1
|
Panmanee W, Tran MTH, Seye SN, Strome ED. Altered S-AdenosylMethionine availability impacts dNTP pools in Saccharomyces cerevisiae. Yeast 2024; 41:513-524. [PMID: 38961653 DOI: 10.1002/yea.3973] [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: 10/19/2023] [Revised: 04/30/2024] [Accepted: 06/22/2024] [Indexed: 07/05/2024] Open
Abstract
Saccharomyces cerevisiae has long been used as a model organism to study genome instability. The SAM1 and SAM2 genes encode AdoMet synthetases, which generate S-AdenosylMethionine (AdoMet) from Methionine (Met) and ATP. Previous work from our group has shown that deletions of the SAM1 and SAM2 genes cause changes to AdoMet levels and impact genome instability in opposite manners. AdoMet is a key product of methionine metabolism and the major methyl donor for methylation events of proteins, RNAs, small molecules, and lipids. The methyl cycle is interrelated to the folate cycle which is involved in de novo synthesis of purine and pyrimidine deoxyribonucleotides (dATP, dTTP, dCTP, and dGTP). AdoMet also plays a role in polyamine production, essential for cell growth and used in detoxification of reactive oxygen species (ROS) and maintenance of the redox status in cells. This is also impacted by the methyl cycle's role in production of glutathione, another ROS scavenger and cellular protectant. We show here that sam2∆/sam2∆ cells, previously characterized with lower levels of AdoMet and higher genome instability, have a higher level of each dNTP (except dTTP), contributing to a higher overall dNTP pool level when compared to wildtype. Unchecked, these increased levels can lead to multiple types of DNA damage which could account for the genome instability increases in these cells.
Collapse
Affiliation(s)
- Warunya Panmanee
- Department of Biological Sciences, Northern Kentucky University, Highland Heights, Kentucky, USA
| | - Men T H Tran
- Department of Biological Sciences, Northern Kentucky University, Highland Heights, Kentucky, USA
| | - Serigne N Seye
- Department of Biological Sciences, Northern Kentucky University, Highland Heights, Kentucky, USA
| | - Erin D Strome
- Department of Biological Sciences, Northern Kentucky University, Highland Heights, Kentucky, USA
| |
Collapse
|
2
|
Poliaková Turan M, Riedo R, Medo M, Pozzato C, Friese-Hamim M, Koch JP, Coggins SA, Li Q, Kim B, Albers J, Aebersold DM, Zamboni N, Zimmer Y, Medová M. E2F1-Associated Purine Synthesis Pathway Is a Major Component of the MET-DNA Damage Response Network. CANCER RESEARCH COMMUNICATIONS 2024; 4:1863-1880. [PMID: 38957115 PMCID: PMC11288008 DOI: 10.1158/2767-9764.crc-23-0370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 05/03/2024] [Accepted: 06/25/2024] [Indexed: 07/04/2024]
Abstract
Various lines of investigation support a signaling interphase shared by receptor tyrosine kinases and the DNA damage response. However, the underlying network nodes and their contribution to the maintenance of DNA integrity remain unknown. We explored MET-related metabolic pathways in which interruption compromises proper resolution of DNA damage. Discovery metabolomics combined with transcriptomics identified changes in pathways relevant to DNA repair following MET inhibition (METi). METi by tepotinib was associated with the formation of γH2AX foci and with significant alterations in major metabolic circuits such as glycolysis, gluconeogenesis, and purine, pyrimidine, amino acid, and lipid metabolism. 5'-Phosphoribosyl-N-formylglycinamide, a de novo purine synthesis pathway metabolite, was consistently decreased in in vitro and in vivo MET-dependent models, and METi-related depletion of dNTPs was observed. METi instigated the downregulation of critical purine synthesis enzymes including phosphoribosylglycinamide formyltransferase, which catalyzes 5'-phosphoribosyl-N-formylglycinamide synthesis. Genes encoding these enzymes are regulated through E2F1, whose levels decrease upon METi in MET-driven cells and xenografts. Transient E2F1 overexpression prevented dNTP depletion and the concomitant METi-associated DNA damage in MET-driven cells. We conclude that DNA damage following METi results from dNTP reduction via downregulation of E2F1 and a consequent decline of de novo purine synthesis. SIGNIFICANCE Maintenance of genome stability prevents disease and affiliates with growth factor receptor tyrosine kinases. We identified de novo purine synthesis as a pathway in which key enzymatic players are regulated through MET receptor and whose depletion via MET targeting explains MET inhibition-associated formation of DNA double-strand breaks. The mechanistic importance of MET inhibition-dependent E2F1 downregulation for interference with DNA integrity has translational implications for MET-targeting-based treatment of malignancies.
Collapse
Affiliation(s)
- Michaela Poliaková Turan
- Department of Radiation Oncology, Inselspital Bern University Hospital, Bern, Switzerland.
- Department for BioMedical Research, Radiation Oncology, University of Bern, Bern, Switzerland.
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland.
| | - Rahel Riedo
- Department of Radiation Oncology, Inselspital Bern University Hospital, Bern, Switzerland.
- Department for BioMedical Research, Radiation Oncology, University of Bern, Bern, Switzerland.
| | - Matúš Medo
- Department of Radiation Oncology, Inselspital Bern University Hospital, Bern, Switzerland.
- Department for BioMedical Research, Radiation Oncology, University of Bern, Bern, Switzerland.
| | - Chiara Pozzato
- Department of Radiation Oncology, Inselspital Bern University Hospital, Bern, Switzerland.
- Department for BioMedical Research, Radiation Oncology, University of Bern, Bern, Switzerland.
| | - Manja Friese-Hamim
- Corporate Animal Using Vendor and Vivarium Governance (SQ-AV), Corporate Sustainability, Quality, Trade Compliance (SQ), Animal Affairs (SQ-A), The Healthcare Business of Merck KGaA, Darmstadt, Germany.
| | - Jonas P. Koch
- Department of Radiation Oncology, Inselspital Bern University Hospital, Bern, Switzerland.
- Department for BioMedical Research, Radiation Oncology, University of Bern, Bern, Switzerland.
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland.
| | - Si’Ana A. Coggins
- Center for Drug Discovery, Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia.
| | - Qun Li
- Center for Drug Discovery, Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia.
| | - Baek Kim
- Center for Drug Discovery, Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia.
- College of Pharmacy, Kyung-Hee University, Seoul, South Korea.
| | - Joachim Albers
- Research Unit Oncology, The Healthcare Business of Merck KGaA, Darmstadt, Germany.
| | - Daniel M. Aebersold
- Department of Radiation Oncology, Inselspital Bern University Hospital, Bern, Switzerland.
- Department for BioMedical Research, Radiation Oncology, University of Bern, Bern, Switzerland.
| | - Nicola Zamboni
- Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland.
- PHRT Swiss Multi-Omics Center, Zurich, Switzerland.
| | - Yitzhak Zimmer
- Department of Radiation Oncology, Inselspital Bern University Hospital, Bern, Switzerland.
- Department for BioMedical Research, Radiation Oncology, University of Bern, Bern, Switzerland.
| | - Michaela Medová
- Department of Radiation Oncology, Inselspital Bern University Hospital, Bern, Switzerland.
- Department for BioMedical Research, Radiation Oncology, University of Bern, Bern, Switzerland.
| |
Collapse
|
3
|
Prasad CB, Oo A, Liu Y, Qiu Z, Zhong Y, Li N, Singh D, Xin X, Cho YJ, Li Z, Zhang X, Yan C, Zheng Q, Wang QE, Guo D, Kim B, Zhang J. The thioredoxin system determines CHK1 inhibitor sensitivity via redox-mediated regulation of ribonucleotide reductase activity. Nat Commun 2024; 15:4667. [PMID: 38821952 PMCID: PMC11143221 DOI: 10.1038/s41467-024-48076-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 04/19/2024] [Indexed: 06/02/2024] Open
Abstract
Checkpoint kinase 1 (CHK1) is critical for cell survival under replication stress (RS). CHK1 inhibitors (CHK1i's) in combination with chemotherapy have shown promising results in preclinical studies but have displayed minimal efficacy with substantial toxicity in clinical trials. To explore combinatorial strategies that can overcome these limitations, we perform an unbiased high-throughput screen in a non-small cell lung cancer (NSCLC) cell line and identify thioredoxin1 (Trx1), a major component of the mammalian antioxidant-system, as a determinant of CHK1i sensitivity. We establish a role for redox recycling of RRM1, the larger subunit of ribonucleotide reductase (RNR), and a depletion of the deoxynucleotide pool in this Trx1-mediated CHK1i sensitivity. Further, the TrxR inhibitor auranofin, an approved anti-rheumatoid arthritis drug, shows a synergistic interaction with CHK1i via interruption of the deoxynucleotide pool. Together, we show a pharmacological combination to treat NSCLC that relies on a redox regulatory link between the Trx system and mammalian RNR activity.
Collapse
Affiliation(s)
- Chandra Bhushan Prasad
- Department of Radiation Oncology, James Cancer Hospital and Richard J. Solove Research Institute, The Ohio State University, Columbus, OH, 43210, USA
| | - Adrian Oo
- Center for ViroScience and Cure, Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA, 30322, USA
| | - Yujie Liu
- Department of Radiation Oncology, James Cancer Hospital and Richard J. Solove Research Institute, The Ohio State University, Columbus, OH, 43210, USA
| | - Zhaojun Qiu
- Department of Radiation Oncology, James Cancer Hospital and Richard J. Solove Research Institute, The Ohio State University, Columbus, OH, 43210, USA
| | - Yaogang Zhong
- Department of Radiation Oncology, James Cancer Hospital and Richard J. Solove Research Institute, The Ohio State University, Columbus, OH, 43210, USA
- The Comprehensive Cancer Center, Center for Cancer Metabolism, The Ohio State University, Columbus, OH, 43210, USA
| | - Na Li
- Department of Radiation Oncology, James Cancer Hospital and Richard J. Solove Research Institute, The Ohio State University, Columbus, OH, 43210, USA
| | - Deepika Singh
- Department of Radiation Oncology, James Cancer Hospital and Richard J. Solove Research Institute, The Ohio State University, Columbus, OH, 43210, USA
| | - Xiwen Xin
- The Ohio State University, Columbus, OH, 43210, USA
| | - Young-Jae Cho
- Center for ViroScience and Cure, Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA, 30322, USA
| | - Zaibo Li
- Department of Pathology, The Ohio State University Wexner Medical Center, College of Medicine, Columbus, OH, 43210, USA
| | - Xiaoli Zhang
- Department of Biomedical Informatics, Wexner Medical Center, College of Medicine, The Ohio State University, Columbus, OH, 43210, USA
| | - Chunhong Yan
- Georgia Cancer Center, Augusta University, Augusta, GA, 30912, USA
| | - Qingfei Zheng
- Department of Radiation Oncology, James Cancer Hospital and Richard J. Solove Research Institute, The Ohio State University, Columbus, OH, 43210, USA
- The Comprehensive Cancer Center, Center for Cancer Metabolism, The Ohio State University, Columbus, OH, 43210, USA
| | - Qi-En Wang
- Department of Radiation Oncology, James Cancer Hospital and Richard J. Solove Research Institute, The Ohio State University, Columbus, OH, 43210, USA
| | - Deliang Guo
- Department of Radiation Oncology, James Cancer Hospital and Richard J. Solove Research Institute, The Ohio State University, Columbus, OH, 43210, USA
- The Comprehensive Cancer Center, Center for Cancer Metabolism, The Ohio State University, Columbus, OH, 43210, USA
| | - Baek Kim
- Center for ViroScience and Cure, Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA, 30322, USA
| | - Junran Zhang
- Department of Radiation Oncology, James Cancer Hospital and Richard J. Solove Research Institute, The Ohio State University, Columbus, OH, 43210, USA.
- The Comprehensive Cancer Center, Center for Cancer Metabolism, The Ohio State University, Columbus, OH, 43210, USA.
- The Comprehensive Cancer Center, Pelotonia Institute for Immuno-Oncology, The Ohio State University, Columbus, OH, 43210, USA.
| |
Collapse
|
4
|
Giang LH, Wu KS, Lee WC, Chu SS, Do AD, Changou CA, Tran HM, Hsieh TH, Chen HH, Hsieh CL, Sung SY, Yu AL, Yen Y, Wong TT, Chang CC. Targeting of RRM2 suppresses DNA damage response and activates apoptosis in atypical teratoid rhabdoid tumor. J Exp Clin Cancer Res 2023; 42:346. [PMID: 38124207 PMCID: PMC10731702 DOI: 10.1186/s13046-023-02911-x] [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: 10/11/2023] [Accepted: 11/19/2023] [Indexed: 12/23/2023] Open
Abstract
BACKGROUND Atypical teratoid rhabdoid tumors (ATRT) is a rare but aggressive malignancy in the central nervous system, predominantly occurring in early childhood. Despite aggressive treatment, the prognosis of ATRT patients remains poor. RRM2, a subunit of ribonucleotide reductase, has been reported as a biomarker for aggressiveness and poor prognostic conditions in several cancers. However, little is known about the role of RRM2 in ATRT. Uncovering the role of RRM2 in ATRT will further promote the development of feasible strategies and effective drugs to treat ATRT. METHODS Expression of RRM2 was evaluated by molecular profiling analysis and was confirmed by IHC in both ATRT patients and PDX tissues. Follow-up in vitro studies used shRNA knockdown RRM2 in three different ATRT cells to elucidate the oncogenic role of RRM2. The efficacy of COH29, an RRM2 inhibitor, was assessed in vitro and in vivo. Western blot and RNA-sequencing were used to determine the mechanisms of RRM2 transcriptional activation in ATRT. RESULTS RRM2 was found to be significantly overexpressed in multiple independent ATRT clinical cohorts through comprehensive bioinformatics and clinical data analysis in this study. The expression level of RRM2 was strongly correlated with poor survival rates in patients. In addition, we employed shRNAs to silence RRM2, which led to significantly decrease in ATRT colony formation, cell proliferation, and migration. In vitro experiments showed that treatment with COH29 resulted in similar but more pronounced inhibitory effect. Therefore, ATRT orthotopic mouse model was utilized to validate this finding, and COH29 treatment showed significant tumor growth suppression and prolong overall survival. Moreover, we provide evidence that COH29 treatment led to genomic instability, suppressed homologous recombinant DNA damage repair, and subsequently induced ATRT cell death through apoptosis in ATRT cells. CONCLUSIONS Collectively, our study uncovers the oncogenic functions of RRM2 in ATRT cell lines, and highlights the therapeutic potential of targeting RRM2 in ATRT. The promising effect of COH29 on ATRT suggests its potential suitability for clinical trials as a novel therapeutic approach for ATRT.
Collapse
Affiliation(s)
- Le Hien Giang
- International Ph.D. Program for Translational Science, College of Medical Science and Technology, Taipei Medical University, Taipei, 11031, Taiwan
- Department of Biology and Genetics, Hai Phong University of Medicine and Pharmacy, Hai Phong, 180000, Vietnam
| | - Kuo-Sheng Wu
- Graduate Institute of Clinical Medicine, College of Medicine, Taipei Medical University, Taipei, 110, Taiwan
| | - Wei-Chung Lee
- Graduate Institute of Clinical Medicine, College of Medicine, Taipei Medical University, Taipei, 110, Taiwan
- The Ph.D. Program for Translational Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei, 110, Taiwan
| | - Shing-Shung Chu
- Graduate Institute of Clinical Medicine, College of Medicine, Taipei Medical University, Taipei, 110, Taiwan
| | - Anh Duy Do
- International Ph.D. Program for Translational Science, College of Medical Science and Technology, Taipei Medical University, Taipei, 11031, Taiwan
- Department of Physiology, Pathophysiology and Immunology, Pham Ngoc Thach University of Medicine, Ho Chi Minh City, 700000, Vietnam
| | - Chun A Changou
- The Ph.D. Program for Translational Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei, 110, Taiwan
- The Ph.D. Program for Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei, 11031, Taiwan
| | - Huy Minh Tran
- Department of Neurosurgery, Faculty of Medicine, University of Medicine and Pharmacy, Ho Chi Minh City, 700000, Vietnam
| | - Tsung-Han Hsieh
- Joint Biobank, Office of Human Research, Taipei Medical University, Taipei, 110, Taiwan
| | - Hsin-Hung Chen
- Division of Pediatric Neurosurgery, Neurological Institute, Taipei Veterans General Hospital, Taipei, 112, Taiwan
| | - Chia-Ling Hsieh
- The Ph.D. Program for Translational Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei, 110, Taiwan
- Laboratory of Translational Medicine, Development Center for Biotechnology, Taipei, 115, Taiwan
| | - Shian-Ying Sung
- International Ph.D. Program for Translational Science, College of Medical Science and Technology, Taipei Medical University, Taipei, 11031, Taiwan
- The Ph.D. Program for Translational Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei, 110, Taiwan
| | - Alice L Yu
- Institute of Stem Cell and Translational Cancer Research, Chang Gung Memorial Hospital at Linkou and Chang Gung University, Taoyuan, 333, Taiwan
- Genomics Research Center, Academia Sinica, Taipei, 115, Taiwan
| | - Yun Yen
- The Ph.D. Program for Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei, 11031, Taiwan
| | - Tai-Tong Wong
- Graduate Institute of Clinical Medicine, College of Medicine, Taipei Medical University, Taipei, 110, Taiwan
- Pediatric Brain Tumor Program, Taipei Cancer Center, Taipei Medical University, Taipei, 110, Taiwan
- Division of Pediatric Neurosurgery, Department of Neurosurgery, Taipei Medical University Hospital and Taipei Neuroscience Institute, Taipei Medical University, Taipei, 110, Taiwan
- Neuroscience Research Center, Taipei Medical University Hospital, Taipei, 110, Taiwan
- TMU Research Center for Cancer Translational Medicine, Taipei Medical University, Taipei, 110, Taiwan
| | - Che-Chang Chang
- International Ph.D. Program for Translational Science, College of Medical Science and Technology, Taipei Medical University, Taipei, 11031, Taiwan.
- The Ph.D. Program for Translational Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei, 110, Taiwan.
- Neuroscience Research Center, Taipei Medical University Hospital, Taipei, 110, Taiwan.
- TMU Research Center for Cancer Translational Medicine, Taipei Medical University, Taipei, 110, Taiwan.
- The Ph.D. Program for Translational Medicine, College of Medical Science and Technology, Taipei Medical University, 6F., Education & Research Building, Shuang-Ho Campus, No. 301, Yuantong Rd., Zhonghe Dist., New Taipei City, 23564, Taiwan.
| |
Collapse
|
5
|
Barbari SR, Beach AK, Markgren JG, Parkash V, Moore EA, Johansson E, Shcherbakova PV. Enhanced polymerase activity permits efficient synthesis by cancer-associated DNA polymerase ϵ variants at low dNTP levels. Nucleic Acids Res 2022; 50:8023-8040. [PMID: 35822874 PMCID: PMC9371911 DOI: 10.1093/nar/gkac602] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 06/13/2022] [Accepted: 06/29/2022] [Indexed: 11/28/2022] Open
Abstract
Amino acid substitutions in the exonuclease domain of DNA polymerase ϵ (Polϵ) cause ultramutated tumors. Studies in model organisms suggested pathogenic mechanisms distinct from a simple loss of exonuclease. These mechanisms remain unclear for most recurrent Polϵ mutations. Particularly, the highly prevalent V411L variant remained a long-standing puzzle with no detectable mutator effect in yeast despite the unequivocal association with ultramutation in cancers. Using purified four-subunit yeast Polϵ, we assessed the consequences of substitutions mimicking human V411L, S459F, F367S, L424V and D275V. While the effects on exonuclease activity vary widely, all common cancer-associated variants have increased DNA polymerase activity. Notably, the analog of Polϵ-V411L is among the strongest polymerases, and structural analysis suggests defective polymerase-to-exonuclease site switching. We further show that the V411L analog produces a robust mutator phenotype in strains that lack mismatch repair, indicating a high rate of replication errors. Lastly, unlike wild-type and exonuclease-dead Polϵ, hyperactive variants efficiently synthesize DNA at low dNTP concentrations. We propose that this characteristic could promote cancer cell survival and preferential participation of mutator polymerases in replication during metabolic stress. Our results support the notion that polymerase fitness, rather than low fidelity alone, is an important determinant of variant pathogenicity.
Collapse
Affiliation(s)
- Stephanie R Barbari
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Annette K Beach
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Joel G Markgren
- Department of Medical Biochemistry and Biophysics, Umeå University, SE-90187 Umeå, Sweden
| | - Vimal Parkash
- Department of Medical Biochemistry and Biophysics, Umeå University, SE-90187 Umeå, Sweden
| | - Elizabeth A Moore
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Erik Johansson
- Department of Medical Biochemistry and Biophysics, Umeå University, SE-90187 Umeå, Sweden
| | - Polina V Shcherbakova
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
| |
Collapse
|
6
|
Zavileyskiy L, Bunik V. Regulation of p53 Function by Formation of Non-Nuclear Heterologous Protein Complexes. Biomolecules 2022; 12:biom12020327. [PMID: 35204825 PMCID: PMC8869670 DOI: 10.3390/biom12020327] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Revised: 02/10/2022] [Accepted: 02/16/2022] [Indexed: 01/10/2023] Open
Abstract
A transcription factor p53 is activated upon cellular exposure to endogenous and exogenous stresses, triggering either homeostatic correction or cell death. Depending on the stress level, often measurable as DNA damage, the dual outcome is supported by p53 binding to a number of regulatory and metabolic proteins. Apart from the nucleus, p53 localizes to mitochondria, endoplasmic reticulum and cytosol. We consider non-nuclear heterologous protein complexes of p53, their structural determinants, regulatory post-translational modifications and the role in intricate p53 functions. The p53 heterologous complexes regulate the folding, trafficking and/or action of interacting partners in cellular compartments. Some of them mainly sequester p53 (HSP proteins, G6PD, LONP1) or its partners (RRM2B, PRKN) in specific locations. Formation of other complexes (with ATP2A2, ATP5PO, BAX, BCL2L1, CHCHD4, PPIF, POLG, SOD2, SSBP1, TFAM) depends on p53 upregulation according to the stress level. The p53 complexes with SIRT2, MUL1, USP7, TXN, PIN1 and PPIF control regulation of p53 function through post-translational modifications, such as lysine acetylation or ubiquitination, cysteine/cystine redox transformation and peptidyl-prolyl cis-trans isomerization. Redox sensitivity of p53 functions is supported by (i) thioredoxin-dependent reduction of p53 disulfides, (ii) inhibition of the thioredoxin-dependent deoxyribonucleotide synthesis by p53 binding to RRM2B and (iii) changed intracellular distribution of p53 through its oxidation by CHCHD4 in the mitochondrial intermembrane space. Increasing knowledge on the structure, function and (patho)physiological significance of the p53 heterologous complexes will enable a fine tuning of the settings-dependent p53 programs, using small molecule regulators of specific protein–protein interactions of p53.
Collapse
Affiliation(s)
- Lev Zavileyskiy
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119991 Moscow, Russia;
| | - Victoria Bunik
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119991 Moscow, Russia;
- Department of Biokinetics, Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
- Department of Biochemistry, Sechenov University, 119991 Moscow, Russia
- Correspondence:
| |
Collapse
|
7
|
Ihle M, Biber S, Schroeder IS, Blattner C, Deniz M, Damia G, Gottifredi V, Wiesmüller L. Impact of the interplay between stemness features, p53 and pol iota on replication pathway choices. Nucleic Acids Res 2021; 49:7457-7475. [PMID: 34165573 PMCID: PMC8287946 DOI: 10.1093/nar/gkab526] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 06/02/2021] [Accepted: 06/09/2021] [Indexed: 12/12/2022] Open
Abstract
Using human embryonic, adult and cancer stem cells/stem cell-like cells (SCs), we demonstrate that DNA replication speed differs in SCs and their differentiated counterparts. While SCs decelerate DNA replication, differentiated cells synthesize DNA faster and accumulate DNA damage. Notably, both replication phenotypes depend on p53 and polymerase iota (POLι). By exploring protein interactions and newly synthesized DNA, we show that SCs promote complex formation of p53 and POLι at replication sites. Intriguingly, in SCs the translocase ZRANB3 is recruited to POLι and required for slow-down of DNA replication. The known role of ZRANB3 in fork reversal suggests that the p53–POLι complex mediates slow but safe bypass of replication barriers in SCs. In differentiated cells, POLι localizes more transiently to sites of DNA synthesis and no longer interacts with p53 facilitating fast POLι-dependent DNA replication. In this alternative scenario, POLι associates with the p53 target p21, which antagonizes PCNA poly-ubiquitination and, thereby potentially disfavors the recruitment of translocases. Altogether, we provide evidence for diametrically opposed DNA replication phenotypes in SCs and their differentiated counterparts putting DNA replication-based strategies in the spotlight for the creation of therapeutic opportunities targeting SCs.
Collapse
Affiliation(s)
- Michaela Ihle
- Department of Obstetrics and Gynecology, Ulm University, Ulm 89075, Germany
| | - Stephanie Biber
- Department of Obstetrics and Gynecology, Ulm University, Ulm 89075, Germany
| | - Insa S Schroeder
- Department of Biophysics, GSI Helmholtz Center for Heavy Ion Research, Darmstadt 64291, Germany
| | - Christine Blattner
- Institute for Biological and Chemical Systems - Biological Information Processing, Karlsruhe Institute of Technology, Karlsruhe 76021, Germany
| | - Miriam Deniz
- Department of Obstetrics and Gynecology, Ulm University, Ulm 89075, Germany
| | - Giovanna Damia
- Department of Oncology, Istituto di Ricerche Farmacologiche Mario Negri-IRCCS Milan, Milan 20156, Italy
| | - Vanesa Gottifredi
- Cell cycle and Genomic Stability Laboratory, Fundación Instituto Leloir, Buenos Aires C1405BWE, Argentina
| | - Lisa Wiesmüller
- Department of Obstetrics and Gynecology, Ulm University, Ulm 89075, Germany
| |
Collapse
|
8
|
Replication Stress, Genomic Instability, and Replication Timing: A Complex Relationship. Int J Mol Sci 2021; 22:ijms22094764. [PMID: 33946274 PMCID: PMC8125245 DOI: 10.3390/ijms22094764] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/26/2021] [Accepted: 04/28/2021] [Indexed: 12/29/2022] Open
Abstract
The replication-timing program constitutes a key element of the organization and coordination of numerous nuclear processes in eukaryotes. This program is established at a crucial moment in the cell cycle and occurs simultaneously with the organization of the genome, thus indicating the vital significance of this process. With recent technological achievements of high-throughput approaches, a very strong link has been confirmed between replication timing, transcriptional activity, the epigenetic and mutational landscape, and the 3D organization of the genome. There is also a clear relationship between replication stress, replication timing, and genomic instability, but the extent to which they are mutually linked to each other is unclear. Recent evidence has shown that replication timing is affected in cancer cells, although the cause and consequence of this effect remain unknown. However, in-depth studies remain to be performed to characterize the molecular mechanisms of replication-timing regulation and clearly identify different cis- and trans-acting factors. The results of these studies will potentially facilitate the discovery of new therapeutic pathways, particularly for personalized medicine, or new biomarkers. This review focuses on the complex relationship between replication timing, replication stress, and genomic instability.
Collapse
|
9
|
Jin CY, Du L, Nuerlan AH, Wang XL, Yang YW, Guo R. High expression of RRM2 as an independent predictive factor of poor prognosis in patients with lung adenocarcinoma. Aging (Albany NY) 2020; 13:3518-3535. [PMID: 33411689 PMCID: PMC7906179 DOI: 10.18632/aging.202292] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Accepted: 10/27/2020] [Indexed: 12/24/2022]
Abstract
Ribonucleotide reductase subunit M2 may play a role as a potential prognostic biomarker in several cancers. In this study, we evaluated whether RRM2 gene expression is associated with the prognosis of patients with lung adenocarcinoma (LUAD) using publicly available data from The Cancer Genome Atlas (TCGA). Wilcoxon signed-rank test and logistic regression were performed to evaluate the association between RRM2 expression and clinical features in patients with LUAD. Kaplan-Meier and Cox regression methods were used to examine the effect of RRM2 expression level in the overall survival, and a nomogram was performed to illustrate the correlation between the RRM2 gene expression and the risk of LUAD. TCGA data set was used for gene set enrichment analysis (GSEA). We also performed a further experiment in vitro to assess the effect of RRM2 expression on the proliferation and invasive abilities of LUAD cells and its key signaling pathway proteins. Our results revealed that the expression level of RRM2 in patients with LUAD was much higher than that in normal tissues (p = 3.99e-32). High expression of RRM2 was significantly associated with tumor stage (IV vs. I: OR = 3.02, p = 0.012) and TNM classification (T2 vs. T1: OR = 1.88, p = 0.001; N2 vs. N0: OR = 2.69, p < 0.001). Kaplan-Meier survival analysis showed that high expression of RRM2 was associated with a worse prognosis of LUAD compared low expression of RRM2 (p = 7.86e-04). Multivariate analysis showed that high RRM2 expression was an independent factor affecting overall survival (HR = 1.29, p < 0.001). The association between RRM2 gene expression and the risk of LUAD was presented in a nomogram. GSEA revealed that the cell cycle, p53 signaling pathway, DNA replication, small cell lung cancer, apoptosis, and pathways in cancer were differentially enriched in patients with high expression of RRM2. RRM2 over-expression promoted the proliferation and invasive abilities of LUAD cells. RRM2 over-expression increased the activation of Bcl-2 and E-cadherin signaling pathways, and reduced the activation of p53 signaling pathway. In summary, high RRM2 expression is an independent predictive factor of poor prognosis in patients with lung adenocarcinoma.
Collapse
Affiliation(s)
- Cheng-Yu Jin
- Department of Chest Surgery, People's Hospital of Xinjiang Uygur Autonomous Region, Urumqi 830001, Xinjiang, China
| | - Liang Du
- Department of Chest Surgery, People's Hospital of Xinjiang Uygur Autonomous Region, Urumqi 830001, Xinjiang, China
| | - A-Han Nuerlan
- Department of Chest Surgery, People's Hospital of Xinjiang Uygur Autonomous Region, Urumqi 830001, Xinjiang, China
| | - Xiao-Lei Wang
- Department of Chest Surgery, People's Hospital of Xinjiang Uygur Autonomous Region, Urumqi 830001, Xinjiang, China
| | - Yong-Wei Yang
- Department of Chest Surgery, People's Hospital of Xinjiang Uygur Autonomous Region, Urumqi 830001, Xinjiang, China
| | - Rui Guo
- Department of Chest Surgery, People's Hospital of Xinjiang Uygur Autonomous Region, Urumqi 830001, Xinjiang, China
| |
Collapse
|
10
|
The Regulatory Properties of the Ccr4-Not Complex. Cells 2020; 9:cells9112379. [PMID: 33138308 PMCID: PMC7692201 DOI: 10.3390/cells9112379] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 10/21/2020] [Accepted: 10/26/2020] [Indexed: 12/12/2022] Open
Abstract
The mammalian Ccr4–Not complex, carbon catabolite repression 4 (Ccr4)-negative on TATA-less (Not), is a large, highly conserved, multifunctional assembly of proteins that acts at different cellular levels to regulate gene expression. In the nucleus, it is involved in the regulation of the cell cycle, chromatin modification, activation and inhibition of transcription initiation, control of transcription elongation, RNA export, nuclear RNA surveillance, and DNA damage repair. In the cytoplasm, the Ccr4–Not complex plays a central role in mRNA decay and affects protein quality control. Most of our original knowledge of the Ccr4–Not complex is derived, primarily, from studies in yeast. More recent studies have shown that the mammalian complex has a comparable structure and similar properties. In this review, we summarize the evidence for the multiple roles of both the yeast and mammalian Ccr4–Not complexes, highlighting their similarities.
Collapse
|
11
|
Puts G, Jarrett S, Leonard M, Matsangos N, Snyder D, Wang Y, Vincent R, Portney B, Abbotts R, McLaughlin L, Zalzman M, Rassool F, Kaetzel D. Metastasis Suppressor NME1 Modulates Choice of Double-Strand Break Repair Pathways in Melanoma Cells by Enhancing Alternative NHEJ while Inhibiting NHEJ and HR. Int J Mol Sci 2020; 21:ijms21165896. [PMID: 32824412 PMCID: PMC7460576 DOI: 10.3390/ijms21165896] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 08/09/2020] [Accepted: 08/13/2020] [Indexed: 01/15/2023] Open
Abstract
Reduced NME1 expression in melanoma cell lines, mouse models of melanoma, and melanoma specimens in human patients is associated with increased metastatic activity. Herein, we investigate the role of NME1 in repair of double-stranded breaks (DSBs) and choice of double-strand break repair (DSBR) pathways in melanoma cells. Using chromatin immunoprecipitation, NME1 was shown to be recruited rapidly and directly to DSBs generated by the homing endonuclease I-PpoI. NME1 was recruited to DSBs within 30 min, in concert with recruitment of ataxia-telangiectasia mutated (ATM) protein, an early step in DSBR complex formation, as well as loss of histone 2B. NME1 was detected up to 5 kb from the break site after DSB induction, suggesting a role in extending chromatin reorganization away from the repair site. shRNA-mediated silencing of NME1 expression led to increases in the homologous recombination (HR) and non-homologous end-joining (NHEJ) pathways of double-strand break repair (DSBR), and reduction in the low fidelity, alternative-NHEJ (A-NHEJ) pathway. These findings suggest low expression of NME1 drives DSBR towards higher fidelity pathways, conferring enhanced genomic stability necessary for rapid and error-free proliferation in invasive and metastatic cells. The novel mechanism highlighted in the current study appears likely to impact metastatic potential and therapy-resistance in advanced melanoma and other cancers.
Collapse
Affiliation(s)
- Gemma Puts
- Department of Biochemistry and Molecular Biology, School of Medicine, University of Maryland, Baltimore, MD 21201, USA; (G.P.); (M.L.); (N.M.); (D.S.); (Y.W.); (R.V.); (B.P.); (M.Z.)
| | - Stuart Jarrett
- Department of Toxicology and Cancer Biology, College of Medicine, University of Kentucky, Lexington, KY 40536, USA;
| | - Mary Leonard
- Department of Biochemistry and Molecular Biology, School of Medicine, University of Maryland, Baltimore, MD 21201, USA; (G.P.); (M.L.); (N.M.); (D.S.); (Y.W.); (R.V.); (B.P.); (M.Z.)
| | - Nicolette Matsangos
- Department of Biochemistry and Molecular Biology, School of Medicine, University of Maryland, Baltimore, MD 21201, USA; (G.P.); (M.L.); (N.M.); (D.S.); (Y.W.); (R.V.); (B.P.); (M.Z.)
| | - Devin Snyder
- Department of Biochemistry and Molecular Biology, School of Medicine, University of Maryland, Baltimore, MD 21201, USA; (G.P.); (M.L.); (N.M.); (D.S.); (Y.W.); (R.V.); (B.P.); (M.Z.)
| | - Ying Wang
- Department of Biochemistry and Molecular Biology, School of Medicine, University of Maryland, Baltimore, MD 21201, USA; (G.P.); (M.L.); (N.M.); (D.S.); (Y.W.); (R.V.); (B.P.); (M.Z.)
| | - Richard Vincent
- Department of Biochemistry and Molecular Biology, School of Medicine, University of Maryland, Baltimore, MD 21201, USA; (G.P.); (M.L.); (N.M.); (D.S.); (Y.W.); (R.V.); (B.P.); (M.Z.)
| | - Benjamin Portney
- Department of Biochemistry and Molecular Biology, School of Medicine, University of Maryland, Baltimore, MD 21201, USA; (G.P.); (M.L.); (N.M.); (D.S.); (Y.W.); (R.V.); (B.P.); (M.Z.)
| | - Rachel Abbotts
- Department of Radiation Oncology, School of Medicine, University of Maryland, Baltimore, MD 21201, USA; (R.A.); (L.M.); (F.R.)
- University of Maryland Marlene and Stewart Greenebaum Comprehensive Cancer Center, Baltimore, MD 21201, USA
| | - Lena McLaughlin
- Department of Radiation Oncology, School of Medicine, University of Maryland, Baltimore, MD 21201, USA; (R.A.); (L.M.); (F.R.)
- University of Maryland Marlene and Stewart Greenebaum Comprehensive Cancer Center, Baltimore, MD 21201, USA
| | - Michal Zalzman
- Department of Biochemistry and Molecular Biology, School of Medicine, University of Maryland, Baltimore, MD 21201, USA; (G.P.); (M.L.); (N.M.); (D.S.); (Y.W.); (R.V.); (B.P.); (M.Z.)
- University of Maryland Marlene and Stewart Greenebaum Comprehensive Cancer Center, Baltimore, MD 21201, USA
- Department of Otorhinolaryngology, School of Medicine, University of Maryland, Baltimore, MD 21201, USA
| | - Feyruz Rassool
- Department of Radiation Oncology, School of Medicine, University of Maryland, Baltimore, MD 21201, USA; (R.A.); (L.M.); (F.R.)
- University of Maryland Marlene and Stewart Greenebaum Comprehensive Cancer Center, Baltimore, MD 21201, USA
| | - David Kaetzel
- Department of Biochemistry and Molecular Biology, School of Medicine, University of Maryland, Baltimore, MD 21201, USA; (G.P.); (M.L.); (N.M.); (D.S.); (Y.W.); (R.V.); (B.P.); (M.Z.)
- University of Maryland Marlene and Stewart Greenebaum Comprehensive Cancer Center, Baltimore, MD 21201, USA
- Correspondence: ; Tel.: +1-410-706-5080; Fax: +1-410-706-8297
| |
Collapse
|
12
|
DNA Damage Response and Metabolic Reprogramming in Health and Disease. Trends Genet 2020; 36:777-791. [PMID: 32684438 DOI: 10.1016/j.tig.2020.06.018] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 06/29/2020] [Accepted: 06/30/2020] [Indexed: 01/08/2023]
Abstract
Nuclear DNA damage contributes to cellular malfunction and the premature onset of age-related diseases, including cancer. Until recently, the canonical DNA damage response (DDR) was thought to represent a collection of nuclear processes that detect, signal and repair damaged DNA. However, recent evidence suggests that beyond nuclear events, the DDR rewires an intricate network of metabolic circuits, fine-tunes protein synthesis, trafficking, and secretion as well as balances growth with defense strategies in response to genotoxic insults. In this review, we discuss how the active DDR signaling mobilizes extranuclear and systemic responses to promote cellular homeostasis and organismal survival in health and disease.
Collapse
|
13
|
Wang L, Sun R, Eriksson S. Basic biochemical characterization of cytosolic enzymes in thymidine nucleotide synthesis in adult rat tissues: implications for tissue specific mitochondrial DNA depletion and deoxynucleoside-based therapy for TK2-deficiency. BMC Mol Cell Biol 2020; 21:33. [PMID: 32345222 PMCID: PMC7189545 DOI: 10.1186/s12860-020-00272-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 03/31/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Deficiency in thymidine kinase 2 (TK2) or p53 inducible ribonucleotide reductase small subunit (p53R2) is associated with tissue specific mitochondrial DNA (mtDNA) depletion. To understand the mechanisms of the tissue specific mtDNA depletion we systematically studied key enzymes in dTMP synthesis in mitochondrial and cytosolic extracts prepared from adult rat tissues. RESULTS In addition to mitochondrial TK2 a cytosolic isoform of TK2 was characterized, which showed similar substrate specificity to the mitochondrial TK2. Total TK activity was highest in spleen and lowest in skeletal muscle. Thymidylate synthase (TS) was detected in cytosols and its activity was high in spleen but low in other tissues. TS protein levels were high in heart, brain and skeletal muscle, which deviated from TS activity levels. The p53R2 proteins were at similar levels in all tissues except liver where it was ~ 6-fold lower. Our results strongly indicate that mitochondria in most tissues are capable of producing enough dTTP for mtDNA replication via mitochondrial TK2, but skeletal muscle mitochondria do not and are most likely dependent on both the salvage and de novo synthesis pathways. CONCLUSION These results provide important information concerning mechanisms for the tissue dependent variation of dTTP synthesis and explained why deficiency in TK2 or p53R2 leads to skeletal muscle dysfunctions. Furthermore, the presence of a putative cytosolic TK2-like enzyme may provide basic knowledge for the understanding of deoxynucleoside-based therapy for mitochondrial disorders.
Collapse
Affiliation(s)
- Liya Wang
- Department of Anatomy, Physiology and Biochemistry, Swedish University of Agricultural Sciences, SE-750 07, Uppsala, Sweden.
| | - Ren Sun
- Department of Anatomy, Physiology and Biochemistry, Swedish University of Agricultural Sciences, SE-750 07, Uppsala, Sweden
| | - Staffan Eriksson
- Department of Anatomy, Physiology and Biochemistry, Swedish University of Agricultural Sciences, SE-750 07, Uppsala, Sweden
| |
Collapse
|
14
|
The yeast Aft1 transcription factor activates ribonucleotide reductase catalytic subunit RNR1 in response to iron deficiency. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1863:194522. [PMID: 32147528 DOI: 10.1016/j.bbagrm.2020.194522] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 02/25/2020] [Accepted: 03/01/2020] [Indexed: 12/18/2022]
Abstract
Eukaryotic ribonucleotide reductases are iron-dependent enzymes that catalyze the rate-limiting step in the de novo synthesis of deoxyribonucleotides. Multiple mechanisms regulate the activity of ribonucleotide reductases in response to genotoxic stresses and iron deficiency. Upon iron starvation, the Saccharomyces cerevisiae Aft1 transcription factor specifically binds to iron-responsive cis elements within the promoter of a group of genes, known as the iron regulon, activating their transcription. Members of the iron regulon participate in iron acquisition, mobilization and recycling, and trigger a genome-wide metabolic remodeling of iron-dependent pathways. Here, we describe a mechanism that optimizes the activity of yeast ribonucleotide reductase when iron is scarce. We demonstrate that Aft1 and the DNA-binding protein Ixr1 enhance the expression of the gene encoding for its catalytic subunit, RNR1, in response to iron limitation, leading to an increase in both mRNA and protein levels. By mutagenesis of the Aft1-binding sites within RNR1 promoter, we conclude that RNR1 activation by iron depletion is important for Rnr1 protein and deoxyribonucleotide synthesis. Remarkably, Aft1 also activates the expression of IXR1 upon iron scarcity through an iron-responsive element located within its promoter. These results provide a novel mechanism for the direct activation of ribonucleotide reductase function by the iron-regulated Aft1 transcription factor.
Collapse
|
15
|
Liu B, Großhans J. The role of dNTP metabolites in control of the embryonic cell cycle. Cell Cycle 2019; 18:2817-2827. [PMID: 31544596 PMCID: PMC6791698 DOI: 10.1080/15384101.2019.1665948] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 09/03/2019] [Accepted: 09/06/2019] [Indexed: 01/06/2023] Open
Abstract
Deoxyribonucleotide metabolites (dNTPs) are the substrates for DNA synthesis. It has been proposed that their availability influences the progression of the cell cycle during development and pathological situations such as tumor growth. The mechanism has remained unclear for the link between cell cycle and dNTP levels beyond their role as substrates. Here, we review recent studies concerned with the dynamics of dNTP levels in early embryos and the role of DNA replication checkpoint as a sensor of dNTP levels.
Collapse
Affiliation(s)
- Boyang Liu
- Institut für Entwicklungsbiochemie, Universitätsmedizin, Georg-August-Universität, Göttingen, Germany
| | - Jörg Großhans
- Institut für Entwicklungsbiochemie, Universitätsmedizin, Georg-August-Universität, Göttingen, Germany
- Entwicklungsgenetik, Fachbereich Biologie, Philipps-Universität, Marburg, Germany
| |
Collapse
|
16
|
Fakouri NB, Hansen TL, Desler C, Anugula S, Rasmussen LJ. From Powerhouse to Perpetrator-Mitochondria in Health and Disease. BIOLOGY 2019; 8:biology8020035. [PMID: 31083572 PMCID: PMC6627154 DOI: 10.3390/biology8020035] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Revised: 02/16/2019] [Accepted: 03/05/2019] [Indexed: 12/22/2022]
Abstract
In this review we discuss the interaction between metabolic stress, mitochondrial dysfunction, and genomic instability. Unrepaired DNA damage in the nucleus resulting from excess accumulation of DNA damages and stalled replication can initiate cellular signaling responses that negatively affect metabolism and mitochondrial function. On the other hand, mitochondrial pathologies can also lead to stress in the nucleus, and cause sensitivity to DNA-damaging agents. These are examples of how hallmarks of cancer and aging are connected and influenced by each other to protect humans from disease.
Collapse
Affiliation(s)
- Nima B Fakouri
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA.
| | - Thomas Lau Hansen
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, 2200 Copenhagen, Denmark.
| | - Claus Desler
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, 2200 Copenhagen, Denmark.
| | - Sharath Anugula
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, 2200 Copenhagen, Denmark.
| | - Lene Juel Rasmussen
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, 2200 Copenhagen, Denmark.
| |
Collapse
|
17
|
Bourbousse C, Vegesna N, Law JA. SOG1 activator and MYB3R repressors regulate a complex DNA damage network in Arabidopsis. Proc Natl Acad Sci U S A 2018; 115:E12453-E12462. [PMID: 30541889 PMCID: PMC6310815 DOI: 10.1073/pnas.1810582115] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
To combat DNA damage, organisms mount a DNA damage response (DDR) that results in cell cycle regulation, DNA repair and, in severe cases, cell death. Underscoring the importance of gene regulation in this response, studies in Arabidopsis have demonstrated that all of the aforementioned processes rely on SUPPRESSOR OF GAMMA RESPONSE 1 (SOG1), a NAC family transcription factor (TF) that has been functionally equated to the mammalian tumor suppressor, p53. However, the expression networks connecting SOG1 to these processes remain largely unknown and, although the DDR spans from minutes to hours, most transcriptomic data correspond to single time-point snapshots. Here, we generated transcriptional models of the DDR from GAMMA (γ)-irradiated wild-type and sog1 seedlings during a 24-hour time course using DREM, the Dynamic Regulatory Events Miner, revealing 11 coexpressed gene groups with distinct biological functions and cis-regulatory features. Within these networks, additional chromatin immunoprecipitation and transcriptomic experiments revealed that SOG1 is the major activator, directly targeting the most strongly up-regulated genes, including TFs, repair factors, and early cell cycle regulators, while three MYB3R TFs are the major repressors, specifically targeting the most strongly down-regulated genes, which mainly correspond to G2/M cell cycle-regulated genes. Together these models reveal the temporal dynamics of the transcriptional events triggered by γ-irradiation and connects these events to TFs and biological processes over a time scale commensurate with key processes coordinated in response to DNA damage, greatly expanding our understanding of the DDR.
Collapse
Affiliation(s)
- Clara Bourbousse
- Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037
| | - Neeraja Vegesna
- Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093
| | - Julie A Law
- Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037;
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093
| |
Collapse
|
18
|
Pamidimukkala NV, Leonard MK, Snyder D, McCorkle JR, Kaetzel DM. Metastasis Suppressor NME1 Directly Activates Transcription of the ALDOC Gene in Melanoma Cells. Anticancer Res 2018; 38:6059-6068. [PMID: 30396920 DOI: 10.21873/anticanres.12956] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2018] [Revised: 09/05/2018] [Accepted: 10/05/2018] [Indexed: 01/01/2023]
Abstract
BACKGROUND/AIM NME/NM23 nucleoside diphosphate kinase 1 (NME1) is a metastasis suppressor gene, exhibiting reduced expression in metastatic cancers and the ability to suppress metastatic activity of cancer cells. We previously identified NME1-regulated genes with prognostic value in human melanoma. This study was conducted in melanoma cell lines aiming to elucidate the mechanism through which NME regulates one of these genes, aldolase C (ALDOC). MATERIALS AND METHODS ALDOC mRNA and protein expression was measured using qRT-PCR and immunoblot analyses. Promoter-luciferase constructs and chromatin immunoprecipitation were employed to measure the impact of NME1 on ALDOC transcription. RESULTS NME1 enhanced ALDOC transcription, evidenced by increased expression of ALDOC pre-mRNA and activity of an ALDOC promoter-luciferase module. NME1 was detected at the ALDOC promoter, and forced NME1 expression resulted in enhanced occupancy of the promoter by NME1, increased presence of epigenetic activation markers (H3K4me3 and H3K27ac), and recruitment of RNA polymerase II. CONCLUSION This is the first study to indicate that NME1 induces transcription through its direct binding to the promoter region of a target gene.
Collapse
Affiliation(s)
- Nidhi V Pamidimukkala
- Department of Biochemistry and Molecular Biology, School of Medicine, University of Maryland-Baltimore, Baltimore, MD, U.S.A
| | - Mary Kathryn Leonard
- Department of Biochemistry and Molecular Biology, School of Medicine, University of Maryland-Baltimore, Baltimore, MD, U.S.A
| | - Devin Snyder
- Department of Biochemistry and Molecular Biology, School of Medicine, University of Maryland-Baltimore, Baltimore, MD, U.S.A
| | | | - David M Kaetzel
- Department of Biochemistry and Molecular Biology, School of Medicine, University of Maryland-Baltimore, Baltimore, MD, U.S.A. .,Markey Cancer Center, University of Kentucky, Lexington, KY, U.S.A.,Marlene and Stewart Greenebaum Comprehensive Cancer Center, University of Maryland-Baltimore, Baltimore, MD, U.S.A
| |
Collapse
|
19
|
Gustafsson NMS, Färnegårdh K, Bonagas N, Ninou AH, Groth P, Wiita E, Jönsson M, Hallberg K, Lehto J, Pennisi R, Martinsson J, Norström C, Hollers J, Schultz J, Andersson M, Markova N, Marttila P, Kim B, Norin M, Olin T, Helleday T. Targeting PFKFB3 radiosensitizes cancer cells and suppresses homologous recombination. Nat Commun 2018; 9:3872. [PMID: 30250201 PMCID: PMC6155239 DOI: 10.1038/s41467-018-06287-x] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 08/24/2018] [Indexed: 12/16/2022] Open
Abstract
The glycolytic PFKFB3 enzyme is widely overexpressed in cancer cells and an emerging anti-cancer target. Here, we identify PFKFB3 as a critical factor in homologous recombination (HR) repair of DNA double-strand breaks. PFKFB3 rapidly relocates into ionizing radiation (IR)-induced nuclear foci in an MRN-ATM-γH2AX-MDC1-dependent manner and co-localizes with DNA damage and HR repair proteins. PFKFB3 relocalization is critical for recruitment of HR proteins, HR activity, and cell survival upon IR. We develop KAN0438757, a small molecule inhibitor that potently targets PFKFB3. Pharmacological PFKFB3 inhibition impairs recruitment of ribonucleotide reductase M2 and deoxynucleotide incorporation upon DNA repair, and reduces dNTP levels. Importantly, KAN0438757 induces radiosensitization in transformed cells while leaving non-transformed cells unaffected. In summary, we identify a key role for PFKFB3 enzymatic activity in HR repair and present KAN0438757, a selective PFKFB3 inhibitor that could potentially be used as a strategy for the treatment of cancer.
Collapse
Affiliation(s)
- Nina M S Gustafsson
- Science for Life Laboratory, Department of Oncology and Pathology, Karolinska Institutet, 171 21, Stockholm, Sweden.
- Kancera AB, Karolinska Science Park, 171 48, Solna, Sweden.
| | - Katarina Färnegårdh
- Kancera AB, Karolinska Science Park, 171 48, Solna, Sweden
- Drug Discovery and Development Platform, Science for Life Laboratory, Department of Organic Chemistry, Stockholm University, Box 1030, S-171 21, Solna, Sweden
| | - Nadilly Bonagas
- Science for Life Laboratory, Department of Oncology and Pathology, Karolinska Institutet, 171 21, Stockholm, Sweden
| | - Anna Huguet Ninou
- Science for Life Laboratory, Department of Oncology and Pathology, Karolinska Institutet, 171 21, Stockholm, Sweden
- Kancera AB, Karolinska Science Park, 171 48, Solna, Sweden
| | - Petra Groth
- Science for Life Laboratory, Department of Oncology and Pathology, Karolinska Institutet, 171 21, Stockholm, Sweden
| | - Elisee Wiita
- Science for Life Laboratory, Department of Oncology and Pathology, Karolinska Institutet, 171 21, Stockholm, Sweden
| | | | - Kenth Hallberg
- SARomics Biostructures AB, Medicon Village, SE-223 81, Lund, Sweden
- Sprint Bioscience, 141 57, Huddinge, Sweden
| | - Jemina Lehto
- Science for Life Laboratory, Department of Oncology and Pathology, Karolinska Institutet, 171 21, Stockholm, Sweden
- Kancera AB, Karolinska Science Park, 171 48, Solna, Sweden
| | - Rosa Pennisi
- Department of Sciences, Roma Tre University, 446 00146 Rome, Italy
| | | | | | - Jessica Hollers
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Johan Schultz
- Kancera AB, Karolinska Science Park, 171 48, Solna, Sweden
| | | | | | - Petra Marttila
- Science for Life Laboratory, Department of Oncology and Pathology, Karolinska Institutet, 171 21, Stockholm, Sweden
| | - Baek Kim
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30322, USA
- Department of Pharmacy, Kyung-Hee University, 02447, Seoul, South Korea
| | - Martin Norin
- Kancera AB, Karolinska Science Park, 171 48, Solna, Sweden
| | - Thomas Olin
- Kancera AB, Karolinska Science Park, 171 48, Solna, Sweden
| | - Thomas Helleday
- Science for Life Laboratory, Department of Oncology and Pathology, Karolinska Institutet, 171 21, Stockholm, Sweden.
- Sheffield Cancer Centre, Department of Oncology and Metabolism, University of Sheffield, S10 2RX, Sheffield, UK.
| |
Collapse
|
20
|
Molecular signature pathway of gene protein interaction in human mitochondrial DNA (mtDNA) metabolism linked disease. INDIAN JOURNAL OF MEDICAL SPECIALITIES 2018. [DOI: 10.1016/j.injms.2018.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
|
21
|
Clb6-Cdc28 Promotes Ribonucleotide Reductase Subcellular Redistribution during S Phase. Mol Cell Biol 2018; 38:MCB.00497-17. [PMID: 29263158 DOI: 10.1128/mcb.00497-17] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 12/11/2017] [Indexed: 11/20/2022] Open
Abstract
A tightly controlled cellular deoxyribonucleotide (deoxynucleoside triphosphate [dNTP]) pool is critical for maintenance of genome integrity. One mode of dNTP pool regulation is through subcellular localization of ribonucleotide reductase (RNR), the enzyme that catalyzes the rate-limiting step of dNTP biosynthesis. In Saccharomyces cerevisiae, the RNR small subunit, Rnr2-Rnr4, is localized to the nucleus, whereas the large subunit, Rnr1, is cytoplasmic. As cells enter S phase or encounter DNA damage, Rnr2-Rnr4 relocalizes to the cytoplasm to form an active holoenzyme complex with Rnr1. Although the DNA damage-induced relocalization requires the checkpoint kinases Mec1-Rad53-Dun1, the S-phase-specific redistribution does not. Here, we report that the S-phase cyclin-cyclin-dependent kinase (CDK) complex Clb6-Cdc28 controls Rnr2-Rnr4 relocalization in S phase. Rnr2 contains a consensus CDK site and exhibits Clb6-dependent phosphorylation in S phase. Deletion of CLB6 or removal of the CDK site results in an increased association of Rnr2 with its nuclear anchor Wtm1, nuclear retention of Rnr2-Rnr4, and an enhanced sensitivity to the RNR inhibitor hydroxyurea. Thus, we propose that Rnr2-Rnr4 redistribution in S phase is triggered by Clb6-Cdc28-mediated phosphorylation of Rnr2, which disrupts the Rnr2-Wtm1 interaction and promotes the release of Rnr2-Rnr4 from the nucleus.
Collapse
|
22
|
Puts GS, Leonard MK, Pamidimukkala NV, Snyder DE, Kaetzel DM. Nuclear functions of NME proteins. J Transl Med 2018; 98:211-218. [PMID: 29058704 PMCID: PMC6136249 DOI: 10.1038/labinvest.2017.109] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2017] [Revised: 06/16/2017] [Accepted: 06/19/2017] [Indexed: 01/09/2023] Open
Abstract
The NME family of proteins is composed of 10 isoforms, designated NME1-10, which are diverse in their enzymatic activities and patterns of subcellular localization. Each contains a conserved domain associated with a nucleoside diphosphate kinase (NDPK) function, although not all are catalytically active. Several of the NME isoforms (NME1, NME5, NME7, and NME8) also exhibit a 3'-5' exonuclease activity, suggesting roles in DNA proofreading and repair. NME1 and NME2 have been shown to translocate to the nucleus, although they lack a canonical nuclear localization signal. Binding of NME1 and NME2 to DNA does not appear to be sequence-specific in a strict sense, but instead is directed to single-stranded regions and/or other non-B-form structures. NME1 and NME2 have been identified as potential canonical transcription factors that regulate gene transcription through their DNA-binding activities. Indeed, the NME1 and NME2 isoforms have been shown to regulate gene expression programs in a number of cellular settings, and this regulatory function has been proposed to underlie their well-recognized ability to suppress the metastatic phenotype of cancer cells. Moreover, NME1 and, more recently, NME3, have been implicated in repair of both single- and double-stranded breaks in DNA. This suggests that reduced expression of NME proteins could contribute to the genomic instability that drives cancer progression. Clearly, a better understanding of the nuclear functions of NME1 and possibly other NME isoforms could provide critical insights into mechanisms underlying malignant progression in cancer. Indeed, clinical data indicate that the subcellular localization of NME1 may be an important prognostic marker in some cancers. This review summarizes putative functions of nuclear NME proteins in DNA binding, transcription, and DNA damage repair, and highlights their possible roles in cancer progression.
Collapse
|
23
|
Guo JR, Li Z, Wang CY, Kei Lam CW, Chen QQ, Zhang WJ, Wai Wong VK, Yao MC, Zhang W. Profiling of ribonucleotides and deoxyribonucleotides pools in response to DNA damage and repair induced by methyl methanesulfonate in cancer and normal cells. Oncotarget 2017; 8:101707-101719. [PMID: 29254198 PMCID: PMC5731908 DOI: 10.18632/oncotarget.21521] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 09/03/2017] [Indexed: 02/04/2023] Open
Abstract
The absolute and relative pool sizes of deoxyribonucleotides (dRNs) are essential in DNA replication fidelity, DNA damage and repair. We found in this study that although DNA damage induced by methyl methanesulfonate (MMS) seemed similar in cancer (HepG2) and normal (LO2) cells, more extensive alterations in ribonucleotides (RNs) and dRNs pools occurred in HepG2 cells indicating that HepG2 cells were more vigilant to DNA damage. After 10 h repair, RNs pools were still severely perturbed in LO2 cells. Compared to LO2 cells, deoxyribonucleotide triphosphates (dNTPs) pools in HepG2 cells elevated by more folds which could facilitate more efficient DNA repair and improve survival probability following DNA damage, although this should definitely lead to higher mutation rates. DNA repair was more efficient in HepG2 cells at S phase and it partly came to an end while DNA repair was still uncompleted in LO2 cells outside S phase. In conclusion, our results demonstrated that HepG2 and LO2 cells presented many differences in nucleotide metabolism, cell cycle checkpoints and DNA repair pathways in response to DNA damage, which could be potential targets for cancer treatment.
Collapse
Affiliation(s)
- Jian-Ru Guo
- State Key Laboratory of Quality Research in Chinese Medicines, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Taipa, China
| | - Zheng Li
- State Key Laboratory of Quality Research in Chinese Medicines, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Taipa, China
| | - Cai-Yun Wang
- State Key Laboratory of Quality Research in Chinese Medicines, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Taipa, China
| | - Christopher Wai Kei Lam
- State Key Laboratory of Quality Research in Chinese Medicines, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Taipa, China
| | - Qian-Qian Chen
- State Key Laboratory of Quality Research in Chinese Medicines, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Taipa, China
| | - Wei-Jia Zhang
- School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Vincent Kam Wai Wong
- State Key Laboratory of Quality Research in Chinese Medicines, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Taipa, China
| | - Mei-Cun Yao
- School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Wei Zhang
- State Key Laboratory of Quality Research in Chinese Medicines, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Taipa, China
| |
Collapse
|
24
|
Kochenova OV, Bezalel-Buch R, Tran P, Makarova AV, Chabes A, Burgers PMJ, Shcherbakova PV. Yeast DNA polymerase ζ maintains consistent activity and mutagenicity across a wide range of physiological dNTP concentrations. Nucleic Acids Res 2017; 45:1200-1218. [PMID: 28180291 PMCID: PMC5388397 DOI: 10.1093/nar/gkw1149] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 10/31/2016] [Accepted: 11/02/2016] [Indexed: 11/12/2022] Open
Abstract
In yeast, dNTP pools expand drastically during DNA damage response. We show that similar dNTP elevation occurs in strains, in which intrinsic replisome defects promote the participation of error-prone DNA polymerase ζ (Polζ) in replication of undamaged DNA. To understand the significance of dNTP pools increase for Polζ function, we studied the activity and fidelity of four-subunit Polζ (Polζ4) and Polζ4-Rev1 (Polζ5) complexes in vitro at ‘normal S-phase’ and ‘damage-response’ dNTP concentrations. The presence of Rev1 inhibited the activity of Polζ and greatly increased the rate of all three ‘X-dCTP’ mispairs, which Polζ4 alone made extremely inefficiently. Both Polζ4 and Polζ5 were most promiscuous at G nucleotides and frequently generated multiple closely spaced sequence changes. Surprisingly, the shift from ‘S-phase’ to ‘damage-response’ dNTP levels only minimally affected the activity, fidelity and error specificity of Polζ complexes. Moreover, Polζ-dependent mutagenesis triggered by replisome defects or UV irradiation in vivo was not decreased when dNTP synthesis was suppressed by hydroxyurea, indicating that Polζ function does not require high dNTP levels. The results support a model wherein dNTP elevation is needed to facilitate non-mutagenic tolerance pathways, while Polζ synthesis represents a unique mechanism of rescuing stalled replication when dNTP supply is low.
Collapse
Affiliation(s)
- Olga V Kochenova
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE, USA
| | - Rachel Bezalel-Buch
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
| | - Phong Tran
- Department of Medical Biochemistry and Biophysics and Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden
| | - Alena V Makarova
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
| | - Andrei Chabes
- Department of Medical Biochemistry and Biophysics and Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden
| | - Peter M J Burgers
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
| | - Polina V Shcherbakova
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE, USA
| |
Collapse
|
25
|
Misselbeck K, Marchetti L, Field MS, Scotti M, Priami C, Stover PJ. A hybrid stochastic model of folate-mediated one-carbon metabolism: Effect of the common C677T MTHFR variant on de novo thymidylate biosynthesis. Sci Rep 2017; 7:797. [PMID: 28400561 PMCID: PMC5429759 DOI: 10.1038/s41598-017-00854-w] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 03/13/2017] [Indexed: 11/19/2022] Open
Abstract
Folate-mediated one-carbon metabolism (FOCM) is an interconnected network of metabolic pathways, including those required for the de novo synthesis of dTMP and purine nucleotides and for remethylation of homocysteine to methionine. Mouse models of folate-responsive neural tube defects (NTDs) indicate that impaired de novo thymidylate (dTMP) synthesis through changes in SHMT expression is causative in folate-responsive NTDs. We have created a hybrid computational model comprised of ordinary differential equations and stochastic simulation. We investigated whether the de novo dTMP synthesis pathway was sensitive to perturbations in FOCM that are known to be associated with human NTDs. This computational model shows that de novo dTMP synthesis is highly sensitive to the common MTHFR C677T polymorphism and that the effect of the polymorphism on FOCM is greater in folate deficiency. Computational simulations indicate that the MTHFR C677T polymorphism and folate deficiency interact to increase the stochastic behavior of the FOCM network, with the greatest instability observed for reactions catalyzed by serine hydroxymethyltransferase (SHMT). Furthermore, we show that de novo dTMP synthesis does not occur in the cytosol at rates sufficient for DNA replication, supporting empirical data indicating that impaired nuclear de novo dTMP synthesis results in uracil misincorporation into DNA.
Collapse
Affiliation(s)
- Karla Misselbeck
- The Microsoft Research - University of Trento Centre for Computational and Systems Biology (COSBI), Piazza Manifattura, 1, 38068, Rovereto (TN), Italy
- Department of Mathematics, University of Trento, Trento, Italy
| | - Luca Marchetti
- The Microsoft Research - University of Trento Centre for Computational and Systems Biology (COSBI), Piazza Manifattura, 1, 38068, Rovereto (TN), Italy
| | - Martha S Field
- Division of Nutritional Sciences, Cornell University, Ithaca, New York, 14853, USA
| | - Marco Scotti
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Düsternbrooker Weg 20, 24105, Kiel, Germany
| | - Corrado Priami
- The Microsoft Research - University of Trento Centre for Computational and Systems Biology (COSBI), Piazza Manifattura, 1, 38068, Rovereto (TN), Italy.
- Department of Mathematics, University of Trento, Trento, Italy.
| | - Patrick J Stover
- Division of Nutritional Sciences, Cornell University, Ithaca, New York, 14853, USA.
| |
Collapse
|
26
|
Pai CC, Kearsey SE. A Critical Balance: dNTPs and the Maintenance of Genome Stability. Genes (Basel) 2017; 8:genes8020057. [PMID: 28146119 PMCID: PMC5333046 DOI: 10.3390/genes8020057] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 01/24/2017] [Indexed: 01/14/2023] Open
Abstract
A crucial factor in maintaining genome stability is establishing deoxynucleoside triphosphate (dNTP) levels within a range that is optimal for chromosomal replication. Since DNA replication is relevant to a wide range of other chromosomal activities, these may all be directly or indirectly affected when dNTP concentrations deviate from a physiologically normal range. The importance of understanding these consequences is relevant to genetic disorders that disturb dNTP levels, and strategies that inhibit dNTP synthesis in cancer chemotherapy and for treatment of other disorders. We review here how abnormal dNTP levels affect DNA replication and discuss the consequences for genome stability.
Collapse
Affiliation(s)
- Chen-Chun Pai
- CRUK-MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, ORCRB, Roosevelt Drive, Oxford OX3 7DQ, UK.
| | - Stephen E Kearsey
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK.
| |
Collapse
|
27
|
Wrigstedt P, Iashin V, Lagerblom K, Keskiväli J, Chernichenko K, Repo T. Syntheses of C-6 Aryl- and Alkynyl-Substituted Thymidines from Thymidine trans-5,6-Bromohydrins. European J Org Chem 2017. [DOI: 10.1002/ejoc.201601219] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Pauli Wrigstedt
- Department of Chemistry; University of Helsinki; P. O. Box 55 (A. I. Virtasen aukio 1) 00014 Helsinki Finland
| | - Vladimir Iashin
- Department of Chemistry; University of Helsinki; P. O. Box 55 (A. I. Virtasen aukio 1) 00014 Helsinki Finland
| | - Kalle Lagerblom
- Department of Chemistry; University of Helsinki; P. O. Box 55 (A. I. Virtasen aukio 1) 00014 Helsinki Finland
| | - Juha Keskiväli
- Department of Chemistry; University of Helsinki; P. O. Box 55 (A. I. Virtasen aukio 1) 00014 Helsinki Finland
| | - Konstantin Chernichenko
- Department of Chemistry; University of Helsinki; P. O. Box 55 (A. I. Virtasen aukio 1) 00014 Helsinki Finland
| | - Timo Repo
- Department of Chemistry; University of Helsinki; P. O. Box 55 (A. I. Virtasen aukio 1) 00014 Helsinki Finland
| |
Collapse
|
28
|
Abstract
Thymidylate (dTMP) biosynthesis plays an essential and exclusive function in DNA synthesis and proper cell division, and therefore has been an attractive therapeutic target. Folate analogs, known as antifolates, and nucleotide analogs that inhibit the enzymatic action of the de novo thymidylate biosynthesis pathway and are commonly used in cancer treatment. In this review, we examine the mechanisms by which the antifolate 5-fluorouracil, as well as other dTMP synthesis inhibitors, function in cancer treatment in light of emerging evidence that dTMP synthesis occurs in the nucleus. Nuclear localization of the de novo dTMP synthesis pathway requires modification of the pathway enzymes by the small ubiquitin-like modifier (SUMO) protein. SUMOylation is required for nuclear localization of the de novo dTMP biosynthesis pathway, and disruption in the SUMO pathway inhibits cell proliferation in several cancer models. We summarize evidence that the nuclear localization of the dTMP biosynthesis pathway is a critical factor in the efficacy of antifolate-based therapies that target dTMP synthesis.
Collapse
|
29
|
Levring TB, Kongsbak M, Rode AKO, Woetmann A, Ødum N, Bonefeld CM, Geisler C. Human CD4+ T cells require exogenous cystine for glutathione and DNA synthesis. Oncotarget 2016; 6:21853-64. [PMID: 26392411 PMCID: PMC4673131 DOI: 10.18632/oncotarget.5213] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 08/24/2015] [Indexed: 12/15/2022] Open
Abstract
Adaptive immune responses require activation and expansion of antigen-specific T cells. Whereas early T cell activation is independent of exogenous cystine (Cys2), T cell proliferation is dependent of Cys2. However, the exact roles of Cys2 in T cell proliferation still need to be determined. The aim of this study was to elucidate why activated human T cells require exogenous Cys2 in order to proliferate. We activated purified naïve human CD4+ T cells and found that glutathione (GSH) levels and DNA synthesis were dependent on Cys2 and increased in parallel with increasing concentrations of Cys2. Vice-versa, the GSH synthesis inhibitor L-buthionine-sulfoximine (BSO) and inhibition of Cys2 uptake with glutamate inhibited GSH and DNA synthesis in parallel. We further found that thioredoxin (Trx) can partly substitute for GSH during DNA synthesis. Finally, we show that GSH or Trx is required for the activity of ribonucleotide reductase (RNR), the enzyme responsible for generation of the deoxyribonucleotide DNA building blocks. In conclusion, we show that activated human T cells require exogenous Cys2 to proliferate and that this is partly explained by the fact that Cys2 is required for production of GSH, which in turn is required for optimal RNR-mediated deoxyribonucleotide synthesis and DNA replication.
Collapse
Affiliation(s)
- Trine B Levring
- Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Martin Kongsbak
- Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Anna K O Rode
- Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Anders Woetmann
- Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Niels Ødum
- Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Charlotte Menné Bonefeld
- Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Carsten Geisler
- Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| |
Collapse
|
30
|
Wrigstedt P, Kavakka J, Heikkinen S, Nieger M, Räisänen M, Repo T. The Reactivity of Thymine and Thymidine 5,6-Epoxides with Organometallic Reagents - A Route to Thymidine (6-4) Photoproduct Analogues. J Org Chem 2016; 81:3848-59. [PMID: 27080560 DOI: 10.1021/acs.joc.6b00495] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
This report describes an efficient procedure for the generation and isolation of various thymine and thymidine 5,6-epoxides from the corresponding trans-5,6-bromohydrins by reaction with triethylamine. The quantitative isolation of the epoxides, accomplished by solvent precipitation of triethylamine hydrobromide, enabled their regiospecific ring-opening at C6 position by organometallic nucleophiles. The reaction was amenable to a broad range of alkyl, aryl, alkenyl, and alkynyl organomagnesium, -zinc, -aluminum, or -boron reagents, although the reactivity was strongly affected by the electronic effects of N3 protecting group. Additionally, the reaction featured excellent cis-diastereoselectivity providing access to C6-carbon-functionalized dihydrothymidine cis-alcohols, which are synthetic derivatives of UV-induced DNA lesions, namely, thymidine (6-4) photoproducts.
Collapse
Affiliation(s)
- Pauli Wrigstedt
- Department of Chemistry, †Laboratory of Inorganic Chemistry and ‡Laboratory of Organic Chemistry, University of Helsinki , P.O. Box 55, Helsinki FIN-00014, Finland
| | - Jari Kavakka
- Department of Chemistry, †Laboratory of Inorganic Chemistry and ‡Laboratory of Organic Chemistry, University of Helsinki , P.O. Box 55, Helsinki FIN-00014, Finland
| | - Sami Heikkinen
- Department of Chemistry, †Laboratory of Inorganic Chemistry and ‡Laboratory of Organic Chemistry, University of Helsinki , P.O. Box 55, Helsinki FIN-00014, Finland
| | - Martin Nieger
- Department of Chemistry, †Laboratory of Inorganic Chemistry and ‡Laboratory of Organic Chemistry, University of Helsinki , P.O. Box 55, Helsinki FIN-00014, Finland
| | - Minna Räisänen
- Department of Chemistry, †Laboratory of Inorganic Chemistry and ‡Laboratory of Organic Chemistry, University of Helsinki , P.O. Box 55, Helsinki FIN-00014, Finland
| | - Timo Repo
- Department of Chemistry, †Laboratory of Inorganic Chemistry and ‡Laboratory of Organic Chemistry, University of Helsinki , P.O. Box 55, Helsinki FIN-00014, Finland
| |
Collapse
|
31
|
Wilhelm T, Ragu S, Magdalou I, Machon C, Dardillac E, Técher H, Guitton J, Debatisse M, Lopez BS. Slow Replication Fork Velocity of Homologous Recombination-Defective Cells Results from Endogenous Oxidative Stress. PLoS Genet 2016; 12:e1006007. [PMID: 27135742 PMCID: PMC4852921 DOI: 10.1371/journal.pgen.1006007] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 04/05/2016] [Indexed: 01/01/2023] Open
Abstract
Replications forks are routinely hindered by different endogenous stresses. Because homologous recombination plays a pivotal role in the reactivation of arrested replication forks, defects in homologous recombination reveal the initial endogenous stress(es). Homologous recombination-defective cells consistently exhibit a spontaneously reduced replication speed, leading to mitotic extra centrosomes. Here, we identify oxidative stress as a major endogenous source of replication speed deceleration in homologous recombination-defective cells. The treatment of homologous recombination-defective cells with the antioxidant N-acetyl-cysteine or the maintenance of the cells at low O2 levels (3%) rescues both the replication fork speed, as monitored by single-molecule analysis (molecular combing), and the associated mitotic extra centrosome frequency. Reciprocally, the exposure of wild-type cells to H2O2 reduces the replication fork speed and generates mitotic extra centrosomes. Supplying deoxynucleotide precursors to H2O2-exposed cells rescued the replication speed. Remarkably, treatment with N-acetyl-cysteine strongly expanded the nucleotide pool, accounting for the replication speed rescue. Remarkably, homologous recombination-defective cells exhibit a high level of endogenous reactive oxygen species. Consistently, homologous recombination-defective cells accumulate spontaneous γH2AX or XRCC1 foci that are abolished by treatment with N-acetyl-cysteine or maintenance at 3% O2. Finally, oxidative stress stimulated homologous recombination, which is suppressed by supplying deoxynucleotide precursors. Therefore, the cellular redox status strongly impacts genome duplication and transmission. Oxidative stress should generate replication stress through different mechanisms, including DNA damage and nucleotide pool imbalance. These data highlight the intricacy of endogenous replication and oxidative stresses, which are both evoked during tumorigenesis and senescence initiation, and emphasize the importance of homologous recombination as a barrier against spontaneous genetic instability triggered by the endogenous oxidative/replication stress axis. Endogenous stress is an important stress because it challenges cells daily. However, endogenous stress is difficult to apprehend. Replication forks are routinely hindered by different endogenous stresses. Because homologous recombination plays a pivotal role in the reactivation of arrested replication forks, defects in homologous recombination reveal the initial endogenous stress(es). Here we identify endogenous oxidative stress among the different potential endogenous stresses as being responsible for spontaneous replication defects in homologous recombination-defective cells. Therefore, oxidative and replication stresses, which are both evoked during tumorigenesis and senescence initiation, are linked, and homologous recombination acts as a barrier against spontaneous genetic instability triggered by endogenous oxidative/replication stress.
Collapse
Affiliation(s)
- Therese Wilhelm
- CNRS UMR 8200, Gustave Roussy Cancer Institute, Université Paris-Saclay, Team labeled “Ligue 2014”, Villejuif, France
| | - Sandrine Ragu
- CNRS UMR 8200, Gustave Roussy Cancer Institute, Université Paris-Saclay, Team labeled “Ligue 2014”, Villejuif, France
| | - Indiana Magdalou
- CNRS UMR 8200, Gustave Roussy Cancer Institute, Université Paris-Saclay, Team labeled “Ligue 2014”, Villejuif, France
| | - Christelle Machon
- Laboratoire de Biochimie et Toxicologie, Hospices Civils de Lyon, Centre Hospitalier Lyon-Sud, Pierre-Bénite, France
- Laboratoire de Chimie Analytique, Université de Lyon, Université Lyon 1, ISPB Faculté de Pharmacie, Lyon, France
| | - Elodie Dardillac
- CNRS UMR 8200, Gustave Roussy Cancer Institute, Université Paris-Saclay, Team labeled “Ligue 2014”, Villejuif, France
| | - Hervé Técher
- Institut Curie, Centre de Recherche, Paris, France, UPMC Université Paris 06, Paris, France, CNRS UMR 3244, Paris, France
| | - Jérôme Guitton
- Laboratoire de Biochimie et Toxicologie, Hospices Civils de Lyon, Centre Hospitalier Lyon-Sud, Pierre-Bénite, France
- Laboratoire de Toxicologie, Université Lyon 1, ISPB, Faculté de Pharmacie, Lyon, France
| | - Michelle Debatisse
- Institut Curie, Centre de Recherche, Paris, France, UPMC Université Paris 06, Paris, France, CNRS UMR 3244, Paris, France
| | - Bernard S. Lopez
- CNRS UMR 8200, Gustave Roussy Cancer Institute, Université Paris-Saclay, Team labeled “Ligue 2014”, Villejuif, France
- * E-mail:
| |
Collapse
|
32
|
The direct interaction of NME3 with Tip60 in DNA repair. Biochem J 2016; 473:1237-45. [DOI: 10.1042/bcj20160122] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Accepted: 03/04/2016] [Indexed: 11/17/2022]
Abstract
Cellular supply of dNTPs via RNR (ribonucleotide reductase) is crucial for DNA replication and repair. It has been shown that DNA-damage-site-specific recruitment of RNR is critical for DNA repair efficiency in quiescent cells. The catalytic function of RNR produces dNDPs. The subsequent step of dNTP formation requires the function of NDP kinase. There are ten isoforms of NDP kinase in human cells. In the present study, we identified NME3 as one specific NDP kinase that interacts directly with Tip60, a histone acetyltransferase, to form a complex with RNR. Our data reveal that NME3 recruitment to DNA damage sites depends on this interaction. Disruption of interaction of NME3 with Tip60 suppressed DNA repair in serum-deprived cells. Thus Tip60 interacts with RNR and NME3 to provide site-specific synthesis of dNTP for facilitating DNA repair in serum-deprived cells which contain low levels of dNTPs.
Collapse
|
33
|
Daly MB, Roth ME, Bonnac L, Maldonado JO, Xie J, Clouser CL, Patterson SE, Kim B, Mansky LM. Dual anti-HIV mechanism of clofarabine. Retrovirology 2016; 13:20. [PMID: 27009333 PMCID: PMC4806454 DOI: 10.1186/s12977-016-0254-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 03/17/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND HIV-1 replication kinetics inherently depends on the availability of cellular dNTPs for viral DNA synthesis. In activated CD4(+) T cells and other rapidly dividing cells, the concentrations of dNTPs are high and HIV-1 reverse transcription occurs in an efficient manner. In contrast, nondividing cells such as macrophages have lower dNTP pools, which restricts efficient reverse transcription. Clofarabine is an FDA approved ribonucleotide reductase inhibitor, which has shown potent antiretroviral activity in transformed cell lines. Here, we explore the potency, toxicity and mechanism of action of clofarabine in the human primary HIV-1 target cells: activated CD4(+) T cells and macrophages. RESULTS Clofarabine is a potent HIV-1 inhibitor in both activated CD4(+) T cells and macrophages. Due to its minimal toxicity in macrophages, clofarabine displays a selectivity index over 300 in this nondividing cell type. The anti-HIV-1 activity of clofarabine correlated with a significant decrease in both cellular dNTP levels and viral DNA synthesis. Additionally, we observed that clofarabine triphosphate was directly incorporated into DNA by HIV-1 reverse transcriptase and blocked processive DNA synthesis, particularly at the low dNTP levels found in macrophages. CONCLUSIONS Taken together, these data provide strong mechanistic evidence that clofarabine is a dual action inhibitor of HIV-1 replication that both limits dNTP substrates for viral DNA synthesis and directly inhibits the DNA polymerase activity of HIV-1 reverse transcriptase.
Collapse
Affiliation(s)
- Michele B Daly
- Center for Drug Discovery, Department of Pediatrics, Emory Center for AIDS Research, Emory University, Children's Healthcare of Atlanta, 1760 Haygood Dr., Atlanta, GA, 30322, USA
| | - Megan E Roth
- Institute for Molecular Virology, University of Minnesota, 18-242 Moos Tower, 515 Delaware St SE, Minneapolis, MN, 55455, USA.,Department of Diagnostic and Biological Sciences, School of Dentistry, University of Minnesota, Minneapolis, MN, 55455, USA.,Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Laurent Bonnac
- Center for Drug Design, Academic Health Center, University of Minnesota, Minneapolis, MN, 55455, USA
| | - José O Maldonado
- Institute for Molecular Virology, University of Minnesota, 18-242 Moos Tower, 515 Delaware St SE, Minneapolis, MN, 55455, USA.,Department of Diagnostic and Biological Sciences, School of Dentistry, University of Minnesota, Minneapolis, MN, 55455, USA.,Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Jiashu Xie
- Center for Drug Design, Academic Health Center, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Christine L Clouser
- Institute for Molecular Virology, University of Minnesota, 18-242 Moos Tower, 515 Delaware St SE, Minneapolis, MN, 55455, USA
| | - Steven E Patterson
- Center for Drug Design, Academic Health Center, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Baek Kim
- Center for Drug Discovery, Department of Pediatrics, Emory Center for AIDS Research, Emory University, Children's Healthcare of Atlanta, 1760 Haygood Dr., Atlanta, GA, 30322, USA.
| | - Louis M Mansky
- Institute for Molecular Virology, University of Minnesota, 18-242 Moos Tower, 515 Delaware St SE, Minneapolis, MN, 55455, USA. .,Department of Diagnostic and Biological Sciences, School of Dentistry, University of Minnesota, Minneapolis, MN, 55455, USA. .,Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN, 55455, USA. .,Center for Drug Design, Academic Health Center, University of Minnesota, Minneapolis, MN, 55455, USA.
| |
Collapse
|
34
|
Sanvisens N, Romero AM, Zhang C, Wu X, An X, Huang M, Puig S. Yeast Dun1 Kinase Regulates Ribonucleotide Reductase Small Subunit Localization in Response to Iron Deficiency. J Biol Chem 2016; 291:9807-17. [PMID: 26970775 DOI: 10.1074/jbc.m116.720862] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Indexed: 12/25/2022] Open
Abstract
Ribonucleotide reductase (RNR) is an essential iron-dependent enzyme that catalyzes deoxyribonucleotide synthesis in eukaryotes. Living organisms have developed multiple strategies to tightly modulate RNR function to avoid inadequate or unbalanced deoxyribonucleotide pools that cause DNA damage and genome instability. Yeast cells activate RNR in response to genotoxic stress and iron deficiency by facilitating redistribution of its small heterodimeric subunit Rnr2-Rnr4 from the nucleus to the cytoplasm, where it forms an active holoenzyme with large Rnr1 subunit. Dif1 protein inhibits RNR by promoting nuclear import of Rnr2-Rnr4. Upon DNA damage, Dif1 phosphorylation by the Dun1 checkpoint kinase and its subsequent degradation enhances RNR function. In this report, we demonstrate that Dun1 kinase triggers Rnr2-Rnr4 redistribution to the cytoplasm in response to iron deficiency. We show that Rnr2-Rnr4 relocalization by low iron requires Dun1 kinase activity and phosphorylation site Thr-380 in the Dun1 activation loop, but not the Dun1 forkhead-associated domain. By using different Dif1 mutant proteins, we uncover that Dun1 phosphorylates Dif1 Ser-104 and Thr-105 residues upon iron scarcity. We observe that the Dif1 phosphorylation pattern differs depending on the stimuli, which suggests different Dun1 activating pathways. Importantly, the Dif1-S104A/T105A mutant exhibits defects in nucleus-to-cytoplasm redistribution of Rnr2-Rnr4 by iron limitation. Taken together, these results reveal that, in response to iron starvation, Dun1 kinase phosphorylates Dif1 to stimulate Rnr2-Rnr4 relocalization to the cytoplasm and promote RNR function.
Collapse
Affiliation(s)
- Nerea Sanvisens
- From the Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), Paterna, Valencia 46980, Spain and
| | - Antonia M Romero
- From the Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), Paterna, Valencia 46980, Spain and
| | - Caiguo Zhang
- the Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado 80045
| | - Xiaorong Wu
- the Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado 80045
| | - Xiuxiang An
- the Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado 80045
| | - Mingxia Huang
- the Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado 80045
| | - Sergi Puig
- From the Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), Paterna, Valencia 46980, Spain and
| |
Collapse
|
35
|
Mohamady S, Taylor SD. Synthesis of Nucleoside Triphosphates from 2'-3'-Protected Nucleosides Using Trimetaphosphate. Org Lett 2016; 18:580-3. [PMID: 26759914 DOI: 10.1021/acs.orglett.5b03624] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Chemists have been attempting to triphosphorylate nucleosides and other alcohols using trimetaphosphate (TriMP) since the 1960s. However, this route appears to have been abandoned due to poor yields. The first practical syntheses of nucleoside triphosphates (NTPs) are reported using TriMP as the key reagent. This was achieved by reacting the tetrabutylammonium salt of TriMP with mesitylenesulfonyl chloride in the presence of DABCO in pyridine followed by the addition of an appropriately protected nucleoside and phthalimide. Quenching the reaction with aqueous buffer followed by hydrolysis of the OH protecting groups gave the NTPs in good yield.
Collapse
Affiliation(s)
- Samy Mohamady
- Faculty of Pharmacy, The British University in Egypt , Cairo-Suez Desert Road, 11837 Cairo, Egypt
| | - Scott D Taylor
- Department of Chemistry, University of Waterloo , 200 University Avenue West, Waterloo, Ontario, Canada N2L 3G1
| |
Collapse
|
36
|
Tsao N, Lee MH, Zhang W, Cheng YC, Chang ZF. The contribution of CMP kinase to the efficiency of DNA repair. Cell Cycle 2015; 14:354-63. [PMID: 25659034 DOI: 10.4161/15384101.2014.987618] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Cellular supply of deoxynucleoside triphosphates (dNTPs) is crucial for DNA replication and repair. In this study, we investigated the role of CMP/UMP kinase (CMPK), an enzyme catalyzes CDP formation, in DNA repair. Knockdown of CMPK delays DNA repair during recovery from UV damage in serum-deprived cells but not in the cells without serum deprivation. Exogenous supply of cytidine or deoxycytidine facilitates DNA repair dependent on CMPK in serum-deprived cells, suggesting that the synthesis of dCDP or CDP determines the rate of repair. However, CMPK knockdown does not affect the steady state level of dCTP in serum-deprived cells. We then found the localization of CMPK at DNA damage sites and its complex formation with Tip60 and ribonucleotide reductase. Our analysis demonstrated that the N-terminal 32-amino-acid of CMPK is required for its recruitment to DNA damage sites in a Tip60-dependent manner. Re-expression of wild-type but not N-terminus deleted CMPK restores the efficiency of DNA repair in CMPK knockdown cells. We proposed that site-specific dCDP formation via CMPK provides a means to facilitate DNA repair in serum-deprived cells.
Collapse
Affiliation(s)
- Ning Tsao
- a Graduate Institute of Biochemistry and Molecular Biology; College of Medicine ; National Taiwan University ; Taipei , Taiwan (R.O.C.)
| | | | | | | | | |
Collapse
|
37
|
Graindorge D, Martineau S, Machon C, Arnoux P, Guitton J, Francesconi S, Frochot C, Sage E, Girard PM. Singlet Oxygen-Mediated Oxidation during UVA Radiation Alters the Dynamic of Genomic DNA Replication. PLoS One 2015; 10:e0140645. [PMID: 26485711 PMCID: PMC4618472 DOI: 10.1371/journal.pone.0140645] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Accepted: 09/29/2015] [Indexed: 02/07/2023] Open
Abstract
UVA radiation (320–400 nm) is a major environmental agent that can exert its deleterious action on living organisms through absorption of the UVA photons by endogenous or exogenous photosensitizers. This leads to the production of reactive oxygen species (ROS), such as singlet oxygen (1O2) and hydrogen peroxide (H2O2), which in turn can modify reversibly or irreversibly biomolecules, such as lipids, proteins and nucleic acids. We have previously reported that UVA-induced ROS strongly inhibit DNA replication in a dose-dependent manner, but independently of the cell cycle checkpoints activation. Here, we report that the production of 1O2 by UVA radiation leads to a transient inhibition of replication fork velocity, a transient decrease in the dNTP pool, a quickly reversible GSH-dependent oxidation of the RRM1 subunit of ribonucleotide reductase and sustained inhibition of origin firing. The time of recovery post irradiation for each of these events can last from few minutes (reduction of oxidized RRM1) to several hours (replication fork velocity and origin firing). The quenching of 1O2 by sodium azide prevents the delay of DNA replication, the decrease in the dNTP pool and the oxidation of RRM1, while inhibition of Chk1 does not prevent the inhibition of origin firing. Although the molecular mechanism remains elusive, our data demonstrate that the dynamic of replication is altered by UVA photosensitization of vitamins via the production of singlet oxygen.
Collapse
Affiliation(s)
- Dany Graindorge
- CNRS UMR 3348, Stress Génotoxiques et Cancer, Orsay, France
- Curie Institute, PSL Research University, Orsay, France
| | - Sylvain Martineau
- CNRS UMR 3348, Stress Génotoxiques et Cancer, Orsay, France
- Curie Institute, PSL Research University, Orsay, France
| | - Christelle Machon
- Centre Hospitalier Lyon-Sud, Hospices Civils de Lyon, Laboratoire de biochimie-toxicologie, Pierre Bénite, France
- Laboratoire de chimie analytique, Université Lyon 1, ISPBL, Faculté de pharmacie, Lyon, France
| | - Philippe Arnoux
- Université de Lorraine, Laboratoire Réactions et Génie des Procédés (LRGP), Nancy, France
- CNRS, UMR7274, Nancy, France
| | - Jérôme Guitton
- Centre Hospitalier Lyon-Sud, Hospices Civils de Lyon, Laboratoire de biochimie-toxicologie, Pierre Bénite, France
- Laboratoire de Toxicologie, Université Lyon 1, ISPBL, Faculté de pharmacie, Lyon, France
| | - Stefania Francesconi
- CNRS UMR 3348, Stress Génotoxiques et Cancer, Orsay, France
- Curie Institute, PSL Research University, Orsay, France
| | - Céline Frochot
- Université de Lorraine, Laboratoire Réactions et Génie des Procédés (LRGP), Nancy, France
- CNRS, UMR7274, Nancy, France
| | - Evelyne Sage
- CNRS UMR 3348, Stress Génotoxiques et Cancer, Orsay, France
- Curie Institute, PSL Research University, Orsay, France
| | - Pierre-Marie Girard
- CNRS UMR 3348, Stress Génotoxiques et Cancer, Orsay, France
- Curie Institute, PSL Research University, Orsay, France
- * E-mail:
| |
Collapse
|
38
|
Kohnken R, Kodigepalli KM, Wu L. Regulation of deoxynucleotide metabolism in cancer: novel mechanisms and therapeutic implications. Mol Cancer 2015; 14:176. [PMID: 26416562 PMCID: PMC4587406 DOI: 10.1186/s12943-015-0446-6] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Accepted: 09/18/2015] [Indexed: 11/16/2022] Open
Abstract
Regulation of intracellular deoxynucleoside triphosphate (dNTP) pool is critical to genomic stability and cancer development. Imbalanced dNTP pools can lead to enhanced mutagenesis and cell proliferation resulting in cancer development. Therapeutic agents that target dNTP synthesis and metabolism are commonly used in treatment of several types of cancer. Despite several studies, the molecular mechanisms that regulate the intracellular dNTP levels and maintain their homeostasis are not completely understood. The discovery of SAMHD1 as the first mammalian dNTP triphosphohydrolase provided new insight into the mechanisms of dNTP regulation. SAMHD1 maintains the homeostatic dNTP levels that regulate DNA replication and damage repair. Recent progress indicates that gene mutations and epigenetic mechanisms lead to downregulation of SAMHD1 activity or expression in multiple cancers. Impaired SAMHD1 function can cause increased dNTP pool resulting in genomic instability and cell-cycle progression, thereby facilitating cancer cell proliferation. This review summarizes the latest advances in understanding the importance of dNTP metabolism in cancer development and the novel function of SAMHD1 in regulating this process.
Collapse
Affiliation(s)
- Rebecca Kohnken
- Center for Retrovirus Research, Department of Veterinary Biosciences, The Ohio State University, 1900 Coffey Road, Columbus, OH, 43210, USA
| | - Karthik M Kodigepalli
- Center for Retrovirus Research, Department of Veterinary Biosciences, The Ohio State University, 1900 Coffey Road, Columbus, OH, 43210, USA
| | - Li Wu
- Center for Retrovirus Research, Department of Veterinary Biosciences, The Ohio State University, 1900 Coffey Road, Columbus, OH, 43210, USA. .,Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, 43210, USA. .,Comprehensive Cancer Center, The Ohio State University, Columbus, OH, 43210, USA.
| |
Collapse
|
39
|
Róna G, Borsos M, Ellis JJ, Mehdi AM, Christie M, Környei Z, Neubrandt M, Tóth J, Bozóky Z, Buday L, Madarász E, Bodén M, Kobe B, Vértessy BG. Dynamics of re-constitution of the human nuclear proteome after cell division is regulated by NLS-adjacent phosphorylation. Cell Cycle 2015; 13:3551-64. [PMID: 25483092 DOI: 10.4161/15384101.2014.960740] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Phosphorylation by the cyclin-dependent kinase 1 (Cdk1) adjacent to nuclear localization signals (NLSs) is an important mechanism of regulation of nucleocytoplasmic transport. However, no systematic survey has yet been performed in human cells to analyze this regulatory process, and the corresponding cell-cycle dynamics have not yet been investigated. Here, we focused on the human proteome and found that numerous proteins, previously not identified in this context, are associated with Cdk1-dependent phosphorylation sites adjacent to their NLSs. Interestingly, these proteins are involved in key regulatory events of DNA repair, epigenetics, or RNA editing and splicing. This finding indicates that cell-cycle dependent events of genome editing and gene expression profiling may be controlled by nucleocytoplasmic trafficking. For in-depth investigations, we selected a number of these proteins and analyzed how point mutations, expected to modify the phosphorylation ability of the NLS segments, perturb nucleocytoplasmic localization. In each case, we found that mutations mimicking hyper-phosphorylation abolish nuclear import processes. To understand the mechanism underlying these phenomena, we performed a video microscopy-based kinetic analysis to obtain information on cell-cycle dynamics on a model protein, dUTPase. We show that the NLS-adjacent phosphorylation by Cdk1 of human dUTPase, an enzyme essential for genomic integrity, results in dynamic cell cycle-dependent distribution of the protein. Non-phosphorylatable mutants have drastically altered protein re-import characteristics into the nucleus during the G1 phase. Our results suggest a dynamic Cdk1-driven mechanism of regulation of the nuclear proteome composition during the cell cycle.
Collapse
Key Words
- Cdc28, cyclin-dependent protein kinase (Cdk) encoded by CDC28
- Cdk1, cyclin-dependent kinase 1
- GO, gene ontology
- NES, nuclear export signal
- NLS, nuclear localization signal
- SNP, single nucleotide polymorphisms
- SV40, Simian virus 40
- UBA1, Ubiquitin-activating enzyme E1
- UNG2, Human Uracil-DNA glycosylase 2
- cNLS, classical nuclear localization signal
- cell cycle
- dNTP, deoxyribonucleotide triphosphate
- dTTP, deoxythymidine triphosphate
- dUMP, deoxyuridine monophosphate
- dUTP, deoxyuridine triphosphate
- dUTPase
- importin
- phosphorylation
- trafficking
Collapse
Affiliation(s)
- Gergely Róna
- a Institute of Enzymology; RCNS; Hungarian Academy of Sciences ; Budapest , Hungary
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
40
|
Molina B, Marchetti F, Gómez L, Ramos S, Torres L, Ortiz R, Altamirano-Lozano M, Carnevale A, Frias S. Hydroxyurea induces chromosomal damage in G2 and enhances the clastogenic effect of mitomycin C in Fanconi anemia cells. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2015; 56:457-467. [PMID: 25663157 DOI: 10.1002/em.21938] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Accepted: 01/05/2015] [Indexed: 06/04/2023]
Abstract
Fanconi's anemia (FA) is a recessive disease; 16 genes are currently recognized in FA. FA proteins participate in the FA/BRCA pathway that plays a crucial role in the repair of DNA damage induced by crosslinking compounds. Hydroxyurea (HU) is an agent that induces replicative stress by inhibiting ribonucleotide reductase (RNR), which synthesizes deoxyribonucleotide triphosphates (dNTPs) necessary for DNA replication and repair. HU is known to activate the FA pathway; however, its clastogenic effects are not well characterized. We have investigated the effects of HU treatment alone or in sequential combination with mitomycin-C (MMC) on FA patient-derived lymphoblastoid cell lines from groups FA-A, B, C, D1/BRCA2, and E and on lymphocytes from two unclassified FA patients. All FA cells showed a significant increase (P < 0.05) in chromosomal aberrations following treatment with HU during the last 3 h before mitosis. Furthermore, when FA cells previously exposed to MMC were treated with HU, we observed an increase of MMC-induced DNA damage that was characterized by high occurrence of DNA breaks and a reduction in rejoined chromosomal aberrations. These findings show that exposure to HU during G2 induces chromosomal aberrations by a mechanism that is independent of its well-known role in replication fork stalling during S-phase and that HU interfered mainly with the rejoining process of DNA damage. We suggest that impaired oxidative stress response, lack of an adequate amount of dNTPs for DNA repair due to RNR inhibition, and interference with cell cycle control checkpoints underlie the clastogenic activity of HU in FA cells. Environ. Mol. Mutagen. 56:457-467, 2015. © 2015 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Bertha Molina
- Laboratorio de Citogenética, Instituto Nacional de Pediatría, México
| | | | - Laura Gómez
- Laboratorio de Citogenética, Instituto Nacional de Pediatría, México
| | - Sandra Ramos
- Laboratorio de Citogenética, Instituto Nacional de Pediatría, México
| | - Leda Torres
- Laboratorio de Citogenética, Instituto Nacional de Pediatría, México
| | - Rocio Ortiz
- Laboratorio de Citometría de Flujo, Universidad Autónoma Metropolitana, Iztapalapa, Mexico
| | | | - Alessandra Carnevale
- Subdirección de Genómica Poblacional, Instituto Nacional de Medicina Genómica, México
| | - Sara Frias
- Laboratorio de Citogenética, Instituto Nacional de Pediatría, México
- Departamento de Medicina, Genómica y Toxicología Ambiental, Instituto de Investigaciones Biomédicas, UNAM, México
| |
Collapse
|
41
|
Mah V, Alavi M, Márquez-Garbán DC, Maresh EL, Kim SR, Horvath S, Bagryanova L, Huerta-Yepez S, Chia D, Pietras R, Goodglick L. Ribonucleotide reductase subunit M2 predicts survival in subgroups of patients with non-small cell lung carcinoma: effects of gender and smoking status. PLoS One 2015; 10:e0127600. [PMID: 26001082 PMCID: PMC4441434 DOI: 10.1371/journal.pone.0127600] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 04/16/2015] [Indexed: 12/25/2022] Open
Abstract
Background Ribonucleotide reductase catalyzes the conversion of ribonucleotide diphosphates to deoxyribonucleotide diphosphates. The functional enzyme consists of two subunits - one large (RRM1) and one small (RRM2 or RRM2b) subunit. Expression levels of each subunit have been implicated in prognostic outcomes in several different types of cancers. Experimental Design Immunohistochemistry for RRM1 and RRM2 was performed on a lung cancer tissue microarray (TMA) and analyzed. 326 patients from the microarray were included in this study. Results In non-small cell lung cancer (NSCLC), RRM2 expression was strongly predictive of disease-specific survival in women, non-smokers and former smokers who had quit at least 10 years prior to being diagnosed with lung cancer. Higher expression was associated with worse survival. This was not the case for men, current smokers and those who had stopped smoking for shorter periods of time. RRM1 was not predictive of survival outcomes in any subset of the patient group. Conclusion RRM2, but not RRM1, is a useful predictor of survival outcome in certain subsets of NSCLC patients.
Collapse
Affiliation(s)
- Vei Mah
- Department of Pathology and Laboratory Medicine, UCLA, Los Angeles, California, 90095, United States of America
- * E-mail:
| | - Mohammad Alavi
- Department of Pathology and Laboratory Medicine, UCLA, Los Angeles, California, 90095, United States of America
| | - Diana C. Márquez-Garbán
- Department of Medicine, Division of Hematology-Oncology, UCLA, Los Angeles, California, 90095, United States of America
- Jonsson Comprehensive Cancer Center, David Geffen School of Medicine at UCLA, Los Angeles, California, 90095, United States of America
| | - Erin L. Maresh
- Department of Pathology and Laboratory Medicine, UCLA, Los Angeles, California, 90095, United States of America
| | - Sara R. Kim
- Department of Pathology and Laboratory Medicine, UCLA, Los Angeles, California, 90095, United States of America
| | - Steve Horvath
- Department of Biostatistics, UCLA, Los Angeles, California, 90095, United States of America
- Department of Human Genetics, UCLA, Los Angeles, California, 90095, United States of America
- Jonsson Comprehensive Cancer Center, David Geffen School of Medicine at UCLA, Los Angeles, California, 90095, United States of America
| | - Lora Bagryanova
- Department of Pathology and Laboratory Medicine, UCLA, Los Angeles, California, 90095, United States of America
| | - Sara Huerta-Yepez
- Unidad de Investigación en Enfermedades Oncológicas, Hospital Infantil de México, Federico Gómez, SSa, México
| | - David Chia
- Department of Pathology and Laboratory Medicine, UCLA, Los Angeles, California, 90095, United States of America
- Jonsson Comprehensive Cancer Center, David Geffen School of Medicine at UCLA, Los Angeles, California, 90095, United States of America
| | - Richard Pietras
- Department of Medicine, Division of Hematology-Oncology, UCLA, Los Angeles, California, 90095, United States of America
- Jonsson Comprehensive Cancer Center, David Geffen School of Medicine at UCLA, Los Angeles, California, 90095, United States of America
| | - Lee Goodglick
- Department of Pathology and Laboratory Medicine, UCLA, Los Angeles, California, 90095, United States of America
- Jonsson Comprehensive Cancer Center, David Geffen School of Medicine at UCLA, Los Angeles, California, 90095, United States of America
| |
Collapse
|
42
|
Tebbi A, Guittet O, Tuphile K, Cabrié A, Lepoivre M. Caspase-dependent Proteolysis of Human Ribonucleotide Reductase Small Subunits R2 and p53R2 during Apoptosis. J Biol Chem 2015; 290:14077-90. [PMID: 25878246 DOI: 10.1074/jbc.m115.649640] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Indexed: 11/06/2022] Open
Abstract
Ribonucleotide reductase (RnR) is a key enzyme synthesizing deoxyribonucleotides for DNA replication and repair. In mammals, the R1 catalytic subunit forms an active complex with either one of the two small subunits R2 and p53R2. Expression of R2 is S phase-specific and required for DNA replication. The p53R2 protein is expressed throughout the cell cycle and in quiescent cells where it provides dNTPs for mitochondrial DNA synthesis. Participation of R2 and p53R2 in DNA repair has also been suggested. In this study, we investigated the fate of the RnR subunits during apoptosis. The p53R2 protein was cleaved in a caspase-dependent manner in K-562 cells treated with inhibitors of the Bcr-Abl oncogenic kinase and in HeLa 229 cells incubated with TNF-α and cycloheximide. The cleavage site was mapped between Asp(342) and Asn(343). Caspase attack released a C-terminal p53R2 peptide of nine residues containing the conserved heptapeptide essential for R1 binding. As a consequence, the cleaved p53R2 protein was inactive. In vitro, purified caspase-3 and -8 could release the C-terminal tail of p53R2. Knocking down these caspases, but not caspase-2, -7, and -10, also inhibited p53R2 cleavage in cells committed to die via the extrinsic death receptor pathway. The R2 subunit was subjected to caspase- and proteasome-dependent proteolysis, which was prevented by siRNA targeting caspase-8. Knocking down caspase-3 was ineffective. Protein R1 was not subjected to degradation. Adding deoxyribonucleosides to restore dNTP pools transiently protected cells from apoptosis. These data identify RnR activity as a prosurvival function inactivated by proteolysis during apoptosis.
Collapse
Affiliation(s)
- Ali Tebbi
- From the Université Paris Sud, Institute of Molecular and Cellular Biochemistry and Biophysics, UMR 8619, 91405 Orsay, France, CNRS, 91405 Orsay, France, and Department of Virology, Institut Pasteur, Pathogenesis of Hepatitis B Virus, 75015 Paris, France
| | - Olivier Guittet
- From the Université Paris Sud, Institute of Molecular and Cellular Biochemistry and Biophysics, UMR 8619, 91405 Orsay, France, CNRS, 91405 Orsay, France, and
| | - Karine Tuphile
- From the Université Paris Sud, Institute of Molecular and Cellular Biochemistry and Biophysics, UMR 8619, 91405 Orsay, France, CNRS, 91405 Orsay, France, and
| | - Aimeric Cabrié
- From the Université Paris Sud, Institute of Molecular and Cellular Biochemistry and Biophysics, UMR 8619, 91405 Orsay, France, CNRS, 91405 Orsay, France, and
| | - Michel Lepoivre
- From the Université Paris Sud, Institute of Molecular and Cellular Biochemistry and Biophysics, UMR 8619, 91405 Orsay, France, CNRS, 91405 Orsay, France, and
| |
Collapse
|
43
|
Horváth A, Batki J, Henn L, Lukacsovich T, Róna G, Erdélyi M, Vértessy BG. dUTPase expression correlates with cell division potential in Drosophila melanogaster. FEBS J 2015; 282:1998-2013. [PMID: 25735890 DOI: 10.1111/febs.13255] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Revised: 01/30/2015] [Accepted: 03/02/2015] [Indexed: 11/30/2022]
Abstract
dUTP pyrophosphatase (dUTPase) is a dNTP-sanitizing enzyme that prevents the appearance of potentially harmful uracil bases in DNA by hydrolyzing cellular dUTP. This function of dUTPase is found to be essential in many organisms including Drosophila melanogaster. Previously, we showed that the expression pattern of dUTPase determines the extent of uracil accumulation in the genome of different tissues. We wished to find the regulatory mechanism that eventually leaves a set of tissues with a uracil-free and intact genome. We found that the expression pattern established by the promoter of Drosophila dUTPase overlaps with mRNA and protein expression, excluding the involvement of other post-transcriptional contributions. This promoter was found to be active in primordial tissues, such as in the imaginal discs of larvae, in the larval brain and in reproductive organs. In the case of brain and imaginal tissues, we observed that the promoter activity depends on a DNA replication-related element motif, the docking site of DNA replication-related element binding factor, which is known as a transcriptional activator of genes involved in replication and proliferation. These results suggest that dUTPase expression is fine-tuned to meet the requirements of DNA synthesis in tissues where the maintenance of genome integrity is of high importance.
Collapse
Affiliation(s)
- András Horváth
- Institute of Enzymology, Hungarian Academy of Sciences, Budapest, Hungary
| | - Júlia Batki
- Institute of Enzymology, Hungarian Academy of Sciences, Budapest, Hungary
| | - László Henn
- Institute of Genetics, Hungarian Academy of Sciences, Szeged, Hungary
| | - Tamás Lukacsovich
- Department of Developmental and Cell Biology, University of California, Irvine, CA, USA
| | - Gergely Róna
- Institute of Enzymology, Hungarian Academy of Sciences, Budapest, Hungary.,Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and Economics, Budapest, Hungary
| | - Miklós Erdélyi
- Institute of Genetics, Hungarian Academy of Sciences, Szeged, Hungary
| | - Beáta G Vértessy
- Institute of Enzymology, Hungarian Academy of Sciences, Budapest, Hungary.,Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and Economics, Budapest, Hungary
| |
Collapse
|
44
|
Zhu C, Tang C, Cao Z, He W, Chen Y, Chen X, Guo K, Ying H. Fully Automated Continuous Meso-flow Synthesis of 5′-Nucleotides and Deoxynucleotides. Org Process Res Dev 2014. [DOI: 10.1021/op5002066] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Chenjie Zhu
- College
of Biotechnology and Pharmaceutical Engineering, Nanjing University of Technology, Nanjing 210009, China
- National Engineering Technique Research Center for Biotechnology, Nanjing 211816, China
| | - Chenglun Tang
- College
of Biotechnology and Pharmaceutical Engineering, Nanjing University of Technology, Nanjing 210009, China
- National Engineering Technique Research Center for Biotechnology, Nanjing 211816, China
| | - Zhi Cao
- College
of Biotechnology and Pharmaceutical Engineering, Nanjing University of Technology, Nanjing 210009, China
- National Engineering Technique Research Center for Biotechnology, Nanjing 211816, China
| | - Wei He
- College
of Biotechnology and Pharmaceutical Engineering, Nanjing University of Technology, Nanjing 210009, China
| | - Yong Chen
- College
of Biotechnology and Pharmaceutical Engineering, Nanjing University of Technology, Nanjing 210009, China
- National Engineering Technique Research Center for Biotechnology, Nanjing 211816, China
| | - Xiaochun Chen
- College
of Biotechnology and Pharmaceutical Engineering, Nanjing University of Technology, Nanjing 210009, China
- National Engineering Technique Research Center for Biotechnology, Nanjing 211816, China
| | - Kai Guo
- College
of Biotechnology and Pharmaceutical Engineering, Nanjing University of Technology, Nanjing 210009, China
| | - Hanjie Ying
- College
of Biotechnology and Pharmaceutical Engineering, Nanjing University of Technology, Nanjing 210009, China
- National Engineering Technique Research Center for Biotechnology, Nanjing 211816, China
| |
Collapse
|
45
|
|
46
|
Spontaneous slow replication fork progression elicits mitosis alterations in homologous recombination-deficient mammalian cells. Proc Natl Acad Sci U S A 2013; 111:763-8. [PMID: 24347643 DOI: 10.1073/pnas.1311520111] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Homologous recombination deficient (HR(-)) mammalian cells spontaneously display reduced replication fork (RF) movement and mitotic extra centrosomes. We show here that these cells present a complex mitotic phenotype, including prolonged metaphase arrest, anaphase bridges, and multipolar segregations. We then asked whether the replication and the mitotic phenotypes are interdependent. First, we determined low doses of hydroxyurea that did not affect the cell cycle distribution or activate CHK1 phosphorylation but did slow the replication fork movement of wild-type cells to the same level than in HR(-) cells. Remarkably, these low hydroxyurea doses generated the same mitotic defects (and to the same extent) in wild-type cells as observed in unchallenged HR(-) cells. Reciprocally, supplying nucleotide precursors to HR(-) cells suppressed both their replication deceleration and mitotic extra centrosome phenotypes. Therefore, subtle replication stress that escapes to surveillance pathways and, thus, fails to prevent cells from entering mitosis alters metaphase progression and centrosome number, resulting in multipolar mitosis. Importantly, multipolar mitosis results in global unbalanced chromosome segregation involving the whole genome, even fully replicated chromosomes. These data highlight the cross-talk between chromosome replication and segregation, and the importance of HR at the interface of these two processes for protection against general genome instability.
Collapse
|
47
|
Leveles I, Németh V, Szabó JE, Harmat V, Nyíri K, Bendes ÁÁ, Papp-Kádár V, Zagyva I, Róna G, Ozohanics O, Vékey K, Tóth J, Vértessy BG. Structure and enzymatic mechanism of a moonlighting dUTPase. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:2298-308. [PMID: 24311572 DOI: 10.1107/s0907444913021136] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Accepted: 07/29/2013] [Indexed: 02/08/2023]
Abstract
Genome integrity requires well controlled cellular pools of nucleotides. dUTPases are responsible for regulating cellular dUTP levels and providing dUMP for dTTP biosynthesis. In Staphylococcus, phage dUTPases are also suggested to be involved in a moonlighting function regulating the expression of pathogenicity-island genes. Staphylococcal phage trimeric dUTPase sequences include a specific insertion that is not found in other organisms. Here, a 2.1 Å resolution three-dimensional structure of a ϕ11 phage dUTPase trimer with complete localization of the phage-specific insert, which folds into a small β-pleated mini-domain reaching out from the dUTPase core surface, is presented. The insert mini-domains jointly coordinate a single Mg2+ ion per trimer at the entrance to the threefold inner channel. Structural results provide an explanation for the role of Asp95, which is suggested to have functional significance in the moonlighting activity, as the metal-ion-coordinating moiety potentially involved in correct positioning of the insert. Enzyme-kinetics studies of wild-type and mutant constructs show that the insert has no major role in dUTP binding or cleavage and provide a description of the elementary steps (fast binding of substrate and release of products). In conclusion, the structural and kinetic data allow insights into both the phage-specific characteristics and the generally conserved traits of ϕ11 phage dUTPase.
Collapse
Affiliation(s)
- Ibolya Leveles
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, 29 Karolina Street, 1113 Budapest, Hungary
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
48
|
Xie M, Yen Y, Owonikoko TK, Ramalingam SS, Khuri FR, Curran WJ, Doetsch PW, Deng X. Bcl2 induces DNA replication stress by inhibiting ribonucleotide reductase. Cancer Res 2013; 74:212-23. [PMID: 24197132 DOI: 10.1158/0008-5472.can-13-1536-t] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
DNA replication stress is an inefficient DNA synthesis process that leads replication forks to progress slowly or stall. Two main factors that cause replication stress are alterations in pools of deoxyribonucleotide (dNTP) precursors required for DNA synthesis and changes in the activity of proteins required for synthesis of dNTPs. Ribonucleotide reductase (RNR), containing regulatory hRRM1 and catalytic hRRM2 subunits, is the enzyme that catalyzes the conversion of ribonucleoside diphosphates (NDP) to deoxyribonucleoside diphosphates (dNDP) and thereby provides dNTP precursors needed for the synthesis of DNA. Here, we demonstrate that either endogenous or exogenous expression of Bcl2 results in decreases in RNR activity and intracellular dNTP, retardation of DNA replication fork progression, and increased rate of fork asymmetry leading to DNA replication stress. Bcl2 colocalizes with hRRM1 and hRRM2 in the cytoplasm and directly interacts via its BH4 domain with hRRM2 but not hRRM1. Removal of the BH4 domain of Bcl2 abrogates its inhibitory effects on RNR activity, dNTP pool level, and DNA replication. Intriguingly, Bcl2 directly inhibits RNR activity by disrupting the functional hRRM1/hRRM2 complex via its BH4 domain. Our findings argue that Bcl2 reduces intracellular dNTPs by inhibiting ribonucleotide reductase activity, thereby providing insight into how Bcl2 triggers DNA replication stress.
Collapse
Affiliation(s)
- Maohua Xie
- Authors' Affiliations: Departments of Radiation Oncology, Hematology and Medical Oncology, and Biochemistry, Emory University School of Medicine and Winship Cancer Institute of Emory University, Atlanta, Georgia; and Department of Clinical and Molecular Pharmacology, City of Hope National Medical Center, Duarte, California
| | | | | | | | | | | | | | | |
Collapse
|
49
|
Yu L, Zhao Y, Quan C, Ji W, Zhu J, Huang Y, Guan R, Sun D, Jin Y, Meng X, Zhang C, Yu Y, Bai J, Sun W, Fu S. Gemcitabine eliminates double minute chromosomes from human ovarian cancer cells. PLoS One 2013; 8:e71988. [PMID: 23991020 PMCID: PMC3750019 DOI: 10.1371/journal.pone.0071988] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2013] [Accepted: 07/05/2013] [Indexed: 11/23/2022] Open
Abstract
Double minute chromosomes are cytogenetic manifestations of gene amplification frequently seen in cancer cells. Genes amplified on double minute chromosomes include oncogenes and multi-drug resistant genes. These genes encode proteins which contribute to cancer formation, cancer progression, and development of resistance to drugs used in cancer treatment. Elimination of double minute chromosomes, and therefore genes amplified on them, is an effective way to decrease the malignancy of cancer cells. We investigated the effectiveness of a cancer drug, gemcitabine, on the loss of double minute chromosomes from the ovarian cancer cell line UACC-1598. Gemcitabine is able to decrease the number of double minute chromosomes in cells at a 7500X lower concentration than the commonly used cancer drug hydroxyurea. Amplified genes present on the double minute chromosomes are decreased at the DNA level upon gemcitabine treatment. Gemcitabine, even at a low nanomolar concentration, is able to cause DNA damage. The selective incorporation of double minutes chromatin and γ-H2AX signals into micronuclei provides a strong link between DNA damage and the loss of double minute chromosomes from gemcitabine treated cells. Cells treated with gemcitabine also showed decreased cell growth, colony formation, and invasion. Together, our results suggest that gemcitabine is effective in decreasing double minute chromosomes and this affects the biology of ovarian cancer cells.
Collapse
Affiliation(s)
- Lisa Yu
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China
| | - Yan Zhao
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China
| | - Chao Quan
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China
| | - Wei Ji
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China
| | - Jing Zhu
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China
| | - Yun Huang
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China
| | - Rongwei Guan
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China
| | - Donglin Sun
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China
| | - Yan Jin
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China
- Key Laboratory of Medical Genetics (Harbin Medical University), Heilongjiang Higher Education Institutions, Harbin, China
| | - Xiangning Meng
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China
| | - Chunyu Zhang
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China
| | - Yang Yu
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China
| | - Jing Bai
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China
| | - Wenjing Sun
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China
| | - Songbin Fu
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China
- Key Laboratory of Medical Genetics (Harbin Medical University), Heilongjiang Higher Education Institutions, Harbin, China
| |
Collapse
|
50
|
Abstract
Primate immunodeficiency viruses are highly specialized lentiviruses that have evolved to successfully infect and persist for the lifetime of the host. Despite encountering numerous potent antiviral factors, HIVs and SIVs are successful pathogens due to the acquisition of equally potent countermeasures in the form of accessory genes. The accessory gene Vpx encoded by HIV-2 and a subset of SIVs have a profound effect on the ability of lentiviruses to infect non-dividing cells, such as macrophages. Although most virus replication occurs in activated CD4(+) T cells, myeloid lineage cells are natural targets of infection and play a central role in virus transmission, dissemination, and persistence. However, myeloid lineage cells are poorly sensitive to lentiviral infection due partly to the high-level expression of a host protein that regulates nucleic acid metabolism named SAMHD1. Degradation of SAMHD1 is induced by Vpx to eliminate this intrinsic antiviral factor. Importantly, SAMHD1 has also been implicated as a negative regulator of the innate immune response, so the interplay between SAMHD1 and Vpx is likely to have significant consequences for virus replication, persistence, and immune control.
Collapse
Affiliation(s)
- Mark Sharkey
- University of Miami Miller School of Medicine, Miami, FL 33136, USA.
| |
Collapse
|