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Oikawa T, Hasegawa J, Handa H, Ohnishi N, Onodera Y, Hashimoto A, Sasaki J, Sasaki T, Ueda K, Sabe H. p53 ensures the normal behavior and modification of G1/S-specific histone H3.1 in the nucleus. Life Sci Alliance 2024; 7:e202402835. [PMID: 38906678 PMCID: PMC11192845 DOI: 10.26508/lsa.202402835] [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: 05/22/2024] [Revised: 06/05/2024] [Accepted: 06/06/2024] [Indexed: 06/23/2024] Open
Abstract
H3.1 histone is predominantly synthesized and enters the nucleus during the G1/S phase of the cell cycle, as a new component of duplicating nucleosomes. Here, we found that p53 is necessary to secure the normal behavior and modification of H3.1 in the nucleus during the G1/S phase, in which p53 increases C-terminal domain nuclear envelope phosphatase 1 (CTDNEP1) levels and decreases enhancer of zeste homolog 2 (EZH2) levels in the H3.1 interactome. In the absence of p53, H3.1 molecules tended to be tethered at or near the nuclear envelope (NE), where they were predominantly trimethylated at lysine 27 (H3K27me3) by EZH2, without forming nucleosomes. This accumulation was likely caused by the high affinity of H3.1 toward phosphatidic acid (PA). p53 reduced nuclear PA levels by increasing levels of CTDNEP1, which activates lipin to convert PA into diacylglycerol. We moreover found that the cytosolic H3 chaperone HSC70 attenuates the H3.1-PA interaction, and our molecular imaging analyses suggested that H3.1 may be anchored around the NE after their nuclear entry. Our results expand our knowledge of p53 function in regulation of the nuclear behavior of H3.1 during the G1/S phase, in which p53 may primarily target nuclear PA and EZH2.
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Affiliation(s)
- Tsukasa Oikawa
- https://ror.org/02e16g702 Department of Molecular Biology, Graduate School of Medicine, Hokkaido University, Sapporo, Japan
| | - Junya Hasegawa
- Department of Biochemical Pathophysiology/Lipid Biology, Medical Research Institute, Tokyo Medical and Dental University, Bunkyo-ku, Japan
| | - Haruka Handa
- https://ror.org/02e16g702 Department of Molecular Biology, Graduate School of Medicine, Hokkaido University, Sapporo, Japan
| | - Naomi Ohnishi
- Cancer Proteomics Group, Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Koto-ku, Japan
| | - Yasuhito Onodera
- https://ror.org/02e16g702 Department of Molecular Biology, Graduate School of Medicine, Hokkaido University, Sapporo, Japan
- https://ror.org/02e16g702 Global Center for Biomedical Science and Engineering, Graduate School of Medicine, Hokkaido University, Sapporo, Japan
| | - Ari Hashimoto
- https://ror.org/02e16g702 Department of Molecular Biology, Graduate School of Medicine, Hokkaido University, Sapporo, Japan
| | - Junko Sasaki
- Department of Biochemical Pathophysiology/Lipid Biology, Medical Research Institute, Tokyo Medical and Dental University, Bunkyo-ku, Japan
| | - Takehiko Sasaki
- Department of Biochemical Pathophysiology/Lipid Biology, Medical Research Institute, Tokyo Medical and Dental University, Bunkyo-ku, Japan
| | - Koji Ueda
- Cancer Proteomics Group, Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Koto-ku, Japan
| | - Hisataka Sabe
- https://ror.org/02e16g702 Department of Molecular Biology, Graduate School of Medicine, Hokkaido University, Sapporo, Japan
- https://ror.org/02e16g702 Institute for Genetic Medicine, Hokkaido University, Sapporo, Japan
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2
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Barreto-Galvez A, Niljikar M, Gagliardi J, Zhang R, Kumar V, Juruwala A, Pradeep A, Shaikh A, Tiwari P, Sharma K, Gerhardt J, Cao J, Kataoka K, Durbin A, Qi J, Ye BH, Madireddy A. Acetyl transferase EP300 deficiency leads to chronic replication stress mediated by defective fork protection at stalled replication forks. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.29.538781. [PMID: 37163075 PMCID: PMC10168362 DOI: 10.1101/2023.04.29.538781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Mutations in the epigenetic regulator and global transcriptional activator, E1A binding protein (EP300), is being increasingly reported in aggressive hematological malignancies including adult T-cell leukemia/lymphoma (ATLL). However, the mechanistic contribution of EP300 dysregulation to cancer initiation and progression are currently unknown. Independent inhibition of EP300 in human cells results in the differential expression of genes involved in regulating the cell cycle, DNA replication and DNA damage response. Nevertheless, specific function played by EP300 in DNA replication initiation, progression and replication fork integrity has not been studied. Here, using ATLL cells as a model to study EP300 deficiency and an p300-selective PROTAC degrader, degrader as a pharmacologic tool, we reveal that EP300-mutated cells display prolonged cell cycle kinetics, due to pronounced dysregulations in DNA replication dynamics leading to persistent genomic instability. Aberrant DNA replication in EP300-mutated cells is characterized by elevated replication origin firing due to increased replisome pausing genome-wide. We demonstrate that EP300 deficiency results in nucleolytic degradation of nascently synthesized DNA at stalled forks due to a prominent defect in fork stabilization and protection. This in turn results in the accumulation of single stranded DNA gaps at collapsed replication forks, in EP300-deficient cells. Inhibition of Mre11 nuclease rescues the ssDNA accumulation indicating a dysregulation in downstream mechanisms that restrain nuclease activity at stalled forks. Importantly, we find that the absence of EP300 results in decreased expression of BRCA2 protein expression and a dependency on POLD3-mediated error-prone replication restart mechanisms. The overall S-phase abnormalities observed lead to under-replicated DNA in G2/M that instigates mitotic DNA synthesis. This in turn is associated with mitotic segregation defects characterized by elevated micronuclei formation, accumulation of cytosolic DNA and transmission of unrepaired inherited DNA lesions in the subsequent G1-phase in EP300-deficient cells. We demonstrate that the DNA replication dynamics of EP300-mutated cells ATLL cells recapitulate features of BRCA-deficient cancers. Altogether these results suggest that mutations in EP300 cause chronic DNA replication stress and defective replication fork restart results in persistent genomic instability that underlie aggressive chemo-resistant tumorigenesis in humans.
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3
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Human cytomegalovirus hijacks host stress response fueling replication stress and genome instability. Cell Death Differ 2022; 29:1639-1653. [PMID: 35194187 PMCID: PMC9346009 DOI: 10.1038/s41418-022-00953-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 02/03/2022] [Accepted: 02/03/2022] [Indexed: 01/01/2023] Open
Abstract
Viral infections enhance cancer risk and threaten host genome integrity. Although human cytomegalovirus (HCMV) proteins have been detected in a wide spectrum of human malignancies and HCMV infections have been implicated in tumorigenesis, the underlying mechanisms remain poorly understood. Here, we employed a range of experimental approaches, including single-molecule DNA fiber analysis, and showed that infection by any of the four commonly used HCMV strains: AD169, Towne, TB40E or VR1814 induced replication stress (RS), as documented by host-cell replication fork asymmetry and formation of 53BP1 foci. The HCMV-evoked RS triggered an ensuing host DNA damage response (DDR) and chromosomal instability in both permissive and non-permissive human cells, the latter being particularly relevant in the context of tumorigenesis, as such cells can survive and proliferate after HCMV infection. The viral major immediate early enhancer and promoter (MIEP) that controls expression of the viral genes IE72 (IE-1) and IE86 (IE-2), contains transcription-factor binding sites shared by promoters of cellular stress-response genes. We found that DNA damaging insults, including those relevant for cancer therapy, enhanced IE72/86 expression. Thus, MIEP has been evolutionary shaped to exploit host DDR. Ectopically expressed IE72 and IE86 also induced RS and increased genomic instability. Of clinical relevance, we show that undergoing standard-of-care genotoxic radio-chemotherapy in patients with HCMV-positive glioblastomas correlated with elevated HCMV protein markers after tumor recurrence. Collectively, these results are consistent with our proposed concept of HCMV hijacking transcription-factor binding sites shared with host stress-response genes. We present a model to explain the potential oncomodulatory effects of HCMV infections through enhanced replication stress, subverted DNA damage response and induced genomic instability.
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4
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The human nucleoporin Tpr protects cells from RNA-mediated replication stress. Nat Commun 2021; 12:3937. [PMID: 34168151 PMCID: PMC8225803 DOI: 10.1038/s41467-021-24224-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 06/04/2021] [Indexed: 12/24/2022] Open
Abstract
Although human nucleoporin Tpr is frequently deregulated in cancer, its roles are poorly understood. Here we show that Tpr depletion generates transcription-dependent replication stress, DNA breaks, and genomic instability. DNA fiber assays and electron microscopy visualization of replication intermediates show that Tpr deficient cells exhibit slow and asymmetric replication forks under replication stress. Tpr deficiency evokes enhanced levels of DNA-RNA hybrids. Additionally, complementary proteomic strategies identify a network of Tpr-interacting proteins mediating RNA processing, such as MATR3 and SUGP2, and functional experiments confirm that their depletion trigger cellular phenotypes shared with Tpr deficiency. Mechanistic studies reveal the interplay of Tpr with GANP, a component of the TREX-2 complex. The Tpr-GANP interaction is supported by their shared protein level alterations in a cohort of ovarian carcinomas. Our results reveal links between nucleoporins, DNA transcription and replication, and the existence of a network physically connecting replication forks with transcription, splicing, and mRNA export machinery.
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5
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Krell K, Harijan D, Ganz D, Doll L, Wagenknecht HA. Postsynthetic Modifications of DNA and RNA by Means of Copper-Free Cycloadditions as Bioorthogonal Reactions. Bioconjug Chem 2020; 31:990-1011. [DOI: 10.1021/acs.bioconjchem.0c00072] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Katja Krell
- Karlsruhe Institute of Technology (KIT), Institute for Organic Chemistry, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
| | - Dennis Harijan
- Karlsruhe Institute of Technology (KIT), Institute for Organic Chemistry, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
| | - Dorothée Ganz
- Karlsruhe Institute of Technology (KIT), Institute for Organic Chemistry, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
| | - Larissa Doll
- Karlsruhe Institute of Technology (KIT), Institute for Organic Chemistry, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
| | - Hans-Achim Wagenknecht
- Karlsruhe Institute of Technology (KIT), Institute for Organic Chemistry, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
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6
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Vanzo R, Bartkova J, Merchut-Maya JM, Hall A, Bouchal J, Dyrskjøt L, Frankel LB, Gorgoulis V, Maya-Mendoza A, Jäättelä M, Bartek J. Autophagy role(s) in response to oncogenes and DNA replication stress. Cell Death Differ 2020; 27:1134-1153. [PMID: 31409894 PMCID: PMC7206042 DOI: 10.1038/s41418-019-0403-9] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 07/26/2019] [Accepted: 07/29/2019] [Indexed: 12/12/2022] Open
Abstract
Autophagy is an evolutionarily conserved process that captures aberrant intracellular proteins and/or damaged organelles for delivery to lysosomes, with implications for cellular and organismal homeostasis, aging and diverse pathologies, including cancer. During cancer development, autophagy may play both tumour-supporting and tumour-suppressing roles. Any relationships of autophagy to the established oncogene-induced replication stress (RS) and the ensuing DNA damage response (DDR)-mediated anti-cancer barrier in early tumorigenesis remain to be elucidated. Here, assessing potential links between autophagy, RS and DDR, we found that autophagy is enhanced in both early and advanced stages of human urinary bladder and prostate tumorigenesis. Furthermore, a high-content, single-cell-level microscopy analysis of human cellular models exposed to diverse genotoxic insults showed that autophagy is enhanced in cells that experienced robust DNA damage, independently of the cell-cycle position. Oncogene- and drug-induced RS triggered first DDR and later autophagy. Unexpectedly, genetic inactivation of autophagy resulted in RS, despite cellular retention of functional mitochondria and normal ROS levels. Moreover, recovery from experimentally induced RS required autophagy to support DNA synthesis. Consistently, RS due to the absence of autophagy could be partly alleviated by exogenous supply of deoxynucleosides. Our results highlight the importance of autophagy for DNA synthesis, suggesting that autophagy may support cancer progression, at least in part, by facilitating tumour cell survival and fitness under replication stress, a feature shared by most malignancies. These findings have implications for better understanding of the role of autophagy in tumorigenesis, as well as for attempts to manipulate autophagy as an anti-tumour therapeutic strategy.
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Affiliation(s)
- Riccardo Vanzo
- Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Jirina Bartkova
- Danish Cancer Society Research Center, Copenhagen, Denmark
- Department of Medical Biochemistry and Biophysics, Division of Genome Biology, Science for Life Laboratory, Karolinska Institute, Stockholm, Sweden
| | | | - Arnaldur Hall
- Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Jan Bouchal
- Department of Clinical and Molecular Pathology, Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czech Republic
| | - Lars Dyrskjøt
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Lisa B Frankel
- Danish Cancer Society Research Center, Copenhagen, Denmark
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
| | - Vassilis Gorgoulis
- Department of Histology and Embryology, School of Medicine, National Kapodistrian University of Athens, Athens, Greece
- Biomedical Research Foundation of the Academy of Athens, Athens, Greece
- Faculty Institute of Cancer Sciences, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | | | - Marja Jäättelä
- Danish Cancer Society Research Center, Copenhagen, Denmark.
| | - Jiri Bartek
- Danish Cancer Society Research Center, Copenhagen, Denmark.
- Department of Medical Biochemistry and Biophysics, Division of Genome Biology, Science for Life Laboratory, Karolinska Institute, Stockholm, Sweden.
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7
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Hjorth-Jensen K, Maya-Mendoza A, Dalgaard N, Sigurðsson JO, Bartek J, Iglesias-Gato D, Olsen JV, Flores-Morales A. SPOP promotes transcriptional expression of DNA repair and replication factors to prevent replication stress and genomic instability. Nucleic Acids Res 2019; 46:9484-9495. [PMID: 30124983 PMCID: PMC6182143 DOI: 10.1093/nar/gky719] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 08/04/2018] [Indexed: 12/21/2022] Open
Abstract
Mutations in SPOP, the gene most frequently point-mutated in primary prostate cancer, are associated with a high degree of genomic instability and deficiency in homologous recombination repair of DNA but the underlying mechanisms behind this defect are currently unknown. Here we demonstrate that SPOP knockdown leads to spontaneous replication stress and impaired recovery from replication fork stalling. We show that this is associated with reduced expression of several key DNA repair and replication factors including BRCA2, ATR, CHK1 and RAD51. Consequently, SPOP knockdown impairs RAD51 foci formation and activation of CHK1 in response to replication stress and compromises recovery from replication fork stalling. An SPOP interactome analysis shows that wild type (WT) SPOP but not mutant SPOP associates with multiple proteins involved in transcription, mRNA splicing and export. Consistent with the association of SPOP with transcription, splicing and RNA export complexes, the decreased expression of BRCA2, ATR, CHK1 and RAD51 occurs at the level of transcription.
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Affiliation(s)
- Kim Hjorth-Jensen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Translational Cancer Research Unit, Danish Cancer Society Research Center, Copenhagen, Denmark
| | | | - Nanna Dalgaard
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Translational Cancer Research Unit, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Jón O Sigurðsson
- Novo Nordisk Foundation Center for Protein Research, Department of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jiri Bartek
- Genome Integrity Unit, Danish Cancer Society Research Center, Copenhagen, Denmark.,Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Science for Life Laboratory, Karolinska Institute, Stockholm, Sweden
| | - Diego Iglesias-Gato
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Translational Cancer Research Unit, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Jesper V Olsen
- Novo Nordisk Foundation Center for Protein Research, Department of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Amilcar Flores-Morales
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Translational Cancer Research Unit, Danish Cancer Society Research Center, Copenhagen, Denmark.,Novo Nordisk Foundation Center for Protein Research, Department of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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8
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Young LA, O'Connor LO, de Renty C, Veldman-Jones MH, Dorval T, Wilson Z, Jones DR, Lawson D, Odedra R, Maya-Mendoza A, Reimer C, Bartek J, Lau A, O'Connor MJ. Differential Activity of ATR and WEE1 Inhibitors in a Highly Sensitive Subpopulation of DLBCL Linked to Replication Stress. Cancer Res 2019; 79:3762-3775. [DOI: 10.1158/0008-5472.can-18-2480] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2018] [Revised: 12/23/2018] [Accepted: 05/20/2019] [Indexed: 11/16/2022]
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9
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Ligasová A, Koberna K. DNA Replication: From Radioisotopes to Click Chemistry. Molecules 2018; 23:molecules23113007. [PMID: 30453631 PMCID: PMC6278288 DOI: 10.3390/molecules23113007] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 11/14/2018] [Accepted: 11/15/2018] [Indexed: 12/14/2022] Open
Abstract
The replication of nuclear and mitochondrial DNA are basic processes assuring the doubling of the genetic information of eukaryotic cells. In research of the basic principles of DNA replication, and also in the studies focused on the cell cycle, an important role is played by artificially-prepared nucleoside and nucleotide analogues that serve as markers of newly synthesized DNA. These analogues are incorporated into the DNA during DNA replication, and are subsequently visualized. Several methods are used for their detection, including the highly popular click chemistry. This review aims to provide the readers with basic information about the various possibilities of the detection of replication activity using nucleoside and nucleotide analogues, and to show the strengths and weaknesses of those different detection systems, including click chemistry for microscopic studies.
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Affiliation(s)
- Anna Ligasová
- Faculty of Medicine and Dentistry, Institute of Molecular and Translational Medicine, Palacký University in Olomouc, Hněvotínská 5, 779 00 Olomouc, Czech Republic.
| | - Karel Koberna
- Faculty of Medicine and Dentistry, Institute of Molecular and Translational Medicine, Palacký University in Olomouc, Hněvotínská 5, 779 00 Olomouc, Czech Republic.
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10
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High speed of fork progression induces DNA replication stress and genomic instability. Nature 2018; 559:279-284. [DOI: 10.1038/s41586-018-0261-5] [Citation(s) in RCA: 275] [Impact Index Per Article: 45.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 05/22/2018] [Indexed: 12/27/2022]
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11
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Fesenko DO, Guseinov TO, Lapa SA, Kuznetsova VE, Shershov VE, Spitsyn MA, Nasedkina TV, Zasedatelev AS, Chudinov AV. Substrate Properties of New Fluorescently Labeled Deoxycytidine Triphosphates in Enzymatic Synthesis of DNA with Polymerases of Families A and B. Mol Biol 2018. [DOI: 10.1134/s0026893318030044] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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12
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Zawada Z, Tatar A, Mocilac P, Buděšínský M, Kraus T. Transport of Nucleoside Triphosphates into Cells by Artificial Molecular Transporters. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201801306] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Zbigniew Zawada
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences; Flemingovo nám. 2 166 10 Praha 6 Czech Republic
| | - Ameneh Tatar
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences; Flemingovo nám. 2 166 10 Praha 6 Czech Republic
| | - Pavle Mocilac
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences; Flemingovo nám. 2 166 10 Praha 6 Czech Republic
| | - Miloš Buděšínský
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences; Flemingovo nám. 2 166 10 Praha 6 Czech Republic
| | - Tomáš Kraus
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences; Flemingovo nám. 2 166 10 Praha 6 Czech Republic
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13
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Zawada Z, Tatar A, Mocilac P, Buděšínský M, Kraus T. Transport of Nucleoside Triphosphates into Cells by Artificial Molecular Transporters. Angew Chem Int Ed Engl 2018; 57:9891-9895. [PMID: 29578619 DOI: 10.1002/anie.201801306] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 03/14/2018] [Indexed: 01/18/2023]
Abstract
Chemically modified nucleoside triphosphates (NTPs) are widely exploited as unnatural metabolites in chemical biology and medicinal chemistry. Because anionic NTPs do not permeate cell membranes, their corresponding neutral precursors are employed in cell-based assays. These precursors become active metabolites after enzymatic conversion, which often proceeds insufficiently. Here we show that metabolically-active NTPs can be directly transported into eukaryotic cells and bacteria by the action of designed synthetic nucleoside triphosphate transporters (SNTTs). The transporter is composed of a receptor, which forms a non-covalent complex with a triphosphate anion, and a cell-penetrating agent, which translocates the complex across the plasma membrane. NTP is then released from the complex in the intracellular milieu and accumulates in nuclei and nucleoli in high concentration. The transport of NTPs proceeds rapidly (seconds to minutes) and selectively even in the presence of other organic anions. We demonstrate that this operationally simple and efficient means of transport of fluorescently labelled NTPs into cells can be used for metabolic labeling of DNA in live cells.
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Affiliation(s)
- Zbigniew Zawada
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 166 10, Praha 6, Czech Republic
| | - Ameneh Tatar
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 166 10, Praha 6, Czech Republic
| | - Pavle Mocilac
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 166 10, Praha 6, Czech Republic
| | - Miloš Buděšínský
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 166 10, Praha 6, Czech Republic
| | - Tomáš Kraus
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 166 10, Praha 6, Czech Republic
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14
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Zhao PA, Rivera-Mulia JC, Gilbert DM. Replication Domains: Genome Compartmentalization into Functional Replication Units. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1042:229-257. [DOI: 10.1007/978-981-10-6955-0_11] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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15
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Maya‐Mendoza A, Jackson DA. Labeling DNA Replication Foci to Visualize Chromosome Territories In Vivo. ACTA ACUST UNITED AC 2017. [DOI: 10.1002/cpcb.19] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
| | - Dean A. Jackson
- Systems Microscopy Centre, Faculty of Life Sciences, The University of Manchester Manchester United Kingdom
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16
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Maya-Mendoza A, Ostrakova J, Kosar M, Hall A, Duskova P, Mistrik M, Merchut-Maya JM, Hodny Z, Bartkova J, Christensen C, Bartek J. Myc and Ras oncogenes engage different energy metabolism programs and evoke distinct patterns of oxidative and DNA replication stress. Mol Oncol 2014; 9:601-16. [PMID: 25435281 PMCID: PMC5528704 DOI: 10.1016/j.molonc.2014.11.001] [Citation(s) in RCA: 87] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Revised: 11/03/2014] [Accepted: 11/05/2014] [Indexed: 10/28/2022] Open
Abstract
Both Myc and Ras oncogenes impact cellular metabolism, deregulate redox homeostasis and trigger DNA replication stress (RS) that compromises genomic integrity. However, how are such oncogene-induced effects evoked and temporally related, to what extent are these kinetic parameters shared by Myc and Ras, and how are these cellular changes linked with oncogene-induced cellular senescence in different cell context(s) remain poorly understood. Here, we addressed the above-mentioned open questions by multifaceted comparative analyses of human cellular models with inducible expression of c-Myc and H-RasV12 (Ras), two commonly deregulated oncoproteins operating in a functionally connected signaling network. Our study of DNA replication parameters using the DNA fiber approach and time-course assessment of perturbations in glycolytic flux, oxygen consumption and production of reactive oxygen species (ROS) revealed the following results. First, overabundance of nuclear Myc triggered RS promptly, already after one day of Myc induction, causing slow replication fork progression and fork asymmetry, even before any metabolic changes occurred. In contrast, Ras overexpression initially induced a burst of cell proliferation and increased the speed of replication fork progression. However, after several days of induction Ras caused bioenergetic metabolic changes that correlated with slower DNA replication fork progression and the ensuing cell cycle arrest, gradually leading to senescence. Second, the observed oncogene-induced RS and metabolic alterations were cell-type/context dependent, as shown by comparative analyses of normal human BJ fibroblasts versus U2-OS sarcoma cells. Third, the energy metabolic reprogramming triggered by Ras was more robust compared to impact of Myc. Fourth, the detected oncogene-induced oxidative stress was due to ROS (superoxide) of non-mitochondrial origin and mitochondrial OXPHOS was reduced (Crabtree effect). Overall, our study provides novel insights into oncogene-evoked metabolic reprogramming, replication and oxidative stress, with implications for mechanisms of tumorigenesis and potential targeting of oncogene addiction.
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Affiliation(s)
| | - Jitka Ostrakova
- Danish Cancer Society Research Center, DK-2100 Copenhagen, Denmark
| | - Martin Kosar
- Danish Cancer Society Research Center, DK-2100 Copenhagen, Denmark; Department of Genome Integrity, Institute of Molecular Genetics, v.v.i., Academy of Sciences of the Czech Republic, CZ-142 20 Prague, Czech Republic
| | - Arnaldur Hall
- Danish Cancer Society Research Center, DK-2100 Copenhagen, Denmark
| | - Pavlina Duskova
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University, CZ-775 15 Olomouc, Czech Republic
| | - Martin Mistrik
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University, CZ-775 15 Olomouc, Czech Republic
| | | | - Zdenek Hodny
- Department of Genome Integrity, Institute of Molecular Genetics, v.v.i., Academy of Sciences of the Czech Republic, CZ-142 20 Prague, Czech Republic
| | - Jirina Bartkova
- Danish Cancer Society Research Center, DK-2100 Copenhagen, Denmark
| | | | - Jiri Bartek
- Danish Cancer Society Research Center, DK-2100 Copenhagen, Denmark; Department of Genome Integrity, Institute of Molecular Genetics, v.v.i., Academy of Sciences of the Czech Republic, CZ-142 20 Prague, Czech Republic; Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University, CZ-775 15 Olomouc, Czech Republic.
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Nascent chromatin capture proteomics determines chromatin dynamics during DNA replication and identifies unknown fork components. Nat Cell Biol 2014; 16:281-93. [PMID: 24561620 DOI: 10.1038/ncb2918] [Citation(s) in RCA: 268] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2012] [Accepted: 01/15/2014] [Indexed: 02/07/2023]
Abstract
To maintain genome function and stability, DNA sequence and its organization into chromatin must be duplicated during cell division. Understanding how entire chromosomes are copied remains a major challenge. Here, we use nascent chromatin capture (NCC) to profile chromatin proteome dynamics during replication in human cells. NCC relies on biotin-dUTP labelling of replicating DNA, affinity purification and quantitative proteomics. Comparing nascent chromatin with mature post-replicative chromatin, we provide association dynamics for 3,995 proteins. The replication machinery and 485 chromatin factors such as CAF-1, DNMT1 and SUV39h1 are enriched in nascent chromatin, whereas 170 factors including histone H1, DNMT3, MBD1-3 and PRC1 show delayed association. This correlates with H4K5K12diAc removal and H3K9me1 accumulation, whereas H3K27me3 and H3K9me3 remain unchanged. Finally, we combine NCC enrichment with experimentally derived chromatin probabilities to predict a function in nascent chromatin for 93 uncharacterized proteins, and identify FAM111A as a replication factor required for PCNA loading. Together, this provides an extensive resource to understand genome and epigenome maintenance.
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Boutorine AS, Novopashina DS, Krasheninina OA, Nozeret K, Venyaminova AG. Fluorescent probes for nucleic Acid visualization in fixed and live cells. Molecules 2013; 18:15357-97. [PMID: 24335616 PMCID: PMC6270009 DOI: 10.3390/molecules181215357] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Revised: 11/20/2013] [Accepted: 12/05/2013] [Indexed: 12/13/2022] Open
Abstract
This review analyses the literature concerning non-fluorescent and fluorescent probes for nucleic acid imaging in fixed and living cells from the point of view of their suitability for imaging intracellular native RNA and DNA. Attention is mainly paid to fluorescent probes for fluorescence microscopy imaging. Requirements for the target-binding part and the fluorophore making up the probe are formulated. In the case of native double-stranded DNA, structure-specific and sequence-specific probes are discussed. Among the latest, three classes of dsDNA-targeting molecules are described: (i) sequence-specific peptides and proteins; (ii) triplex-forming oligonucleotides and (iii) polyamide oligo(N-methylpyrrole/N-methylimidazole) minor groove binders. Polyamides seem to be the most promising targeting agents for fluorescent probe design, however, some technical problems remain to be solved, such as the relatively low sequence specificity and the high background fluorescence inside the cells. Several examples of fluorescent probe applications for DNA imaging in fixed and living cells are cited. In the case of intracellular RNA, only modified oligonucleotides can provide such sequence-specific imaging. Several approaches for designing fluorescent probes are considered: linear fluorescent probes based on modified oligonucleotide analogs, molecular beacons, binary fluorescent probes and template-directed reactions with fluorescence probe formation, FRET donor-acceptor pairs, pyrene excimers, aptamers and others. The suitability of all these methods for living cell applications is discussed.
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Affiliation(s)
- Alexandre S. Boutorine
- Muséum National d’Histoire Naturelle, CNRS, UMR 7196, INSERM, U565, 57 rue Cuvier, B.P. 26, Paris Cedex 05, F-75231, France; E-Mail:
| | - Darya S. Novopashina
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences, Lavrentyev Ave., 8, Novosibirsk 630090, Russia; E-Mails: (D.S.N.); (O.A.K.); (A.G.V.)
| | - Olga A. Krasheninina
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences, Lavrentyev Ave., 8, Novosibirsk 630090, Russia; E-Mails: (D.S.N.); (O.A.K.); (A.G.V.)
- Department of Natural Sciences, Novosibirsk State University, Pirogova Str., 2, Novosibirsk 630090, Russia
| | - Karine Nozeret
- Muséum National d’Histoire Naturelle, CNRS, UMR 7196, INSERM, U565, 57 rue Cuvier, B.P. 26, Paris Cedex 05, F-75231, France; E-Mail:
| | - Alya G. Venyaminova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences, Lavrentyev Ave., 8, Novosibirsk 630090, Russia; E-Mails: (D.S.N.); (O.A.K.); (A.G.V.)
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