1
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Wang W, Yan T, Guo X, Cai H, Liang C, Huang L, Wang Y, Ma P, Qi S. KAP1 phosphorylation promotes the survival of neural stem cells after ischemia/reperfusion by maintaining the stability of PCNA. Stem Cell Res Ther 2022; 13:290. [PMID: 35799276 PMCID: PMC9264526 DOI: 10.1186/s13287-022-02962-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 04/17/2022] [Indexed: 11/28/2022] Open
Abstract
Aims To explore the function of phosphorylation of KAP1 (p-KAP1) at the serine-824 site (S824) in the proliferation and apoptosis of endogenous neural stem cells (NSCs) after cerebral ischemic/reperfusion (I/R). Methods The apoptosis and proliferation of C17.2 cells transfected with the p-KAP1-expression plasmids and the expression of proliferation cell nuclear antigen (PCNA) and p-KAP1 were detected by immunofluorescence and Western blotting after the Oxygen Glucose deprivation/reperfusion model (OGD/R). The interaction of p-KAP1 and CUL4A with PCNA was analyzed by immunoprecipitation. In the rats MCAO model, we performed the adeno-associated virus (AAV) 2/9 gene delivery of p-KAP1 mutants to verify the proliferation of endogenous NSCs and the colocalization of PCNA and CUL4A by immunofluorescence. Results The level of p-KAP1 was significantly down-regulated in the stroke model in vivo and in vitro. Simulated p-KAP1(S824) significantly increased the proliferation of C17.2 cells and the expression of PCNA after OGD/R. Simulated p-KAP1(S824) enhanced the binding of p-KAP1 and PCNA and decreased the interaction between PCNA and CUL4A in C17.2 cells subjected to OGD/R. The AAV2/9-mediated p-KAP1(S824) increased endogenous NSCs proliferation, PCNA expression, p-KAP1 binding to PCNA, and improved neurological function in the rat MCAO model. Conclusions Our findings confirmed that simulated p-KAP1(S824) improved the survival and proliferation of endogenous NSCs. The underlying mechanism is that highly expressed p-KAP1(S824) promotes binding to PCNA, and inhibits the binding of CUL4A to PCNA. This reduced CUL4A-mediated ubiquitination degradation to increase the stability of PCNA and promote the survival and proliferation of NSCs. Supplementary Information The online version contains supplementary material available at 10.1186/s13287-022-02962-5.
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Affiliation(s)
- Wan Wang
- School of Medical Technology, Xuzhou Key Laboratory of Laboratory Diagnostics, Xuzhou Medical University, Xuzhou, 221004, China.,Department of Laboratory Medicine, Affiliated Hospital of Xuzhou Medical University, Xuzhou, 221002, China
| | - Tianqing Yan
- School of Medical Technology, Xuzhou Key Laboratory of Laboratory Diagnostics, Xuzhou Medical University, Xuzhou, 221004, China
| | - Xinjian Guo
- School of Medical Technology, Xuzhou Key Laboratory of Laboratory Diagnostics, Xuzhou Medical University, Xuzhou, 221004, China
| | - Heng Cai
- School of Medical Technology, Xuzhou Key Laboratory of Laboratory Diagnostics, Xuzhou Medical University, Xuzhou, 221004, China
| | - Chang Liang
- School of Basic Medical Science, Xuzhou Medical University, Xuzhou, 221004, China
| | - Linyan Huang
- School of Medical Technology, Xuzhou Key Laboratory of Laboratory Diagnostics, Xuzhou Medical University, Xuzhou, 221004, China
| | - Yanling Wang
- School of Medical Technology, Xuzhou Key Laboratory of Laboratory Diagnostics, Xuzhou Medical University, Xuzhou, 221004, China
| | - Ping Ma
- School of Medical Technology, Xuzhou Key Laboratory of Laboratory Diagnostics, Xuzhou Medical University, Xuzhou, 221004, China. .,Department of Laboratory Medicine, Affiliated Hospital of Xuzhou Medical University, Xuzhou, 221002, China.
| | - Suhua Qi
- School of Medical Technology, Xuzhou Key Laboratory of Laboratory Diagnostics, Xuzhou Medical University, Xuzhou, 221004, China. .,Pharmacology College, Xuzhou Medical University, Xuzhou, 221004, China.
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2
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Jang SW, Kim JM. Mutation of aspartic acid 199 in USP1 disrupts its deubiquitinating activity and impairs DNA repair. FEBS Lett 2021; 595:1997-2006. [PMID: 34128540 DOI: 10.1002/1873-3468.14152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 06/08/2021] [Accepted: 06/10/2021] [Indexed: 11/06/2022]
Abstract
The deubiquitinating enzyme USP1 contains highly conserved motifs forming its catalytic center. Recently, the COSMIC mutation database identified a mutation in USP1 at Asp-199 in endometrial cancer. Here, we investigated the role of Asp-199 for USP1 function. The mutation of aspartic acid to alanine (D199A) resulted in failure of USP1 to undergo autocleavage and form a complex with ubiquitin, indicating D199A Usp1 is catalytically inactive. The D199A mutation did not affect the interaction with Uaf1. Moreover, D199A Usp1 had defects in deubiquitination of FANCD2 and PCNA and displayed reduced FANCD2 foci formation and DNA repair efficiency. Furthermore, mutation of Asp-199 to glutamic acid resulted in phenotypes similar to the D199A mutation. Collectively, our findings demonstrate the importance of Asp-199 for USP1 activity and suggest the implications of USP1 downregulation in cancer.
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Affiliation(s)
- Seok Won Jang
- Department of Pharmacology, Chonnam National University Medical School, Jellanamdo, Korea
| | - Jung Min Kim
- Department of Pharmacology, Chonnam National University Medical School, Jellanamdo, Korea
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3
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Sun Y, Saha LK, Saha S, Jo U, Pommier Y. Debulking of topoisomerase DNA-protein crosslinks (TOP-DPC) by the proteasome, non-proteasomal and non-proteolytic pathways. DNA Repair (Amst) 2020; 94:102926. [DOI: 10.1016/j.dnarep.2020.102926] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Revised: 07/06/2020] [Accepted: 07/07/2020] [Indexed: 01/24/2023]
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4
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bioPROTACs as versatile modulators of intracellular therapeutic targets including proliferating cell nuclear antigen (PCNA). Proc Natl Acad Sci U S A 2020; 117:5791-5800. [PMID: 32123106 DOI: 10.1073/pnas.1920251117] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Targeted degradation approaches such as proteolysis targeting chimeras (PROTACs) offer new ways to address disease through tackling challenging targets and with greater potency, efficacy, and specificity over traditional approaches. However, identification of high-affinity ligands to serve as PROTAC starting points remains challenging. As a complementary approach, we describe a class of molecules termed biological PROTACs (bioPROTACs)-engineered intracellular proteins consisting of a target-binding domain directly fused to an E3 ubiquitin ligase. Using GFP-tagged proteins as model substrates, we show that there is considerable flexibility in both the choice of substrate binders (binding positions, scaffold-class) and the E3 ligases. We then identified a highly effective bioPROTAC against an oncology target, proliferating cell nuclear antigen (PCNA) to elicit rapid and robust PCNA degradation and associated effects on DNA synthesis and cell cycle progression. Overall, bioPROTACs are powerful tools for interrogating degradation approaches, target biology, and potentially for making therapeutic impacts.
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5
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Gui W, Paudel P, Zhuang Z. Activity-Based Ubiquitin Probes for Investigation of Deubiquitinases. COMPREHENSIVE NATURAL PRODUCTS III 2020. [PMCID: PMC7157470 DOI: 10.1016/b978-0-12-409547-2.14672-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Ubiquitination is emerging as an important post-translational modification (PTM) for numerous cellular functions including protein degradation, DNA damage repair and tolerance, and cell cycle progression. Compared with other small-molecule modifiers found in phosphorylation, acetylation and glycosylation, ubiquitin is a small protein modifier that exists as either a single ubiquitin or a polyubiquitin chain. Furthermore, the polyubiquitin chains are formed via various linkages imparting an additional layer of specificity in cellular signaling. In order to adequately study ubiquitin signaling and particularly deubiquitination, a number of ubiquitin activity-based probes (ABPs) were developed and utilized in understanding the deubiquitinase (DUBs) function. Here, we focus on the current state of the DUB ABP development and their application in understanding DUB function and specificity for polyubiquitin chains and ubiquitinated proteins.
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6
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Cao K, Wang H, Fang Y, Wang Y, Wei L, Chen X, Jiang Z, Wei X, Hu Y. Histone Deacetylase 4 Promotes Osteosarcoma Cell Proliferation and Invasion by Regulating Expression of Proliferating Cell Nuclear Antigen. Front Oncol 2019; 9:870. [PMID: 31552187 PMCID: PMC6743440 DOI: 10.3389/fonc.2019.00870] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 08/21/2019] [Indexed: 01/01/2023] Open
Abstract
Background/Aims: Osteosarcoma (OS) is commonly characterized by lower survival rates and high incidences of local recurrence due to its highly aggressive nature and metastatic tendencies. Studies have shown that histone deacetylase 4 (HDAC4) and proliferating cell nuclear antigen (PCNA) are highly expressed in cancers. Nevertheless, the roles of HDAC4 and PCNA in osteosarcoma (OS) remain unclear. This research aimed to study the expression of HDAC4 and PCNA and their relation to cell proliferation and invasion in human OS. Methods: The levels of HDAC4 and PCNA mRNA and protein were tested in human OS and osteochondroma (OC) tissues. The overexpression and knockdown of HDAC4 in OS cell lines were used to determine the effect of HDAC4 on the expression and degradation of PCNA. The effect of HDAC4 on cell proliferation, invasion and apoptosis was also detected. Additionally, we explored the interaction between HDAC4 and PCNA. Results: The results showed that both HDAC4 and PCNA were increased in human OS tissues. Overexpression of the HDAC4 protein increased the protein level of PCNA, had no effect on the PCNA mRNA level, and decreased the level of ubiquitinated PCNA. We found that overexpression of HDAC4 promoted cell proliferation and invasion and inhibited apoptosis. The opposite effects were observed when HDAC4 was knocked down. The results also showed that HDAC4 could bind to PCNA directly. Conclusions: Our findings suggest that HDAC4 could promote OS cell proliferation and invasion by regulating the expression of PCNA. Thus, our research indicates that HDAC4 may be a potential target for therapy in OS.
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Affiliation(s)
- Kun Cao
- Department of Orthopaedics, First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Hao Wang
- Department of Orthopaedics, First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Yueyang Fang
- Department of Orthopaedics, First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Yuan Wang
- Department of Orthopaedics, First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Lei Wei
- Department of Orthopaedics and Department of Surgery, Warren Alpert Medical School of Brown University/Rhode Island Hospital (RIH), Providence, RI, United States
| | - Xi Chen
- Department of Orthopaedics, First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Zheng Jiang
- Department of Orthopaedics, First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Xiaochun Wei
- Shanxi Key Laboratory of Bone and Soft Tissue Injury Repair, Department of Orthopaedics, Second Hospital of Shanxi Medical University, Taiyuan, China
| | - Yong Hu
- Department of Orthopaedics, First Affiliated Hospital of Anhui Medical University, Hefei, China
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7
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Aleksandrov R, Dotchev A, Poser I, Krastev D, Georgiev G, Panova G, Babukov Y, Danovski G, Dyankova T, Hubatsch L, Ivanova A, Atemin A, Nedelcheva-Veleva MN, Hasse S, Sarov M, Buchholz F, Hyman AA, Grill SW, Stoynov SS. Protein Dynamics in Complex DNA Lesions. Mol Cell 2019; 69:1046-1061.e5. [PMID: 29547717 DOI: 10.1016/j.molcel.2018.02.016] [Citation(s) in RCA: 101] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Revised: 12/26/2017] [Accepted: 02/09/2018] [Indexed: 12/13/2022]
Abstract
A single mutagen can generate multiple different types of DNA lesions. How different repair pathways cooperate in complex DNA lesions, however, remains largely unclear. Here we measured, clustered, and modeled the kinetics of recruitment and dissociation of 70 DNA repair proteins to laser-induced DNA damage sites in HeLa cells. The precise timescale of protein recruitment reveals that error-prone translesion polymerases are considerably delayed compared to error-free polymerases. We show that this is ensured by the delayed recruitment of RAD18 to double-strand break sites. The time benefit of error-free polymerases disappears when PARP inhibition significantly delays PCNA recruitment. Moreover, removal of PCNA from complex DNA damage sites correlates with RPA loading during 5'-DNA end resection. Our systematic study of the dynamics of DNA repair proteins in complex DNA lesions reveals the multifaceted coordination between the repair pathways and provides a kinetics-based resource to study genomic instability and anticancer drug impact.
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Affiliation(s)
- Radoslav Aleksandrov
- Institute of Molecular Biology, Bulgarian Academy of Sciences, Acad. G. Bonchev Str. Bl.21, 1113 Sofia, Bulgaria
| | - Anton Dotchev
- Institute of Molecular Biology, Bulgarian Academy of Sciences, Acad. G. Bonchev Str. Bl.21, 1113 Sofia, Bulgaria
| | - Ina Poser
- Max Planck Institute for Molecular Cell Biology and Genetics, 108 Pfotenhauerstr., 01307 Dresden, Germany
| | - Dragomir Krastev
- Max Planck Institute for Molecular Cell Biology and Genetics, 108 Pfotenhauerstr., 01307 Dresden, Germany
| | - Georgi Georgiev
- Faculty of Mathematics and Informatics, Sofia University, St. Kliment Ohridski, 5 James Bourchier Blvd., 1164 Sofia, Bulgaria
| | - Greta Panova
- Department of Mathematics, University of Pennsylvania, 209 South 33rd Street, Philadelphia, PA 19104, USA
| | - Yordan Babukov
- Institute of Molecular Biology, Bulgarian Academy of Sciences, Acad. G. Bonchev Str. Bl.21, 1113 Sofia, Bulgaria; Faculty of Mathematics and Informatics, Sofia University, St. Kliment Ohridski, 5 James Bourchier Blvd., 1164 Sofia, Bulgaria
| | - Georgi Danovski
- Institute of Molecular Biology, Bulgarian Academy of Sciences, Acad. G. Bonchev Str. Bl.21, 1113 Sofia, Bulgaria
| | - Teodora Dyankova
- Institute of Molecular Biology, Bulgarian Academy of Sciences, Acad. G. Bonchev Str. Bl.21, 1113 Sofia, Bulgaria
| | - Lars Hubatsch
- Max Planck Institute for Molecular Cell Biology and Genetics, 108 Pfotenhauerstr., 01307 Dresden, Germany
| | - Aneliya Ivanova
- Institute of Molecular Biology, Bulgarian Academy of Sciences, Acad. G. Bonchev Str. Bl.21, 1113 Sofia, Bulgaria
| | - Aleksandar Atemin
- Institute of Molecular Biology, Bulgarian Academy of Sciences, Acad. G. Bonchev Str. Bl.21, 1113 Sofia, Bulgaria
| | - Marina N Nedelcheva-Veleva
- Institute of Molecular Biology, Bulgarian Academy of Sciences, Acad. G. Bonchev Str. Bl.21, 1113 Sofia, Bulgaria
| | - Susanne Hasse
- Max Planck Institute for Molecular Cell Biology and Genetics, 108 Pfotenhauerstr., 01307 Dresden, Germany
| | - Mihail Sarov
- Max Planck Institute for Molecular Cell Biology and Genetics, 108 Pfotenhauerstr., 01307 Dresden, Germany
| | - Frank Buchholz
- Max Planck Institute for Molecular Cell Biology and Genetics, 108 Pfotenhauerstr., 01307 Dresden, Germany; Medical Systems Biology, UCC, Medical Faculty Carl Gustav Carus, TU Dresden, Fetscherstr. 74, 01307 Dresden, Germany
| | - Anthony A Hyman
- Max Planck Institute for Molecular Cell Biology and Genetics, 108 Pfotenhauerstr., 01307 Dresden, Germany
| | - Stephan W Grill
- Max Planck Institute for Molecular Cell Biology and Genetics, 108 Pfotenhauerstr., 01307 Dresden, Germany
| | - Stoyno S Stoynov
- Institute of Molecular Biology, Bulgarian Academy of Sciences, Acad. G. Bonchev Str. Bl.21, 1113 Sofia, Bulgaria.
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8
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Czerwińska J, Nowak M, Wojtczak P, Dziuban-Lech D, Cieśla JM, Kołata D, Gajewska B, Barańczyk-Kuźma A, Robinson AR, Shane HL, Gregg SQ, Rigatti LH, Yousefzadeh MJ, Gurkar AU, McGowan SJ, Kosicki K, Bednarek M, Zarakowska E, Gackowski D, Oliński R, Speina E, Niedernhofer LJ, Tudek B. ERCC1-deficient cells and mice are hypersensitive to lipid peroxidation. Free Radic Biol Med 2018; 124:79-96. [PMID: 29860127 PMCID: PMC6098728 DOI: 10.1016/j.freeradbiomed.2018.05.088] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 05/28/2018] [Accepted: 05/29/2018] [Indexed: 01/01/2023]
Abstract
Lipid peroxidation (LPO) products are relatively stable and abundant metabolites, which accumulate in tissues of mammals with aging, being able to modify all cellular nucleophiles, creating protein and DNA adducts including crosslinks. Here, we used cells and mice deficient in the ERCC1-XPF endonuclease required for nucleotide excision repair and the repair of DNA interstrand crosslinks to ask if specifically LPO-induced DNA damage contributes to loss of cell and tissue homeostasis. Ercc1-/- mouse embryonic fibroblasts were more sensitive than wild-type (WT) cells to the LPO products: 4-hydroxy-2-nonenal (HNE), crotonaldehyde and malondialdehyde. ERCC1-XPF hypomorphic mice were hypersensitive to CCl4 and a diet rich in polyunsaturated fatty acids, two potent inducers of endogenous LPO. To gain insight into the mechanism of how LPO influences DNA repair-deficient cells, we measured the impact of the major endogenous LPO product, HNE, on WT and Ercc1-/- cells. HNE inhibited proliferation, stimulated ROS and LPO formation, induced DNA base damage, strand breaks, error-prone translesion DNA synthesis and cellular senescence much more potently in Ercc1-/- cells than in DNA repair-competent control cells. HNE also deregulated base excision repair and energy production pathways. Our observations that ERCC1-deficient cells and mice are hypersensitive to LPO implicates LPO-induced DNA damage in contributing to cellular demise and tissue degeneration, notably even when the source of LPO is dietary polyunsaturated fats.
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Affiliation(s)
- Jolanta Czerwińska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland.
| | - Małgorzata Nowak
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland.
| | - Patrycja Wojtczak
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland.
| | - Dorota Dziuban-Lech
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland.
| | - Jarosław M Cieśla
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland.
| | - Daria Kołata
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland.
| | - Beata Gajewska
- Department of Biochemistry, Medical University of Warsaw, Warsaw, Poland.
| | | | - Andria R Robinson
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA; University of Pittsburgh Medical Center Hillman Cancer Center, Pittsburgh, PA, USA.
| | - Hillary L Shane
- University of Pittsburgh Medical Center Hillman Cancer Center, Pittsburgh, PA, USA.
| | - Siobhán Q Gregg
- University of Pittsburgh Medical Center Hillman Cancer Center, Pittsburgh, PA, USA; Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
| | - Lora H Rigatti
- University of Pittsburgh Medical Center Hillman Cancer Center, Pittsburgh, PA, USA.
| | - Matthew J Yousefzadeh
- Department of Molecular Medicine, Center on Aging, The Scripps Research Institute, Jupiter, FL, USA.
| | - Aditi U Gurkar
- Department of Molecular Medicine, Center on Aging, The Scripps Research Institute, Jupiter, FL, USA.
| | - Sara J McGowan
- Department of Molecular Medicine, Center on Aging, The Scripps Research Institute, Jupiter, FL, USA.
| | - Konrad Kosicki
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland.
| | - Małgorzata Bednarek
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland.
| | - Ewelina Zarakowska
- Department of Clinical Biochemistry, Faculty of Pharmacy, Collegium Medicum, Nicolaus Copernicus University in Toruń, Bydgoszcz, Poland.
| | - Daniel Gackowski
- Department of Clinical Biochemistry, Faculty of Pharmacy, Collegium Medicum, Nicolaus Copernicus University in Toruń, Bydgoszcz, Poland.
| | - Ryszard Oliński
- Department of Clinical Biochemistry, Faculty of Pharmacy, Collegium Medicum, Nicolaus Copernicus University in Toruń, Bydgoszcz, Poland.
| | - Elżbieta Speina
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland.
| | - Laura J Niedernhofer
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA; University of Pittsburgh Medical Center Hillman Cancer Center, Pittsburgh, PA, USA; Department of Molecular Medicine, Center on Aging, The Scripps Research Institute, Jupiter, FL, USA.
| | - Barbara Tudek
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland; Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland.
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9
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Lee MYWT, Wang X, Zhang S, Zhang Z, Lee EYC. Regulation and Modulation of Human DNA Polymerase δ Activity and Function. Genes (Basel) 2017; 8:genes8070190. [PMID: 28737709 PMCID: PMC5541323 DOI: 10.3390/genes8070190] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Revised: 07/07/2017] [Accepted: 07/11/2017] [Indexed: 12/28/2022] Open
Abstract
This review focuses on the regulation and modulation of human DNA polymerase δ (Pol δ). The emphasis is on the mechanisms that regulate the activity and properties of Pol δ in DNA repair and replication. The areas covered are the degradation of the p12 subunit of Pol δ, which converts it from a heterotetramer (Pol δ4) to a heterotrimer (Pol δ3), in response to DNA damage and also during the cell cycle. The biochemical mechanisms that lead to degradation of p12 are reviewed, as well as the properties of Pol δ4 and Pol δ3 that provide insights into their functions in DNA replication and repair. The second focus of the review involves the functions of two Pol δ binding proteins, polymerase delta interaction protein 46 (PDIP46) and polymerase delta interaction protein 38 (PDIP38), both of which are multi-functional proteins. PDIP46 is a novel activator of Pol δ4, and the impact of this function is discussed in relation to its potential roles in DNA replication. Several new models for the roles of Pol δ3 and Pol δ4 in leading and lagging strand DNA synthesis that integrate a role for PDIP46 are presented. PDIP38 has multiple cellular localizations including the mitochondria, the spliceosomes and the nucleus. It has been implicated in a number of cellular functions, including the regulation of specialized DNA polymerases, mitosis, the DNA damage response, mouse double minute 2 homolog (Mdm2) alternative splicing and the regulation of the NADPH oxidase 4 (Nox4).
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Affiliation(s)
- Marietta Y W T Lee
- Department Biochemistry and Molecular Biology, New York Medical College, Valhalla, NY 10595, USA.
| | - Xiaoxiao Wang
- Department Biochemistry and Molecular Biology, New York Medical College, Valhalla, NY 10595, USA.
| | - Sufang Zhang
- Department Biochemistry and Molecular Biology, New York Medical College, Valhalla, NY 10595, USA.
| | - Zhongtao Zhang
- Department Biochemistry and Molecular Biology, New York Medical College, Valhalla, NY 10595, USA.
| | - Ernest Y C Lee
- Department Biochemistry and Molecular Biology, New York Medical College, Valhalla, NY 10595, USA.
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10
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Huseinovic A, van Leeuwen JS, van Welsem T, Stulemeijer I, van Leeuwen F, Vermeulen NPE, Kooter JM, Vos JC. The effect of acetaminophen on ubiquitin homeostasis in Saccharomyces cerevisiae. PLoS One 2017; 12:e0173573. [PMID: 28291796 PMCID: PMC5349473 DOI: 10.1371/journal.pone.0173573] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 02/23/2017] [Indexed: 02/05/2023] Open
Abstract
Acetaminophen (APAP), although considered a safe drug, is one of the major causes of acute liver failure by overdose, and therapeutic chronic use can cause serious health problems. Although the reactive APAP metabolite N-acetyl-p-benzoquinoneimine (NAPQI) is clearly linked to liver toxicity, toxicity of APAP is also found without drug metabolism of APAP to NAPQI. To get more insight into mechanisms of APAP toxicity, a genome-wide screen in Saccharomyces cerevisiae for APAP-resistant deletion strains was performed. In this screen we identified genes related to the DNA damage response. Next, we investigated the link between genotype and APAP-induced toxicity or resistance by performing a more detailed screen with a library containing mutants of 1522 genes related to nuclear processes, like DNA repair and chromatin remodelling. We identified 233 strains that had an altered growth rate relative to wild type, of which 107 showed increased resistance to APAP and 126 showed increased sensitivity. Gene Ontology analysis identified ubiquitin homeostasis, regulation of transcription of RNA polymerase II genes, and the mitochondria-to-nucleus signalling pathway to be associated with APAP resistance, while histone exchange and modification, and vesicular transport were connected to APAP sensitivity. Indeed, we observed a link between ubiquitin levels and APAP resistance, whereby ubiquitin deficiency conferred resistance to APAP toxicity while ubiquitin overexpression resulted in sensitivity. The toxicity profile of various chemicals, APAP, and its positional isomer AMAP on a series of deletion strains with ubiquitin deficiency showed a unique resistance pattern for APAP. Furthermore, exposure to APAP increased the level of free ubiquitin and influenced the ubiquitination of proteins. Together, these results uncover a role for ubiquitin homeostasis in APAP-induced toxicity.
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Affiliation(s)
- Angelina Huseinovic
- AIMMS-Division of Molecular Toxicology, Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, Amsterdam, The Netherlands
| | - Jolanda S. van Leeuwen
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Tibor van Welsem
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Iris Stulemeijer
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Fred van Leeuwen
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Nico P. E. Vermeulen
- AIMMS-Division of Molecular Toxicology, Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, Amsterdam, The Netherlands
| | - Jan M. Kooter
- AIMMS-Department of Molecular Cell Biology, Section Genetics, VU University Amsterdam, Amsterdam, The Netherlands
| | - J. Chris Vos
- AIMMS-Division of Molecular Toxicology, Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, Amsterdam, The Netherlands
- * E-mail:
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11
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Wilson RHC, Biasutto AJ, Wang L, Fischer R, Baple EL, Crosby AH, Mancini EJ, Green CM. PCNA dependent cellular activities tolerate dramatic perturbations in PCNA client interactions. DNA Repair (Amst) 2016; 50:22-35. [PMID: 28073635 PMCID: PMC5264654 DOI: 10.1016/j.dnarep.2016.12.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Revised: 12/16/2016] [Accepted: 12/19/2016] [Indexed: 01/04/2023]
Abstract
We assess the cellular effects of the mutation that causes PARD (PCNAS228I). Cells from affected individuals are sensitive to T2AA and T3. PCNAS228I impairs interactions between PCNA and Cdt1, DNMT1, PolD3 and PolD4. The PIP-box of p21 retains binding to PCNAS228I. PCNA-dependent degradation and the cell cycle are only subtly altered by PCNAS228I.
Proliferating cell nuclear antigen (PCNA) is an essential cofactor for DNA replication and repair, recruiting multiple proteins to their sites of action. We examined the effects of the PCNAS228I mutation that causes PCNA-associated DNA repair disorder (PARD). Cells from individuals affected by PARD are sensitive to the PCNA inhibitors T3 and T2AA, showing that the S228I mutation has consequences for undamaged cells. Analysis of the binding between PCNA and PCNA-interacting proteins (PIPs) shows that the S228I change dramatically impairs the majority of these interactions, including that of Cdt1, DNMT1, PolD3p66 and PolD4p12. In contrast p21 largely retains the ability to bind PCNAS228I. This property is conferred by the p21 PIP box sequence itself, which is both necessary and sufficient for PCNAS228I binding. Ubiquitination of PCNA is unaffected by the S228I change, which indirectly alters the structure of the inter-domain connecting loop. Despite the dramatic in vitro effects of the PARD mutation on PIP-degron binding, there are only minor alterations to the stability of p21 and Cdt1 in cells from affected individuals. Overall our data suggests that reduced affinity of PCNAS228I for specific clients causes subtle cellular defects in undamaged cells which likely contribute to the etiology of PARD.
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Affiliation(s)
- Rosemary H C Wilson
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - Antonio J Biasutto
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - Lihao Wang
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - Roman Fischer
- Target Discovery Institute, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK
| | - Emma L Baple
- University of Exeter Medical School, Barrack Road, Exeter, EX2 5DW, UK
| | - Andrew H Crosby
- University of Exeter Medical School, Barrack Road, Exeter, EX2 5DW, UK
| | - Erika J Mancini
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK; School of Life Sciences, University of Sussex, Falmer, Brighton, BN1 9RH, UK
| | - Catherine M Green
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK.
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12
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PCNA SUMOylation protects against PCNA polyubiquitination-mediated, Rad59-dependent, spontaneous, intrachromosomal gene conversion. Mutat Res 2016; 791-792:10-18. [PMID: 27505077 DOI: 10.1016/j.mrfmmm.2016.08.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 06/29/2016] [Accepted: 08/01/2016] [Indexed: 11/23/2022]
Abstract
Homologous recombination is crucial in both the maintenance of genome stability and the generation of genetic diversity. Recently, multiple aspects of the recombination machinery functioning at arrested DNA replication forks have been established, yet the roles of diverse modifications of PCNA, the key platform organizing the replication complex, in intrachromosomal recombination have not been comprehensively elucidated. Here, we report how PCNA SUMOylation and/or polyubiquitination affects recombination between direct repeats in S. cerevisiae. Our results show that these PCNA modifications primarily affect gene conversion, whereas their effect on the recombination-mediated deletion of intervening sequence is much less obvious. Siz1-dependent PCNA SUMOylation strongly limits Rad52/Rad51/Rad59-dependent gene conversion. A 5- to 10-fold increase in the frequency of such recombination events is observed in Siz1-defective strains, but this increase is fully suppressed when PCNA polyubiquitination is also compromised. PCNA polyubiquitination can stimulate gene conversion in both PCNA SUMOylation-proficient and SUMOylation-deficient strains. On the other hand, in PCNA polyubiquitination-deficient strains, the lack of PCNA SUMOylation does not affect GC levels. Therefore, we postulate that the antirecombinogenic activity of Siz1 mainly concerns recombination induced by PCNA polyubiquitination. In the absence of PCNA SUMOylation, the frequency of PCNA polyubiquitination-mediated gene conversion is not only increased, but it is also channeled into the Rad59-dependent pathway. Additionally, we show a weak inhibitory effect of Rad5 on Rad52/Rad59-directed single-strand annealing.
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13
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Chen CW, Tsao N, Huang LY, Yen Y, Liu X, Lehman C, Wang YH, Tseng MC, Chen YJ, Ho YC, Chen CF, Chang ZF. The Impact of dUTPase on Ribonucleotide Reductase-Induced Genome Instability in Cancer Cells. Cell Rep 2016; 16:1287-1299. [PMID: 27452458 DOI: 10.1016/j.celrep.2016.06.094] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2016] [Revised: 05/04/2016] [Accepted: 06/28/2016] [Indexed: 02/07/2023] Open
Abstract
The appropriate supply of dNTPs is critical for cell growth and genome integrity. Here, we investigated the interrelationship between dUTP pyrophosphatase (dUTPase) and ribonucleotide reductase (RNR) in the regulation of genome stability. Our results demonstrate that reducing the expression of dUTPase increases genome stress in cancer. Analysis of clinical samples reveals a significant correlation between the combination of low dUTPase and high R2, a subunit of RNR, and a poor prognosis in colorectal and breast cancer patients. Furthermore, overexpression of R2 in non-tumorigenic cells progressively increases genome stress, promoting transformation. These cells display alterations in replication fork progression, elevated genomic uracil, and breaks at AT-rich common fragile sites. Consistently, overexpression of dUTPase abolishes R2-induced genome instability. Thus, the expression level of dUTPase determines the role of high R2 in driving genome instability in cancer cells.
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Affiliation(s)
- Chih-Wei Chen
- Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei 112, Taiwan
| | - Ning Tsao
- Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei 100, Taiwan
| | - Lin-Yi Huang
- Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei 112, Taiwan
| | - Yun Yen
- Department of Molecular Pharmacology, City of Hope National Medical Center and Beckman Research Institute, Duarte, CA 91010, USA; Taipei Medical University, Taipei 110, Taiwan
| | - Xiyong Liu
- Taipei Medical University, Taipei 110, Taiwan; California Cancer Institute, Sino-American Cancer Foundation, Temple City, CA 91780, USA
| | - Christine Lehman
- Department of Cancer Biology, Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem, NC 27157-1016, USA
| | - Yuh-Hwa Wang
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Mei-Chun Tseng
- Institute of Chemistry, Academia Sinica, Nankang, Taipei 115, Taiwan
| | - Yu-Ju Chen
- Department of Chemistry, National Taiwan University, Taipei 100, Taiwan; Institute of Chemistry, Academia Sinica, Nankang, Taipei 115, Taiwan
| | - Yi-Chi Ho
- Institute of Chemistry, Academia Sinica, Nankang, Taipei 115, Taiwan
| | - Chian-Feng Chen
- VYM Genome Research Center, National Yang-Ming University, Taipei 112, Taiwan
| | - Zee-Fen Chang
- Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei 112, Taiwan.
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14
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Ramadan K, Halder S, Wiseman K, Vaz B. Strategic role of the ubiquitin-dependent segregase p97 (VCP or Cdc48) in DNA replication. Chromosoma 2016; 126:17-32. [PMID: 27086594 DOI: 10.1007/s00412-016-0587-4] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Revised: 03/10/2016] [Accepted: 03/16/2016] [Indexed: 01/01/2023]
Abstract
Genome amplification (DNA synthesis) is one of the most demanding cellular processes in all proliferative cells. The DNA replication machinery (also known as the replisome) orchestrates genome amplification during S-phase of the cell cycle. Genetic material is particularly vulnerable to various events that can challenge the replisome during its assembly, activation (firing), progression (elongation) and disassembly from chromatin (termination). Any disturbance of the replisome leads to stalling of the DNA replication fork and firing of dormant replication origins, a process known as DNA replication stress. DNA replication stress is considered to be one of the main causes of sporadic cancers and other pathologies related to tissue degeneration and ageing. The mechanisms of replisome assembly and elongation during DNA synthesis are well understood. However, once DNA synthesis is complete, the process of replisome disassembly, and its removal from chromatin, remains unclear. In recent years, a growing body of evidence has alluded to a central role in replisome regulation for the ubiquitin-dependent protein segregase p97, also known as valosin-containing protein (VCP) in metazoans and Cdc48 in lower eukaryotes. By orchestrating the spatiotemporal turnover of the replisome, p97 plays an essential role in DNA replication. In this review, we will summarise our current knowledge about how p97 controls the replisome from replication initiation, to elongation and finally termination. We will also further examine the more recent findings concerning the role of p97 and how mutations in p97 cofactors, also known as adaptors, cause DNA replication stress induced genomic instability that leads to cancer and accelerated ageing. To our knowledge, this is the first comprehensive review concerning the mechanisms involved in the regulation of DNA replication by p97.
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Affiliation(s)
- Kristijan Ramadan
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Roosevelt Drive, Oxford, OX3 7DQ, UK.
| | - Swagata Halder
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Roosevelt Drive, Oxford, OX3 7DQ, UK
| | - Katherine Wiseman
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Roosevelt Drive, Oxford, OX3 7DQ, UK
| | - Bruno Vaz
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Roosevelt Drive, Oxford, OX3 7DQ, UK
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15
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Wang Z, Huang M, Ma X, Li H, Tang T, Guo C. REV1 promotes PCNA monoubiquitination through interacting with ubiquitinated RAD18. J Cell Sci 2016; 129:1223-33. [DOI: 10.1242/jcs.179408] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 01/18/2016] [Indexed: 01/11/2023] Open
Abstract
Translesion DNA synthesis (TLS) is one mode of DNA damage tolerance, which plays an important role in genome mutagenesis and chromatin integrity maintenance. PCNA monoubiquitination is one of the key factors for TLS pathway choice. So far, it remains unclear how TLS pathway is elaborately regulated. Here, we report that TLS polymerase REV1 can promote PCNA monoubiquitination after UV radiation. Further studies revealed that this stimulatory effect is mediated through the enhanced interaction between REV1 and ubiquitinated RAD18, which facilitates the release of nonubiquitinated RAD18 from ubiquitinated RAD18 trapping followed by more RAD18 recruiting to chromatin for its TLS function. Furthermore, we found that this stimulatory effect could also be detected after exposure to hydroxyurea or mitomycin C, but not methyl methanesulfonate (MMS), which is in line with the fact that ubiquitinated RAD18 could not be detected after exposure to MMS.
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Affiliation(s)
- Zhifeng Wang
- Key Laboratory of Genomic and Precision Medicine, China Gastrointestinal Cancer Research Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Min Huang
- Key Laboratory of Genomic and Precision Medicine, China Gastrointestinal Cancer Research Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiaolu Ma
- Key Laboratory of Genomic and Precision Medicine, China Gastrointestinal Cancer Research Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Huiming Li
- Key Laboratory of Genomic and Precision Medicine, China Gastrointestinal Cancer Research Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Tieshan Tang
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Caixia Guo
- Key Laboratory of Genomic and Precision Medicine, China Gastrointestinal Cancer Research Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
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16
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Chen X, Bosques L, Sung P, Kupfer GM. A novel role for non-ubiquitinated FANCD2 in response to hydroxyurea-induced DNA damage. Oncogene 2015; 35:22-34. [PMID: 25893307 DOI: 10.1038/onc.2015.68] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Revised: 01/30/2015] [Accepted: 02/02/2015] [Indexed: 12/20/2022]
Abstract
Fanconi anemia (FA) is a genetic disease of bone marrow failure, cancer susceptibility, and sensitivity to DNA crosslinking agents. FANCD2, the central protein of the FA pathway, is monoubiquitinated upon DNA damage, such as crosslinkers and replication blockers such as hydroxyurea (HU). Even though FA cells demonstrate unequivocal sensitivity to crosslinkers, such as mitomycin C (MMC), we find that they are largely resistant to HU, except for cells absent for expression of FANCD2. FANCD2, RAD51 and RAD18 form a complex, which is enhanced upon HU exposure. Surprisingly, although FANCD2 is required for this enhanced interaction, its monoubiquitination is not. Similarly, non-ubiquitinated FANCD2 can still support proliferation cell nuclear antigen (PCNA) monoubiquitination. RAD51, but not BRCA2, is also required for PCNA monoubiquitination in response to HU, suggesting that this function is independent of homologous recombination (HR). We further show that translesion (TLS) polymerase PolH chromatin localization is decreased in FANCD2 deficient cells, FANCD2 siRNA knockdown cells and RAD51 siRNA knockdown cells, and PolH knockdown results in HU sensitivity only. Our data suggest that FANCD2 and RAD51 have an important role in PCNA monoubiquitination and TLS in a FANCD2 monoubiquitination and HR-independent manner in response to HU. This effect is not observed with MMC treatment, suggesting a non-canonical function for the FA pathway in response to different types of DNA damage.
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Affiliation(s)
- X Chen
- Department of Pediatrics, Section of Hematology/Oncology, Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA.,Department of Pathology, Section of Hematology/Oncology, Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
| | - L Bosques
- Department of Pediatrics, Section of Hematology/Oncology, Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA.,Department of Pathology, Section of Hematology/Oncology, Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
| | - P Sung
- Department of Molecular, Cellular, and Developmental Biology, Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
| | - G M Kupfer
- Department of Pediatrics, Section of Hematology/Oncology, Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA.,Department of Pathology, Section of Hematology/Oncology, Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
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17
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Yang Q, Ou C, Liu M, Xiao W, Wen C, Sun F. NRAGE promotes cell proliferation by stabilizing PCNA in a ubiquitin-proteasome pathway in esophageal carcinomas. Carcinogenesis 2014; 35:1643-51. [PMID: 24710624 DOI: 10.1093/carcin/bgu084] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Neurotrophin receptor-interacting melanoma antigen-encoding gene homolog (NRAGE) is generally recognized as a tumor suppressor as it induces cell apoptosis and suppresses cell metastasis. However, it has recently been reported that NRAGE is overexpressed in lung cancer, melanoma and colon cancer, implicating a complicated role of NRAGE as we have expected. In the study, we aim to elucidate the functional roles and molecular mechanisms of NRAGE in esophageal carcinoma. We found that both NRAGE mRNA and protein were significantly overexpressed in esophageal tumor tissues. Consistently, both in vivo and in vitro analyses demonstrated that knockdown of NRAGE apparently inhibited cell growth, and cell cycle analysis further demonstrated that NRAGE knockdown cells were mainly arrested in G2M cell phase, accompanied with an apparent reduction of S phase. In the process of exploring molecular mechanisms, we found that either knockdown in vitro or knockout in vivo of NRAGE reduced proliferating cell nuclear antigen (PCNA) protein, expression of which could completely rescue the inhibited proliferation in NRAGE defective cells. Furthermore, NRAGE physically interacted with PCNA in esophageal cancer cells through DNA polymerase III subunit, and knockdown of NRAGE facilitated PCNA K48-linked polyubiquitination, leading PCNA to the proteasome-dependent degradation and a ubiquitin-specific protease USP10 was identified to be a key regulator in the process of K48 polyubiquitination in NRAGE-deleted cells. In conclusion, our study highlights a unique role of NRAGE and implies that NRAGE is likely to be an attractive oncotarget in developing novel genetic anticancer therapeutic strategies for esophageal squamous cell carcinomas.
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Affiliation(s)
- Qingyuan Yang
- Department of Clinical Laboratory Medicine, Tenth People's Hospital of Tongji University, Shanghai 200072, China, Department of Clinical Laboratory, The Affiliated Tumor Hospital of Guangxi Medical University, Nanning 530021, China, Jiangsu Key Laboratory for Molecular and Medical Biotechnology, Nanjing Normal University, Nanjing 210023, China and The Central Laboratory, Tenth People's Hospital of Tongji University, Shanghai 200072, China
| | - Chao Ou
- Department of Clinical Laboratory, The Affiliated Tumor Hospital of Guangxi Medical University, Nanning 530021, China
| | - Mei Liu
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, Nanjing Normal University, Nanjing 210023, China and
| | - Weifan Xiao
- The Central Laboratory, Tenth People's Hospital of Tongji University, Shanghai 200072, China
| | - Chuanjun Wen
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, Nanjing Normal University, Nanjing 210023, China and
| | - Fenyong Sun
- Department of Clinical Laboratory Medicine, Tenth People's Hospital of Tongji University, Shanghai 200072, China, Department of Clinical Laboratory, The Affiliated Tumor Hospital of Guangxi Medical University, Nanning 530021, China, Jiangsu Key Laboratory for Molecular and Medical Biotechnology, Nanjing Normal University, Nanjing 210023, China and The Central Laboratory, Tenth People's Hospital of Tongji University, Shanghai 200072, China
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18
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Villamil MA, Liang Q, Zhuang Z. The WD40-repeat protein-containing deubiquitinase complex: catalysis, regulation, and potential for therapeutic intervention. Cell Biochem Biophys 2014; 67:111-26. [PMID: 23797609 DOI: 10.1007/s12013-013-9637-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Ubiquitination has emerged as an essential signaling mechanism in eukaryotes. Deubiquitinases (DUBs) counteract the activities of the ubiquitination machinery and provide another level of control in cellular ubiquitination. Not surprisingly, DUBs are subjected to stringent regulations. Besides regulation by the noncatalytic domains present in the DUB sequences, DUB-interacting proteins are increasingly realized as essential regulators for DUB activity and function. This review focuses on DUBs that are associated with WD40-repeat proteins. Many human ubiquitin-specific proteases (USPs) were found to interact with WD40-repeat proteins, but little is known as to how this interaction regulates the activity and function of USPs. In recent years, significant progress has been made in understanding a prototypical WD40-repeat protein-containing DUB complex that comprises USP1 and USP1-associated factor 1 (UAF1). It has been shown that UAF1 activates USP1 through a potential active-site modulation, and the complex formation between USP1 and UAF1 is regulated by serine phosphorylation. Recently, human USPs have been recognized as a promising target class for inhibitor discovery. Small molecule inhibitors targeting several human USPs have been reported. USP1 is involved in two major DNA damage response pathways, DNA translesion synthesis and the Fanconi anemia pathway. Inhibiting the USP1/UAF1 deubiquitinase complex represents a new strategy to potentiate cancer cells to DNA-crosslinking agents and to overcome resistance that has plagued clinical cancer chemotherapy. The progress in inhibitor discovery against USPs and the WD40-repeat protein-containing USP complex will be discussed.
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Affiliation(s)
- Mark A Villamil
- Department of Chemistry and Biochemistry, University of Delaware, 214A Drake Hall, Newark, DE 19716, USA
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19
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Zhu Q, Chang Y, Yang J, Wei Q. Post-translational modifications of proliferating cell nuclear antigen: A key signal integrator for DNA damage response (Review). Oncol Lett 2014; 7:1363-1369. [PMID: 24765138 PMCID: PMC3997659 DOI: 10.3892/ol.2014.1943] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Accepted: 02/13/2014] [Indexed: 12/02/2022] Open
Abstract
Previous studies have shown that the post-translational modifications of proliferating cell nuclear antigen (PCNA) may be crucial in influencing the cellular choice between different pathways, such as the cell cycle checkpoint, DNA repair or apoptosis pathways, in order to maintain genomic stability. DNA damage leads to replication stress and the subsequent induction of PCNA modification by small ubiquitin (Ub)-related modifiers and Ub, which has been identified to affect multiple biological processes of genomic DNA. Thus far, much has been learned concerning the behavior of modified PCNA as a key signal integrator in response to DNA damage. In humans and yeast, modified PCNA activates DNA damage bypass via an error-prone or error-free pathway to prevent the breakage of DNA replication forks, which may potentially induce double-strand breaks and subsequent chromosomal rearrangements. However, the exact mechanisms by which these pathways work and by what means the modified PCNA is involved in these processes remain elusive. Thus, the improved understanding of PCNA modification and its implications for DNA damage response may provide us with more insight into the mechanisms by which human cells regulate aberrant recombination events, and cancer initiation and development. The present review focuses on the post-translational modifications of PCNA and its important functions in mediating mammalian cellular response to different types of DNA damage.
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Affiliation(s)
- Qiong Zhu
- Battalion Two of Cadet Brigade, Third Military Medical University, Chongqing 400038, P.R. China
| | - Yuxiao Chang
- Battalion Two of Cadet Brigade, Third Military Medical University, Chongqing 400038, P.R. China
| | - Jin Yang
- Department of Cell Biology, Third Military Medical University, Chongqing 400038, P.R. China
| | - Quanfang Wei
- Department of Cell Biology, Third Military Medical University, Chongqing 400038, P.R. China
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20
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Liang Q, Dexheimer TS, Zhang P, Rosenthal AS, Villamil MA, You C, Zhang Q, Chen J, Ott CA, Sun H, Luci DK, Yuan B, Simeonov A, Jadhav A, Xiao H, Wang Y, Maloney DJ, Zhuang Z. A selective USP1-UAF1 inhibitor links deubiquitination to DNA damage responses. Nat Chem Biol 2014; 10:298-304. [PMID: 24531842 DOI: 10.1038/nchembio.1455] [Citation(s) in RCA: 186] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2013] [Accepted: 12/11/2013] [Indexed: 12/31/2022]
Abstract
Protein ubiquitination and deubiquitination are central to the control of a large number of cellular pathways and signaling networks in eukaryotes. Although the essential roles of ubiquitination have been established in the eukaryotic DNA damage response, the deubiquitination process remains poorly defined. Chemical probes that perturb the activity of deubiquitinases (DUBs) are needed to characterize the cellular function of deubiquitination. Here we report ML323 (2), a highly potent inhibitor of the USP1-UAF1 deubiquitinase complex with excellent selectivity against human DUBs, deSUMOylase, deneddylase and unrelated proteases. Using ML323, we interrogated deubiquitination in the cellular response to UV- and cisplatin-induced DNA damage and revealed new insights into the requirement of deubiquitination in the DNA translesion synthesis and Fanconi anemia pathways. Moreover, ML323 potentiates cisplatin cytotoxicity in non-small cell lung cancer and osteosarcoma cells. Our findings point to USP1-UAF1 as a key regulator of the DNA damage response and a target for overcoming resistance to the platinum-based anticancer drugs.
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Affiliation(s)
- Qin Liang
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware, USA
| | - Thomas S Dexheimer
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland, USA
| | - Ping Zhang
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware, USA
| | - Andrew S Rosenthal
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland, USA
| | - Mark A Villamil
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware, USA
| | - Changjun You
- Department of Chemistry, University of California-Riverside, Riverside, California, USA
| | - Qiuting Zhang
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, Jiangxi, China
| | - Junjun Chen
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware, USA
| | - Christine A Ott
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware, USA
| | - Hongmao Sun
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland, USA
| | - Diane K Luci
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland, USA
| | - Bifeng Yuan
- Department of Chemistry, University of California-Riverside, Riverside, California, USA
| | - Anton Simeonov
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland, USA
| | - Ajit Jadhav
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland, USA
| | - Hui Xiao
- Laboratory of Macromolecular Analysis and Proteomics, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Yinsheng Wang
- Department of Chemistry, University of California-Riverside, Riverside, California, USA
| | - David J Maloney
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland, USA
| | - Zhihao Zhuang
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware, USA
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21
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Lee MYWT, Zhang S, Lin SHS, Wang X, Darzynkiewicz Z, Zhang Z, Lee EYC. The tail that wags the dog: p12, the smallest subunit of DNA polymerase δ, is degraded by ubiquitin ligases in response to DNA damage and during cell cycle progression. Cell Cycle 2013; 13:23-31. [PMID: 24300032 DOI: 10.4161/cc.27407] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
DNA polymerase δ (Pol δ) is a key enzyme in eukaryotic DNA replication. Human Pol δ is a heterotetramer whose p12 subunit is degraded in response to DNA damage, leading to the in vivo conversion of Pol δ4 to Pol δ3. Two E3 ubiquitin ligases, RNF8 and CRL4(Cdt2), participate in the DNA damage-induced degradation of p12. We discuss how these E3 ligases integrate the formation of Pol δ3 and ubiquitinated PCNA for DNA repair processes. CRL4(Cdt2) partially degrades p12 during normal cell cycle progression, thereby generating Pol δ3 during S phase. This novel finding extends the current view of the role of Pol δ3 in DNA repair and leads to the hypothesis that it participates in DNA replication. The coordinated regulation of licensing factors and Pol δ3 by CRL4(Cdt2) now opens new avenues for control of DNA replication. A parallel study of Pol δ4 and Pol δ3 in Okazaki fragment processing provides evidence for a role of Pol δ3 in DNA replication. We discuss several new perspectives of the role of the 2 forms of Pol δ in DNA replication and repair, as well the significance of the integration of p12 regulation in DNA repair and cell cycle progression.
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Affiliation(s)
- Marietta Y W T Lee
- Department of Biochemistry and Molecular Biology; New York Medical College; Valhalla, NY USA
| | - Sufang Zhang
- Department of Biochemistry and Molecular Biology; New York Medical College; Valhalla, NY USA
| | - Szu Hua Sharon Lin
- Department of Biochemistry and Molecular Biology; New York Medical College; Valhalla, NY USA
| | - Xiaoxiao Wang
- Department of Biochemistry and Molecular Biology; New York Medical College; Valhalla, NY USA
| | - Zbigniew Darzynkiewicz
- Department of Pathology; Brander Cancer Research Institute; New York Medical College; Valhalla, NY USA
| | - Zhongtao Zhang
- Department of Biochemistry and Molecular Biology; New York Medical College; Valhalla, NY USA
| | - Ernest Y C Lee
- Department of Biochemistry and Molecular Biology; New York Medical College; Valhalla, NY USA
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22
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Neelsen KJ, Zanini IM, Mijic S, Herrador R, Zellweger R, Ray Chaudhuri A, Creavin KD, Blow JJ, Lopes M. Deregulated origin licensing leads to chromosomal breaks by rereplication of a gapped DNA template. Genes Dev 2013; 27:2537-42. [PMID: 24298053 PMCID: PMC3861667 DOI: 10.1101/gad.226373.113] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Accepted: 10/30/2013] [Indexed: 01/01/2023]
Abstract
Deregulated origin licensing and rereplication promote genome instability and tumorigenesis by largely elusive mechanisms. Investigating the consequences of Early mitotic inhibitor 1 (Emi1) depletion in human cells, previously associated with rereplication, we show by DNA fiber labeling that origin reactivation occurs rapidly, well before accumulation of cells with >4N DNA, and is associated with checkpoint-blind ssDNA gaps and replication fork reversal. Massive RPA chromatin loading, formation of small chromosomal fragments, and checkpoint activation occur only later, once cells complete bulk DNA replication. We propose that deregulated origin firing leads to undetected discontinuities on newly replicated DNA, which ultimately cause breakage of rereplicating forks.
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Affiliation(s)
- Kai J. Neelsen
- Institute of Molecular Cancer Research, University of Zurich, CH-8057 Zurich, Switzerland
| | - Isabella M.Y. Zanini
- Institute of Molecular Cancer Research, University of Zurich, CH-8057 Zurich, Switzerland
| | - Sofija Mijic
- Institute of Molecular Cancer Research, University of Zurich, CH-8057 Zurich, Switzerland
| | - Raquel Herrador
- Institute of Molecular Cancer Research, University of Zurich, CH-8057 Zurich, Switzerland
| | - Ralph Zellweger
- Institute of Molecular Cancer Research, University of Zurich, CH-8057 Zurich, Switzerland
| | - Arnab Ray Chaudhuri
- Institute of Molecular Cancer Research, University of Zurich, CH-8057 Zurich, Switzerland
| | - Kevin D. Creavin
- Centre for Gene Regulation and Expression, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - J. Julian Blow
- Centre for Gene Regulation and Expression, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Massimo Lopes
- Institute of Molecular Cancer Research, University of Zurich, CH-8057 Zurich, Switzerland
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23
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Ganoth A, Tsfadia Y, Wiener R. Ubiquitin: Molecular modeling and simulations. J Mol Graph Model 2013; 46:29-40. [DOI: 10.1016/j.jmgm.2013.09.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Revised: 09/09/2013] [Accepted: 09/10/2013] [Indexed: 01/18/2023]
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24
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Reuther S, Reiter M, Raabe A, Dikomey E. Effect of irradiation on the expression of DNA repair genes studied in human fibroblasts by real-time qPCR using three methods of reference gene validation. RADIATION AND ENVIRONMENTAL BIOPHYSICS 2013; 52:463-469. [PMID: 23884658 DOI: 10.1007/s00411-013-0482-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Accepted: 07/09/2013] [Indexed: 06/02/2023]
Abstract
The aim of this study was to determine the effects of ionizing radiation on gene expression by using for a first time a qPCR platform specifically established for the detection of 94 DNA repair genes but also to test the robustness of these results by using three analytical methods (global pattern recognition, ΔΔCq/Normfinder and ΔΔCq/Genorm). Study was focused on these genes because DNA repair is known primarily to determine the radiation response. Six strains of normal human fibroblasts were exposed to 2 Gy, and changes in gene expression were analyzed 24 h thereafter. A significant change in gene expression was found for only few genes, but the genes detected were mostly different for the three analytical methods used. For GPR, a significant change was found for four genes, in contrast to the eight or nine genes when applying ΔΔCq/Genorm or ΔΔCq/Normfinder, respectively. When using all three methods, a significant change in expression was only seen for GADD45A and PCNA. These data demonstrate that (1) the genes identified to show an altered expression upon irradiation strongly depend on the analytical method applied, and that (2) overall GADD45A and PCNA appear to play a central role in this response, while no significant change is induced for any of the other DNA repair genes tested.
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Affiliation(s)
- Sebastian Reuther
- Laboratory of Radiobiology & Experimental Radiooncology, Center of Oncology, University Medical Center Hamburg-Eppendorf, 20246, Hamburg, Germany
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25
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Leng L, Xu C, Wei C, Zhang J, Liu B, Ma J, Li N, Qin W, Zhang W, Zhang C, Xing X, Zhai L, Yang F, Li M, Jin C, Yuan Y, Xu P, Qin J, Xie H, He F, Wang J. A Proteomics Strategy for the Identification of FAT10-Modified Sites by Mass Spectrometry. J Proteome Res 2013; 13:268-76. [PMID: 23862649 DOI: 10.1021/pr400395k] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ling Leng
- State Key Laboratory of Proteomics,
Beijing Proteome Research Center, National Center for Protein Sciences
Beijing, Beijing Institute of Radiation Medicine, Beijing 102206, China
- National Engineering Research Center for Protein Drugs, Beijing 102206, China
| | - Changming Xu
- Department of Automatic Control,
College of Mechatronics and Automation, National University of Defense Technology, Changsha 410073, China
| | - Chao Wei
- Institute of Basic Medical Science,
Chinese Academy of Medical Science and School of Basic Medicine, Peking Union Medical College, Beijing 10005, China
| | - Jiyang Zhang
- Department of Automatic Control,
College of Mechatronics and Automation, National University of Defense Technology, Changsha 410073, China
| | - Boya Liu
- State Key Laboratory of Proteomics,
Beijing Proteome Research Center, National Center for Protein Sciences
Beijing, Beijing Institute of Radiation Medicine, Beijing 102206, China
- National Engineering Research Center for Protein Drugs, Beijing 102206, China
| | - Jie Ma
- State Key Laboratory of Proteomics,
Beijing Proteome Research Center, National Center for Protein Sciences
Beijing, Beijing Institute of Radiation Medicine, Beijing 102206, China
- National Engineering Research Center for Protein Drugs, Beijing 102206, China
| | - Ning Li
- State Key Laboratory of Proteomics,
Beijing Proteome Research Center, National Center for Protein Sciences
Beijing, Beijing Institute of Radiation Medicine, Beijing 102206, China
- National Engineering Research Center for Protein Drugs, Beijing 102206, China
| | - Weijie Qin
- State Key Laboratory of Proteomics,
Beijing Proteome Research Center, National Center for Protein Sciences
Beijing, Beijing Institute of Radiation Medicine, Beijing 102206, China
- National Engineering Research Center for Protein Drugs, Beijing 102206, China
| | - Wanjun Zhang
- State Key Laboratory of Proteomics,
Beijing Proteome Research Center, National Center for Protein Sciences
Beijing, Beijing Institute of Radiation Medicine, Beijing 102206, China
- National Engineering Research Center for Protein Drugs, Beijing 102206, China
| | - Chengpu Zhang
- State Key Laboratory of Proteomics,
Beijing Proteome Research Center, National Center for Protein Sciences
Beijing, Beijing Institute of Radiation Medicine, Beijing 102206, China
- National Engineering Research Center for Protein Drugs, Beijing 102206, China
| | - Xiaohua Xing
- State Key Laboratory of Proteomics,
Beijing Proteome Research Center, National Center for Protein Sciences
Beijing, Beijing Institute of Radiation Medicine, Beijing 102206, China
- National Engineering Research Center for Protein Drugs, Beijing 102206, China
| | - Linhui Zhai
- State Key Laboratory of Proteomics,
Beijing Proteome Research Center, National Center for Protein Sciences
Beijing, Beijing Institute of Radiation Medicine, Beijing 102206, China
- National Engineering Research Center for Protein Drugs, Beijing 102206, China
| | - Fan Yang
- State Key Laboratory of Proteomics,
Beijing Proteome Research Center, National Center for Protein Sciences
Beijing, Beijing Institute of Radiation Medicine, Beijing 102206, China
- National Engineering Research Center for Protein Drugs, Beijing 102206, China
| | - Mansheng Li
- State Key Laboratory of Proteomics,
Beijing Proteome Research Center, National Center for Protein Sciences
Beijing, Beijing Institute of Radiation Medicine, Beijing 102206, China
- National Engineering Research Center for Protein Drugs, Beijing 102206, China
| | - Chaozhi Jin
- State Key Laboratory of Proteomics,
Beijing Proteome Research Center, National Center for Protein Sciences
Beijing, Beijing Institute of Radiation Medicine, Beijing 102206, China
- National Engineering Research Center for Protein Drugs, Beijing 102206, China
| | - Yanzhi Yuan
- State Key Laboratory of Proteomics,
Beijing Proteome Research Center, National Center for Protein Sciences
Beijing, Beijing Institute of Radiation Medicine, Beijing 102206, China
- National Engineering Research Center for Protein Drugs, Beijing 102206, China
| | - Ping Xu
- State Key Laboratory of Proteomics,
Beijing Proteome Research Center, National Center for Protein Sciences
Beijing, Beijing Institute of Radiation Medicine, Beijing 102206, China
- National Engineering Research Center for Protein Drugs, Beijing 102206, China
| | - Jun Qin
- State Key Laboratory of Proteomics,
Beijing Proteome Research Center, National Center for Protein Sciences
Beijing, Beijing Institute of Radiation Medicine, Beijing 102206, China
- National Engineering Research Center for Protein Drugs, Beijing 102206, China
- Baylor College of Medicine, Houston, Texas 77030, United States
| | - Hongwei Xie
- Department of Automatic Control,
College of Mechatronics and Automation, National University of Defense Technology, Changsha 410073, China
| | - Fuchu He
- State Key Laboratory of Proteomics,
Beijing Proteome Research Center, National Center for Protein Sciences
Beijing, Beijing Institute of Radiation Medicine, Beijing 102206, China
- National Engineering Research Center for Protein Drugs, Beijing 102206, China
| | - Jian Wang
- State Key Laboratory of Proteomics,
Beijing Proteome Research Center, National Center for Protein Sciences
Beijing, Beijing Institute of Radiation Medicine, Beijing 102206, China
- National Engineering Research Center for Protein Drugs, Beijing 102206, China
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26
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Zhang S, Zhao H, Darzynkiewicz Z, Zhou P, Zhang Z, Lee EYC, Lee MYWT. A novel function of CRL4(Cdt2): regulation of the subunit structure of DNA polymerase δ in response to DNA damage and during the S phase. J Biol Chem 2013; 288:29550-61. [PMID: 23913683 DOI: 10.1074/jbc.m113.490466] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
DNA polymerase δ (Pol δ4) is a heterotetrameric enzyme, whose p12 subunit is degraded in response to DNA damage, leaving behind a trimer (Pol δ3) with altered enzymatic characteristics that participate in gap filling during DNA repair. We demonstrate that CRL4(Cdt2), a key regulator of cell cycle progression that targets replication licensing factors, also targets the p12 subunit of Pol δ4 in response to DNA damage and on entry into S phase. Evidence for the involvement of CRL4(Cdt2) included demonstration that p12 possesses a proliferating cell nuclear antigen-interacting protein-degron (PIP-degron) and that knockdown of the components of the CRL4(Cdt2) complex inhibited the degradation of p12 in response to DNA damage. Analysis of p12 levels in synchronized cell populations showed that p12 is partially degraded in S phase and that this is affected by knockdowns of CUL4A or CUL4B. Laser scanning cytometry of overexpressed wild type p12 and a mutant resistant to degradation showed that the reduction in p12 levels during S phase was prevented by mutation of p12. Thus, CRL4(Cdt2) also regulates the subunit composition of Pol δ during the cell cycle. These studies reveal a novel function of CRL4(Cdt2), i.e. the direct regulation of DNA polymerase δ, adding to its known functions in the regulation of the licensing of replication origins and expanding the scope of its overall control of DNA replication. The formation of Pol δ3 in S phase as a normal aspect of cell cycle progression leads to the novel implications that it is involved in DNA replication as well as DNA repair.
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Affiliation(s)
- Sufang Zhang
- From the Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla, New York 10595
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27
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Arbel-Eden A, Joseph-Strauss D, Masika H, Printzental O, Rachi E, Simchen G. Trans-Lesion DNA Polymerases May Be Involved in Yeast Meiosis. G3 (BETHESDA, MD.) 2013; 3:633-644. [PMID: 23550131 PMCID: PMC3618350 DOI: 10.1534/g3.113.005603] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2013] [Accepted: 02/09/2013] [Indexed: 12/14/2022]
Abstract
Trans-lesion DNA polymerases (TLSPs) enable bypass of DNA lesions during replication and are also induced under stress conditions. Being only weakly dependent on their template during replication, TLSPs introduce mutations into DNA. The low processivity of these enzymes ensures that they fall off their template after a few bases are synthesized and are then replaced by the more accurate replicative polymerase. We find that the three TLSPs of budding yeast Saccharomyces cerevisiae Rev1, PolZeta (Rev3 and Rev7), and Rad30 are induced during meiosis at a time when DNA double-strand breaks (DSBs) are formed and homologous chromosomes recombine. Strains deleted for one or any combination of the three TLSPs undergo normal meiosis. However, in the triple-deletion mutant, there is a reduction in both allelic and ectopic recombination. We suggest that trans-lesion polymerases are involved in the processing of meiotic double-strand breaks that lead to mutations. In support of this notion, we report significant yeast two-hybrid (Y2H) associations in meiosis-arrested cells between the TLSPs and DSB proteins Rev1-Spo11, Rev1-Mei4, and Rev7-Rec114, as well as between Rev1 and Rad30 We suggest that the involvement of TLSPs in processing of meiotic DSBs could be responsible for the considerably higher frequency of mutations reported during meiosis compared with that found in mitotically dividing cells, and therefore may contribute to faster evolutionary divergence than previously assumed.
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Affiliation(s)
- Ayelet Arbel-Eden
- Department of Genetics, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
- Department of Medical Laboratory Sciences, Hadassah Academic College, Jerusalem 91010, Israel
| | | | - Hagit Masika
- Department of Genetics, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Oxana Printzental
- Department of Genetics, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Eléanor Rachi
- Department of Genetics, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Giora Simchen
- Department of Genetics, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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28
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Parsons JL, Nicolay NH, Sharma RA. Biological and therapeutic relevance of nonreplicative DNA polymerases to cancer. Antioxid Redox Signal 2013; 18:851-73. [PMID: 22794079 PMCID: PMC3557440 DOI: 10.1089/ars.2011.4203] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Apart from surgical approaches, the treatment of cancer remains largely underpinned by radiotherapy and pharmacological agents that cause damage to cellular DNA, which ultimately causes cancer cell death. DNA polymerases, which are involved in the repair of cellular DNA damage, are therefore potential targets for inhibitors for improving the efficacy of cancer therapy. They can be divided, according to their main function, into two groups, namely replicative and nonreplicative enzymes. At least 15 different DNA polymerases, including their homologs, have been discovered to date, which vary considerably in processivity and fidelity. Many of the nonreplicative (specialized) DNA polymerases replicate DNA in an error-prone fashion, and they have been shown to participate in multiple DNA damage repair and tolerance pathways, which are often aberrant in cancer cells. Alterations in DNA repair pathways involving DNA polymerases have been linked with cancer survival and with treatment response to radiotherapy or to classes of cytotoxic drugs routinely used for cancer treatment, particularly cisplatin, oxaliplatin, etoposide, and bleomycin. Indeed, there are extensive preclinical data to suggest that DNA polymerase inhibition may prove to be a useful approach for increasing the effectiveness of therapies in patients with cancer. Furthermore, specialized DNA polymerases warrant examination of their potential use as clinical biomarkers to select for particular cancer therapies, to individualize treatment for patients.
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Affiliation(s)
- Jason L Parsons
- Cancer Research UK-Medical Research Council, Oncology Department, Gray Institute for Radiation Oncology and Biology, University of Oxford, Oxford, United Kingdom
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29
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Zhang S, Zhou Y, Sarkeshik A, Yates JR, Thomson TM, Zhang Z, Lee EYC, Lee MYWT. Identification of RNF8 as a ubiquitin ligase involved in targeting the p12 subunit of DNA polymerase δ for degradation in response to DNA damage. J Biol Chem 2012; 288:2941-50. [PMID: 23233665 DOI: 10.1074/jbc.m112.423392] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
DNA polymerase δ consists of four subunits, one of which, p12, is degraded in response to DNA damage through the ubiquitin-proteasome pathway. However, the identities of the ubiquitin ligase(s) that are responsible for the proximal biochemical events in triggering proteasomal degradation of p12 are unknown. We employed a classical approach to identifying a ubiquitin ligase that is involved in p12 degradation. Using UbcH5c as ubiquitin-conjugating enzyme, a ubiquitin ligase activity that polyubiquitinates p12 was purified from HeLa cells. Proteomic analysis revealed that RNF8, a RING finger ubiquitin ligase that plays an important role in the DNA damage response, was the only ubiquitin ligase present in the purified preparation. In vivo, DNA damage-induced p12 degradation was significantly reduced by shRNA knockdown of RNF8 in cultured human cells and in RNF8(-/-) mouse epithelial cells. These studies provide the first identification of a ubiquitin ligase activity that is involved in the DNA damage-induced destruction of p12. The identification of RNF8 allows new insights into the integration of the control of p12 degradation by different DNA damage signaling pathways.
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Affiliation(s)
- Sufang Zhang
- Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla, New York 10595, USA
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30
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Lee MYWT, Zhang S, Lin SHS, Chea J, Wang X, LeRoy C, Wong A, Zhang Z, Lee EYC. Regulation of human DNA polymerase delta in the cellular responses to DNA damage. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2012; 53:683-698. [PMID: 23047826 DOI: 10.1002/em.21743] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2012] [Revised: 08/28/2012] [Accepted: 08/29/2012] [Indexed: 06/01/2023]
Abstract
The p12 subunit of polymerase delta (Pol δ) is degraded in response to DNA damage induced by UV, alkylating agents, oxidative, and replication stresses. This leads to the conversion of the Pol δ4 holoenzyme to the heterotrimer, Pol δ3. We review studies that establish that Pol δ3 formation is an event that could have a major impact on cellular processes in genomic surveillance, DNA replication, and DNA repair. p12 degradation is dependent on the apical ataxia telangiectasia and Rad3 related (ATR) kinase and is mediated by the ubiquitin-proteasome system. Pol δ3 exhibits properties of an "antimutator" polymerase, suggesting that it could contribute to an increased surveillance against mutagenesis, for example, when Pol δ carries out bypass synthesis past small base lesions that engage in spurious base pairing. Chromatin immunoprecipitation analysis and examination of the spatiotemporal recruitment of Pol δ to sites of DNA damage show that Pol δ3 is the primary form of Pol δ associated with cyclobutane pyrimidine dimer lesions and therefore should be considered as the operative form of Pol δ engaged in DNA repair. We propose a model for the switching of Pol δ with translesion polymerases, incorporating the salient features of the recently determined structure of monoubiquitinated proliferating cell nuclear antigen and emphasizing the role of Pol δ3. Because of the critical role of Pol δ activity in DNA replication and repair, the formation of Pol δ3 in response to DNA damage opens the prospect that pleiotropic effects may ensue. This opens the horizons for future exploration of how this novel response to DNA damage contributes to genomic stability.
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Affiliation(s)
- Marietta Y W T Lee
- Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla, NY 10595, USA.
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31
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Walsh E, Wang X, Lee MY, Eckert KA. Mechanism of replicative DNA polymerase delta pausing and a potential role for DNA polymerase kappa in common fragile site replication. J Mol Biol 2012; 425:232-43. [PMID: 23174185 DOI: 10.1016/j.jmb.2012.11.016] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2012] [Revised: 11/12/2012] [Accepted: 11/12/2012] [Indexed: 11/16/2022]
Abstract
Common fragile sites (CFSs) are hot spots of chromosomal breakage, and CFS breakage models involve perturbations of DNA replication. Here, we analyzed the contribution of specific repetitive DNA sequence elements within CFSs to the inhibition of DNA synthesis by replicative and specialized DNA polymerases (Pols). The efficiency of in vitro DNA synthesis was quantitated using templates corresponding to regions within FRA16D and FRA3B harboring AT-rich microsatellite and quasi-palindrome (QP) sequences. QPs were predicted to form stems of ~75-100% self-homology, separated by 3-9 bases of intervening sequences. Analysis of DNA synthesis progression by human Pol δ demonstrated significant synthesis perturbation both at [A](n) and [TA](n) repeats in a length-dependent manner and at short (<40 base pairs) QP sequences. DNA synthesis by the Y-family polymerase κ was significantly more efficient than Pol δ through both types of repetitive elements. Using DNA trap experiments, we show that Pol δ pauses within CFS sequences are sites of enzyme dissociation, and dissociation was observed in the presence of RFC-loaded PCNA. We propose that enrichment of microsatellite and QP elements at CFS regions contributes to fragility by perturbing replication through multiple mechanisms, including replicative Pol pausing and dissociation. Our finding that Pol δ dissociates at specific CFS sequences is significant, since dissociation of the replication machinery and inability to efficiently recover the replication fork can lead to fork collapse and/or formation of double-strand breaks in vivo. Our biochemical studies also extend the potential involvement of Y-family polymerases in CFS maintenance to include polymerase κ.
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Affiliation(s)
- Erin Walsh
- Cellular and Molecular Biology Graduate Program, Penn State University College of Medicine, Hershey, PA 17033, USA
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32
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Chea J, Zhang S, Zhao H, Zhang Z, Lee EYC, Darzynkiewicz Z, Lee MYWT. Spatiotemporal recruitment of human DNA polymerase delta to sites of UV damage. Cell Cycle 2012; 11:2885-95. [PMID: 22801543 DOI: 10.4161/cc.21280] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Human DNA polymerase δ (Pol δ) is involved in various DNA damage responses in addition to its central role in DNA replication. The Pol δ4 holoenzyme consists of four subunits, p125, p50, p68 and p12. It has been established that the p12 subunit is rapidly degraded in response to DNA damage by UV leading to the in vivo conversion of Pol δ4 to Pol δ3, a trimeric form lacking the p12 subunit. We provide the first analysis of the time-dependent recruitment of the individual Pol δ subunits to sites of DNA damage produced by UV irradiation through 5 μm polycarbonate filters by immunofluorescence microscopy and laser scanning cytometry (LSC). Quantitative analysis demonstrates that the recruitments of the three large subunits was near complete by 2 h and did not change significantly up to 4 h after UV exposure. However, the recruitment of p12 was incomplete even at 4 h, with about 70% of the Pol δ lacking the p12 subunit. ChIP analysis of Pol δ after global UV irradiation further demonstrates that only p125, p50 and p68 were present. Thus, Pol δ3 is the predominant form of Pol δ at sites of UV damage as a result of p12 degradation. Using LSC, we have further confirmed that Pol δ was recruited to CPD damage sites in all phases of the cell cycle. Collectively, our results show that Pol δ at the DNA damage site is the Pol δ trimer lacking p12 regardless of the cell cycle phase.
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Affiliation(s)
- Jennifer Chea
- Department of Biochemistry and Molecular Biology; New York Medical College; Valhalla, NY USA
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33
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Altmannová V, Kolesár P, Krejčí L. SUMO Wrestles with Recombination. Biomolecules 2012; 2:350-75. [PMID: 24970142 PMCID: PMC4030836 DOI: 10.3390/biom2030350] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2012] [Revised: 06/27/2012] [Accepted: 07/13/2012] [Indexed: 01/21/2023] Open
Abstract
DNA double-strand breaks (DSBs) comprise one of the most toxic DNA lesions, as the failure to repair a single DSB has detrimental consequences on the cell. Homologous recombination (HR) constitutes an error-free repair pathway for the repair of DSBs. On the other hand, when uncontrolled, HR can lead to genome rearrangements and needs to be tightly regulated. In recent years, several proteins involved in different steps of HR have been shown to undergo modification by small ubiquitin-like modifier (SUMO) peptide and it has been suggested that deficient sumoylation impairs the progression of HR. This review addresses specific effects of sumoylation on the properties of various HR proteins and describes its importance for the homeostasis of DNA repetitive sequences. The article further illustrates the role of sumoylation in meiotic recombination and the interplay between SUMO and other post-translational modifications.
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Affiliation(s)
| | - Peter Kolesár
- Department of Biology, Masaryk University, Brno 62500, Czech Republic.
| | - Lumír Krejčí
- Department of Biology, Masaryk University, Brno 62500, Czech Republic.
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34
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35
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Spasser L, Brik A. Chemistry and Biology of the Ubiquitin Signal. Angew Chem Int Ed Engl 2012; 51:6840-62. [DOI: 10.1002/anie.201200020] [Citation(s) in RCA: 117] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2012] [Indexed: 01/07/2023]
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36
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Zhang Z, Zhang S, Lin SHS, Wang X, Wu L, Lee EYC, Lee MYWT. Structure of monoubiquitinated PCNA: implications for DNA polymerase switching and Okazaki fragment maturation. Cell Cycle 2012; 11:2128-36. [PMID: 22592530 DOI: 10.4161/cc.20595] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Ubiquitination of proliferating cell nuclear antigen (PCNA) to ub-PCNA is essential for DNA replication across bulky template lesions caused by UV radiation and alkylating agents, as ub-PCNA orchestrates the recruitment and switching of translesion synthesis (TLS) polymerases with replication polymerases. This allows replication to proceed, leaving the DNA to be repaired subsequently. Defects in a TLS polymerase, Pol η, lead to a form of Xeroderma pigmentosum, a disease characterized by severe skin sensitivity to sunlight damage and an increased incidence of skin cancer. Structurally, however, information on how ub-PCNA orchestrates the switching of these two classes of polymerases is lacking. We have solved the structure of ub-PCNA and demonstrate that the ubiquitin molecules in ub-PCNA are radially extended away from the PCNA without structural contact aside from the isopeptide bond linkage. This unique orientation provides an open platform for the recruitment of TLS polymerases through ubiquitin-interacting domains. However, the ubiquitin moieties, to the side of the equatorial PCNA plane, can place spatial constraints on the conformational flexibility of proteins bound to ub-PCNA. We show that ub-PCNA is impaired in its ability to support the coordinated actions of Fen1 and Pol δ in assays mimicking Okazaki fragment processing. This provides evidence for the novel concept that ub-PCNA may modulate additional DNA transactions other than TLS polymerase recruitment and switching.
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Affiliation(s)
- Zhongtao Zhang
- Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla, NY, USA.
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37
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Gali H, Juhasz S, Morocz M, Hajdu I, Fatyol K, Szukacsov V, Burkovics P, Haracska L. Role of SUMO modification of human PCNA at stalled replication fork. Nucleic Acids Res 2012; 40:6049-59. [PMID: 22457066 PMCID: PMC3401441 DOI: 10.1093/nar/gks256] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
DNA double-strand breaks (DSBs) can be generated not only by reactive agents but also as a result of replication fork collapse at unrepaired DNA lesions. Whereas ubiquitylation of proliferating cell nuclear antigen (PCNA) facilitates damage bypass, modification of yeast PCNA by small ubiquitin-like modifier (SUMO) controls recombination by providing access for the Srs2 helicase to disrupt Rad51 nucleoprotein filaments. However, in human cells, the roles of PCNA SUMOylation have not been explored. Here, we characterize the modification of human PCNA by SUMO in vivo as well as in vitro. We establish that human PCNA can be SUMOylated at multiple sites including its highly conserved K164 residue and that SUMO modification is facilitated by replication factor C (RFC). We also show that expression of SUMOylation site PCNA mutants leads to increased DSB formation in the Rad18−/− cell line where the effect of Rad18-dependent K164 PCNA ubiquitylation can be ruled out. Moreover, expression of PCNA-SUMO1 fusion prevents DSB formation as well as inhibits recombination if replication stalls at DNA lesions. These findings suggest the importance of SUMO modification of human PCNA in preventing replication fork collapse to DSB and providing genome stability.
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Affiliation(s)
- Himabindu Gali
- Institute of Genetics, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
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Hegde ML, Izumi T, Mitra S. Oxidized base damage and single-strand break repair in mammalian genomes: role of disordered regions and posttranslational modifications in early enzymes. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2012; 110:123-53. [PMID: 22749145 DOI: 10.1016/b978-0-12-387665-2.00006-7] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Oxidative genome damage induced by reactive oxygen species includes oxidized bases, abasic (AP) sites, and single-strand breaks, all of which are repaired via the evolutionarily conserved base excision repair/single-strand break repair (BER/SSBR) pathway. BER/SSBR in mammalian cells is complex, with preferred and backup sub-pathways, and is linked to genome replication and transcription. The early BER/SSBR enzymes, namely, DNA glycosylases (DGs) and the end-processing proteins such as abasic endonuclease 1 (APE1), form complexes with downstream repair (and other noncanonical) proteins via pairwise interactions. Furthermore, a unique feature of mammalian early BER/SSBR enzymes is the presence of a disordered terminal extension that is absent in their Escherichia coli prototypes. These nonconserved segments usually contain organelle-targeting signals, common interaction interfaces, and sites of posttranslational modifications that may be involved in regulating their repair function including lesion scanning. Finally, the linkage of BER/SSBR deficiency to cancer, aging, and human neurodegenerative diseases, and therapeutic targeting of BER/SSBR are discussed.
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Affiliation(s)
- Muralidhar L Hegde
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, USA
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Fushman D, Wilkinson KD. Structure and recognition of polyubiquitin chains of different lengths and linkage. F1000 BIOLOGY REPORTS 2011; 3:26. [PMID: 22162729 PMCID: PMC3229271 DOI: 10.3410/b3-26] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The polyubiquitin signal is post-translationally attached to a large number of proteins, often directing formation of macromolecular complexes resulting in the translocation, assembly or degradation of the attached protein. Recent structural and functional studies reveal general mechanisms by which different architectures and length of the signal are distinguished.
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Affiliation(s)
- David Fushman
- Department of Chemistry and Biochemistry, University of MarylandCollege Park, MD 20742USA
| | - Keith D. Wilkinson
- Department of Biochemistry, Emory University School of MedicineAtlanta, GA 30322USA
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