi
- Cardiovascular Endocrinology Laboratory, Baker Heart and Diabetes Institute, Melbourne, Australia
| | - Alexander Cowcher
- Centre for Endocrinology and Metabolism, Hudson Institute of Medical Research, Clayton, Australia
| | - James Morgan
- Centre for Endocrinology and Metabolism, Hudson Institute of Medical Research, Clayton, Australia
| | - Jun Yang
- Centre for Endocrinology and Metabolism, Hudson Institute of Medical Research, Clayton, Australia
| | - Peter J Fuller
- Centre for Endocrinology and Metabolism, Hudson Institute of Medical Research, Clayton, Australia
| | - Morag J Young
- Cardiovascular Endocrinology Laboratory, Baker Heart and Diabetes Institute, Melbourne, Australia
- University of Melbourne and Baker HDI Department of Cardiometabolic Health and Disease, Melbourne, Australia
| |
Collapse
|
8
|
Extended DNA binding interfaces beyond the canonical SAP domain contribute to the function of replication stress regulator SDE2 at DNA replication forks. J Biol Chem 2022; 298:102268. [PMID: 35850305 PMCID: PMC9399289 DOI: 10.1016/j.jbc.2022.102268] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 07/05/2022] [Accepted: 07/07/2022] [Indexed: 11/25/2022] Open
Abstract
Elevated DNA replication stress causes instability of the DNA replication fork and increased DNA mutations, which underlies tumorigenesis. The DNA replication stress regulator silencing-defective 2 (SDE2) is known to bind to TIMELESS (TIM), a protein of the fork protection complex, and enhances its stability, thereby supporting replisome activity at DNA replication forks. However, the DNA-binding activity of SDE2 is not well defined. Here, we structurally and functionally characterize a new conserved DNA-binding motif related to the SAP (SAF-A/B, Acinus, PIAS) domain in human SDE2 and establish its preference for ssDNA. Our NMR solution structure of the SDE2SAP domain reveals a helix-extended loop-helix core with the helices aligned parallel to each other, consistent with known canonical SAP folds. Notably, we have shown that the DNA interaction of this SAP domain extends beyond the core SAP domain and is augmented by two lysine residues in the C-terminal tail, which is uniquely positioned adjacent to the SAP motif and conserved in the pre-mRNA splicing factor SF3A3. Furthermore, we found that mutation in the SAP domain and extended C terminus not only disrupts ssDNA binding but also impairs TIM localization at replication forks, thus inhibiting efficient fork progression. Taken together, our results establish SDE2SAP as an essential element for SDE2 to exert its role in preserving replication fork integrity via fork protection complex regulation and highlight the structural diversity of the DNA–protein interactions achieved by a specialized DNA-binding motif.
Collapse
|
9
|
Grabarczyk DB. The Fork Protection Complex: A Regulatory Hub at the Head of the Replisome. Subcell Biochem 2022; 99:83-107. [PMID: 36151374 DOI: 10.1007/978-3-031-00793-4_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
As well as accurately duplicating DNA, the eukaryotic replisome performs a variety of other crucial tasks to maintain genomic stability. For example, organizational elements, like cohesin, must be transferred from the front of the fork to the new strands, and when there is replication stress, forks need to be protected and checkpoint signalling activated. The Tof1-Csm3 (or Timeless-Tipin in humans) Fork Protection Complex (FPC) ensures efficient replisome progression and is required for a range of replication-associated activities. Recent studies have begun to reveal the structure of this complex, and how it functions within the replisome to perform its diverse roles. The core of the FPC acts as a DNA grip on the front of the replisome to regulate fork progression. Other flexibly linked domains and motifs mediate interactions with proteins and specific DNA structures, enabling the FPC to act as a hub at the head of the replication fork.
Collapse
Affiliation(s)
- Daniel B Grabarczyk
- Rudolf Virchow Center for Integrative and Translational Bioimaging, Institute for Structural Biology, University of Würzburg, Würzburg, Germany.
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria.
| |
Collapse
|
10
|
Yoshizawa-Sugata N, Yamazaki S, Mita-Yoshida K, Ono T, Nishito Y, Masai H. Loss of full-length DNA replication regulator Rif1 in two-cell embryos is associated with zygotic transcriptional activation. J Biol Chem 2021; 297:101367. [PMID: 34736895 PMCID: PMC8686075 DOI: 10.1016/j.jbc.2021.101367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 10/17/2021] [Accepted: 10/20/2021] [Indexed: 11/21/2022] Open
Abstract
Rif1 regulates DNA replication timing and double-strand break repair, and its depletion induces transcriptional bursting of two-cell (2C) zygote-specific genes in mouse ES cells. However, how Rif1 regulates zygotic transcription is unclear. We show here that Rif1 depletion promotes the formation of a unique Zscan4 enhancer structure harboring both histone H3 lysine 27 acetylation (H3K27ac) and moderate levels of silencing chromatin mark H3K9me3. Curiously, another enhancer mark H3K4me1 is missing, whereas DNA methylation is still maintained in the structure, which spreads across gene bodies and neighboring regions within the Zscan4 gene cluster. We also found by function analyses of Rif1 domains in ES cells that ectopic expression of Rif1 lacking N-terminal domain results in upregulation of 2C transcripts. This appears to be caused by dominant negative inhibition of endogenous Rif1 protein localization at the nuclear periphery through formation of hetero-oligomers between the N-terminally truncated and endogenous forms. Strikingly, in murine 2C embryos, most of Rif1-derived polypeptides are expressed as truncated forms in soluble nuclear or cytosolic fraction and are likely nonfunctional. Toward the morula stage, the full-length form of Rif1 gradually increased. Our results suggest that the absence of the functional full-length Rif1 due to its instability or alternative splicing and potential inactivation of Rif1 through dominant inhibition by N-terminally truncated Rif1 polypeptides may be involved in 2C-specific transcription program.
Collapse
Key Words
- 2c, two-cell (embryo)
- 4-oht, 4-hydroxytamoxifen
- dox, doxycycline
- erv, endogenous retrovirus
- es, embryonic stem
- hpf, hours post fertilization
- idr, intrinsic disordered region
- ivf, in vitro fertilization
- kd, knockdown
- ko, knockout
- rt, room temperature
Collapse
Affiliation(s)
| | - Satoshi Yamazaki
- Genome Dynamics Project, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Kaoru Mita-Yoshida
- Center for Basic Technology Research, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Tomio Ono
- Center for Basic Technology Research, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Yasumasa Nishito
- Center for Basic Technology Research, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Hisao Masai
- Genome Dynamics Project, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan.
| |
Collapse
|
11
|
Rageul J, Park JJ, Zeng PP, Lee EA, Yang J, Hwang S, Lo N, Weinheimer AS, Schärer OD, Yeo JE, Kim H. SDE2 integrates into the TIMELESS-TIPIN complex to protect stalled replication forks. Nat Commun 2020; 11:5495. [PMID: 33127907 PMCID: PMC7603486 DOI: 10.1038/s41467-020-19162-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 09/28/2020] [Indexed: 01/07/2023] Open
Abstract
Protecting replication fork integrity during DNA replication is essential for maintaining genome stability. Here, we report that SDE2, a PCNA-associated protein, plays a key role in maintaining active replication and counteracting replication stress by regulating the replication fork protection complex (FPC). SDE2 directly interacts with the FPC component TIMELESS (TIM) and enhances its stability, thereby aiding TIM localization to replication forks and the coordination of replisome progression. Like TIM deficiency, knockdown of SDE2 leads to impaired fork progression and stalled fork recovery, along with a failure to activate CHK1 phosphorylation. Moreover, loss of SDE2 or TIM results in an excessive MRE11-dependent degradation of reversed forks. Together, our study uncovers an essential role for SDE2 in maintaining genomic integrity by stabilizing the FPC and describes a new role for TIM in protecting stalled replication forks. We propose that TIM-mediated fork protection may represent a way to cooperate with BRCA-dependent fork stabilization. The fork protection complex (FPC), including the proteins TIMELESS and TIPIN, stabilizes the replisome to ensure unperturbed fork progression during DNA replication. Here the authors reveal that that SDE2, a PCNA-associated protein, plays an important role in maintaining active replication and protecting stalled forks by regulating the replication fork protection complex (FPC).
Collapse
Affiliation(s)
- Julie Rageul
- Department of Pharmacological Sciences, State University of New York at Stony Brook, Stony Brook, New York, 11794, USA
| | - Jennifer J Park
- Department of Pharmacological Sciences, State University of New York at Stony Brook, Stony Brook, New York, 11794, USA
| | - Ping Ping Zeng
- Department of Pharmacological Sciences, State University of New York at Stony Brook, Stony Brook, New York, 11794, USA
| | - Eun-A Lee
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, 44919, Republic of Korea
| | - Jihyeon Yang
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, 44919, Republic of Korea
| | - Sunyoung Hwang
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, 44919, Republic of Korea
| | - Natalie Lo
- Department of Pharmacological Sciences, State University of New York at Stony Brook, Stony Brook, New York, 11794, USA
| | - Alexandra S Weinheimer
- Department of Biochemistry and Cell Biology, State University of New York at Stony Brook, Stony Brook, New York, 11794, USA
| | - Orlando D Schärer
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, 44919, Republic of Korea.,Department of Biological Sciences, School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, 44919, Republic of Korea
| | - Jung-Eun Yeo
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, 44919, Republic of Korea.
| | - Hyungjin Kim
- Department of Pharmacological Sciences, State University of New York at Stony Brook, Stony Brook, New York, 11794, USA. .,Stony Brook Cancer Center, Renaissance School of Medicine at Stony Brook University, Stony Brook, New York, 11794, USA.
| |
Collapse
|
12
|
Grabarczyk DB. Crystal structure and interactions of the Tof1-Csm3 (Timeless-Tipin) fork protection complex. Nucleic Acids Res 2020; 48:6996-7004. [PMID: 32469068 PMCID: PMC7337906 DOI: 10.1093/nar/gkaa456] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 05/14/2020] [Accepted: 05/20/2020] [Indexed: 11/13/2022] Open
Abstract
The Tof1-Csm3 fork protection complex has a central role in the replisome-it promotes the progression of DNA replication forks and protects them when they stall, while also enabling cohesion establishment and checkpoint responses. Here, I present the crystal structure of the Tof1-Csm3 complex from Chaetomium thermophilum at 3.1 Å resolution. The structure reveals that both proteins together form an extended alpha helical repeat structure, which suggests a mechanical or scaffolding role for the complex. Expanding on this idea, I characterize a DNA interacting region and a cancer-associated Mrc1 binding site. This study provides the molecular basis for understanding the functions of the Tof1-Csm3 complex, its human orthologue the Timeless-Tipin complex and additionally the Drosophila circadian rhythm protein Timeless.
Collapse
Affiliation(s)
- Daniel B Grabarczyk
- Rudolf Virchow Center for Experimental Biomedicine, Institute for Structural Biology, University of Würzburg, Josef-Schneider-Str. 2, Würzburg, Germany
| |
Collapse
|
13
|
Chakraborty A, Aziz F, Roh E, Le LTM, Dey R, Zhang T, Rathore MG, Biswas AS, Bode AM, Dong Z. Knock-down of the TIM/TIPIN complex promotes apoptosis in melanoma cells. Oncotarget 2020; 11:1846-1861. [PMID: 32499870 PMCID: PMC7244016 DOI: 10.18632/oncotarget.27572] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 04/10/2020] [Indexed: 11/25/2022] Open
Abstract
The Timeless (TIM) and it's interacting partner TIPIN protein complex is well known for its role in replication checkpoints and normal DNA replication processes. Recent studies revealed the involvement of TIM and TIPIN in human malignancies; however, no evidence is available regarding the expression of the TIM/TIPIN protein complex or its potential role in melanoma. Therefore, we investigated the role of this complex in melanoma. To assess the role of the TIM/TIPIN complex in melanoma, we analyzed TIM/TIPIN expression data from the publicly accessible TCGA online database, Western blot analysis, and RT-qPCR in a panel of melanoma cell lines. Lentivirus-mediated TIM/TIPIN knockdown in A375 melanoma cells was used to examine proliferation, colony formation, and apoptosis. A xenograft tumor formation assay was also performed. The TIM/TIPIN complex is frequently overexpressed in melanoma cells compared to normal melanocytes. We also discovered that the overexpression of TIM and TIPIN was significantly associated with poorer prognosis of melanoma patients. Furthermore, we observed that shRNA-mediated knockdown of TIM and TIPIN reduced cell viability and proliferation due to the induction of apoptosis and increased levels of γH2AX, a marker of DNA damage. In a xenograft tumor nude mouse model, shRNA-knockdown of TIM/TIPIN significantly reduced tumor growth. Our results suggest that the TIM/TIPIN complex plays an important role in tumorigenesis of melanoma, which might reveal novel approaches for the development of new melanoma therapies. Our studies also provide a beginning structural basis for understanding the assembly of the TIM/TIPIN complex. Further mechanistic investigations are needed to determine the complex’s potential as a biomarker of melanoma susceptibility. Targeting TIM/TIPIN might be a potential therapeutic strategy against melanoma.
Collapse
Affiliation(s)
- Abhijit Chakraborty
- The Hormel Institute, University of Minnesota, Austin, MN 55912, USA.,Immunology, Allergy and Rheumatology Section, Baylor College of Medicine, Houston, TX 77030, USA
| | - Faisal Aziz
- The Hormel Institute, University of Minnesota, Austin, MN 55912, USA
| | - Eunmiri Roh
- The Hormel Institute, University of Minnesota, Austin, MN 55912, USA
| | - Le Thi My Le
- The Hormel Institute, University of Minnesota, Austin, MN 55912, USA
| | - Raja Dey
- The Hormel Institute, University of Minnesota, Austin, MN 55912, USA
| | - Tianshun Zhang
- The Hormel Institute, University of Minnesota, Austin, MN 55912, USA
| | - Moeez G Rathore
- The Hormel Institute, University of Minnesota, Austin, MN 55912, USA
| | - Aalekhya Sharma Biswas
- The Hormel Institute, University of Minnesota, Austin, MN 55912, USA.,Pediatric Gastroenterology and Liver Center, Baylor College of Medicine, Houston, Texas, Houston, TX 77030, USA
| | - Ann M Bode
- The Hormel Institute, University of Minnesota, Austin, MN 55912, USA
| | - Zigang Dong
- The Hormel Institute, University of Minnesota, Austin, MN 55912, USA.,College of Medicine, Zhengzhou University, Zhengzhou, Henan Province 450052, China
| |
Collapse
|
14
|
Yang CC, Kato H, Shindo M, Masai H. Cdc7 activates replication checkpoint by phosphorylating the Chk1-binding domain of Claspin in human cells. eLife 2019; 8:50796. [PMID: 31889509 PMCID: PMC6996922 DOI: 10.7554/elife.50796] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 12/30/2019] [Indexed: 01/05/2023] Open
Abstract
Replication checkpoint is essential for maintaining genome integrity in response to various replication stresses as well as during the normal growth. The evolutionally conserved ATR-Claspin-Chk1 pathway is induced during replication checkpoint activation. Cdc7 kinase, required for initiation of DNA replication at replication origins, has been implicated in checkpoint activation but how it is involved in this pathway has not been known. Here, we show that Cdc7 is required for Claspin-Chk1 interaction in human cancer cells by phosphorylating CKBD (Chk1-binding-domain) of Claspin. The residual Chk1 activation in Cdc7-depleted cells is lost upon further depletion of casein kinase1 (CK1γ1), previously reported to phosphorylate CKBD. Thus, Cdc7, in conjunction with CK1γ1, facilitates the interaction between Claspin and Chk1 through phosphorylating CKBD. We also show that, whereas Cdc7 is predominantly responsible for CKBD phosphorylation in cancer cells, CK1γ1 plays a major role in non-cancer cells, providing rationale for targeting Cdc7 for cancer cell-specific cell killing.
Collapse
Affiliation(s)
- Chi-Chun Yang
- Department of Genome Medicine, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Hiroyuki Kato
- Department of Genome Medicine, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Mayumi Shindo
- Protein Analyses Laboratory, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Hisao Masai
- Department of Genome Medicine, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| |
Collapse
|
15
|
Nyine M, Uwimana B, Akech V, Brown A, Ortiz R, Doležel J, Lorenzen J, Swennen R. Association genetics of bunch weight and its component traits in East African highland banana (Musa spp. AAA group). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:3295-3308. [PMID: 31529270 PMCID: PMC6820618 DOI: 10.1007/s00122-019-03425-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 09/06/2019] [Indexed: 05/06/2023]
Abstract
The major quantitative trait loci associated with bunch weight and its component traits in the East African highland banana-breeding population are located on chromosome 3. Bunch weight increase is one of the major objectives of banana improvement programs, but little is known about the loci controlling bunch weight and its component traits. Here we report for the first time some genomic loci associated with bunch weight and its component traits in banana as revealed through a genome-wide association study. A banana-breeding population of 307 genotypes varying in ploidy was phenotyped in three locations under different environmental conditions, and data were collected on bunch weight, number of hands and fruits; fruit length and circumference; and diameter of both fruit and pulp for three crop cycles. The population was genotyped with genotyping by sequencing and 27,178 single nucleotide polymorphisms (SNPs) were generated. The association between SNPs and the best linear unbiased predictors of traits was performed with TASSEL v5 using a mixed linear model accounting for population structure and kinship. Using Bonferroni correction, false discovery rate, and long-range linkage disequilibrium (LD), 25 genomic loci were identified with significant SNPs and most were localized on chromosome 3. Most SNPs were located in genes encoding uncharacterized and hypothetical proteins, but some mapped to transcription factors and genes involved in cell cycle regulation. Inter-chromosomal LD of SNPs was present in the population, but none of the SNPs were significantly associated with the traits. The clustering of significant SNPs on chromosome 3 supported our hypothesis that fruit filling in this population was under control of a few quantitative trait loci with major effects.
Collapse
Affiliation(s)
- Moses Nyine
- International Institute of Tropical Agriculture, P.O. Box 7878, Kampala, Uganda
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Brigitte Uwimana
- International Institute of Tropical Agriculture, P.O. Box 7878, Kampala, Uganda
| | - Violet Akech
- International Institute of Tropical Agriculture, P.O. Box 7878, Kampala, Uganda
| | - Allan Brown
- International Institute of Tropical Agriculture c/o Nelson Mandela African Institution of Science and Technology, P.O. Box 447, Arusha, Tanzania
| | - Rodomiro Ortiz
- Department of Plant Breeding, Swedish University of Agricultural Sciences, P.O. Box 101, 23053, Alnarp, Sweden
| | - Jaroslav Doležel
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, 78371, Olomouc, Czech Republic
| | - Jim Lorenzen
- International Institute of Tropical Agriculture, P.O. Box 7878, Kampala, Uganda
- Bill and Melinda Gates Foundation, Seattle, 23350, USA
| | - Rony Swennen
- International Institute of Tropical Agriculture c/o Nelson Mandela African Institution of Science and Technology, P.O. Box 447, Arusha, Tanzania.
- Laboratory of Tropical Crop Improvement, Division of Crop Biotechnics, Katholieke Universiteit, 3001, Leuven, Belgium.
- Bioversity International, 3001, Leuven, Belgium.
| |
Collapse
|
16
|
Pineau C, Hikmet F, Zhang C, Oksvold P, Chen S, Fagerberg L, Uhlén M, Lindskog C. Cell Type-Specific Expression of Testis Elevated Genes Based on Transcriptomics and Antibody-Based Proteomics. J Proteome Res 2019; 18:4215-4230. [PMID: 31429579 DOI: 10.1021/acs.jproteome.9b00351] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
One of the most complex organs in the human body is the testis, where spermatogenesis takes place. This physiological process involves thousands of genes and proteins that are activated and repressed, making testis the organ with the highest number of tissue-specific genes. However, the function of a large proportion of the corresponding proteins remains unknown and testis harbors many missing proteins (MPs), defined as products of protein-coding genes that lack experimental mass spectrometry evidence. Here, an integrated omics approach was used for exploring the cell type-specific protein expression of genes with an elevated expression in testis. By combining genome-wide transcriptomics analysis with immunohistochemistry, more than 500 proteins with distinct testicular protein expression patterns were identified, and these were selected for in-depth characterization of their in situ expression in eight different testicular cell types. The cell type-specific protein expression patterns allowed us to identify six distinct clusters of expression at different stages of spermatogenesis. The analysis highlighted numerous poorly characterized proteins in each of these clusters whose expression overlapped with that of known proteins involved in spermatogenesis, including 85 proteins with an unknown function and 60 proteins that previously have been classified as MPs. Furthermore, we were able to characterize the in situ distribution of several proteins that previously lacked spatial information and cell type-specific expression within the testis. The testis elevated expression levels both at the RNA and protein levels suggest that these proteins are related to testis-specific functions. In summary, the study demonstrates the power of combining genome-wide transcriptomics analysis with antibody-based protein profiling to explore the cell type-specific expression of both well-known proteins and MPs. The analyzed proteins constitute important targets for further testis-specific research in male reproductive disorders.
Collapse
Affiliation(s)
- Charles Pineau
- Univ Rennes , Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail), UMR_S 1085 , 35042 Rennes Cedex, France.,Protim , Univ Rennes , 35042 Rennes Cedex, France
| | - Feria Hikmet
- Uppsala University , Department of Immunology, Genetics and Pathology, Rudbeck Laboratory , 75185 Uppsala , Sweden
| | - Cheng Zhang
- Science for Life Laboratory , School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH-Royal Institute of Technology , 17121 Stockholm , Sweden
| | - Per Oksvold
- Science for Life Laboratory , School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH-Royal Institute of Technology , 17121 Stockholm , Sweden
| | - Shuqi Chen
- Science for Life Laboratory , School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH-Royal Institute of Technology , 17121 Stockholm , Sweden
| | - Linn Fagerberg
- Science for Life Laboratory , School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH-Royal Institute of Technology , 17121 Stockholm , Sweden
| | - Mathias Uhlén
- Science for Life Laboratory , School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH-Royal Institute of Technology , 17121 Stockholm , Sweden
| | - Cecilia Lindskog
- Uppsala University , Department of Immunology, Genetics and Pathology, Rudbeck Laboratory , 75185 Uppsala , Sweden
| |
Collapse
|
17
|
Moiseeva TN, Bakkenist CJ. Regulation of the initiation of DNA replication in human cells. DNA Repair (Amst) 2018; 72:99-106. [PMID: 30266203 DOI: 10.1016/j.dnarep.2018.09.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 09/07/2018] [Indexed: 12/31/2022]
Abstract
The origin of species would not have been possible without high fidelity DNA replication and complex genomes evolved with mechanisms that control the initiation of DNA replication at multiple origins on multiple chromosomes such that the genome is duplicated once and only once. The mechanisms that control the assembly and activation of the replicative helicase and the initiation of DNA replication in yeast and Xenopus egg extract systems have been identified and reviewed [1,2]. The goal of this review is to organize currently available data on the mechanisms that control the initiation of DNA replication in human cells.
Collapse
Affiliation(s)
- Tatiana N Moiseeva
- Department of Radiation Oncology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
| | - Christopher J Bakkenist
- Department of Radiation Oncology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA; Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| |
Collapse
|
18
|
Kottemann MC, Conti BA, Lach FP, Smogorzewska A. Removal of RTF2 from Stalled Replisomes Promotes Maintenance of Genome Integrity. Mol Cell 2017; 69:24-35.e5. [PMID: 29290612 DOI: 10.1016/j.molcel.2017.11.035] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Revised: 09/25/2017] [Accepted: 11/29/2017] [Indexed: 11/27/2022]
Abstract
The protection and efficient restart of stalled replication forks is critical for the maintenance of genome integrity. Here, we identify a regulatory pathway that promotes stalled forks recovery from replication stress. We show that the mammalian replisome component C20orf43/RTF2 (homologous to S. pombe Rtf2) must be removed for fork restart to be optimal. We further show that the proteasomal shuttle proteins DDI1 and DDI2 are required for RTF2 removal from stalled forks. Persistence of RTF2 at stalled forks results in fork restart defects, hyperactivation of the DNA damage signal, accumulation of single-stranded DNA (ssDNA), sensitivity to replication drugs, and chromosome instability. These results establish that RTF2 removal is a key determinant for the ability of cells to manage replication stress and maintain genome integrity.
Collapse
Affiliation(s)
- Molly C Kottemann
- Laboratory of Genome Maintenance, The Rockefeller University, New York, NY 10065, USA
| | - Brooke A Conti
- Laboratory of Genome Maintenance, The Rockefeller University, New York, NY 10065, USA
| | - Francis P Lach
- Laboratory of Genome Maintenance, The Rockefeller University, New York, NY 10065, USA
| | - Agata Smogorzewska
- Laboratory of Genome Maintenance, The Rockefeller University, New York, NY 10065, USA.
| |
Collapse
|
19
|
Hau PM, Tsao SW. Epstein-Barr Virus Hijacks DNA Damage Response Transducers to Orchestrate Its Life Cycle. Viruses 2017; 9:v9110341. [PMID: 29144413 PMCID: PMC5707548 DOI: 10.3390/v9110341] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 10/30/2017] [Accepted: 11/08/2017] [Indexed: 12/12/2022] Open
Abstract
The Epstein–Barr virus (EBV) is a ubiquitous virus that infects most of the human population. EBV infection is associated with multiple human cancers, including Burkitt’s lymphoma, Hodgkin’s lymphoma, a subset of gastric carcinomas, and almost all undifferentiated non-keratinizing nasopharyngeal carcinoma. Intensive research has shown that EBV triggers a DNA damage response (DDR) during primary infection and lytic reactivation. The EBV-encoded viral proteins have been implicated in deregulating the DDR signaling pathways. The consequences of DDR inactivation lead to genomic instability and promote cellular transformation. This review summarizes the current understanding of the relationship between EBV infection and the DDR transducers, including ATM (ataxia telangiectasia mutated), ATR (ATM and Rad3-related), and DNA-PK (DNA-dependent protein kinase), and discusses how EBV manipulates the DDR signaling pathways to complete the replication process of viral DNA during lytic reactivation.
Collapse
Affiliation(s)
- Pok Man Hau
- Department of Anatomical and Cellular Pathology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China.
| | - Sai Wah Tsao
- School of Biomedical Science, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China.
| |
Collapse
|
20
|
Alternative Lengthening of Telomeres Mediated by Mitotic DNA Synthesis Engages Break-Induced Replication Processes. Mol Cell Biol 2017; 37:MCB.00226-17. [PMID: 28760773 DOI: 10.1128/mcb.00226-17] [Citation(s) in RCA: 135] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2017] [Accepted: 07/20/2017] [Indexed: 01/05/2023] Open
Abstract
Alternative lengthening of telomeres (ALT) is a telomerase-independent telomere maintenance mechanism that occurs in a subset of cancers. By analyzing telomerase-positive cells and their human TERC knockout-derived ALT human cell lines, we show that ALT cells harbor more fragile telomeres representing telomere replication problems. ALT-associated replication defects trigger mitotic DNA synthesis (MiDAS) at telomeres in a RAD52-dependent, but RAD51-independent, manner. Telomeric MiDAS is a conservative DNA synthesis process, potentially mediated by break-induced replication, similar to type II ALT survivors in Saccharomyces cerevisiae Replication stresses induced by ectopic oncogenic expression of cyclin E, G-quadruplexes, or R-loop formation facilitate the ALT pathway and lead to telomere clustering, a hallmark of ALT cancers. The TIMELESS/TIPIN complex suppresses telomere clustering and telomeric MiDAS, whereas the SMC5/6 complex promotes them. In summary, ALT cells exhibit more telomere replication defects that result in persistent DNA damage responses at telomeres, leading to the engagement of telomeric MiDAS (spontaneous mitotic telomere synthesis) that is triggered by DNA replication stress, a potential driver of genomic duplications in cancer.
Collapse
|
21
|
Holzer S, Degliesposti G, Kilkenny ML, Maslen SL, Matak-Vinkovíc D, Skehel M, Pellegrini L. Crystal structure of the N-terminal domain of human Timeless and its interaction with Tipin. Nucleic Acids Res 2017; 45:5555-5563. [PMID: 28334766 PMCID: PMC5605233 DOI: 10.1093/nar/gkx139] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 02/24/2017] [Indexed: 11/13/2022] Open
Abstract
Human Timeless is involved in replication fork stabilization, S-phase checkpoint activation and establishment of sister chromatid cohesion. In the cell, Timeless forms a constitutive heterodimeric complex with Tipin. Here we present the 1.85 Å crystal structure of a large N-terminal segment of human Timeless, spanning amino acids 1-463, and we show that this region of human Timeless harbours a partial binding site for Tipin. Furthermore, we identify minimal regions of the two proteins that are required for the formation of a stable Timeless-Tipin complex and provide evidence that the Timeless-Tipin interaction is based on a composite binding interface comprising different domains of Timeless.
Collapse
Affiliation(s)
- Sandro Holzer
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| | | | - Mairi L Kilkenny
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| | - Sarah L Maslen
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | | | - Mark Skehel
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Luca Pellegrini
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| |
Collapse
|
22
|
Escorcia W, Forsburg SL. Destabilization of the replication fork protection complex disrupts meiotic chromosome segregation. Mol Biol Cell 2017; 28:2978-2997. [PMID: 28855376 PMCID: PMC5662257 DOI: 10.1091/mbc.e17-02-0101] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Revised: 08/21/2017] [Accepted: 08/23/2017] [Indexed: 12/17/2022] Open
Abstract
The replication fork protection complex (FPC) coordinates multiple processes that are crucial for unimpeded passage of the replisome through various barriers and difficult to replicate areas of the genome. We examine the function of Swi1 and Swi3, fission yeast's primary FPC components, to elucidate how replication fork stability contributes to DNA integrity in meiosis. We report that destabilization of the FPC results in reduced spore viability, delayed replication, changes in recombination, and chromosome missegregation in meiosis I and meiosis II. These phenotypes are linked to accumulation and persistence of DNA damage markers in meiosis and to problems with cohesion stability at the centromere. These findings reveal an important connection between meiotic replication fork stability and chromosome segregation, two processes with major implications to human reproductive health.
Collapse
Affiliation(s)
- Wilber Escorcia
- Program in Molecular & Computational Biology, University of Southern California, Los Angeles, CA 90089-2910
| | - Susan L Forsburg
- Program in Molecular & Computational Biology, University of Southern California, Los Angeles, CA 90089-2910
| |
Collapse
|
23
|
The Intra-S Checkpoint Responses to DNA Damage. Genes (Basel) 2017; 8:genes8020074. [PMID: 28218681 PMCID: PMC5333063 DOI: 10.3390/genes8020074] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2017] [Revised: 02/08/2017] [Accepted: 02/08/2017] [Indexed: 02/03/2023] Open
Abstract
Faithful duplication of the genome is a challenge because DNA is susceptible to damage by a number of intrinsic and extrinsic genotoxins, such as free radicals and UV light. Cells activate the intra-S checkpoint in response to damage during S phase to protect genomic integrity and ensure replication fidelity. The checkpoint prevents genomic instability mainly by regulating origin firing, fork progression, and transcription of G1/S genes in response to DNA damage. Several studies hint that regulation of forks is perhaps the most critical function of the intra-S checkpoint. However, the exact role of the checkpoint at replication forks has remained elusive and controversial. Is the checkpoint required for fork stability, or fork restart, or to prevent fork reversal or fork collapse, or activate repair at replication forks? What are the factors that the checkpoint targets at stalled replication forks? In this review, we will discuss the various pathways activated by the intra-S checkpoint in response to damage to prevent genomic instability.
Collapse
|
24
|
Michael AK, Fribourgh JL, Van Gelder RN, Partch CL. Animal Cryptochromes: Divergent Roles in Light Perception, Circadian Timekeeping and Beyond. Photochem Photobiol 2017; 93:128-140. [PMID: 27891621 DOI: 10.1111/php.12677] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 10/09/2016] [Indexed: 12/15/2022]
Abstract
Cryptochromes are evolutionarily related to the light-dependent DNA repair enzyme photolyase, serving as major regulators of circadian rhythms in insects and vertebrate animals. There are two types of cryptochromes in the animal kingdom: Drosophila-like CRYs that act as nonvisual photopigments linking circadian rhythms to the environmental light/dark cycle, and vertebrate-like CRYs that do not appear to sense light directly, but control the generation of circadian rhythms by acting as transcriptional repressors. Some animals have both types of CRYs, while others possess only one. Cryptochromes have two domains, the photolyase homology region (PHR) and an extended, intrinsically disordered C-terminus. While all animal CRYs share a high degree of sequence and structural homology in their PHR domains, the C-termini are divergent in both length and sequence identity. Recently, cryptochrome function has been shown to extend beyond its pivotal role in circadian clocks, participating in regulation of the DNA damage response, cancer progression and glucocorticoid signaling, as well as being implicated as possible magnetoreceptors. In this review, we provide a historical perspective on the discovery of animal cryptochromes, examine similarities and differences of the two types of animal cryptochromes and explore some of the divergent roles for this class of proteins.
Collapse
Affiliation(s)
- Alicia K Michael
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA
| | - Jennifer L Fribourgh
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA
| | | | - Carrie L Partch
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA.,Center for Circadian Biology, University of California San Diego, San Diego, CA
| |
Collapse
|
25
|
Xu X, Wang JT, Li M, Liu Y. TIMELESS Suppresses the Accumulation of Aberrant CDC45·MCM2-7·GINS Replicative Helicase Complexes on Human Chromatin. J Biol Chem 2016; 291:22544-22558. [PMID: 27587400 PMCID: PMC5077192 DOI: 10.1074/jbc.m116.719963] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Revised: 08/31/2016] [Indexed: 07/24/2023] Open
Abstract
The replication licensing factor CDC6 recruits the MCM2-7 replicative helicase to the replication origin, where MCM2-7 is activated to initiate DNA replication. MCM2-7 is activated by both the CDC7-Dbf4 kinase and cyclin-dependent kinase and via interactions with CDC45 and go-ichi-ni-san complex (GINS) to form the CDC45·MCM2-7·GINS (CMG) helicase complex. TIMELESS (TIM) is important for the subsequent coupling of CMG activity to DNA polymerases for efficient DNA synthesis. However, the mechanism by which TIM regulates CMG activity for proper replication fork progression remains unclear. Here we show that TIM interacts with MCM2-7 prior to the initiation of DNA replication. TIM depletion in various human cell lines results in the accumulation of aberrant CMG helicase complexes on chromatin. Importantly, the presence of these abnormal CMG helicase complexes is not restricted to cells undergoing DNA synthesis. Furthermore, even though these aberrant CMG complexes interact with the DNA polymerases on human chromatin, these complexes are not phosphorylated properly by cyclin-dependent kinase/CDC7-Dbf4 kinase and exhibit reduced DNA unwinding activity. This phenomenon coincides with a significant accumulation of the p27 and p21 replication inhibitors, reduced chromatin association of CDC6 and cyclin E, and a delay in S phase entry. Our results provide the first evidence that TIM is required for the correct chromatin association of the CMG complex to allow efficient DNA replication.
Collapse
Affiliation(s)
- Xiaohua Xu
- From the Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, Duarte, California 91010-3000
| | - Jiin-Tarng Wang
- From the Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, Duarte, California 91010-3000
| | - Min Li
- From the Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, Duarte, California 91010-3000
| | - Yilun Liu
- From the Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, Duarte, California 91010-3000
| |
Collapse
|
26
|
Yang CC, Suzuki M, Yamakawa S, Uno S, Ishii A, Yamazaki S, Fukatsu R, Fujisawa R, Sakimura K, Tsurimoto T, Masai H. Claspin recruits Cdc7 kinase for initiation of DNA replication in human cells. Nat Commun 2016; 7:12135. [PMID: 27401717 PMCID: PMC4945878 DOI: 10.1038/ncomms12135] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2016] [Accepted: 06/03/2016] [Indexed: 11/09/2022] Open
Abstract
Claspin transmits replication stress signal from ATR to Chk1 effector kinase as a mediator. It also plays a role in efficient replication fork progression during normal growth. Here we have generated conditional knockout of Claspin and show that Claspin knockout mice are dead by E12.5 and Claspin knockout mouse embryonic fibroblast (MEF) cells show defect in S phase. Using the mutant cell lines, we report the crucial roles of the acidic patch (AP) near the C terminus of Claspin in initiation of DNA replication. Cdc7 kinase binds to AP and this binding is required for phosphorylation of Mcm. AP is involved also in intramolecular interaction with a N-terminal segment, masking the DNA-binding domain and a newly identified PIP motif, and Cdc7-mediated phosphorylation reduces the intramolecular interaction. Our results suggest a new role of Claspin in initiation of DNA replication during normal S phase through the recruitment of Cdc7 that facilitates phosphorylation of Mcm proteins. Claspin mediates the transmission of a replication-stress signal from ATR to Chk1 and is necessary for efficient fork progression. Here the authors demonstrate that the C-terminal acidic patch is important for this role due to its interaction with Cdc7.
Collapse
Affiliation(s)
- Chi-Chun Yang
- Department of Genome Medicine, Tokyo Metropolitan Institute of Medical Science, 4-6-1 Kamikitazawa, Setagaya-ku, Tokyo 156-8506, Japan
| | - Masahiro Suzuki
- Department of Genome Medicine, Tokyo Metropolitan Institute of Medical Science, 4-6-1 Kamikitazawa, Setagaya-ku, Tokyo 156-8506, Japan
| | - Shiori Yamakawa
- Department of Genome Medicine, Tokyo Metropolitan Institute of Medical Science, 4-6-1 Kamikitazawa, Setagaya-ku, Tokyo 156-8506, Japan
| | - Syuzi Uno
- Department of Genome Medicine, Tokyo Metropolitan Institute of Medical Science, 4-6-1 Kamikitazawa, Setagaya-ku, Tokyo 156-8506, Japan
| | - Ai Ishii
- Department of Genome Medicine, Tokyo Metropolitan Institute of Medical Science, 4-6-1 Kamikitazawa, Setagaya-ku, Tokyo 156-8506, Japan
| | - Satoshi Yamazaki
- Department of Genome Medicine, Tokyo Metropolitan Institute of Medical Science, 4-6-1 Kamikitazawa, Setagaya-ku, Tokyo 156-8506, Japan
| | - Rino Fukatsu
- Department of Genome Medicine, Tokyo Metropolitan Institute of Medical Science, 4-6-1 Kamikitazawa, Setagaya-ku, Tokyo 156-8506, Japan
| | - Ryo Fujisawa
- Department of Biology, Faculty of Science, Kyushu University 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Kenji Sakimura
- Department of Cellular Neurobiology, Brain Research Institute, Niigata University, Niigata 951-8585, Japan
| | - Toshiki Tsurimoto
- Department of Biology, Faculty of Science, Kyushu University 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Hisao Masai
- Department of Genome Medicine, Tokyo Metropolitan Institute of Medical Science, 4-6-1 Kamikitazawa, Setagaya-ku, Tokyo 156-8506, Japan
| |
Collapse
|
27
|
Jang SW, Jung JK, Kim JM. Replication Protein A (RPA) deficiency activates the Fanconi anemia DNA repair pathway. Cell Cycle 2016; 15:2336-45. [PMID: 27398742 DOI: 10.1080/15384101.2016.1201621] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The Fanconi anemia (FA) pathway regulates DNA inter-strand crosslink (ICL) repair. Despite our greater understanding of the role of FA in ICL repair, its function in the preventing spontaneous genome instability is not well understood. Here, we show that depletion of replication protein A (RPA) activates the FA pathway. RPA1 deficiency increases chromatin recruitment of FA core complex, leading to FANCD2 monoubiquitination (FANCD2-Ub) and foci formation in the absence of DNA damaging agents. Importantly, ATR depletion, but not ATM, abolished RPA1 depletion-induced FANCD2-Ub, suggesting that ATR activation mediated FANCD2-Ub. Interestingly, we found that depletion of hSSB1/2-INTS3, a single-stranded DNA-binding protein complex, induces FANCD2-Ub, like RPA1 depletion. More interestingly, depletion of either RPA1 or INTS3 caused increased accumulation of DNA damage in FA pathway deficient cell lines. Taken together, these results indicate that RPA deficiency induces activation of the FA pathway in an ATR-dependent manner, which may play a role in the genome maintenance.
Collapse
Affiliation(s)
- Seok-Won Jang
- a Department of Pharmacology , Medical Research Center for Gene Regulation, Chonnam National University Medical School , Gwangju , Korea
| | - Jin Ki Jung
- a Department of Pharmacology , Medical Research Center for Gene Regulation, Chonnam National University Medical School , Gwangju , Korea
| | - Jung Min Kim
- a Department of Pharmacology , Medical Research Center for Gene Regulation, Chonnam National University Medical School , Gwangju , Korea
| |
Collapse
|
28
|
Gadaleta MC, Das MM, Tanizawa H, Chang YT, Noma KI, Nakamura TM, Noguchi E. Swi1Timeless Prevents Repeat Instability at Fission Yeast Telomeres. PLoS Genet 2016; 12:e1005943. [PMID: 26990647 PMCID: PMC4798670 DOI: 10.1371/journal.pgen.1005943] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 02/25/2016] [Indexed: 01/09/2023] Open
Abstract
Genomic instability associated with DNA replication stress is linked to cancer and genetic pathologies in humans. If not properly regulated, replication stress, such as fork stalling and collapse, can be induced at natural replication impediments present throughout the genome. The fork protection complex (FPC) is thought to play a critical role in stabilizing stalled replication forks at several known replication barriers including eukaryotic rDNA genes and the fission yeast mating-type locus. However, little is known about the role of the FPC at other natural impediments including telomeres. Telomeres are considered to be difficult to replicate due to the presence of repetitive GT-rich sequences and telomere-binding proteins. However, the regulatory mechanism that ensures telomere replication is not fully understood. Here, we report the role of the fission yeast Swi1Timeless, a subunit of the FPC, in telomere replication. Loss of Swi1 causes telomere shortening in a telomerase-independent manner. Our epistasis analyses suggest that heterochromatin and telomere-binding proteins are not major impediments for telomere replication in the absence of Swi1. Instead, repetitive DNA sequences impair telomere integrity in swi1Δ mutant cells, leading to the loss of repeat DNA. In the absence of Swi1, telomere shortening is accompanied with an increased recruitment of Rad52 recombinase and more frequent amplification of telomere/subtelomeres, reminiscent of tumor cells that utilize the alternative lengthening of telomeres pathway (ALT) to maintain telomeres. These results suggest that Swi1 ensures telomere replication by suppressing recombination and repeat instability at telomeres. Our studies may also be relevant in understanding the potential role of Swi1Timeless in regulation of telomere stability in cancer cells. In every round of the cell cycle, cells must accurately replicate their full genetic information. This process is highly regulated, as defects during DNA replication cause genomic instability, leading to various genetic disorders including cancers. To thwart these problems, cells carry an array of complex mechanisms to deal with various obstacles found across the genome that can hamper DNA replication and cause DNA damage. Understanding how these mechanisms are regulated and orchestrated is of paramount importance in the field. In this report, we describe how Swi1, a Timeless-related protein in fission yeast, regulates efficient replication of telomeres, which are considered to be difficult to replicate due to the presence of repetitive DNA and telomere-binding proteins. We show that Swi1 prevents telomere damage and maintains telomere length by protecting integrity of telomeric repeats. Swi1-mediated telomere maintenance is independent of telomerase activity, and loss of Swi1 causes hyper-activation of recombination-based telomere maintenance, which generates heterogeneous telomeres. Similar telomerase-independent and recombination-dependent mechanism is utilized by approximately 15% of human cancers, linking telomere replication defects with cancer development. Thus, our study may be relevant in understanding the role of telomere replication defects in the development of cancers in humans.
Collapse
Affiliation(s)
- Mariana C. Gadaleta
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Mukund M. Das
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Hideki Tanizawa
- Gene Expression and Regulation Program, The Wistar Institute, Philadelphia, Pennsylvania, United States of America
| | - Ya-Ting Chang
- Department of Biochemistry and Molecular Genetics, College of Medicine, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Ken-ichi Noma
- Gene Expression and Regulation Program, The Wistar Institute, Philadelphia, Pennsylvania, United States of America
| | - Toru M. Nakamura
- Department of Biochemistry and Molecular Genetics, College of Medicine, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Eishi Noguchi
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, Pennsylvania, United States of America
- * E-mail:
| |
Collapse
|
29
|
A Timeless Link Between Circadian Patterns and Disease. Trends Mol Med 2016; 22:68-81. [DOI: 10.1016/j.molmed.2015.11.007] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Revised: 11/16/2015] [Accepted: 11/18/2015] [Indexed: 02/06/2023]
|
30
|
Calì F, Bharti SK, Di Perna R, Brosh RM, Pisani FM. Tim/Timeless, a member of the replication fork protection complex, operates with the Warsaw breakage syndrome DNA helicase DDX11 in the same fork recovery pathway. Nucleic Acids Res 2015; 44:705-17. [PMID: 26503245 PMCID: PMC4737141 DOI: 10.1093/nar/gkv1112] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Accepted: 10/13/2015] [Indexed: 11/15/2022] Open
Abstract
We present evidence that Tim establishes a physical and functional interaction with DDX11, a super-family 2 iron-sulfur cluster DNA helicase genetically linked to the chromosomal instability disorder Warsaw breakage syndrome. Tim stimulates DDX11 unwinding activity on forked DNA substrates up to 10-fold and on bimolecular anti-parallel G-quadruplex DNA structures and three-stranded D-loop approximately 4–5-fold. Electrophoretic mobility shift assays revealed that Tim enhances DDX11 binding to DNA, suggesting that the observed stimulation derives from an improved ability of DDX11 to interact with the nucleic acid substrate. Surface plasmon resonance measurements indicate that DDX11 directly interacts with Tim. DNA fiber track assays with HeLa cells exposed to hydroxyurea demonstrated that Tim or DDX11 depletion significantly reduced replication fork progression compared to control cells; whereas no additive effect was observed by co-depletion of both proteins. Moreover, Tim and DDX11 are epistatic in promoting efficient resumption of stalled DNA replication forks in hydroxyurea-treated cells. This is consistent with the finding that association of the two endogenous proteins in the cell extract chromatin fraction is considerably increased following hydroxyurea exposure. Overall, our studies provide evidence that Tim and DDX11 physically and functionally interact and act in concert to preserve replication fork progression in perturbed conditions.
Collapse
Affiliation(s)
- Federica Calì
- Istituto di Biochimica delle Proteine, Consiglio Nazionale delle Ricerche, Via Pietro Castellino, 111. 80131 - Napoli, Italy
| | - Sanjay Kumar Bharti
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, NIH Biomedical Research Center, 251 Bayview Blvd, Baltimore, MD 21224 USA
| | - Roberta Di Perna
- Istituto di Biochimica delle Proteine, Consiglio Nazionale delle Ricerche, Via Pietro Castellino, 111. 80131 - Napoli, Italy
| | - Robert M Brosh
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, NIH Biomedical Research Center, 251 Bayview Blvd, Baltimore, MD 21224 USA
| | - Francesca M Pisani
- Istituto di Biochimica delle Proteine, Consiglio Nazionale delle Ricerche, Via Pietro Castellino, 111. 80131 - Napoli, Italy
| |
Collapse
|
31
|
Xie S, Mortusewicz O, Ma HT, Herr P, Poon RYC, Poon RRY, Helleday T, Qian C. Timeless Interacts with PARP-1 to Promote Homologous Recombination Repair. Mol Cell 2015; 60:163-76. [PMID: 26344098 DOI: 10.1016/j.molcel.2015.07.031] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Revised: 05/01/2015] [Accepted: 07/29/2015] [Indexed: 12/21/2022]
Abstract
Human Timeless helps stabilize replication forks during normal DNA replication and plays a critical role in activation of the S phase checkpoint and proper establishment of sister chromatid cohesion. However, it remains elusive whether Timeless is involved in the repair of damaged DNA. Here, we identify that Timeless physically interacts with PARP-1 independent of poly(ADP-ribosyl)ation. We present high-resolution crystal structures of Timeless PAB (PARP-1-binding domain) in free form and in complex with PARP-1 catalytic domain. Interestingly, Timeless PAB domain specifically recognizes PARP-1, but not PARP-2 or PARP-3. Timeless-PARP-1 interaction does not interfere with PARP-1 enzymatic activity. We demonstrate that rapid and transient accumulation of Timeless at laser-induced DNA damage sites requires PARP-1, but not poly(ADP-ribosyl)ation and that Timeless is co-trapped with PARP-1 at DNA lesions upon PARP inhibition. Furthermore, we show that Timeless and PARP-1 interaction is required for efficient homologous recombination repair.
Collapse
Affiliation(s)
- Si Xie
- School of Biomedical Sciences, The University of Hong Kong, Hong Kong
| | - Oliver Mortusewicz
- Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 21 Stockholm, Sweden
| | - Hoi Tang Ma
- Division of Life Science, Hong Kong University of Science and Technology, Hong Kong
| | - Patrick Herr
- Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 21 Stockholm, Sweden
| | - Randy Y C Poon
- Division of Life Science, Hong Kong University of Science and Technology, Hong Kong
| | - Randy R Y Poon
- Division of Life Science, Hong Kong University of Science and Technology, Hong Kong
| | - Thomas Helleday
- Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 21 Stockholm, Sweden.
| | - Chengmin Qian
- School of Biomedical Sciences, The University of Hong Kong, Hong Kong.
| |
Collapse
|
32
|
Hao J, de Renty C, Li Y, Xiao H, Kemp MG, Han Z, DePamphilis ML, Zhu W. And-1 coordinates with Claspin for efficient Chk1 activation in response to replication stress. EMBO J 2015; 34:2096-110. [PMID: 26082189 DOI: 10.15252/embj.201488016] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2014] [Accepted: 05/08/2015] [Indexed: 11/09/2022] Open
Abstract
The replisome is important for DNA replication checkpoint activation, but how specific components of the replisome coordinate with ATR to activate Chk1 in human cells remains largely unknown. Here, we demonstrate that And-1, a replisome component, acts together with ATR to activate Chk1. And-1 is phosphorylated at T826 by ATR following replication stress, and this phosphorylation is required for And-1 to accumulate at the damage sites, where And-1 promotes the interaction between Claspin and Chk1, thereby stimulating efficient Chk1 activation by ATR. Significantly, And-1 binds directly to ssDNA and facilitates the association of Claspin with ssDNA. Furthermore, And-1 associates with replication forks and is required for the recovery of stalled forks. These studies establish a novel ATR-And-1 axis as an important regulator for efficient Chk1 activation and reveal a novel mechanism of how the replisome regulates the replication checkpoint and genomic stability.
Collapse
Affiliation(s)
- Jing Hao
- Department of Biochemistry and Molecular Medicine, The George Washington University Medical School, Washington, DC, USA
| | | | - Yongming Li
- Department of Biochemistry and Molecular Medicine, The George Washington University Medical School, Washington, DC, USA
| | - Haijie Xiao
- Department of Biochemistry and Molecular Medicine, The George Washington University Medical School, Washington, DC, USA
| | - Michael G Kemp
- Department of Biological Sciences, Florida Institute of Technology, Melbourne, FL, USA
| | - Zhiyong Han
- Department of Biochemistry and Molecular Medicine, The George Washington University Medical School, Washington, DC, USA
| | | | - Wenge Zhu
- Department of Biochemistry and Molecular Medicine, The George Washington University Medical School, Washington, DC, USA
| |
Collapse
|
33
|
Baldeyron C, Brisson A, Tesson B, Némati F, Koundrioukoff S, Saliba E, De Koning L, Martel E, Ye M, Rigaill G, Meseure D, Nicolas A, Gentien D, Decaudin D, Debatisse M, Depil S, Cruzalegui F, Pierré A, Roman-Roman S, Tucker GC, Dubois T. TIPIN depletion leads to apoptosis in breast cancer cells. Mol Oncol 2015; 9:1580-98. [PMID: 26004086 DOI: 10.1016/j.molonc.2015.04.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Revised: 03/10/2015] [Accepted: 04/23/2015] [Indexed: 12/31/2022] Open
Abstract
Triple-negative breast cancer (TNBC) is the breast cancer subgroup with the most aggressive clinical behavior. Alternatives to conventional chemotherapy are required to improve the survival of TNBC patients. Gene-expression analyses for different breast cancer subtypes revealed significant overexpression of the Timeless-interacting protein (TIPIN), which is involved in the stability of DNA replication forks, in the highly proliferative associated TNBC samples. Immunohistochemistry analysis showed higher expression of TIPIN in the most proliferative and aggressive breast cancer subtypes including TNBC, and no TIPIN expression in healthy breast tissues. The depletion of TIPIN by RNA interference impairs the proliferation of both human breast cancer and non-tumorigenic cell lines. However, this effect may be specifically associated with apoptosis in breast cancer cells. TIPIN silencing results in higher levels of single-stranded DNA (ssDNA), indicative of replicative stress (RS), in TNBC compared to non-tumorigenic cells. Upon TIPIN depletion, the speed of DNA replication fork was significantly decreased in all BC cells. However, TIPIN-depleted TNBC cells are unable to fire additional replication origins in response to RS and therefore undergo apoptosis. TIPIN knockdown in TNBC cells decreases tumorigenicity in vitro and delays tumor growth in vivo. Our findings suggest that TIPIN is important for the maintenance of DNA replication and represents a potential treatment target for the worst prognosis associated breast cancers, such as TNBC.
Collapse
Affiliation(s)
- Céline Baldeyron
- Institut Curie, Centre de Recherche, Paris, F-75248, France; Breast Cancer Biology Group, Department of Translational Research, Paris, F-75248, France
| | - Amélie Brisson
- Institut Curie, Centre de Recherche, Paris, F-75248, France; Breast Cancer Biology Group, Department of Translational Research, Paris, F-75248, France
| | - Bruno Tesson
- Institut Curie, Centre de Recherche, Paris, F-75248, France; Breast Cancer Biology Group, Department of Translational Research, Paris, F-75248, France; INSERM, U900, Bioinformatics, Biostatistics, Epidemiology and Computational Systems Biology of Cancer, Paris, F-75248, France; Mines ParisTech, Fontainebleau, F-77300, France
| | - Fariba Némati
- Institut Curie, Centre de Recherche, Paris, F-75248, France; Laboratory of Preclinical Investigation, Department of Translational Research, Paris, F-75248, France
| | - Stéphane Koundrioukoff
- Institut Curie, Centre de Recherche, Paris, F-75248, France; CNRS, UMR 3244, Paris, F-75248, France; Université Pierre and Marie Curie Paris VI, Paris, F-75005, France
| | - Elie Saliba
- Institut Curie, Centre de Recherche, Paris, F-75248, France; Breast Cancer Biology Group, Department of Translational Research, Paris, F-75248, France
| | - Leanne De Koning
- Institut Curie, Centre de Recherche, Paris, F-75248, France; RPPA Platform, Department of Translational Research, Paris, F-75248, France
| | - Elise Martel
- Institut Curie, Investigative Pathology Platform, Paris, F-75248, France
| | - Mengliang Ye
- Institut Curie, Centre de Recherche, Paris, F-75248, France; Breast Cancer Biology Group, Department of Translational Research, Paris, F-75248, France
| | - Guillem Rigaill
- Unité de Recherche en Génomique Végétale, INRA-CNRS-Université d'Evry Val d'Essonne, Evry, F-91057, France
| | - Didier Meseure
- Institut Curie, Investigative Pathology Platform, Paris, F-75248, France
| | - André Nicolas
- Institut Curie, Investigative Pathology Platform, Paris, F-75248, France
| | - David Gentien
- Institut Curie, Centre de Recherche, Paris, F-75248, France; Platform of Molecular Biology Facilities, Department of Translational Research, Paris, F-75248, France
| | - Didier Decaudin
- Institut Curie, Centre de Recherche, Paris, F-75248, France; Laboratory of Preclinical Investigation, Department of Translational Research, Paris, F-75248, France
| | - Michelle Debatisse
- Institut Curie, Centre de Recherche, Paris, F-75248, France; CNRS, UMR 3244, Paris, F-75248, France; Université Pierre and Marie Curie Paris VI, Paris, F-75005, France
| | - Stéphane Depil
- Institut de Recherches SERVIER, Pôle Innovation Thérapeutique Oncologie, Croissy-sur-Seine, F-78290, France
| | - Francisco Cruzalegui
- Institut de Recherches SERVIER, Pôle Innovation Thérapeutique Oncologie, Croissy-sur-Seine, F-78290, France
| | - Alain Pierré
- Institut de Recherches SERVIER, Pôle Innovation Thérapeutique Oncologie, Croissy-sur-Seine, F-78290, France
| | - Sergio Roman-Roman
- Institut Curie, Centre de Recherche, Paris, F-75248, France; Breast Cancer Biology Group, Department of Translational Research, Paris, F-75248, France
| | - Gordon C Tucker
- Institut de Recherches SERVIER, Pôle Innovation Thérapeutique Oncologie, Croissy-sur-Seine, F-78290, France
| | - Thierry Dubois
- Institut Curie, Centre de Recherche, Paris, F-75248, France; Breast Cancer Biology Group, Department of Translational Research, Paris, F-75248, France.
| |
Collapse
|
34
|
Inaguma Y, Ito H, Hara A, Iwamoto I, Matsumoto A, Yamagata T, Tabata H, Nagata KI. Morphological characterization of mammalian Timeless in the mouse brain development. Neurosci Res 2015; 92:21-8. [DOI: 10.1016/j.neures.2014.10.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Revised: 10/24/2014] [Accepted: 10/28/2014] [Indexed: 01/14/2023]
|
35
|
Abstract
Analysis of cellular DNA content and measurement of pulse-labeled newly replicated DNA by flow cytometry are useful techniques for cell cycle studies. In this chapter, we describe the protocols for cell cycle synchronization of mammalian cells, including time course designs and consideration of cell types to achieve successful experiments, along with the methods for detection of DNA. Some selected applications dealing with siRNA-mediated knockdown are also presented.
Collapse
|
36
|
Uzunova SD, Zarkov AS, Ivanova AM, Stoynov SS, Nedelcheva-Veleva MN. The subunits of the S-phase checkpoint complex Mrc1/Tof1/Csm3: dynamics and interdependence. Cell Div 2014; 9:4. [PMID: 25379053 PMCID: PMC4221646 DOI: 10.1186/1747-1028-9-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Accepted: 10/17/2014] [Indexed: 01/22/2023] Open
Abstract
Background The S-phase checkpoint aims to prevent cells from generation of extensive single-stranded DNA that predisposes to genome instability. The S. cerevisiae complex Tof1/Csm3/Mrc1 acts to restrain the replicative MCM helicase when DNA synthesis is prohibited. Keeping the replication machinery intact allows restart of the replication fork when the block is relieved. Although the subunits of the Tof1/Csm3/Mrc1 complex are well studied, the impact of every single subunit on the triple complex formation and function needs to be established. Findings This work studies the cellular localization and the chromatin binding of GFP-tagged subunits when the complex is intact and when a subunit is missing. We demonstrate that the complex is formed in cell nucleus, not the cytoplasm, as Tof1, Csm3 and Mrc1 enter the nucleus independently from one another. Via in situ chromatin binding assay we show that a Tof1-Csm3 dimer formation and chromatin binding is required to ensure the attachment of Mrc1 to chromatin. Our study indicates that the translocation into the nucleus is not the process to regulate the timing of chromatin association of Mrc1. We also studied the nuclear behavior of Mrc1 subunit in the process of adaptation to the presence hydroxyurea. Our results indicate that after prolonged HU incubation, cells bypass the S-phase checkpoint and proceed throughout the cell cycle. This process is accompanied by Mrc1 chromatin detachment and Rad53 dephosphorylation. Conclusions In S. cerevisiae the subunits of the S-phase checkpoint complex Mrc1/Tof1/Csm3 independently enter the cell nucleus, where a Tof1-Csm3 dimer is formed to ensure the chromatin binding of Mrc1 and favor DNA replication and S-phase checkpoint fork arrest. In the process of adaptation to the presence of hydroxyurea Mrc1 is detached from chromatin and Rad53 checkpoint activity is diminished in order to allow S-phase checkpoint escape and completion of the cell cycle.
Collapse
Affiliation(s)
- Sonya Dimitrova Uzunova
- Institute of Molecular Biology "Roumen Tsanev", Bulgarian Academy of Sciences, 21 "Acad. George Bonchev" Str., 1113 Sofia, Bulgaria
| | - Alexander Stefanov Zarkov
- Institute of Molecular Biology "Roumen Tsanev", Bulgarian Academy of Sciences, 21 "Acad. George Bonchev" Str., 1113 Sofia, Bulgaria
| | - Anna Marianova Ivanova
- Institute of Molecular Biology "Roumen Tsanev", Bulgarian Academy of Sciences, 21 "Acad. George Bonchev" Str., 1113 Sofia, Bulgaria
| | - Stoyno Stefanov Stoynov
- Institute of Molecular Biology "Roumen Tsanev", Bulgarian Academy of Sciences, 21 "Acad. George Bonchev" Str., 1113 Sofia, Bulgaria
| | | |
Collapse
|
37
|
Witosch J, Wolf E, Mizuno N. Architecture and ssDNA interaction of the Timeless-Tipin-RPA complex. Nucleic Acids Res 2014; 42:12912-27. [PMID: 25348395 PMCID: PMC4227788 DOI: 10.1093/nar/gku960] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
The Timeless-Tipin (Tim-Tipin) complex, also referred to as the fork protection complex, is involved in coordination of DNA replication. Tim-Tipin is suggested to be recruited to replication forks via Replication Protein A (RPA) but details of the interaction are unknown. Here, using cryo-EM and biochemical methods, we characterized complex formation of Tim-Tipin, RPA and single-stranded DNA (ssDNA). Tim-Tipin and RPA form a 258 kDa complex with a 1:1:1 stoichiometry. The cryo-EM 3D reconstruction revealed a globular architecture of the Tim-Tipin-RPA complex with a ring-like and a U-shaped domain covered by a RPA lid. Interestingly, RPA in the complex adopts a horse shoe-like shape resembling its conformation in the presence of long ssDNA (>30 nucleotides). Furthermore, the recruitment of the Tim-Tipin-RPA complex to ssDNA is modulated by the RPA conformation and requires RPA to be in the more compact 30 nt ssDNA binding mode. The dynamic formation and disruption of the Tim-Tipin-RPA-ssDNA complex implicates the RPA-based recruitment of Tim-Tipin to the replication fork.
Collapse
Affiliation(s)
- Justine Witosch
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Eva Wolf
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany Department of Physiological Chemistry and Center For Integrated Protein Science Munich (CIPSM), Butenandt Institute, Ludwig Maximilians University of Munich, Butenandtstrasse 5, 81377 Munich, Germany Institut für allgemeine Botanik, Johannes Gutenberg-University, Johannes-von-Müller-Weg 6, 55128 Mainz, Germany and Institute of Molecular Biology (IMB), Mainz, Germany
| | - Naoko Mizuno
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| |
Collapse
|
38
|
Abstract
Cell-cycle checkpoints are generally global in nature: one unattached kinetochore prevents the segregation of all chromosomes; stalled replication forks inhibit late origin firing throughout the genome. A potential exception to this rule is the regulation of replication fork progression by the S-phase DNA damage checkpoint. In this case, it is possible that the checkpoint is global, and it slows all replication forks in the genome. However, it is also possible that the checkpoint acts locally at sites of DNA damage, and only slows those forks that encounter DNA damage. Whether the checkpoint regulates forks globally or locally has important mechanistic implications for how replication forks deal with damaged DNA during S-phase.
Collapse
|
39
|
Feldkamp MD, Mason AC, Eichman BF, Chazin WJ. Structural analysis of replication protein A recruitment of the DNA damage response protein SMARCAL1. Biochemistry 2014; 53:3052-61. [PMID: 24730652 PMCID: PMC4020579 DOI: 10.1021/bi500252w] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
![]()
SWI/SNF-related,
matrix-associated, actin-dependent regulator of
chromatin, subfamily A-like1 (SMARCAL1) is a recently identified DNA
damage response protein involved in remodeling stalled replication
forks. The eukaryotic single-strand DNA binding protein replication
protein A (RPA) recruits SMARCAL1 to stalled forks in vivo and facilitates regression of forks containing leading strand gaps.
Both activities are mediated by a direct interaction between an RPA
binding motif (RBM) at the N-terminus of SMARCAL1 and the C-terminal
winged-helix domain of the RPA 32 kDa subunit (RPA32C). Here we report
a biophysical and structural characterization of the SMARCAL1–RPA
interaction. Isothermal titration calorimetry and circular dichroism
spectroscopy revealed that RPA32C binds SMARCAL1-RBM with a Kd of 2.5 μM and induces a disorder-to-helix
transition. The crystal structure of RPA32C was refined to 1.4 Å
resolution, and the SMARCAL1-RBM binding site was mapped on the structure
on the basis of nuclear magnetic resonance chemical shift perturbations.
Conservation of the interaction surface to other RBM-containing proteins
allowed construction of a model for the RPA32C/SMARCAL1-RBM complex.
The implications of our results are discussed with respect to the
recruitment of SMARCAL1 and other DNA damage response and repair proteins
to stalled replication forks.
Collapse
Affiliation(s)
- Michael D Feldkamp
- Department of Biochemistry, ‡Department of Biological Sciences, §Department of Chemistry, and ∥Center for Structural Biology, Vanderbilt University , Nashville, Tennessee 37232, United States
| | | | | | | |
Collapse
|
40
|
Hosono Y, Abe T, Higuchi M, Kajii K, Sakuraba S, Tada S, Enomoto T, Seki M. Tipin functions in the protection against topoisomerase I inhibitor. J Biol Chem 2014; 289:11374-11384. [PMID: 24573676 DOI: 10.1074/jbc.m113.531707] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The replication fork temporarily stalls when encountering an obstacle on the DNA, and replication resumes after the barrier is removed. Simultaneously, activation of the replication checkpoint delays the progression of S phase and inhibits late origin firing. Camptothecin (CPT), a topoisomerase I (Top1) inhibitor, acts as a DNA replication barrier by inducing the covalent retention of Top1 on DNA. The Timeless-Tipin complex, a component of the replication fork machinery, plays a role in replication checkpoint activation and stabilization of the replication fork. However, the role of the Timeless-Tipin complex in overcoming the CPT-induced replication block remains elusive. Here, we generated viable TIPIN gene knock-out (KO) DT40 cells showing delayed S phase progression and increased cell death. TIPIN KO cells were hypersensitive to CPT. However, homologous recombination and replication checkpoint were activated normally, whereas DNA synthesis activity was markedly decreased in CPT-treated TIPIN KO cells. Proteasome-dependent degradation of chromatin-bound Top1 was induced in TIPIN KO cells upon CPT treatment, and pretreatment with aphidicolin, a DNA polymerase inhibitor, suppressed both CPT sensitivity and Top1 degradation. Taken together, our data indicate that replication forks formed without Tipin may collide at a high rate with Top1 retained on DNA by CPT treatment, leading to CPT hypersensitivity and Top1 degradation in TIPIN KO cells.
Collapse
Affiliation(s)
- Yoshifumi Hosono
- Molecular Cell Biology Laboratory, Graduate School of Pharmaceutical Sciences, Tohoku University, Aoba 6-3, Aramaki, Aoba-ku, Sendai 980-8578, Japan
| | - Takuya Abe
- Instituto FIRC di Oncologia Molecolare (IFOM), Fondazione Italiana per la Ricerca sul Cancro (FIRC) Institute for Molecular Oncology Foundation, IFOM-Istituto Europeo di Oncologia Campus, Via Adamello 16, 20139 Milan, Italy
| | - Masato Higuchi
- Molecular Cell Biology Laboratory, Graduate School of Pharmaceutical Sciences, Tohoku University, Aoba 6-3, Aramaki, Aoba-ku, Sendai 980-8578, Japan
| | - Kosa Kajii
- Department of Biochemistry, Tohoku Pharmaceutical University, 4-4-1 Komatsushima, Aoba-ku, Sendai, Miyagi 981-8558, Japan
| | - Shuichi Sakuraba
- Molecular Cell Biology Laboratory, Graduate School of Pharmaceutical Sciences, Tohoku University, Aoba 6-3, Aramaki, Aoba-ku, Sendai 980-8578, Japan
| | - Shusuke Tada
- Faculty of Pharmaceutical Sciences, Teikyo Heisei University, 4-21-2 Nakano, Nakano-ku, Tokyo 164-8530, Japan, and
| | - Takemi Enomoto
- Molecular Cell Biology Laboratory, Research Institute of Pharmaceutical Sciences, Faculty of Pharmacy, Musashino University, 1-1-20 Shinmachi, Nishitokyo-shi, Tokyo 202-8585, Japan
| | - Masayuki Seki
- Department of Biochemistry, Tohoku Pharmaceutical University, 4-4-1 Komatsushima, Aoba-ku, Sendai, Miyagi 981-8558, Japan,.
| |
Collapse
|
41
|
Kang TH, Leem SH. Modulation of ATR-mediated DNA damage checkpoint response by cryptochrome 1. Nucleic Acids Res 2014; 42:4427-34. [PMID: 24489120 PMCID: PMC3985666 DOI: 10.1093/nar/gku094] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Mammalian cryptochromes (Crys) are essential circadian clock factors implicated in diverse clock-independent physiological functions, including DNA damage responses. Here we show that Cry1 modulates the ATR-mediated DNA damage checkpoint (DDC) response by interacting with Timeless (Tim) in a time-of-day-dependent manner. The DDC capacity in response to UV irradiation showed a circadian rhythm. Interestingly, clock-deficient Cry1 and Cry2 double knockout (CryDKO) cells retained substantial DDC capacity compared with clock-proficient wild-type cells, although the Cry1-modulated oscillation of the DDC capacity was abolished in CryDKO cells. We found temporal interaction of Cry1 and Tim in the nucleus. When Cry1 was expressed in the nucleus, it was critical for circadian ATR activity. We regenerated rhythmic DDC responses by ectopically expressing Cry1 in CryDKO cells. In addition, we also investigated the DDC capacity in the liver of mice that were intraperitoneally injected with cisplatin at different circadian times (CT). When mice were injected at CT20, about 2-fold higher expression of phosphorylated minichromosome maintenance protein 2 (p-MCM2) was detected compared with mice injected at CT08, which consequently affected the removal rate of cisplatin-DNA adducts from genomic DNA. Taken together, our data demonstrate the intimate interaction between the circadian clock and the DDC system during genotoxic stress in clock-ticking cells.
Collapse
Affiliation(s)
- Tae-Hong Kang
- Department of Biological Science, Dong-A University, Hadan2-dong, Saha-gu, Busan 604-714, South Korea
| | | |
Collapse
|
42
|
Interplay between the cell cycle and double-strand break response in mammalian cells. Methods Mol Biol 2014; 1170:41-59. [PMID: 24906308 DOI: 10.1007/978-1-4939-0888-2_3] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
The cell cycle is intimately associated with the ability of cells to sense and respond to and repair DNA damage. Understanding how cell cycle progression, particularly DNA replication and cell division, are regulated and how DNA damage can affect these processes has been the subject of intense research. Recent evidence suggests that the repair of DNA damage is regulated by the cell cycle, and that cell cycle factors are closely associated with repair factors and participate in cellular decisions regarding how to respond to and repair damage. Precise regulation of cell cycle progression in the presence of DNA damage is essential to maintain genomic stability and avoid the accumulation of chromosomal aberrations that can promote tumor formation. In this review, we discuss the current understanding of how mammalian cells induce cell cycle checkpoints in response to DNA double-strand breaks. In addition, we discuss how cell cycle factors modulate DNA repair pathways to facilitate proper repair of DNA lesions.
Collapse
|
43
|
Mao Y, Fu A, Leaderer D, Zheng T, Chen K, Zhu Y. Potential cancer-related role of circadian gene TIMELESS suggested by expression profiling and in vitro analyses. BMC Cancer 2013; 13:498. [PMID: 24161199 PMCID: PMC3924353 DOI: 10.1186/1471-2407-13-498] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2013] [Accepted: 10/04/2013] [Indexed: 02/08/2023] Open
Abstract
Background The circadian clock and cell cycle are two global regulatory systems that have pervasive behavioral and physiological effects on eukaryotic cells, and both play a role in cancer development. Recent studies have indicated that the circadian and cell cycle regulator, TIMELESS, may serve as a molecular bridge between these two regulatory systems. Methods To assess the role of TIMELESS in tumorigenesis, we analyzed TIMELESS expression data from publically accessible online databases. A loss-of-function analysis was then performed using TIMELESS-targeting siRNA oligos followed by a whole-genome expression microarray and network analysis. We further tested the effect of TIMELESS down-regulation on cell proliferation rates of a breast and cervical cancer cell line, as suggested by the results of our network analysis. Results TIMELESS was found to be frequently overexpressed in different tumor types compared to normal controls. Elevated expression of TIMELESS was significantly associated with more advanced tumor stage and poorer breast cancer prognosis. We identified a cancer-relevant network of transcripts with altered expression following TIMELESS knockdown which contained many genes with known functions in cancer development and progression. Furthermore, we observed that TIMELESS knockdown significantly decreased cell proliferation rate. Conclusions Our results suggest a potential role for TIMELESS in tumorigenesis, which warrants further investigation of TIMELESS expression as a potential biomarker of cancer susceptibility and prognostic outcome.
Collapse
Affiliation(s)
| | | | | | | | | | - Yong Zhu
- Department of Environmental Health Sciences, Yale School of Public Health, New Haven, CT 06520, USA.
| |
Collapse
|
44
|
Sirbu BM, Cortez D. DNA damage response: three levels of DNA repair regulation. Cold Spring Harb Perspect Biol 2013; 5:a012724. [PMID: 23813586 DOI: 10.1101/cshperspect.a012724] [Citation(s) in RCA: 174] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Genome integrity is challenged by DNA damage from both endogenous and environmental sources. This damage must be repaired to allow both RNA and DNA polymerases to accurately read and duplicate the information in the genome. Multiple repair enzymes scan the DNA for problems, remove the offending damage, and restore the DNA duplex. These repair mechanisms are regulated by DNA damage response kinases including DNA-PKcs, ATM, and ATR that are activated at DNA lesions. These kinases improve the efficiency of DNA repair by phosphorylating repair proteins to modify their activities, by initiating a complex series of changes in the local chromatin structure near the damage site, and by altering the overall cellular environment to make it more conducive to repair. In this review, we focus on these three levels of regulation to illustrate how the DNA damage kinases promote efficient repair to maintain genome integrity and prevent disease.
Collapse
Affiliation(s)
- Bianca M Sirbu
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37027, USA
| | | |
Collapse
|
45
|
O’Reilly LP, Zhang X, Smithgall TE. Individual Src-family tyrosine kinases direct the degradation or protection of the clock protein Timeless via differential ubiquitylation. Cell Signal 2013; 25:860-6. [PMID: 23266470 PMCID: PMC3595377 DOI: 10.1016/j.cellsig.2012.12.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2012] [Revised: 12/05/2012] [Accepted: 12/17/2012] [Indexed: 01/10/2023]
Abstract
Timeless was originally identified in Drosophila as an essential component of circadian cycle regulation, where its function is tightly controlled at the protein level by tyrosine phosphorylation and subsequent degradation. In mammals, Timeless has also been implicated in circadian rhythms as well as cell cycle control and embryonic development. Here we report that mammalian Timeless is an SH3 domain-binding protein and substrate for several members of the Src protein-tyrosine kinase family, including Fyn, Hck, c-Src and c-Yes. Co-expression of Tim with Fyn or Hck was followed by ubiquitylation and subsequent degradation in human 293T cells. While c-Src and c-Yes also promoted Tim ubiquitylation, in this case ubiquitylation correlated with Tim protein accumulation rather than degradation. Both c-Src and c-Yes selectively promoted modification of Tim through Lys63-linked polyubiquitin, which may explain the differential effects on Tim protein turnover. These data show distinct and opposing roles for individual Src-family members in the regulation of Tim protein levels, suggesting a unique mechanism for the regulation of Tim function in mammals.
Collapse
Affiliation(s)
- Linda P. O’Reilly
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Xiong Zhang
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Thomas E. Smithgall
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| |
Collapse
|
46
|
Ashton NW, Bolderson E, Cubeddu L, O'Byrne KJ, Richard DJ. Human single-stranded DNA binding proteins are essential for maintaining genomic stability. BMC Mol Biol 2013; 14:9. [PMID: 23548139 PMCID: PMC3626794 DOI: 10.1186/1471-2199-14-9] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Accepted: 03/20/2013] [Indexed: 12/25/2022] Open
Abstract
The double-stranded conformation of cellular DNA is a central aspect of DNA stabilisation and protection. The helix preserves the genetic code against chemical and enzymatic degradation, metabolic activation, and formation of secondary structures. However, there are various instances where single-stranded DNA is exposed, such as during replication or transcription, in the synthesis of chromosome ends, and following DNA damage. In these instances, single-stranded DNA binding proteins are essential for the sequestration and processing of single-stranded DNA. In order to bind single-stranded DNA, these proteins utilise a characteristic and evolutionary conserved single-stranded DNA-binding domain, the oligonucleotide/oligosaccharide-binding (OB)-fold. In the current review we discuss a subset of these proteins involved in the direct maintenance of genomic stability, an important cellular process in the conservation of cellular viability and prevention of malignant transformation. We discuss the central roles of single-stranded DNA binding proteins from the OB-fold domain family in DNA replication, the restart of stalled replication forks, DNA damage repair, cell cycle-checkpoint activation, and telomere maintenance.
Collapse
Affiliation(s)
- Nicholas W Ashton
- Genome Stability Laboratory, Cancer and Ageing Research Program, Institute of Health and Biomedical Innovation, Translational Research Institute, Queensland University of Technology, Woolloongabba, Queensland, 4102, Australia
| | | | | | | | | |
Collapse
|
47
|
Aria V, De Felice M, Di Perna R, Uno S, Masai H, Syväoja JE, van Loon B, Hübscher U, Pisani FM. The human Tim-Tipin complex interacts directly with DNA polymerase epsilon and stimulates its synthetic activity. J Biol Chem 2013; 288:12742-52. [PMID: 23511638 DOI: 10.1074/jbc.m112.398073] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The Tim-Tipin complex plays an important role in the S phase checkpoint and replication fork stability in metazoans, but the molecular mechanism underlying its biological function is poorly understood. Here, we present evidence that the recombinant human Tim-Tipin complex (and Tim alone) markedly enhances the synthetic activity of DNA polymerase ε. In contrast, no significant effect on the synthetic ability of human DNA polymerase α and δ by Tim-Tipin was observed. Surface plasmon resonance measurements and co-immunoprecipitation experiments revealed that recombinant DNA polymerase ε directly interacts with either Tim or Tipin. In addition, the results of DNA band shift assays suggest that the Tim-Tipin complex (or Tim alone) is able to associate with DNA polymerase ε bound to a 40-/80-mer DNA ligand. Our results are discussed in view of the molecular dynamics at the human DNA replication fork.
Collapse
Affiliation(s)
- Valentina Aria
- Istituto di Biochimica delle Proteine, Consiglio Nazionale delle Ricerche, Via P. Castellino 111, 80131 Naples, Italy
| | | | | | | | | | | | | | | | | |
Collapse
|
48
|
Human Tim-Tipin complex affects the biochemical properties of the replicative DNA helicase and DNA polymerases. Proc Natl Acad Sci U S A 2013; 110:2523-7. [PMID: 23359676 DOI: 10.1073/pnas.1222494110] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Tim (Timeless) and Tipin (Tim-interacting protein) form a stable heterodimeric complex that influences checkpoint responses and replication fork progression. We report that the Tim-Tipin complex interacts with essential replication fork proteins and affects their biochemical properties. The Tim-Tipin complex, reconstituted and purified using the baculovirus expression system, interacts directly with Mcm complexes and inhibits the single-stranded DNA-dependent ATPase activities of the Mcm2-7 and Mcm4/6/7 complexes, the DNA unwinding activity of the Mcm4/6/7 complex, and the DNA unwinding and ATPase activity of Cdc45-Mcm2-7-GINS complex, the presumed replicative DNA helicase in eukaryotes. Although stable interactions between Tim-Tipin and DNA polymerases (pols) were not observed in immunoprecipitation experiments with purified proteins, Tim was shown to interact with DNA pols α, δ, and ε in cells. Furthermore, the Tim-Tipin complex significantly stimulated the pol activities of DNA pols α, δ, and ε in vitro. The effects of Tim-Tipin on the catalytic activities of the Mcm complexes and DNA pols are mediated by the Tim protein alone, and distinct regions of the Tim protein are responsible for the inhibition of Mcm complex activities and stimulation of DNA pols. These results suggest that the Tim-Tipin complex might play a role in coupling DNA unwinding and DNA synthesis by directly affecting the catalytic activities of replication fork proteins.
Collapse
|
49
|
Roseaulin LC, Noguchi C, Martinez E, Ziegler MA, Toda T, Noguchi E. Coordinated degradation of replisome components ensures genome stability upon replication stress in the absence of the replication fork protection complex. PLoS Genet 2013; 9:e1003213. [PMID: 23349636 PMCID: PMC3547854 DOI: 10.1371/journal.pgen.1003213] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2011] [Accepted: 11/15/2012] [Indexed: 11/18/2022] Open
Abstract
The stabilization of the replisome complex is essential in order to achieve highly processive DNA replication and preserve genomic integrity. Conversely, it would also be advantageous for the cell to abrogate replisome functions to prevent inappropriate replication when fork progression is adversely perturbed. However, such mechanisms remain elusive. Here we report that replicative DNA polymerases and helicases, the major components of the replisome, are degraded in concert in the absence of Swi1, a subunit of the replication fork protection complex. In sharp contrast, ORC and PCNA, which are also required for DNA replication, were stably maintained. We demonstrate that this degradation of DNA polymerases and helicases is dependent on the ubiquitin-proteasome system, in which the SCF(Pof3) ubiquitin ligase is involved. Consistently, we show that Pof3 interacts with DNA polymerase ε. Remarkably, forced accumulation of replisome components leads to abnormal DNA replication and mitotic catastrophes in the absence of Swi1. Swi1 is known to prevent fork collapse at natural replication block sites throughout the genome. Therefore, our results suggest that the cell elicits a program to degrade replisomes upon replication stress in the absence of Swi1. We also suggest that this program prevents inappropriate duplication of the genome, which in turn contributes to the preservation of genomic integrity.
Collapse
Affiliation(s)
- Laura C. Roseaulin
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Chiaki Noguchi
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Esteban Martinez
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Melissa A. Ziegler
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Takashi Toda
- Laboratory of Cell Regulation, Cancer Research UK, London Research Institute, Lincoln's Inn Field Laboratories, London, United Kingdom
| | - Eishi Noguchi
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, Pennsylvania, United States of America
| |
Collapse
|
50
|
Abstract
The eukaryotic cell replicates its chromosomal DNA with almost absolute fidelity in the course of every cell cycle. This accomplishment is remarkable considering that the conditions for DNA replication are rarely ideal. The replication machinery encounters a variety of obstacles on the chromosome, including damaged template DNA. In addition, a number of chromosome regions are considered to be difficult to replicate owing to DNA secondary structures and DNA binding proteins required for various transactions on the chromosome. Under these conditions, replication forks stall or break, posing grave threats to genomic integrity. How does the cell combat such stressful conditions during DNA replication? The replication fork protection complex (FPC) may help answer this question. Recent studies have demonstrated that the FPC is required for the smooth passage of replication forks at difficult-to-replicate genomic regions and plays a critical role in coordinating multiple genome maintenance processes at the replication fork.
Collapse
Affiliation(s)
- Adam R. Leman
- Department of Biochemistry and Molecular Biology; Drexel University College of Medicine; Philadelphia, PA USA
| | - Eishi Noguchi
- Department of Biochemistry and Molecular Biology; Drexel University College of Medicine; Philadelphia, PA USA
| |
Collapse
|