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Olsen JG, Prestel A, Kassem N, Broendum SS, Shamim HM, Simonsen S, Grysbæk M, Mortensen J, Rytkjær LL, Haxholm GW, Marabini R, Holmberg C, Carr AM, Crehuet R, Nielsen O, Kragelund BB. Checkpoint activation by Spd1: a competition-based system relying on tandem disordered PCNA binding motifs. Nucleic Acids Res 2024; 52:2030-2044. [PMID: 38261971 PMCID: PMC10939359 DOI: 10.1093/nar/gkae011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 12/18/2023] [Accepted: 01/02/2024] [Indexed: 01/25/2024] Open
Abstract
DNA regulation, replication and repair are processes fundamental to all known organisms and the sliding clamp proliferating cell nuclear antigen (PCNA) is central to all these processes. S-phase delaying protein 1 (Spd1) from S. pombe, an intrinsically disordered protein that causes checkpoint activation by inhibiting the enzyme ribonucleotide reductase, has one of the most divergent PCNA binding motifs known. Using NMR spectroscopy, in vivo assays, X-ray crystallography, calorimetry, and Monte Carlo simulations, an additional PCNA binding motif in Spd1, a PIP-box, is revealed. The two tandemly positioned, low affinity sites exchange rapidly on PCNA exploiting the same binding sites. Increasing or decreasing the binding affinity between Spd1 and PCNA through mutations of either motif compromised the ability of Spd1 to cause checkpoint activation in yeast. These results pinpoint a role for PCNA in Spd1-mediated checkpoint activation and suggest that its tandemly positioned short linear motifs create a neatly balanced competition-based system, involving PCNA, Spd1 and the small ribonucleotide reductase subunit, Suc22R2. Similar mechanisms may be relevant in other PCNA binding ligands where divergent binding motifs so far have gone under the PIP-box radar.
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Affiliation(s)
- Johan G Olsen
- Structural Biology and NMR Laboratory, The Linderstrøm-Lang Centre for Protein Science and REPIN, Department of Biology, Ole Maaloes Vej 5, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Andreas Prestel
- Structural Biology and NMR Laboratory, The Linderstrøm-Lang Centre for Protein Science and REPIN, Department of Biology, Ole Maaloes Vej 5, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Noah Kassem
- Structural Biology and NMR Laboratory, The Linderstrøm-Lang Centre for Protein Science and REPIN, Department of Biology, Ole Maaloes Vej 5, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Sebastian S Broendum
- Structural Biology and NMR Laboratory, The Linderstrøm-Lang Centre for Protein Science and REPIN, Department of Biology, Ole Maaloes Vej 5, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Hossain Mohammad Shamim
- Cell cycle and Genome Stability Group, Functional Genomics, Department of Biology, Ole Maaloes Vej 5, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Signe Simonsen
- Structural Biology and NMR Laboratory, The Linderstrøm-Lang Centre for Protein Science and REPIN, Department of Biology, Ole Maaloes Vej 5, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Martin Grysbæk
- Cell cycle and Genome Stability Group, Functional Genomics, Department of Biology, Ole Maaloes Vej 5, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Josefine Mortensen
- Cell cycle and Genome Stability Group, Functional Genomics, Department of Biology, Ole Maaloes Vej 5, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Louise Lund Rytkjær
- Cell cycle and Genome Stability Group, Functional Genomics, Department of Biology, Ole Maaloes Vej 5, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Gitte W Haxholm
- Structural Biology and NMR Laboratory, The Linderstrøm-Lang Centre for Protein Science and REPIN, Department of Biology, Ole Maaloes Vej 5, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Riccardo Marabini
- Structural Biology and NMR Laboratory, The Linderstrøm-Lang Centre for Protein Science and REPIN, Department of Biology, Ole Maaloes Vej 5, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Christian Holmberg
- Cell cycle and Genome Stability Group, Functional Genomics, Department of Biology, Ole Maaloes Vej 5, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Antony M Carr
- Genome Damage and Stability Centre, University of Sussex, John Maynard Smith Building, Falmer, BN1 9RQ, Brighton
| | - Ramon Crehuet
- Institute for Advanced Chemistry of Catalonia (IQAC), CSIC, c/ Jordi Girona 18-26, 08034 Barcelona
| | - Olaf Nielsen
- Cell cycle and Genome Stability Group, Functional Genomics, Department of Biology, Ole Maaloes Vej 5, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Birthe B Kragelund
- Structural Biology and NMR Laboratory, The Linderstrøm-Lang Centre for Protein Science and REPIN, Department of Biology, Ole Maaloes Vej 5, University of Copenhagen, 2200 Copenhagen N, Denmark
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González-Magaña A, Blanco FJ. Human PCNA Structure, Function and Interactions. Biomolecules 2020; 10:biom10040570. [PMID: 32276417 PMCID: PMC7225939 DOI: 10.3390/biom10040570] [Citation(s) in RCA: 132] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 04/01/2020] [Accepted: 04/03/2020] [Indexed: 12/13/2022] Open
Abstract
Proliferating cell nuclear antigen (PCNA) is an essential factor in DNA replication and repair. It forms a homotrimeric ring that embraces the DNA and slides along it, anchoring DNA polymerases and other DNA editing enzymes. It also interacts with regulatory proteins through a sequence motif known as PCNA Interacting Protein box (PIP-box). We here review the latest contributions to knowledge regarding the structure-function relationships in human PCNA, particularly the mechanism of sliding, and of the molecular recognition of canonical and non-canonical PIP motifs. The unique binding mode of the oncogene p15 is described in detail, and the implications of the recently discovered structure of PCNA bound to polymerase δ are discussed. The study of the post-translational modifications of PCNA and its partners may yield therapeutic opportunities in cancer treatment, in addition to illuminating the way PCNA coordinates the dynamic exchange of its many partners in DNA replication and repair.
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Affiliation(s)
- Amaia González-Magaña
- CIC bioGUNE, Bizkaia Science and Technology Park, bld 800, 48160 Derio, Bizkaia, Spain;
| | - Francisco J. Blanco
- CIC bioGUNE, Bizkaia Science and Technology Park, bld 800, 48160 Derio, Bizkaia, Spain;
- IKERBASQUE, Basque Foundation for Science, Maria Diaz de Haro 3, 6 solairua, 48013 Bilbao, Bizkaia, Spain
- Correspondence:
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Motnenko A, Liang CC, Yang D, Lopez-Martinez D, Yoshikawa Y, Zhan B, Ward KE, Tian J, Haas W, Spingardi P, Kessler BM, Kriaucionis S, Gygi SP, Cohn MA. Identification of UHRF2 as a novel DNA interstrand crosslink sensor protein. PLoS Genet 2018; 14:e1007643. [PMID: 30335751 PMCID: PMC6193622 DOI: 10.1371/journal.pgen.1007643] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 08/17/2018] [Indexed: 02/04/2023] Open
Abstract
The Fanconi Anemia (FA) pathway is important for repairing interstrand crosslinks (ICLs) between the Watson-Crick strands of the DNA double helix. An initial and essential stage in the repair process is the detection of the ICL. Here, we report the identification of UHRF2, a paralogue of UHRF1, as an ICL sensor protein. UHRF2 is recruited to ICLs in the genome within seconds of their appearance. We show that UHRF2 cooperates with UHRF1, to ensure recruitment of FANCD2 to ICLs. A direct protein-protein interaction is formed between UHRF1 and UHRF2, and between either UHRF1 and UHRF2, and FANCD2. Importantly, we demonstrate that the essential monoubiquitination of FANCD2 is stimulated by UHRF1/UHRF2. The stimulation is mediating by a retention of FANCD2 on chromatin, allowing for its monoubiquitination by the FA core complex. Taken together, we uncover a mechanism of ICL sensing by UHRF2, leading to FANCD2 recruitment and retention at ICLs, in turn facilitating activation of FANCD2 by monoubiquitination.
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Affiliation(s)
- Anna Motnenko
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Chih-Chao Liang
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Di Yang
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | | | - Yasunaga Yoshikawa
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Bao Zhan
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Katherine E. Ward
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Jiayang Tian
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Wilhelm Haas
- Department of Cell Biology, Harvard Medical School, Boston, MA, United States of America Medicine, Kitasato University, Aomori, Japan
| | - Paolo Spingardi
- Ludwig Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Benedikt M. Kessler
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Skirmantas Kriaucionis
- Ludwig Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Steven P. Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA, United States of America Medicine, Kitasato University, Aomori, Japan
| | - Martin A. Cohn
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
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Maneuvers on PCNA Rings during DNA Replication and Repair. Genes (Basel) 2018; 9:genes9080416. [PMID: 30126151 PMCID: PMC6116012 DOI: 10.3390/genes9080416] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 08/08/2018] [Accepted: 08/09/2018] [Indexed: 12/20/2022] Open
Abstract
DNA replication and repair are essential cellular processes that ensure genome duplication and safeguard the genome from deleterious mutations. Both processes utilize an abundance of enzymatic functions that need to be tightly regulated to ensure dynamic exchange of DNA replication and repair factors. Proliferating cell nuclear antigen (PCNA) is the major coordinator of faithful and processive replication and DNA repair at replication forks. Post-translational modifications of PCNA, ubiquitination and acetylation in particular, regulate the dynamics of PCNA-protein interactions. Proliferating cell nuclear antigen (PCNA) monoubiquitination elicits ‘polymerase switching’, whereby stalled replicative polymerase is replaced with a specialized polymerase, while PCNA acetylation may reduce the processivity of replicative polymerases to promote homologous recombination-dependent repair. While regulatory functions of PCNA ubiquitination and acetylation have been well established, the regulation of PCNA-binding proteins remains underexplored. Considering the vast number of PCNA-binding proteins, many of which have similar PCNA binding affinities, the question arises as to the regulation of the strength and sequence of their binding to PCNA. Here I provide an overview of post-translational modifications on both PCNA and PCNA-interacting proteins and discuss their relevance for the regulation of the dynamic processes of DNA replication and repair.
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Jin C, Xiong D, Li HR, Jiang JH, Qi JC, Ding JY. Loss of UHRF2 Is Associated With Non-small Cell Lung Carcinoma Progression. J Cancer 2018; 9:2994-3005. [PMID: 30210621 PMCID: PMC6134831 DOI: 10.7150/jca.25876] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2018] [Accepted: 06/09/2018] [Indexed: 01/12/2023] Open
Abstract
Recent evidence indicated ubiquitin like with PHD and ring finger domains 2 (UHRF2) was involved in various human diseases, especially in cancer, however, its roles in cancer are still in dispute. Here, we found UHRF2 expression was decreased in lung cancer tissues compared with adjacent normal tissues by referring to the Oncomine Database, which was further identified by immunoblotting and quantitative real-time polymerase chain reaction assays. Secondly, we found knockdown of UHRF2 in A549 and 95-D cell lines enhanced the capability of proliferation, invasion and migration, while forced UHRF2 expression inhibited NSCLC cells proliferation,invasion and migration. Mechanistically, dot-blot and western blot assays indicated that the level of UHRF2 was positively correlated with 5-hmC level by affecting ten-eleven translocation 2 (TET2) expression. Clinically, UHRF2 downregulation is significantly correlated with a malignant phenotype, including larger tumor size and poor differentiation. Moreover, UHRF2 downregulated correlates with shorter overall survival(OS). Conclusion: Our findings indicate that UHRF2 is a tumor suppressor in NSCLC by influence TET2 expression and serve as a potential therapeutic target in NSCLC.
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Affiliation(s)
- Chun Jin
- Department of Thoracic Surgery, The Affiliated Zhongshan Hospital of Fudan University, Shanghai 200032, P. R. China
| | - Dian Xiong
- Department of Cardiothoracic Surgery, The Second Affiliated Hospital of Nanchang University, Jiangxi Province 330000, P. R. China
| | - Hao-Ran Li
- Department of Thoracic Surgery, The Affiliated Zhongshan Hospital of Fudan University, Shanghai 200032, P. R. China
| | - Jia-Hao Jiang
- Department of Thoracic Surgery, The Affiliated Zhongshan Hospital of Fudan University, Shanghai 200032, P. R. China
| | - Jian-Chao Qi
- Department of emergency surgery, Fujian Provincial Hospital, Fu Zhou, Fujian Province,350001, China
| | - Jian-Yong Ding
- Department of Thoracic Surgery, The Affiliated Zhongshan Hospital of Fudan University, Shanghai 200032, P. R. China
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