1
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He Q, Wang F, O'Donnell ME, Li H. Cryo-EM reveals a nearly complete PCNA loading process and unique features of the human alternative clamp loader CTF18-RFC. Proc Natl Acad Sci U S A 2024; 121:e2319727121. [PMID: 38669181 DOI: 10.1073/pnas.2319727121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 03/15/2024] [Indexed: 04/28/2024] Open
Abstract
The DNA sliding clamp PCNA is a multipurpose platform for DNA polymerases and many other proteins involved in DNA metabolism. The topologically closed PCNA ring needs to be cracked open and loaded onto DNA by a clamp loader, e.g., the well-studied pentameric ATPase complex RFC (RFC1-5). The CTF18-RFC complex is an alternative clamp loader found recently to bind the leading strand DNA polymerase ε and load PCNA onto leading strand DNA, but its structure and the loading mechanism have been unknown. By cryo-EM analysis of in vitro assembled human CTF18-RFC-DNA-PCNA complex, we have captured seven loading intermediates, revealing a detailed PCNA loading mechanism onto a 3'-ss/dsDNA junction by CTF18-RFC. Interestingly, the alternative loader has evolved a highly mobile CTF18 AAA+ module likely to lower the loading activity, perhaps to avoid competition with the RFC and to limit its role to leading strand clamp loading. To compensate for the lost stability due to the mobile AAA+ module, CTF18 has evolved a unique β-hairpin motif that reaches across RFC2 to interact with RFC5, thereby stabilizing the pentameric complex. Further, we found that CTF18 also contains a separation pin to locally melt DNA from the 3'-end of the primer; this ensures its ability to load PCNA to any 3'-ss/dsDNA junction, facilitated by the binding energy of the E-plug to the major groove. Our study reveals unique structural features of the human CTF18-RFC and contributes to a broader understanding of PCNA loading by the alternative clamp loaders.
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Affiliation(s)
- Qing He
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI 49503
| | - Feng Wang
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI 49503
| | - Michael E O'Donnell
- DNA Replication Laboratory, The Rockefeller University, New York, NY 10065
- HHMI, The Rockefeller University, New York, NY 10065
| | - Huilin Li
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI 49503
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2
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Zheng F, Yao NY, Georgescu RE, Li H, O’Donnell ME. Structure of the PCNA unloader Elg1-RFC. Sci Adv 2024; 10:eadl1739. [PMID: 38427736 PMCID: PMC10906927 DOI: 10.1126/sciadv.adl1739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 01/26/2024] [Indexed: 03/03/2024]
Abstract
During DNA replication, the proliferating cell nuclear antigen (PCNA) clamps are loaded onto primed sites for each Okazaki fragment synthesis by the AAA+ heteropentamer replication factor C (RFC). PCNA encircling duplex DNA is quite stable and is removed from DNA by the dedicated clamp unloader Elg1-RFC. Here, we show the cryo-EM structure of Elg1-RFC in various states with PCNA. The structures reveal essential features of Elg1-RFC that explain how it is dedicated to PCNA unloading. Specifically, Elg1 contains two external loops that block opening of the Elg1-RFC complex for DNA binding, and an "Elg1 plug" domain that fills the central DNA binding chamber, thereby reinforcing the exclusive PCNA unloading activity of Elg1-RFC. Elg1-RFC was capable of unloading PCNA using non-hydrolyzable AMP-PNP. Both RFC and Elg1-RFC could remove PCNA from covalently closed circular DNA, indicating that PCNA unloading occurs by a mechanism that is distinct from PCNA loading. Implications for the PCNA unloading mechanism are discussed.
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Affiliation(s)
- Fengwei Zheng
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, USA
| | - Nina Y. Yao
- DNA Replication Laboratory and Howard Hughes Medical Institute, The Rockefeller University, NY, New York, USA
| | - Roxana E. Georgescu
- DNA Replication Laboratory and Howard Hughes Medical Institute, The Rockefeller University, NY, New York, USA
| | - Huilin Li
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, USA
| | - Michael E. O’Donnell
- DNA Replication Laboratory and Howard Hughes Medical Institute, The Rockefeller University, NY, New York, USA
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3
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Actis M, Fujii N, Mackey ZB. A phenotypic screen with Trypanosoma brucei for discovering small molecules that target the SLiM-binding pocket of proliferating cell nuclear antigen orthologs. Chem Biol Drug Des 2024; 103:e14361. [PMID: 37767622 DOI: 10.1111/cbdd.14361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 09/05/2023] [Accepted: 09/12/2023] [Indexed: 09/29/2023]
Abstract
Proliferating cell nuclear antigen (PCNA) is a homo-trimeric protein complex that clamps around DNA to tether DNA polymerases to the template during replication and serves as a hub for many other interacting proteins. It regulates DNA metabolic processes and other vital cellar functions through the binding of proteins having short linear motifs (SLiMs) like the PIP-box (PCNA-interacting protein-box) or the APIM (AlkB homolog 2 PCNA-interacting motif) in the hydrophobic pocket where SLiMs bind. However, overproducing TbPCNA or human PCNA (hPCNA) in the pathogenic protist Trypanosoma brucei triggers a dominant-negative phenotype of arrested proliferation. The mechanism for arresting T. brucei proliferation requires the overproduced PCNA orthologs to have functional intact SLiM-binding pocket. Sight-directed mutagenesis studies showed that T. brucei overproducing PCNA variants with disrupted SLiM-binding pockets grew normally. We hypothesized that chemically disrupting the SLiM-binding pocket would restore proliferation in T. brucei, overproducing PCNA orthologs. Testing this hypothesis is the proof-of-concept for a T. brucei-based PCNA screening assay. The assay design is to discover bioactive small molecules that restore proliferation in T. brucei strains that overproduce PCNA orthologs, likely by disrupting interactions in the SLiM-binding pocket. The pilot screen for this assay discovered two hit compounds that linked to predetermined PCNA targets. Compound #1, a known hPCNA inhibitor, had selective bioactivity to hPCNA overproduced in T. brucei, validating the assay. Compound #6 had promiscuous bioactivity for hPCNA and TbPCNA but is the first compound discovered with bioactivity for inhibiting TbPCNA.
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Affiliation(s)
- Marisa Actis
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Naoaki Fujii
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Zachary B Mackey
- Biochemistry Department, Fralin Life Science Institute Virginia Tech, Blacksburg, Virginia, USA
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4
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Gu L, Li M, Li CM, Haratipour P, Lingeman R, Jossart J, Gutova M, Flores L, Hyde C, Kenjić N, Li H, Chung V, Li H, Lomenick B, Von Hoff DD, Synold TW, Aboody KS, Liu Y, Horne D, Hickey RJ, Perry JJP, Malkas LH. Small molecule targeting of transcription-replication conflict for selective chemotherapy. Cell Chem Biol 2023; 30:1235-1247.e6. [PMID: 37531956 PMCID: PMC10592352 DOI: 10.1016/j.chembiol.2023.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 02/12/2023] [Accepted: 07/10/2023] [Indexed: 08/04/2023]
Abstract
Targeting transcription replication conflicts, a major source of endogenous DNA double-stranded breaks and genomic instability could have important anticancer therapeutic implications. Proliferating cell nuclear antigen (PCNA) is critical to DNA replication and repair processes. Through a rational drug design approach, we identified a small molecule PCNA inhibitor, AOH1996, which selectively kills cancer cells. AOH1996 enhances the interaction between PCNA and the largest subunit of RNA polymerase II, RPB1, and dissociates PCNA from actively transcribed chromatin regions, while inducing DNA double-stranded breaks in a transcription-dependent manner. Attenuation of RPB1 interaction with PCNA, by a point mutation in RPB1's PCNA-binding region, confers resistance to AOH1996. Orally administrable and metabolically stable, AOH1996 suppresses tumor growth as a monotherapy or as a combination treatment but causes no discernable side effects. Inhibitors of transcription replication conflict resolution may provide a new and unique therapeutic avenue for exploiting this cancer-selective vulnerability.
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Affiliation(s)
- Long Gu
- Department of Molecular Diagnostics & Experimental Therapeutics, Beckman Research Institute of City of Hope, Duarte, CA, USA.
| | - Min Li
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Caroline M Li
- Department of Molecular Diagnostics & Experimental Therapeutics, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Pouya Haratipour
- Department of Cancer Biology & Molecular Medicine, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Robert Lingeman
- Department of Molecular Diagnostics & Experimental Therapeutics, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Jennifer Jossart
- Department of Molecular Diagnostics & Experimental Therapeutics, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Margarita Gutova
- Department of Developmental & Stem Cell Biology, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Linda Flores
- Department of Developmental & Stem Cell Biology, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Caitlyn Hyde
- Department of Developmental & Stem Cell Biology, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Nikola Kenjić
- Department of Biochemistry, University of California Riverside, Riverside, CA, USA
| | - Haiqing Li
- Department of Genomics, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Vincent Chung
- Department of Medical Oncology, City of Hope, Duarte, CA, USA
| | - Hongzhi Li
- Department of Bioinformatics, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Brett Lomenick
- Proteome Exploration Laboratory, California Institute of Technology, Pasadena, CA, USA
| | - Daniel D Von Hoff
- Clinical Translational Research Division, Translational Genomics Research Institute, 445N 5th Street, Phoenix, AZ 85004, USA
| | - Timothy W Synold
- Department of Medical Oncology and Therapeutics Research, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Karen S Aboody
- Department of Developmental & Stem Cell Biology, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Yilun Liu
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - David Horne
- Department of Cancer Biology & Molecular Medicine, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Robert J Hickey
- Department of Cancer Biology & Molecular Medicine, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - J Jefferson P Perry
- Department of Molecular Diagnostics & Experimental Therapeutics, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Linda H Malkas
- Department of Molecular Diagnostics & Experimental Therapeutics, Beckman Research Institute of City of Hope, Duarte, CA, USA
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Shao Z, Yang J, Gao Y, Zhang Y, Zhao X, Shao Q, Zhang W, Cao C, Liu H, Gan J. Structural and functional studies of PCNA from African swine fever virus. J Virol 2023; 97:e0074823. [PMID: 37534905 PMCID: PMC10506467 DOI: 10.1128/jvi.00748-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 06/16/2023] [Indexed: 08/04/2023] Open
Abstract
Proliferating cell nuclear antigen (PCNA) belongs to the DNA sliding clamp family. Via interacting with various partner proteins, PCNA plays critical roles in DNA replication, DNA repair, chromatin assembly, epigenetic inheritance, chromatin remodeling, and many other fundamental biological processes. Although PCNA and PCNA-interacting partner networks are conserved across species, PCNA of a given species is rarely functional in heterologous systems, emphasizing the importance of more representative PCNA studies. Here, we report two crystal structures of PCNA from African swine fever virus (ASFV), which is the only member of the Asfarviridae family. Compared to the eukaryotic and archaeal PCNAs and the sliding clamp structural homologs from other viruses, AsfvPCNA possesses unique sequences and/or conformations at several regions, such as the J-loop, interdomain-connecting loop (IDCL), P-loop, and C-tail, which are involved in partner recognition or modification of sliding clamps. In addition to double-stranded DNA binding, we also demonstrate that AsfvPCNA can modestly enhance the ligation activity of the AsfvLIG protein. The unique structural features of AsfvPCNA can serve as a potential target for the development of ASFV-specific inhibitors and help combat the deadly virus. IMPORTANCE Two high-resolution crystal structures of African swine fever virus proliferating cell nuclear antigen (AsfvPCNA) are presented here. Structural comparison revealed that AsfvPCNA is unique at several regions, such as the J-loop, the interdomain-connecting loop linker, and the P-loop, which may play important roles in ASFV-specific partner selection of AsfvPCNA. Unlike eukaryotic and archaeal PCNAs, AsfvPCNA possesses high double-stranded DNA-binding affinity. Besides DNA binding, AsfvPCNA can also modestly enhance the ligation activity of the AsfvLIG protein, which is essential for the replication and repair of ASFV genome. The unique structural features make AsfvPCNA a potential target for drug development, which will help combat the deadly virus.
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Affiliation(s)
- Zhiwei Shao
- Shanghai Public Health Clinical Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Jie Yang
- Shanghai Public Health Clinical Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Yanqing Gao
- Shanghai Public Health Clinical Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Yixi Zhang
- Shanghai Public Health Clinical Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Xin Zhao
- Shanghai Public Health Clinical Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Qiyuan Shao
- Shanghai Public Health Clinical Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Weizhen Zhang
- Shanghai Public Health Clinical Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Chulei Cao
- Shanghai Public Health Clinical Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Hehua Liu
- Shanghai Public Health Clinical Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Jianhua Gan
- Shanghai Public Health Clinical Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
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6
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Sverzhinsky A, Tomkinson AE, Pascal JM. Cryo-EM structures and biochemical insights into heterotrimeric PCNA regulation of DNA ligase. Structure 2022; 30:371-385.e5. [PMID: 34838188 PMCID: PMC8897274 DOI: 10.1016/j.str.2021.11.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 10/04/2021] [Accepted: 11/03/2021] [Indexed: 12/15/2022]
Abstract
DNA ligases act in the final step of many DNA repair pathways and are commonly regulated by the DNA sliding clamp proliferating cell nuclear antigen (PCNA), but there are limited insights into the physical basis for this regulation. Here, we use single-particle cryoelectron microscopy (cryo-EM) to analyze an archaeal DNA ligase and heterotrimeric PCNA in complex with a single-strand DNA break. The cryo-EM structures highlight a continuous DNA-binding surface formed between DNA ligase and PCNA that supports the distorted conformation of the DNA break undergoing repair and contributes to PCNA stimulation of DNA ligation. DNA ligase is conformationally flexible within the complex, with its domains fully ordered only when encircling the repaired DNA to form a stacked ring structure with PCNA. The structures highlight DNA ligase structural transitions while docked on PCNA, changes in DNA conformation during ligation, and the potential for DNA ligase domains to regulate PCNA accessibility to other repair factors.
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Affiliation(s)
- Aleksandr Sverzhinsky
- Department of Biochemistry and Molecular Medicine, Faculty of Medicine, Université de Montréal, Québec H3T 1J4, Canada
| | - Alan E Tomkinson
- Departments of Internal Medicine, Molecular Genetics and Microbiology, and University of New Mexico Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM 87131, USA
| | - John M Pascal
- Department of Biochemistry and Molecular Medicine, Faculty of Medicine, Université de Montréal, Québec H3T 1J4, Canada.
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Kladova OA, Alekseeva IV, Saparbaev M, Fedorova OS, Kuznetsov NA. Modulation of the Apurinic/Apyrimidinic Endonuclease Activity of Human APE1 and of Its Natural Polymorphic Variants by Base Excision Repair Proteins. Int J Mol Sci 2020; 21:ijms21197147. [PMID: 32998246 PMCID: PMC7583023 DOI: 10.3390/ijms21197147] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 09/24/2020] [Accepted: 09/25/2020] [Indexed: 11/25/2022] Open
Abstract
Human apurinic/apyrimidinic endonuclease 1 (APE1) is known to be a critical player of the base excision repair (BER) pathway. In general, BER involves consecutive actions of DNA glycosylases, AP endonucleases, DNA polymerases, and DNA ligases. It is known that these proteins interact with APE1 either at upstream or downstream steps of BER. Therefore, we may propose that even a minor disturbance of protein–protein interactions on the DNA template reduces coordination and repair efficiency. Here, the ability of various human DNA repair enzymes (such as DNA glycosylases OGG1, UNG2, and AAG; DNA polymerase Polβ; or accessory proteins XRCC1 and PCNA) to influence the activity of wild-type (WT) APE1 and its seven natural polymorphic variants (R221C, N222H, R237A, G241R, M270T, R274Q, and P311S) was tested. Förster resonance energy transfer–based kinetic analysis of abasic site cleavage in a model DNA substrate was conducted to detect the effects of interacting proteins on the activity of WT APE1 and its single-nucleotide polymorphism (SNP) variants. The results revealed that WT APE1 activity was stimulated by almost all tested DNA repair proteins. For the SNP variants, the matters were more complicated. Analysis of two SNP variants, R237A and G241R, suggested that a positive charge in this area of the APE1 surface impairs the protein–protein interactions. In contrast, variant R221C (where the affected residue is located near the DNA-binding site) showed permanently lower activation relative to WT APE1, whereas neighboring SNP N222H did not cause a noticeable difference as compared to WT APE1. Buried substitution P311S had an inconsistent effect, whereas each substitution at the DNA-binding site, M270T and R274Q, resulted in the lowest stimulation by BER proteins. Protein–protein molecular docking was performed between repair proteins to identify amino acid residues involved in their interactions. The data uncovered differences in the effects of BER proteins on APE1, indicating an important role of protein–protein interactions in the coordination of the repair pathway.
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Affiliation(s)
- Olga A. Kladova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia; (O.A.K.); (I.V.A.)
| | - Irina V. Alekseeva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia; (O.A.K.); (I.V.A.)
| | - Murat Saparbaev
- Groupe «Mechanisms of DNA Repair and Carcinogenesis», Equipe Labellisée LIGUE 2016, CNRS UMR9019, Université Paris-Saclay, Gustave Roussy Cancer Campus, CEDEX, F-94805 Villejuif, France;
| | - Olga S. Fedorova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia; (O.A.K.); (I.V.A.)
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia
- Correspondence: (O.S.F.); (N.A.K.)
| | - Nikita A. Kuznetsov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia; (O.A.K.); (I.V.A.)
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia
- Correspondence: (O.S.F.); (N.A.K.)
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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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Kowalska E, Strzałka W, Oyama T. A crystallization and preliminary X-ray diffraction study of the Arabidopsis thaliana proliferating cell nuclear antigen (PCNA2) alone and in a complex with a PIP-box peptide from Flap endonuclease 1. Acta Biochim Pol 2020; 67:49-52. [PMID: 32188236 DOI: 10.18388/abp.2020_2896] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 02/10/2020] [Indexed: 11/10/2022]
Abstract
DNA replication is an important event for all living organisms and the mechanism is essentially conserved from archaea, bacteria to eukaryotes. Proliferating cell nuclear antigen (PCNA) acts as the universal platform for many DNA transacting proteins. Flap endonuclease 1 (FEN1) is one such enzyme whose activity is largely affected by the interaction with PCNA. To elucidate the key interactions between plant PCNA and FEN1 and possible structural change of PCNA caused by binding of FEN1 at the atomic level, crystallization and preliminary studies of X-ray diffraction of crystals of Arabidopsis thaliana PCNA2 (AtPCNA2) alone and in a complex with a peptide derived from AtFEN1, which contains a typical PCNA-interacting protein (PIP)-box motif, were performed. Both peptide-free and peptide-bound AtPCNA2s were crystallized using the same reservoir solution but in different crystal systems, indicating that the peptide affected the intermolecular interactions in the crystals. Crystals of AtPCNA2 belonged to the hexagonal space group P63, while those of the peptide-bound AtPCNA2 belonged to the rhombohedral space group H3, both of which could contain the functional homo-trimers.
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Affiliation(s)
- Ewa Kowalska
- Department of Plant Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Krakow, Poland
| | - Wojciech Strzałka
- Department of Plant Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Krakow, Poland
| | - Takuji Oyama
- Faculty of Life and Environmental Sciences, University of Yamanashi, 4-4-37 Takeda, Kofu, Yamanashi 400-8510, Japan
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Tan W, Murphy VJ, Charron A, van Twest S, Sharp M, Constantinou A, Parker MW, Crismani W, Bythell-Douglas R, Deans AJ. Preparation and purification of mono-ubiquitinated proteins using Avi-tagged ubiquitin. PLoS One 2020; 15:e0229000. [PMID: 32092106 PMCID: PMC7039436 DOI: 10.1371/journal.pone.0229000] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 01/27/2020] [Indexed: 01/13/2023] Open
Abstract
Site-specific conjugation of ubiquitin onto a range of DNA repair proteins regulates their critical functions in the DNA damage response. Biochemical and structural characterization of these functions are limited by an absence of tools for the purification of DNA repair proteins in purely the ubiquitinated form. To overcome this barrier, we designed a ubiquitin fusion protein that is N-terminally biotinylated and can be conjugated by E3 RING ligases onto various substrates. Biotin affinity purification of modified proteins, followed by cleavage of the affinity tag leads to release of natively-mono-ubiquitinated substrates. As proof-of-principle, we applied this method to several substrates of mono-ubiquitination in the Fanconi anemia (FA)-BRCA pathway of DNA interstrand crosslink repair. These include the FANCI:FANCD2 complex, the PCNA trimer and BRCA1 modified nucleosomes. This method provides a simple approach to study the role of mono-ubiquitination in DNA repair or any other mono-ubiquitination signaling pathways.
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Affiliation(s)
- Winnie Tan
- Genome Stability Unit, St. Vincent’s Institute of Medical Research, Fitzroy, Victoria, Australia
- Department of Medicine (St. Vincent’s Health), The University of Melbourne, Victoria, Australia
| | - Vincent J. Murphy
- Genome Stability Unit, St. Vincent’s Institute of Medical Research, Fitzroy, Victoria, Australia
| | - Aude Charron
- Genome Stability Unit, St. Vincent’s Institute of Medical Research, Fitzroy, Victoria, Australia
- National Graduate School of Chemistry of Montpellier (ENSCM), Montpellier, France
| | - Sylvie van Twest
- Genome Stability Unit, St. Vincent’s Institute of Medical Research, Fitzroy, Victoria, Australia
| | - Michael Sharp
- Genome Stability Unit, St. Vincent’s Institute of Medical Research, Fitzroy, Victoria, Australia
| | - Angelos Constantinou
- Institute of Human Genetics (IGH), Centre National de la Recherche Scientifique (CNRS), Université de Montpellier (UM), Montpellier, France
| | - Michael W. Parker
- Structural Biology Unit, St. Vincent’s Institute of Medical Research, Fitzroy, Victoria, Australia
- Bio21 Institute, University of Melbourne, Parkville, Victoria, Australia
| | - Wayne Crismani
- Genome Stability Unit, St. Vincent’s Institute of Medical Research, Fitzroy, Victoria, Australia
- Department of Medicine (St. Vincent’s Health), The University of Melbourne, Victoria, Australia
| | - Rohan Bythell-Douglas
- Genome Stability Unit, St. Vincent’s Institute of Medical Research, Fitzroy, Victoria, Australia
- Department of Medicine (St. Vincent’s Health), The University of Melbourne, Victoria, Australia
| | - Andrew J. Deans
- Genome Stability Unit, St. Vincent’s Institute of Medical Research, Fitzroy, Victoria, Australia
- Department of Medicine (St. Vincent’s Health), The University of Melbourne, Victoria, Australia
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11
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Zambrello MA, Craft DL, Hoch JC, Rovnyak D, Schuyler AD. The influence of the probability density function on spectral quality in nonuniformly sampled multidimensional NMR. J Magn Reson 2020; 311:106671. [PMID: 31951863 PMCID: PMC7781205 DOI: 10.1016/j.jmr.2019.106671] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 12/13/2019] [Accepted: 12/14/2019] [Indexed: 05/23/2023]
Abstract
The goal of nonuniform sampling (NUS) is to select a subset of free induction decays (FIDs) from the conventional, uniform grid in a manner that sufficiently samples short evolution times needed for improved sensitivity and long evolution times needed for enhanced resolution. In addition to specifying the number of FIDs to be collected from a uniform grid, NUS schemes also specify the distribution of the selected FIDs, which directly impacts sampling-induced artifacts. Sampling schemes typically address these heuristic guidelines by utilizing a probability density function (PDF) to bias the distribution of sampled evolution times. Given this common approach, schemes differentiate themselves by how the evolution times are distributed within the envelope of the PDF. Here, we employ maximum entropy reconstruction and utilize in situ receiver operating characteristic (IROC) to conduct a critical comparison of the sensitivity and resolution that can be achieved by three types of biased sampling schemes: exponential (PDF is exponentially decaying), Poisson-gap (PDF derived from a sine function), and quantile-directed (PDF defined by simple polynomial decay). This methodology reveals practical insights and trends regarding how the sampling schemes and bias can provide the highest sensitivity and resolution for two nonuniformly sampled dimensions in a three-dimensional biomolecular NMR experiment. The IROC analysis circumvents the limitations of common metrics when used with nonlinear spectral estimation (a characteristic of all methods used with NUS) by quantifying the spectral quality via synthetic signals that are added to the empirical dataset. Recovery of these synthetic signals provides a proxy for the quality of the empirical portion of the spectrum. The central finding is that differences in spectral quality are primarily driven by the strength of bias in the PDF. In addition, a sampling coverage threshold is observed that appears to be connected to the dependence of each NUS method on its random seed. The differences between sampling schemes and biases are most relevant below 20% coverage where seed-dependence is high, whereas at higher coverages, the performance metrics for all of the sampling schemes begin to converge and approach a seed-independent regime. The results presented here show that aggressive sampling at low coverage can produce high-quality spectra by employing a sampling scheme that adheres to a decaying PDF with a bias to a broad range of short evolution times and includes relatively few FIDs at long evolution times.
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Affiliation(s)
- Matthew A Zambrello
- UConn Health, Department of Molecular Biology and Biophysics, Farmington, CT 06030, USA
| | - D Levi Craft
- Bucknell University, Department of Chemistry, Lewisburg, PA 17837, USA
| | - Jeffrey C Hoch
- UConn Health, Department of Molecular Biology and Biophysics, Farmington, CT 06030, USA
| | - David Rovnyak
- Bucknell University, Department of Chemistry, Lewisburg, PA 17837, USA
| | - Adam D Schuyler
- UConn Health, Department of Molecular Biology and Biophysics, Farmington, CT 06030, USA.
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12
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Lowran K, Campbell L, Popp P, Wu CG. Assembly of a G-Quadruplex Repair Complex by the FANCJ DNA Helicase and the REV1 Polymerase. Genes (Basel) 2019; 11:E5. [PMID: 31861576 PMCID: PMC7017153 DOI: 10.3390/genes11010005] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Accepted: 12/17/2019] [Indexed: 12/14/2022] Open
Abstract
The FANCJ helicase unfolds G-quadruplexes (G4s) in human cells to support DNA replication. This action is coupled to the recruitment of REV1 polymerase to synthesize DNA across from a guanine template. The precise mechanisms of these reactions remain unclear. While FANCJ binds to G4s with an AKKQ motif, it is not known whether this site recognizes damaged G4 structures. FANCJ also has a PIP-like (PCNA Interacting Protein) region that may recruit REV1 to G4s either directly or through interactions mediated by PCNA protein. In this work, we measured the affinities of a FANCJ AKKQ peptide for G4s formed by (TTAGGG)4 and (GGGT)4 using fluorescence spectroscopy and biolayer interferometry (BLI). The effects of 8-oxoguanine (8oxoG) on these interactions were tested at different positions. BLI assays were then performed with a FANCJ PIP to examine its recruitment of REV1 and PCNA. FANCJ AKKQ bound tightly to a TTA loop and was sequestered away from the 8oxoG. Reducing the loop length between guanine tetrads increased the affinity of the peptide for 8oxoG4s. FANCJ PIP targeted both REV1 and PCNA but favored interactions with the REV1 polymerase. The impact of these results on the remodeling of damaged G4 DNA is discussed herein.
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Affiliation(s)
- Kaitlin Lowran
- Department of Chemistry, Oakland University, Rochester, MI 48309, USA; (K.L.); (L.C.)
| | - Laura Campbell
- Department of Chemistry, Oakland University, Rochester, MI 48309, USA; (K.L.); (L.C.)
| | - Phillip Popp
- Case Western Reserve University, Cleveland, OH 44106, USA;
| | - Colin G. Wu
- Department of Chemistry, Oakland University, Rochester, MI 48309, USA; (K.L.); (L.C.)
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13
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Xu M, Qin J, Wang L, Lee HJ, Kao CY, Liu D, Songyang Z, Chen J, Tsai MJ, Tsai SY. Nuclear receptors regulate alternative lengthening of telomeres through a novel noncanonical FANCD2 pathway. Sci Adv 2019; 5:eaax6366. [PMID: 31633027 PMCID: PMC6785246 DOI: 10.1126/sciadv.aax6366] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 09/14/2019] [Indexed: 05/07/2023]
Abstract
Alternative lengthening of telomeres (ALT) is known to use homologous recombination (HR) to replicate telomeric DNA in a telomerase-independent manner. However, the detailed process remains largely undefined. It was reported that nuclear receptors COUP-TFII and TR4 are recruited to the enriched GGGTCA variant repeats embedded within ALT telomeres, implicating nuclear receptors in regulating ALT activity. Here, we identified a function of nuclear receptors in ALT telomere maintenance that involves a direct interaction between COUP-TFII/TR4 and FANCD2, the key protein in the Fanconi anemia (FA) DNA repair pathway. The COUP-TFII/TR4-FANCD2 complex actively induces the DNA damage response by recruiting endonuclease MUS81 and promoting the loading of the PCNA-POLD3 replication complex in ALT telomeres. Furthermore, the COUP-TFII/TR4-mediated ALT telomere pathway does not require the FA core complex or the monoubiquitylation of FANCD2, key steps in the canonical FA pathway. Thus, our findings reveal that COUP-TFII/TR4 regulates ALT telomere maintenance through a novel noncanonical FANCD2 pathway.
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Affiliation(s)
- Mafei Xu
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Jun Qin
- CAS Key Laboratory of Tissue Microenvironment and Tumor, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Leiming Wang
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Hui-Ju Lee
- Center for Immunotherapy Research, Houston Methodist Research Institute, Houston, TX, USA
| | - Chung-Yang Kao
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Dan Liu
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Zhou Songyang
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
- School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
- Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China
| | - Junjie Chen
- Department of Experimental Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ming-Jer Tsai
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
- Program in Developmental Biology, Baylor College of Medicine, Houston, TX, USA
| | - Sophia Y. Tsai
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
- Program in Developmental Biology, Baylor College of Medicine, Houston, TX, USA
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14
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Daitchman D, Greenblatt HM, Levy Y. Diffusion of ring-shaped proteins along DNA: case study of sliding clamps. Nucleic Acids Res 2019; 46:5935-5949. [PMID: 29860305 PMCID: PMC6158715 DOI: 10.1093/nar/gky436] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 05/08/2018] [Indexed: 12/13/2022] Open
Abstract
Several DNA-binding proteins, such as topoisomerases, helicases and sliding clamps, have a toroidal (i.e. ring) shape that topologically traps DNA, with this quality being essential to their function. Many DNA-binding proteins that function, for example, as transcription factors or enzymes were shown to be able to diffuse linearly (i.e. slide) along DNA during the search for their target binding sites. The protein's sliding properties and ability to search DNA, which often also involves hopping and dissociation, are expected to be different when it encircles the DNA. In this study, we explored the linear diffusion of four ring-shaped proteins of very similar structure: three sliding clamps (PCNA, β-clamp, and the gp45) and the 9-1-1 protein, with a particular focus on PCNA. Coarse-grained molecular dynamics simulations were performed to decipher the sliding mechanism adopted by these ring-shaped proteins and to determine how the molecular properties of the inner and outer ring govern its search speed. We designed in silico variants to dissect the contributions of ring geometry and electrostatics to the sliding speed of ring-shaped proteins along DNA. We found that the toroidal proteins diffuse when they are tilted relative to the DNA axis and able to rotate during translocation, but that coupling between rotation and translocation is quite weak. Their diffusion speed is affected by the shape of the inner ring and, to a lesser extent, by its electrostatic properties. However, breaking the symmetry of the electrostatic potential can result in deviation of the DNA from the center of the ring and cause slower linear diffusion. The findings are discussed in light of earlier computational and experimental studies on the sliding of clamps.
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Affiliation(s)
- Dina Daitchman
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Harry M Greenblatt
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Yaakov Levy
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
- To whom correspondence should be addressed. Tel: +972 8 9344587;
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15
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Pudgerd A, Chotwiwatthanakun C, Kruangkum T, Itsathitphaisarn O, Sritunyalucksana K, Vanichviriyakit R. The hematopoietic organ of Macrobrachium rosenbergii: Structure, organization and immune status. Fish Shellfish Immunol 2019; 88:415-423. [PMID: 30872029 DOI: 10.1016/j.fsi.2019.03.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 02/26/2019] [Accepted: 03/07/2019] [Indexed: 06/09/2023]
Abstract
The hematopoietic organ (HO) of the giant freshwater prawn Macrobrachium rosenbergii is a discrete, whitish mass located in the epigastric region of the cephalothorax, posterior to the brain. It is composed of hematopoietic cells arranged in a thick layer of numerous lobules that surround a central hemal sinus from which they are separated by a thin sheath. At the center of the sinus is the muscular cor frontale. The lobules extend radially outward from the sinus in three developmental zones. Basal Zone 1 nearest the sinus contains large hematopoietic stem cells with euchromatic nuclei that stain positive for proliferation cell nuclear antigen (PCNA). Zone 2 contains smaller, actively dividing cells as indicated by positive 5-bromo-20-deoxyuridine (BrdU) staining. Distal Zone 3 contains small, loosely packed cells with heterochromatic nuclei, many cytoplasmic granules and vesicles indicating that they will eventually differentiate into hemocytes and enter circulation. Three main arteries, namely the ophthalmic and the 2 branches of the antennary, connect the heart to the HO. Use of India ink and 0.1 μm fluorescent micro-beads injected into the heart revealed that the cor frontale could immediately remove foreign particles from hemolymph by filtration. Fluorescent beads were also detected in the hematopoietic tissue at 30 min after injection, indicating that it could be penetrated by foreign particles. However, the fluorescent signal completely disappeared from the whole HO after 4 h, indicating its role in removal of foreign particles. In conclusion, the present study demonstrated for the first time the detailed histological structures of the HO of M. rosenbergii and its relationship to hematopoiesis and removal of foreign particles from hemolymph.
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Affiliation(s)
- Arnon Pudgerd
- Center of Excellence for Shrimp Molecular Biology and Biotechnology (Centex Shrimp), Faculty of Science, Mahidol University, Faculty of Science, Mahidol University, Rama VI Rd., Bangkok, 10400, Thailand; Department of Anatomy, Faculty of Science, Mahidol University, Rama VI Rd., Bangkok, 10400, Thailand
| | - Charoonroj Chotwiwatthanakun
- Center of Excellence for Shrimp Molecular Biology and Biotechnology (Centex Shrimp), Faculty of Science, Mahidol University, Faculty of Science, Mahidol University, Rama VI Rd., Bangkok, 10400, Thailand; Mahidol University, Nakhonsawan Campus, Nakhonsawan, 60000, Thailand
| | - Thanapong Kruangkum
- Center of Excellence for Shrimp Molecular Biology and Biotechnology (Centex Shrimp), Faculty of Science, Mahidol University, Faculty of Science, Mahidol University, Rama VI Rd., Bangkok, 10400, Thailand; Department of Anatomy, Faculty of Science, Mahidol University, Rama VI Rd., Bangkok, 10400, Thailand
| | - Ornchuma Itsathitphaisarn
- Center of Excellence for Shrimp Molecular Biology and Biotechnology (Centex Shrimp), Faculty of Science, Mahidol University, Faculty of Science, Mahidol University, Rama VI Rd., Bangkok, 10400, Thailand; Department of Biochemistry, Faculty of Science, Mahidol University, Rama VI Rd., Bangkok, 10400, Thailand
| | - Kallaya Sritunyalucksana
- Center of Excellence for Shrimp Molecular Biology and Biotechnology (Centex Shrimp), Faculty of Science, Mahidol University, Faculty of Science, Mahidol University, Rama VI Rd., Bangkok, 10400, Thailand; Shrimp-pathogen Interaction (SPI) Laboratory, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Yothi Office, Rama VI Rd., Bangkok, 10400, Thailand
| | - Rapeepun Vanichviriyakit
- Center of Excellence for Shrimp Molecular Biology and Biotechnology (Centex Shrimp), Faculty of Science, Mahidol University, Faculty of Science, Mahidol University, Rama VI Rd., Bangkok, 10400, Thailand; Department of Anatomy, Faculty of Science, Mahidol University, Rama VI Rd., Bangkok, 10400, Thailand.
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16
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Krishnamoorthy V, Khanna R, Parnaik VK. E3 ubiquitin ligase HECW2 targets PCNA and lamin B1. Biochim Biophys Acta Mol Cell Res 2018; 1865:1088-1104. [PMID: 29753763 DOI: 10.1016/j.bbamcr.2018.05.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 04/20/2018] [Accepted: 05/07/2018] [Indexed: 12/21/2022]
Abstract
Lamins constitute the major architectural proteins of the nuclear lamina that help in maintaining nuclear organization. Mutations in lamins are associated with diverse degenerative diseases, collectively termed laminopathies. HECW2, a HECT-type E3 ubiquitin ligase, is transcriptionally upregulated in HeLa cells expressing Emery-Dreifuss muscular dystrophy-causing-lamin A mutants. However, the role of HECW2 upregulation in mediating downstream effects in lamin mutant-expressing cells was previously unexplored. Here, we show that HECW2 interacts with two lamin A-binding proteins, proliferating cell nuclear antigen (PCNA), via a canonical PCNA-interacting protein (PIP) motif, and lamin B1. HECW2 mediates their ubiquitination and targets them for proteasomal degradation. Cells expressing lamin A mutants G232E and Q294P, in which HECW2 is upregulated, show increased proteasomal degradation of PCNA and lamin B1 most likely mediated by HECW2. Our findings establish HECW2 as an E3 ubiquitin ligase for PCNA and lamin B1 which regulates their levels in laminopathic cells. We also found that HECW2 interacts with wild-type lamin A and ubiquitinates it and this interaction is reduced in case of lamin mutants G232E and Q294P. Our findings suggest that interplay among HECW2, lamin A, PCNA, and lamin B1 determines their respective homeostatic levels in the cell and dysregulation of these interactions may contribute to the pathogenicity of laminopathies.
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Affiliation(s)
| | - Richa Khanna
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Veena K Parnaik
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India.
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17
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Iwata F, Hirakawa H, Nagamune T. A Stable Artificial Multienzymatic Complex Using a Heterotrimeric Protein From Metallosphaera sedula. Biotechnol J 2018; 13:e1700662. [PMID: 29663675 DOI: 10.1002/biot.201700662] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Revised: 02/24/2018] [Indexed: 01/02/2023]
Abstract
Bacterial cytochrome P450 monooxygenases (P450s) are promising biocatalysts for chemical syntheses because they catalyze a variety of oxidations on non-activated hydrocarbons using O2 . However, the requirement of two auxiliary proteins, an electron transfer protein and a reductase, for the catalysis is a major bottleneck for in vitro applications of these monooxygenases. The authors previous study showed that artificial assembly of a bacterial P450 with its auxiliary proteins using a heterotrimeric proliferating cell nuclear antigen (PCNA) from Sulfolobus solfataricus yields a self-sufficient P450, but partial dissociation of P450 from the complex at catalytic concentrations reduces the apparent specific activity of this self-sufficient P450. In this study, a Metallosphaera sedula PCNA is used, which is currently the most stable heterotrimeric PCNA, to assemble a bacterial P450 with its auxiliary proteins at submicromolar protein concentrations. The apparent specific monooxygenase activity of the M. sedula PCNA-assembled P450 with auxiliary proteins is saturated at protein concentrations of 40 nM, and is 2.1-fold higher than that of the S. solfataricus PCNA-assembled P450. Therefore, M. sedula PCNA represents a versatile tool to facilitate multiple enzymatic reactions, including the P450 monooxygenase system.
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Affiliation(s)
- Fumiya Iwata
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Tokyo 113-8656, Japan
| | - Hidehiko Hirakawa
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Tokyo 113-8656, Japan
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Teruyuki Nagamune
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Tokyo 113-8656, Japan
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo 113-8656, Japan
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18
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Gadkari VV, Harvey SR, Raper AT, Chu WT, Wang J, Wysocki VH, Suo Z. Investigation of sliding DNA clamp dynamics by single-molecule fluorescence, mass spectrometry and structure-based modeling. Nucleic Acids Res 2018; 46:3103-3118. [PMID: 29529283 PMCID: PMC5888646 DOI: 10.1093/nar/gky125] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 01/23/2018] [Accepted: 02/12/2018] [Indexed: 12/20/2022] Open
Abstract
Proliferating cell nuclear antigen (PCNA) is a trimeric ring-shaped clamp protein that encircles DNA and interacts with many proteins involved in DNA replication and repair. Despite extensive structural work to characterize the monomeric, dimeric, and trimeric forms of PCNA alone and in complex with interacting proteins, no structure of PCNA in a ring-open conformation has been published. Here, we use a multidisciplinary approach, including single-molecule Förster resonance energy transfer (smFRET), native ion mobility-mass spectrometry (IM-MS), and structure-based computational modeling, to explore the conformational dynamics of a model PCNA from Sulfolobus solfataricus (Sso), an archaeon. We found that Sso PCNA samples ring-open and ring-closed conformations even in the absence of its clamp loader complex, replication factor C, and transition to the ring-open conformation is modulated by the ionic strength of the solution. The IM-MS results corroborate the smFRET findings suggesting that PCNA dynamics are maintained in the gas phase and further establishing IM-MS as a reliable strategy to investigate macromolecular motions. Our molecular dynamic simulations agree with the experimental data and reveal that ring-open PCNA often adopts an out-of-plane left-hand geometry. Collectively, these results implore future studies to define the roles of PCNA dynamics in DNA loading and other PCNA-mediated interactions.
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Affiliation(s)
- Varun V Gadkari
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
- The Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA
| | - Sophie R Harvey
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
- School of Chemistry, Manchester Institute of Biotechnology, University of Manchester, Manchester M1 7DN, UK
| | - Austin T Raper
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
- The Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA
| | - Wen-Ting Chu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P.R. China
| | - Jin Wang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P.R. China
- Department of Chemistry and Physics, State University of New York at Stony Brook, Stony Brook, NY 11794-3400, USA
| | - Vicki H Wysocki
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Zucai Suo
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
- The Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA
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19
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Kondratick CM, Litman JM, Shaffer KV, Washington MT, Dieckman LM. Crystal structures of PCNA mutant proteins defective in gene silencing suggest a novel interaction site on the front face of the PCNA ring. PLoS One 2018; 13:e0193333. [PMID: 29499038 PMCID: PMC5834165 DOI: 10.1371/journal.pone.0193333] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 02/08/2018] [Indexed: 11/19/2022] Open
Abstract
Proliferating cell nuclear antigen (PCNA), a homotrimeric protein, is the eukaryotic sliding clamp that functions as a processivity factor for polymerases during DNA replication. Chromatin association factor 1 (CAF-1) is a heterotrimeric histone chaperone protein that is required for coupling chromatin assembly with DNA replication in eukaryotes. CAF-1 association with replicating DNA, and the targeting of newly synthesized histones to sites of DNA replication and repair requires its interaction with PCNA. Genetic studies have identified three mutant forms of PCNA in yeast that cause defects in gene silencing and exhibit altered association of CAF-1 to chromatin in vivo, as well as inhibit binding to CAF-1 in vitro. Three of these mutant forms of PCNA, encoded by the pol30-6, pol30-8, and the pol30-79 alleles, direct the synthesis of PCNA proteins with the amino acid substitutions D41A/D42A, R61A/D63A, and L126A/I128A, respectively. Interestingly, these double alanine substitutions are located far away from each other within the PCNA protein. To understand the structural basis of the interaction between PCNA and CAF-1 and how disruption of this interaction leads to reduced gene silencing, we determined the X-ray crystal structures of each of these mutant PCNA proteins. All three of the substitutions caused disruptions of a surface cavity on the front face of the PCNA ring, which is formed in part by three loops comprised of residues 21–24, 41–44, and 118–134. We suggest that this cavity is a novel binding pocket required for the interaction between PCNA and CAF-1, and that this region in PCNA also represents a potential binding site for other PCNA-binding proteins.
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Affiliation(s)
- Christine M. Kondratick
- Department of Biochemistry, University of Iowa College of Medicine, Iowa City, IA, United States of America
| | - Jacob M. Litman
- Department of Biochemistry, University of Iowa College of Medicine, Iowa City, IA, United States of America
| | - Kurt V. Shaffer
- Department of Chemistry, Creighton University, Omaha, NE, United States of America
| | - M. Todd Washington
- Department of Biochemistry, University of Iowa College of Medicine, Iowa City, IA, United States of America
| | - Lynne M. Dieckman
- Department of Chemistry, Creighton University, Omaha, NE, United States of America
- * E-mail:
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20
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Sebesta M, Cooper CDO, Ariza A, Carnie CJ, Ahel D. Structural insights into the function of ZRANB3 in replication stress response. Nat Commun 2017; 8:15847. [PMID: 28621305 PMCID: PMC5481773 DOI: 10.1038/ncomms15847] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2016] [Accepted: 05/08/2017] [Indexed: 01/24/2023] Open
Abstract
Strategies to resolve replication blocks are critical for the maintenance of genome stability. Among the factors implicated in the replication stress response is the ATP-dependent endonuclease ZRANB3. Here, we present the structure of the ZRANB3 HNH (His-Asn-His) endonuclease domain and provide a detailed analysis of its activity. We further define PCNA as a key regulator of ZRANB3 function, which recruits ZRANB3 to stalled replication forks and stimulates its endonuclease activity. Finally, we present the co-crystal structures of PCNA with two specific motifs in ZRANB3: the PIP box and the APIM motif. Our data provide important structural insights into the PCNA-APIM interaction, and reveal unexpected similarities between the PIP box and the APIM motif. We propose that PCNA and ATP-dependency serve as a multi-layered regulatory mechanism that modulates ZRANB3 activity at replication forks. Importantly, our findings allow us to interpret the functional significance of cancer associated ZRANB3 mutations.
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Affiliation(s)
- Marek Sebesta
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | | | - Antonio Ariza
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | | | - Dragana Ahel
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
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21
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Prakash A, Moharana K, Wallace SS, Doublié S. Destabilization of the PCNA trimer mediated by its interaction with the NEIL1 DNA glycosylase. Nucleic Acids Res 2017; 45:2897-2909. [PMID: 27994037 PMCID: PMC5389659 DOI: 10.1093/nar/gkw1282] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 11/11/2016] [Accepted: 12/12/2016] [Indexed: 12/12/2022] Open
Abstract
The base excision repair (BER) pathway repairs oxidized lesions in the DNA that result from reactive oxygen species generated in cells. If left unrepaired, these damaged DNA bases can disrupt cellular processes such as replication. NEIL1 is one of the 11 human DNA glycosylases that catalyze the first step of the BER pathway, i.e. recognition and excision of DNA lesions. NEIL1 interacts with essential replication proteins such as the ring-shaped homotrimeric proliferating cellular nuclear antigen (PCNA). We isolated a complex formed between NEIL1 and PCNA (±DNA) using size exclusion chromatography (SEC). This interaction was confirmed using native gel electrophoresis and mass spectrometry. Stokes radii measured by SEC hinted that PCNA in complex with NEIL1 (±DNA) was no longer a trimer. Height measurements and images obtained by atomic force microscopy also demonstrated the dissociation of the PCNA homotrimer in the presence of NEIL1 and DNA, while small-angle X-ray scattering analysis confirmed the NEIL1 mediated PCNA trimer dissociation and formation of a 1:1:1 NEIL1-DNA-PCNA(monomer) complex. Furthermore, ab initio shape reconstruction provides insights into the solution structure of this previously unreported complex. Together, these data point to a potential mechanistic switch between replication and BER.
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Affiliation(s)
- Aishwarya Prakash
- Department of Oncologic Sciences, Mitchell Cancer Institute, University of South Alabama, 1660 Springhill Avenue, Mobile, AL 36604-1405, USA
| | - Kedar Moharana
- Department of Microbiology and Molecular Genetics, The Markey Center for Molecular Genetics, University of Vermont, Stafford Hall, 95 Carrigan Drive, Burlington, VT 05405-0068, USA
| | - Susan S. Wallace
- Department of Microbiology and Molecular Genetics, The Markey Center for Molecular Genetics, University of Vermont, Stafford Hall, 95 Carrigan Drive, Burlington, VT 05405-0068, USA
| | - Sylvie Doublié
- Department of Microbiology and Molecular Genetics, The Markey Center for Molecular Genetics, University of Vermont, Stafford Hall, 95 Carrigan Drive, Burlington, VT 05405-0068, USA
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22
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Billon P, Li J, Lambert JP, Chen Y, Tremblay V, Brunzelle JS, Gingras AC, Verreault A, Sugiyama T, Couture JF, Côté J. Acetylation of PCNA Sliding Surface by Eco1 Promotes Genome Stability through Homologous Recombination. Mol Cell 2016; 65:78-90. [PMID: 27916662 DOI: 10.1016/j.molcel.2016.10.033] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Revised: 10/09/2016] [Accepted: 10/24/2016] [Indexed: 11/19/2022]
Abstract
During DNA replication, proliferating cell nuclear antigen (PCNA) adopts a ring-shaped structure to promote processive DNA synthesis, acting as a sliding clamp for polymerases. Known posttranslational modifications function at the outer surface of the PCNA ring to favor DNA damage bypass. Here, we demonstrate that acetylation of lysine residues at the inner surface of PCNA is induced by DNA lesions. We show that cohesin acetyltransferase Eco1 targets lysine 20 at the sliding surface of the PCNA ring in vitro and in vivo in response to DNA damage. Mimicking constitutive acetylation stimulates homologous recombination and robustly suppresses the DNA damage sensitivity of mutations in damage tolerance pathways. In comparison to the unmodified trimer, structural differences are observed at the interface between protomers in the crystal structure of the PCNA-K20ac ring. Thus, acetylation regulates PCNA sliding on DNA in the presence of DNA damage, favoring homologous recombination linked to sister-chromatid cohesion.
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Affiliation(s)
- Pierre Billon
- St-Patrick Research Group in Basic Oncology, Laval University Cancer Research Center, Centre de Recherche du CHU de Québec-Axe Oncologie, Quebec City, QC G1R 3S3, Canada
| | - Jian Li
- Department of Biological Sciences and Molecular and Cellular Biology Graduate Program, Ohio University, Athens, OH 45701, USA
| | - Jean-Philippe Lambert
- The Lunenfeld-Tanenbaum Research Institute at Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Yizhang Chen
- Department of Biological Sciences and Molecular and Cellular Biology Graduate Program, Ohio University, Athens, OH 45701, USA
| | - Véronique Tremblay
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada
| | - Joseph S Brunzelle
- Department of Molecular Pharmacology and Biological Chemistry, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Anne-Claude Gingras
- The Lunenfeld-Tanenbaum Research Institute at Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Alain Verreault
- Institute for Research in Immunology and Cancer and Département de Pathologie et Biologie Cellulaire, Université de Montréal, Montreal, QC H3C 3J7, Canada
| | - Tomohiko Sugiyama
- Department of Biological Sciences and Molecular and Cellular Biology Graduate Program, Ohio University, Athens, OH 45701, USA
| | - Jean-Francois Couture
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada
| | - Jacques Côté
- St-Patrick Research Group in Basic Oncology, Laval University Cancer Research Center, Centre de Recherche du CHU de Québec-Axe Oncologie, Quebec City, QC G1R 3S3, Canada.
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23
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Abstract
Post-translational protein modification by ubiquitin (Ub) and ubiquitin-like (Ubl) proteins such as small ubiquitin-like modifier (SUMO) regulates processes including protein homeostasis, the DNA damage response, and the cell cycle. Proliferating cell nuclear antigen (PCNA) is modified by Ub or poly-Ub at lysine (Lys)164 after DNA damage to recruit repair factors. Yeast PCNA is modified by SUMO on Lys164 and Lys127 during S-phase to recruit the anti-recombinogenic helicase Srs2. Lys164 modification requires specialized E2/E3 enzyme pairs for SUMO or Ub conjugation. For SUMO, Lys164 modification is strictly dependent on the E3 ligase Siz1, suggesting the E3 alters E2 specificity to promote Lys164 modification. The structural basis for substrate interactions in activated E3/E2–Ub/Ubl complexes remains unclear. Here we report an engineered E2 protein and cross-linking strategies that trap an E3/E2–Ubl/substrate complex for structure determination, illustrating how an E3 can bypass E2 specificity to force-feed a substrate lysine into the E2 active site.
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24
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Altieri AS, Ladner JE, Li Z, Robinson H, Sallman ZF, Marino JP, Kelman Z. A small protein inhibits proliferating cell nuclear antigen by breaking the DNA clamp. Nucleic Acids Res 2016; 44:6232-41. [PMID: 27141962 PMCID: PMC5181682 DOI: 10.1093/nar/gkw351] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Accepted: 04/19/2016] [Indexed: 12/18/2022] Open
Abstract
Proliferating cell nuclear antigen (PCNA) forms a trimeric ring that encircles duplex DNA and acts as an anchor for a number of proteins involved in DNA metabolic processes. PCNA has two structurally similar domains (I and II) linked by a long loop (inter-domain connector loop, IDCL) on the outside of each monomer of the trimeric structure that makes up the DNA clamp. All proteins that bind to PCNA do so via a PCNA-interacting peptide (PIP) motif that binds near the IDCL. A small protein, called TIP, binds to PCNA and inhibits PCNA-dependent activities although it does not contain a canonical PIP motif. The X-ray crystal structure of TIP bound to PCNA reveals that TIP binds to the canonical PIP interaction site, but also extends beyond it through a helix that relocates the IDCL. TIP alters the relationship between domains I and II within the PCNA monomer such that the trimeric ring structure is broken, while the individual domains largely retain their native structure. Small angle X-ray scattering (SAXS) confirms the disruption of the PCNA trimer upon addition of the TIP protein in solution and together with the X-ray crystal data, provides a structural basis for the mechanism of PCNA inhibition by TIP.
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Affiliation(s)
- Amanda S Altieri
- Institute for Bioscience and Biotechnology Research, University of Maryland and the National Institute of Standards and Technology, 9600 Gudelsky Drive, Rockville, MD 20850, USA
| | - Jane E Ladner
- Institute for Bioscience and Biotechnology Research, University of Maryland and the National Institute of Standards and Technology, 9600 Gudelsky Drive, Rockville, MD 20850, USA
| | - Zhuo Li
- Institute for Bioscience and Biotechnology Research, University of Maryland and the National Institute of Standards and Technology, 9600 Gudelsky Drive, Rockville, MD 20850, USA Third Institute of Oceanography, State Oceanic Administration, 184 Daxue Road, Xiamen, Fujian 361005, China
| | - Howard Robinson
- National Synchrotron Light Source, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Zahur F Sallman
- Institute for Bioscience and Biotechnology Research, University of Maryland and the National Institute of Standards and Technology, 9600 Gudelsky Drive, Rockville, MD 20850, USA Biomolecular Labeling Laboratory, Institute for Bioscience and Biotechnology Research, University of Maryland and the National Institute of Standards and Technology, 9600 Gudelsky Drive, Rockville, MD 20850, USA
| | - John P Marino
- Institute for Bioscience and Biotechnology Research, University of Maryland and the National Institute of Standards and Technology, 9600 Gudelsky Drive, Rockville, MD 20850, USA
| | - Zvi Kelman
- Institute for Bioscience and Biotechnology Research, University of Maryland and the National Institute of Standards and Technology, 9600 Gudelsky Drive, Rockville, MD 20850, USA Biomolecular Labeling Laboratory, Institute for Bioscience and Biotechnology Research, University of Maryland and the National Institute of Standards and Technology, 9600 Gudelsky Drive, Rockville, MD 20850, USA
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25
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Ganguly R, Wen AM, Myer AB, Czech T, Sahu S, Steinmetz NF, Raman P. Anti-atherogenic effect of trivalent chromium-loaded CPMV nanoparticles in human aortic smooth muscle cells under hyperglycemic conditions in vitro. Nanoscale 2016; 8:6542-6554. [PMID: 26935414 PMCID: PMC5136293 DOI: 10.1039/c6nr00398b] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Atherosclerosis, a major macrovascular complication associated with diabetes, poses a tremendous burden on national health care expenditure. Despite extensive efforts, cost-effective remedies are unknown. Therapies for atherosclerosis are challenged by a lack of targeted drug delivery approaches. Toward this goal, we turn to a biology-derived drug delivery system utilizing nanoparticles formed by the plant virus, Cowpea mosaic virus (CPMV). The aim herein is to investigate the anti-atherogenic potential of the beneficial mineral nutrient, trivalent chromium, loaded CPMV nanoparticles in human aortic smooth muscle cells (HASMC) under hyperglycemic conditions. A non-covalent loading protocol is established yielding CrCl3-loaded CPMV (CPMV-Cr) carrying 2000 drug molecules per particle. Using immunofluorescence microscopy, we show that CPMV-Cr is readily taken up by HASMC in vitro. In glucose (25 mM)-stimulated cells, 100 nM CPMV-Cr inhibits HASMC proliferation concomitant to attenuated proliferating cell nuclear antigen (PCNA, proliferation marker) expression. This is accompanied by attenuation in high glucose-induced phospho-p38 and pAkt expression. Moreover, CPMV-Cr inhibits the expression of pro-inflammatory cytokines, transforming growth factor-β (TGF-β) and nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB), in glucose-stimulated HASMCs. Finally glucose-stimulated lipid uptake is remarkably abrogated by CPMV-Cr, revealed by Oil Red O staining. Together, these data provide key cellular evidence for an atheroprotective effect of CPMV-Cr in vascular smooth muscle cells (VSMC) under hyperglycemic conditions that may promote novel therapeutic ventures for diabetic atherosclerosis.
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Affiliation(s)
- Rituparna Ganguly
- Department of Integrative Medical Sciences, Northeast Ohio Medical University, 4209 State Route 44, Rootstown, OH 44272-0095, USA. and School of Biomedical Sciences, Kent State University, Kent, OH, USA
| | - Amy M Wen
- Department of Biomedical Engineering, 10990 Euclid Avenue and Case Western Reserve University, Cleveland, OH, USA
| | - Ashley B Myer
- Department of Integrative Medical Sciences, Northeast Ohio Medical University, 4209 State Route 44, Rootstown, OH 44272-0095, USA.
| | - Tori Czech
- Department of Integrative Medical Sciences, Northeast Ohio Medical University, 4209 State Route 44, Rootstown, OH 44272-0095, USA.
| | - Soumyadip Sahu
- Department of Integrative Medical Sciences, Northeast Ohio Medical University, 4209 State Route 44, Rootstown, OH 44272-0095, USA. and School of Biomedical Sciences, Kent State University, Kent, OH, USA
| | - Nicole F Steinmetz
- Department of Biomedical Engineering, 10990 Euclid Avenue and Case Western Reserve University, Cleveland, OH, USA and Department of Radiology, 10990 Euclid Avenue and Case Western Reserve University, Cleveland, OH, USA and Department of Materials Science and Engineering, 10990 Euclid Avenue and Case Western Reserve University, Cleveland, OH, USA and Department of Macromolecular Science and Engineering, 10990 Euclid Avenue and Case Western Reserve University, Cleveland, OH, USA and Case Comprehensive Cancer Center, 10990 Euclid Avenue and Case Western Reserve University, Cleveland, OH, USA
| | - Priya Raman
- Department of Integrative Medical Sciences, Northeast Ohio Medical University, 4209 State Route 44, Rootstown, OH 44272-0095, USA. and School of Biomedical Sciences, Kent State University, Kent, OH, USA
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26
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LuCore SD, Litman JM, Powers KT, Gao S, Lynn AM, Tollefson WTA, Fenn TD, Washington MT, Schnieders MJ. Dead-End Elimination with a Polarizable Force Field Repacks PCNA Structures. Biophys J 2015; 109:816-26. [PMID: 26287633 PMCID: PMC4547145 DOI: 10.1016/j.bpj.2015.06.062] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Revised: 06/07/2015] [Accepted: 06/29/2015] [Indexed: 11/15/2022] Open
Abstract
A balance of van der Waals, electrostatic, and hydrophobic forces drive the folding and packing of protein side chains. Although such interactions between residues are often approximated as being pairwise additive, in reality, higher-order many-body contributions that depend on environment drive hydrophobic collapse and cooperative electrostatics. Beginning from dead-end elimination, we derive the first algorithm, to our knowledge, capable of deterministic global repacking of side chains compatible with many-body energy functions. The approach is applied to seven PCNA x-ray crystallographic data sets with resolutions 2.5-3.8 Å (mean 3.0 Å) using an open-source software. While PDB_REDO models average an Rfree value of 29.5% and MOLPROBITY score of 2.71 Å (77th percentile), dead-end elimination with the polarizable AMOEBA force field lowered Rfree by 2.8-26.7% and improved mean MOLPROBITY score to atomic resolution at 1.25 Å (100th percentile). For structural biology applications that depend on side-chain repacking, including x-ray refinement, homology modeling, and protein design, the accuracy limitations of pairwise additivity can now be eliminated via polarizable or quantum mechanical potentials.
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Affiliation(s)
- Stephen D LuCore
- Department of Biomedical Engineering, University of Iowa, Iowa City, Iowa
| | - Jacob M Litman
- Department of Biochemistry, University of Iowa, Iowa City, Iowa
| | - Kyle T Powers
- Department of Biochemistry, University of Iowa, Iowa City, Iowa
| | - Shibo Gao
- Department of Biochemistry, University of Iowa, Iowa City, Iowa
| | - Ava M Lynn
- Department of Biomedical Engineering, University of Iowa, Iowa City, Iowa
| | | | | | | | - Michael J Schnieders
- Department of Biomedical Engineering, University of Iowa, Iowa City, Iowa; Department of Biochemistry, University of Iowa, Iowa City, Iowa.
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27
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Tsutakawa SE, Yan C, Xu X, Weinacht CP, Freudenthal BD, Yang K, Zhuang Z, Washington MT, Tainer JA, Ivanov I. Structurally distinct ubiquitin- and sumo-modified PCNA: implications for their distinct roles in the DNA damage response. Structure 2015; 23:724-733. [PMID: 25773143 DOI: 10.1016/j.str.2015.02.008] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Revised: 01/28/2015] [Accepted: 02/09/2015] [Indexed: 11/18/2022]
Abstract
Proliferating cell nuclear antigen (PCNA) is a pivotal replication protein, which also controls cellular responses to DNA damage. Posttranslational modification of PCNA by SUMO and ubiquitin modulate these responses. How the modifiers alter PCNA-dependent DNA repair and damage tolerance pathways is largely unknown. We used hybrid methods to identify atomic models of PCNAK107-Ub and PCNAK164-SUMO consistent with small-angle X-ray scattering data of these complexes in solution. We show that SUMO and ubiquitin have distinct modes of association to PCNA. Ubiquitin adopts discrete docked binding positions. By contrast, SUMO associates by simple tethering and adopts extended flexible conformations. These structural differences are the result of the opposite electrostatic potentials of SUMO and Ub. The unexpected contrast in conformational behavior of Ub-PCNA and SUMO-PCNA has implications for interactions with partner proteins, interacting surfaces accessibility, and access points for pathway regulation.
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Affiliation(s)
- Susan E Tsutakawa
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720 USA
| | - Chunli Yan
- Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30302 USA
| | - Xiaojun Xu
- Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30302 USA
| | | | - Bret D Freudenthal
- Department of Biochemistry, University of Iowa College of Medicine, Iowa City, IA 52242 USA
| | - Kun Yang
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716 USA
| | - Zhihao Zhuang
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716 USA
| | - M Todd Washington
- Department of Biochemistry, University of Iowa College of Medicine, Iowa City, IA 52242 USA
| | - John A Tainer
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720 USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, 92037 USA
- Skaggs Institute for Chemical Biology, La Jolla, CA, 92037 USA
| | - Ivaylo Ivanov
- Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30302 USA
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28
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Yin L, Xie Y, Yin S, Lv X, Zhang J, Gu Z, Sun H, Liu S. The S-nitrosylation status of PCNA localized in cytosol impacts the apoptotic pathway in a Parkinson's disease paradigm. PLoS One 2015; 10:e0117546. [PMID: 25675097 PMCID: PMC4326459 DOI: 10.1371/journal.pone.0117546] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Accepted: 12/27/2014] [Indexed: 12/14/2022] Open
Abstract
It is generally accepted that nitric oxide (NO) or its derivatives, reactive nitrogen species (RNS), are involved in the development of Parkinson’s disease (PD). Recently, emerging evidence in the study of PD has indicated that protein S-nitrosylation triggers the signaling changes in neurons. In this study, SH-SY5Y cells treated with rotenone were used as a model of neuronal death in PD. The treated cells underwent significant apoptosis, which was accompanied by an increase in intracellular NO in a rotenone dose-dependent manner. The CyDye switch approach was employed to screen for changes in S-nitrosylated (SNO) proteins in response to the rotenone treatment. Seven proteins with increased S-nitrosylation were identified in the treated SH-SY5Y cells, which included proliferating cell nuclear antigen (PCNA). Although PCNA is generally located in the nucleus and participates in DNA replication and repair, significant PCNA was identified in the SH-SY5Y cytosol. Using immunoprecipitation and pull-down approaches, PCNA was found to interact with caspase-9; using mass spectrometry, the two cysteine residues PCNA-Cys81 and -Cys162 were identified as candidate S-nitrosylated residues. In addition, the evidence obtained from in vitro and the cell model studies indicated that the S-nitrosylation of PCNA-Cys81 affected the interaction between PCNA and caspase-9. Furthermore, the interaction of PCNA and caspase-9 partially blocked caspase-9 activation, indicating that the S-nitrosylation of cytosolic PCNA may be a mediator of the apoptotic pathway.
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Affiliation(s)
- Liang Yin
- Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yingying Xie
- Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Songyue Yin
- Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Xiaolei Lv
- Beijing Protein Innovation, Beijing, China
| | - Jia Zhang
- Beijing Protein Innovation, Beijing, China
| | - Zezong Gu
- Department of Pathology and Anatomical Sciences, University of Missouri School of Medicine, Columbia, Missouri, United States of America
| | - Haidan Sun
- Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- * E-mail: (HS); (SL)
| | - Siqi Liu
- Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- Beijing Protein Innovation, Beijing, China
- * E-mail: (HS); (SL)
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29
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Abstract
The expanding roles of PCNA in functional assembly of DNA replication and repair complexes motivated investigation of the structural and dynamic properties guiding specificity of PCNA-protein interactions. A series of biochemical and computational analyses were combined to evaluate the PIP Box recognition features impacting complex formation. The results indicate subtle differences in topological and molecular descriptors distinguishing both affinity and stoichiometry of binding among PCNA-peptide complexes through cooperative effects. These features were validated using peptide mimics of p85α and Akt, two previously unreported PCNA binding partners. This study characterizes for the first time a reverse PIP Box interaction with PCNA. Small molecule ligand binding at the PIP Box interaction site confirmed the adaptive nature of the protein in dictating overall shape and implicates allosterism in transmitting biological effects.
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Affiliation(s)
- Anthony M. Pedley
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana, United States of America
| | - Markus A. Lill
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana, United States of America
| | - V. Jo Davisson
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana, United States of America
- * E-mail:
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30
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Baple EL, Chambers H, Cross HE, Fawcett H, Nakazawa Y, Chioza BA, Harlalka GV, Mansour S, Sreekantan-Nair A, Patton MA, Muggenthaler M, Rich P, Wagner K, Coblentz R, Stein CK, Last JI, Taylor AMR, Jackson AP, Ogi T, Lehmann AR, Green CM, Crosby AH. Hypomorphic PCNA mutation underlies a human DNA repair disorder. J Clin Invest 2014; 124:3137-46. [PMID: 24911150 PMCID: PMC4071375 DOI: 10.1172/jci74593] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Accepted: 04/17/2014] [Indexed: 11/17/2022] Open
Abstract
Numerous human disorders, including Cockayne syndrome, UV-sensitive syndrome, xeroderma pigmentosum, and trichothiodystrophy, result from the mutation of genes encoding molecules important for nucleotide excision repair. Here, we describe a syndrome in which the cardinal clinical features include short stature, hearing loss, premature aging, telangiectasia, neurodegeneration, and photosensitivity, resulting from a homozygous missense (p.Ser228Ile) sequence alteration of the proliferating cell nuclear antigen (PCNA). PCNA is a highly conserved sliding clamp protein essential for DNA replication and repair. Due to this fundamental role, mutations in PCNA that profoundly impair protein function would be incompatible with life. Interestingly, while the p.Ser228Ile alteration appeared to have no effect on protein levels or DNA replication, patient cells exhibited marked abnormalities in response to UV irradiation, displaying substantial reductions in both UV survival and RNA synthesis recovery. The p.Ser228Ile change also profoundly altered PCNA's interaction with Flap endonuclease 1 and DNA Ligase 1, DNA metabolism enzymes. Together, our findings detail a mutation of PCNA in humans associated with a neurodegenerative phenotype, displaying clinical and molecular features common to other DNA repair disorders, which we showed to be attributable to a hypomorphic amino acid alteration.
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Affiliation(s)
- Emma L. Baple
- Medical Research, RILD Wellcome Wolfson Centre, University of Exeter Medical School, Exeter, Devon, United Kingdom. Department of Zoology, University of Cambridge, Cambridge, United Kingdom. Department of Ophthalmology, University of Arizona College of Medicine, Tucson, Arizona, USA. Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton, United Kingdom. Nagasaki University Research Centre for Genomic Instability and Carcinogenesis (NRGIC), Nagasaki, Japan. Department of Molecular Medicine, Atomic Bomb Disease Institute, Nagasaki University, Nagasaki, Japan. SW Thames Regional Genetics Service, St. George’s Healthcare NHS Trust, London, United Kingdom. Department of Neuroradiology, St. George’s Hospital, London, United Kingdom. Windows of Hope Genetic Study, Walnut Creek, Ohio, USA. SUNY Upstate Medical University, Syracuse, New York, USA. School of Cancer Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom. MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom. Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Helen Chambers
- Medical Research, RILD Wellcome Wolfson Centre, University of Exeter Medical School, Exeter, Devon, United Kingdom. Department of Zoology, University of Cambridge, Cambridge, United Kingdom. Department of Ophthalmology, University of Arizona College of Medicine, Tucson, Arizona, USA. Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton, United Kingdom. Nagasaki University Research Centre for Genomic Instability and Carcinogenesis (NRGIC), Nagasaki, Japan. Department of Molecular Medicine, Atomic Bomb Disease Institute, Nagasaki University, Nagasaki, Japan. SW Thames Regional Genetics Service, St. George’s Healthcare NHS Trust, London, United Kingdom. Department of Neuroradiology, St. George’s Hospital, London, United Kingdom. Windows of Hope Genetic Study, Walnut Creek, Ohio, USA. SUNY Upstate Medical University, Syracuse, New York, USA. School of Cancer Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom. MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom. Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Harold E. Cross
- Medical Research, RILD Wellcome Wolfson Centre, University of Exeter Medical School, Exeter, Devon, United Kingdom. Department of Zoology, University of Cambridge, Cambridge, United Kingdom. Department of Ophthalmology, University of Arizona College of Medicine, Tucson, Arizona, USA. Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton, United Kingdom. Nagasaki University Research Centre for Genomic Instability and Carcinogenesis (NRGIC), Nagasaki, Japan. Department of Molecular Medicine, Atomic Bomb Disease Institute, Nagasaki University, Nagasaki, Japan. SW Thames Regional Genetics Service, St. George’s Healthcare NHS Trust, London, United Kingdom. Department of Neuroradiology, St. George’s Hospital, London, United Kingdom. Windows of Hope Genetic Study, Walnut Creek, Ohio, USA. SUNY Upstate Medical University, Syracuse, New York, USA. School of Cancer Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom. MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom. Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Heather Fawcett
- Medical Research, RILD Wellcome Wolfson Centre, University of Exeter Medical School, Exeter, Devon, United Kingdom. Department of Zoology, University of Cambridge, Cambridge, United Kingdom. Department of Ophthalmology, University of Arizona College of Medicine, Tucson, Arizona, USA. Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton, United Kingdom. Nagasaki University Research Centre for Genomic Instability and Carcinogenesis (NRGIC), Nagasaki, Japan. Department of Molecular Medicine, Atomic Bomb Disease Institute, Nagasaki University, Nagasaki, Japan. SW Thames Regional Genetics Service, St. George’s Healthcare NHS Trust, London, United Kingdom. Department of Neuroradiology, St. George’s Hospital, London, United Kingdom. Windows of Hope Genetic Study, Walnut Creek, Ohio, USA. SUNY Upstate Medical University, Syracuse, New York, USA. School of Cancer Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom. MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom. Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Yuka Nakazawa
- Medical Research, RILD Wellcome Wolfson Centre, University of Exeter Medical School, Exeter, Devon, United Kingdom. Department of Zoology, University of Cambridge, Cambridge, United Kingdom. Department of Ophthalmology, University of Arizona College of Medicine, Tucson, Arizona, USA. Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton, United Kingdom. Nagasaki University Research Centre for Genomic Instability and Carcinogenesis (NRGIC), Nagasaki, Japan. Department of Molecular Medicine, Atomic Bomb Disease Institute, Nagasaki University, Nagasaki, Japan. SW Thames Regional Genetics Service, St. George’s Healthcare NHS Trust, London, United Kingdom. Department of Neuroradiology, St. George’s Hospital, London, United Kingdom. Windows of Hope Genetic Study, Walnut Creek, Ohio, USA. SUNY Upstate Medical University, Syracuse, New York, USA. School of Cancer Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom. MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom. Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Barry A. Chioza
- Medical Research, RILD Wellcome Wolfson Centre, University of Exeter Medical School, Exeter, Devon, United Kingdom. Department of Zoology, University of Cambridge, Cambridge, United Kingdom. Department of Ophthalmology, University of Arizona College of Medicine, Tucson, Arizona, USA. Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton, United Kingdom. Nagasaki University Research Centre for Genomic Instability and Carcinogenesis (NRGIC), Nagasaki, Japan. Department of Molecular Medicine, Atomic Bomb Disease Institute, Nagasaki University, Nagasaki, Japan. SW Thames Regional Genetics Service, St. George’s Healthcare NHS Trust, London, United Kingdom. Department of Neuroradiology, St. George’s Hospital, London, United Kingdom. Windows of Hope Genetic Study, Walnut Creek, Ohio, USA. SUNY Upstate Medical University, Syracuse, New York, USA. School of Cancer Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom. MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom. Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Gaurav V. Harlalka
- Medical Research, RILD Wellcome Wolfson Centre, University of Exeter Medical School, Exeter, Devon, United Kingdom. Department of Zoology, University of Cambridge, Cambridge, United Kingdom. Department of Ophthalmology, University of Arizona College of Medicine, Tucson, Arizona, USA. Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton, United Kingdom. Nagasaki University Research Centre for Genomic Instability and Carcinogenesis (NRGIC), Nagasaki, Japan. Department of Molecular Medicine, Atomic Bomb Disease Institute, Nagasaki University, Nagasaki, Japan. SW Thames Regional Genetics Service, St. George’s Healthcare NHS Trust, London, United Kingdom. Department of Neuroradiology, St. George’s Hospital, London, United Kingdom. Windows of Hope Genetic Study, Walnut Creek, Ohio, USA. SUNY Upstate Medical University, Syracuse, New York, USA. School of Cancer Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom. MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom. Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Sahar Mansour
- Medical Research, RILD Wellcome Wolfson Centre, University of Exeter Medical School, Exeter, Devon, United Kingdom. Department of Zoology, University of Cambridge, Cambridge, United Kingdom. Department of Ophthalmology, University of Arizona College of Medicine, Tucson, Arizona, USA. Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton, United Kingdom. Nagasaki University Research Centre for Genomic Instability and Carcinogenesis (NRGIC), Nagasaki, Japan. Department of Molecular Medicine, Atomic Bomb Disease Institute, Nagasaki University, Nagasaki, Japan. SW Thames Regional Genetics Service, St. George’s Healthcare NHS Trust, London, United Kingdom. Department of Neuroradiology, St. George’s Hospital, London, United Kingdom. Windows of Hope Genetic Study, Walnut Creek, Ohio, USA. SUNY Upstate Medical University, Syracuse, New York, USA. School of Cancer Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom. MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom. Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Ajith Sreekantan-Nair
- Medical Research, RILD Wellcome Wolfson Centre, University of Exeter Medical School, Exeter, Devon, United Kingdom. Department of Zoology, University of Cambridge, Cambridge, United Kingdom. Department of Ophthalmology, University of Arizona College of Medicine, Tucson, Arizona, USA. Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton, United Kingdom. Nagasaki University Research Centre for Genomic Instability and Carcinogenesis (NRGIC), Nagasaki, Japan. Department of Molecular Medicine, Atomic Bomb Disease Institute, Nagasaki University, Nagasaki, Japan. SW Thames Regional Genetics Service, St. George’s Healthcare NHS Trust, London, United Kingdom. Department of Neuroradiology, St. George’s Hospital, London, United Kingdom. Windows of Hope Genetic Study, Walnut Creek, Ohio, USA. SUNY Upstate Medical University, Syracuse, New York, USA. School of Cancer Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom. MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom. Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Michael A. Patton
- Medical Research, RILD Wellcome Wolfson Centre, University of Exeter Medical School, Exeter, Devon, United Kingdom. Department of Zoology, University of Cambridge, Cambridge, United Kingdom. Department of Ophthalmology, University of Arizona College of Medicine, Tucson, Arizona, USA. Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton, United Kingdom. Nagasaki University Research Centre for Genomic Instability and Carcinogenesis (NRGIC), Nagasaki, Japan. Department of Molecular Medicine, Atomic Bomb Disease Institute, Nagasaki University, Nagasaki, Japan. SW Thames Regional Genetics Service, St. George’s Healthcare NHS Trust, London, United Kingdom. Department of Neuroradiology, St. George’s Hospital, London, United Kingdom. Windows of Hope Genetic Study, Walnut Creek, Ohio, USA. SUNY Upstate Medical University, Syracuse, New York, USA. School of Cancer Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom. MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom. Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Martina Muggenthaler
- Medical Research, RILD Wellcome Wolfson Centre, University of Exeter Medical School, Exeter, Devon, United Kingdom. Department of Zoology, University of Cambridge, Cambridge, United Kingdom. Department of Ophthalmology, University of Arizona College of Medicine, Tucson, Arizona, USA. Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton, United Kingdom. Nagasaki University Research Centre for Genomic Instability and Carcinogenesis (NRGIC), Nagasaki, Japan. Department of Molecular Medicine, Atomic Bomb Disease Institute, Nagasaki University, Nagasaki, Japan. SW Thames Regional Genetics Service, St. George’s Healthcare NHS Trust, London, United Kingdom. Department of Neuroradiology, St. George’s Hospital, London, United Kingdom. Windows of Hope Genetic Study, Walnut Creek, Ohio, USA. SUNY Upstate Medical University, Syracuse, New York, USA. School of Cancer Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom. MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom. Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Phillip Rich
- Medical Research, RILD Wellcome Wolfson Centre, University of Exeter Medical School, Exeter, Devon, United Kingdom. Department of Zoology, University of Cambridge, Cambridge, United Kingdom. Department of Ophthalmology, University of Arizona College of Medicine, Tucson, Arizona, USA. Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton, United Kingdom. Nagasaki University Research Centre for Genomic Instability and Carcinogenesis (NRGIC), Nagasaki, Japan. Department of Molecular Medicine, Atomic Bomb Disease Institute, Nagasaki University, Nagasaki, Japan. SW Thames Regional Genetics Service, St. George’s Healthcare NHS Trust, London, United Kingdom. Department of Neuroradiology, St. George’s Hospital, London, United Kingdom. Windows of Hope Genetic Study, Walnut Creek, Ohio, USA. SUNY Upstate Medical University, Syracuse, New York, USA. School of Cancer Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom. MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom. Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Karin Wagner
- Medical Research, RILD Wellcome Wolfson Centre, University of Exeter Medical School, Exeter, Devon, United Kingdom. Department of Zoology, University of Cambridge, Cambridge, United Kingdom. Department of Ophthalmology, University of Arizona College of Medicine, Tucson, Arizona, USA. Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton, United Kingdom. Nagasaki University Research Centre for Genomic Instability and Carcinogenesis (NRGIC), Nagasaki, Japan. Department of Molecular Medicine, Atomic Bomb Disease Institute, Nagasaki University, Nagasaki, Japan. SW Thames Regional Genetics Service, St. George’s Healthcare NHS Trust, London, United Kingdom. Department of Neuroradiology, St. George’s Hospital, London, United Kingdom. Windows of Hope Genetic Study, Walnut Creek, Ohio, USA. SUNY Upstate Medical University, Syracuse, New York, USA. School of Cancer Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom. MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom. Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Roselyn Coblentz
- Medical Research, RILD Wellcome Wolfson Centre, University of Exeter Medical School, Exeter, Devon, United Kingdom. Department of Zoology, University of Cambridge, Cambridge, United Kingdom. Department of Ophthalmology, University of Arizona College of Medicine, Tucson, Arizona, USA. Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton, United Kingdom. Nagasaki University Research Centre for Genomic Instability and Carcinogenesis (NRGIC), Nagasaki, Japan. Department of Molecular Medicine, Atomic Bomb Disease Institute, Nagasaki University, Nagasaki, Japan. SW Thames Regional Genetics Service, St. George’s Healthcare NHS Trust, London, United Kingdom. Department of Neuroradiology, St. George’s Hospital, London, United Kingdom. Windows of Hope Genetic Study, Walnut Creek, Ohio, USA. SUNY Upstate Medical University, Syracuse, New York, USA. School of Cancer Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom. MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom. Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Constance K. Stein
- Medical Research, RILD Wellcome Wolfson Centre, University of Exeter Medical School, Exeter, Devon, United Kingdom. Department of Zoology, University of Cambridge, Cambridge, United Kingdom. Department of Ophthalmology, University of Arizona College of Medicine, Tucson, Arizona, USA. Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton, United Kingdom. Nagasaki University Research Centre for Genomic Instability and Carcinogenesis (NRGIC), Nagasaki, Japan. Department of Molecular Medicine, Atomic Bomb Disease Institute, Nagasaki University, Nagasaki, Japan. SW Thames Regional Genetics Service, St. George’s Healthcare NHS Trust, London, United Kingdom. Department of Neuroradiology, St. George’s Hospital, London, United Kingdom. Windows of Hope Genetic Study, Walnut Creek, Ohio, USA. SUNY Upstate Medical University, Syracuse, New York, USA. School of Cancer Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom. MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom. Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - James I. Last
- Medical Research, RILD Wellcome Wolfson Centre, University of Exeter Medical School, Exeter, Devon, United Kingdom. Department of Zoology, University of Cambridge, Cambridge, United Kingdom. Department of Ophthalmology, University of Arizona College of Medicine, Tucson, Arizona, USA. Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton, United Kingdom. Nagasaki University Research Centre for Genomic Instability and Carcinogenesis (NRGIC), Nagasaki, Japan. Department of Molecular Medicine, Atomic Bomb Disease Institute, Nagasaki University, Nagasaki, Japan. SW Thames Regional Genetics Service, St. George’s Healthcare NHS Trust, London, United Kingdom. Department of Neuroradiology, St. George’s Hospital, London, United Kingdom. Windows of Hope Genetic Study, Walnut Creek, Ohio, USA. SUNY Upstate Medical University, Syracuse, New York, USA. School of Cancer Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom. MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom. Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - A. Malcolm R. Taylor
- Medical Research, RILD Wellcome Wolfson Centre, University of Exeter Medical School, Exeter, Devon, United Kingdom. Department of Zoology, University of Cambridge, Cambridge, United Kingdom. Department of Ophthalmology, University of Arizona College of Medicine, Tucson, Arizona, USA. Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton, United Kingdom. Nagasaki University Research Centre for Genomic Instability and Carcinogenesis (NRGIC), Nagasaki, Japan. Department of Molecular Medicine, Atomic Bomb Disease Institute, Nagasaki University, Nagasaki, Japan. SW Thames Regional Genetics Service, St. George’s Healthcare NHS Trust, London, United Kingdom. Department of Neuroradiology, St. George’s Hospital, London, United Kingdom. Windows of Hope Genetic Study, Walnut Creek, Ohio, USA. SUNY Upstate Medical University, Syracuse, New York, USA. School of Cancer Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom. MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom. Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Andrew P. Jackson
- Medical Research, RILD Wellcome Wolfson Centre, University of Exeter Medical School, Exeter, Devon, United Kingdom. Department of Zoology, University of Cambridge, Cambridge, United Kingdom. Department of Ophthalmology, University of Arizona College of Medicine, Tucson, Arizona, USA. Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton, United Kingdom. Nagasaki University Research Centre for Genomic Instability and Carcinogenesis (NRGIC), Nagasaki, Japan. Department of Molecular Medicine, Atomic Bomb Disease Institute, Nagasaki University, Nagasaki, Japan. SW Thames Regional Genetics Service, St. George’s Healthcare NHS Trust, London, United Kingdom. Department of Neuroradiology, St. George’s Hospital, London, United Kingdom. Windows of Hope Genetic Study, Walnut Creek, Ohio, USA. SUNY Upstate Medical University, Syracuse, New York, USA. School of Cancer Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom. MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom. Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Tomoo Ogi
- Medical Research, RILD Wellcome Wolfson Centre, University of Exeter Medical School, Exeter, Devon, United Kingdom. Department of Zoology, University of Cambridge, Cambridge, United Kingdom. Department of Ophthalmology, University of Arizona College of Medicine, Tucson, Arizona, USA. Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton, United Kingdom. Nagasaki University Research Centre for Genomic Instability and Carcinogenesis (NRGIC), Nagasaki, Japan. Department of Molecular Medicine, Atomic Bomb Disease Institute, Nagasaki University, Nagasaki, Japan. SW Thames Regional Genetics Service, St. George’s Healthcare NHS Trust, London, United Kingdom. Department of Neuroradiology, St. George’s Hospital, London, United Kingdom. Windows of Hope Genetic Study, Walnut Creek, Ohio, USA. SUNY Upstate Medical University, Syracuse, New York, USA. School of Cancer Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom. MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom. Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Alan R. Lehmann
- Medical Research, RILD Wellcome Wolfson Centre, University of Exeter Medical School, Exeter, Devon, United Kingdom. Department of Zoology, University of Cambridge, Cambridge, United Kingdom. Department of Ophthalmology, University of Arizona College of Medicine, Tucson, Arizona, USA. Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton, United Kingdom. Nagasaki University Research Centre for Genomic Instability and Carcinogenesis (NRGIC), Nagasaki, Japan. Department of Molecular Medicine, Atomic Bomb Disease Institute, Nagasaki University, Nagasaki, Japan. SW Thames Regional Genetics Service, St. George’s Healthcare NHS Trust, London, United Kingdom. Department of Neuroradiology, St. George’s Hospital, London, United Kingdom. Windows of Hope Genetic Study, Walnut Creek, Ohio, USA. SUNY Upstate Medical University, Syracuse, New York, USA. School of Cancer Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom. MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom. Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Catherine M. Green
- Medical Research, RILD Wellcome Wolfson Centre, University of Exeter Medical School, Exeter, Devon, United Kingdom. Department of Zoology, University of Cambridge, Cambridge, United Kingdom. Department of Ophthalmology, University of Arizona College of Medicine, Tucson, Arizona, USA. Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton, United Kingdom. Nagasaki University Research Centre for Genomic Instability and Carcinogenesis (NRGIC), Nagasaki, Japan. Department of Molecular Medicine, Atomic Bomb Disease Institute, Nagasaki University, Nagasaki, Japan. SW Thames Regional Genetics Service, St. George’s Healthcare NHS Trust, London, United Kingdom. Department of Neuroradiology, St. George’s Hospital, London, United Kingdom. Windows of Hope Genetic Study, Walnut Creek, Ohio, USA. SUNY Upstate Medical University, Syracuse, New York, USA. School of Cancer Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom. MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom. Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Andrew H. Crosby
- Medical Research, RILD Wellcome Wolfson Centre, University of Exeter Medical School, Exeter, Devon, United Kingdom. Department of Zoology, University of Cambridge, Cambridge, United Kingdom. Department of Ophthalmology, University of Arizona College of Medicine, Tucson, Arizona, USA. Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton, United Kingdom. Nagasaki University Research Centre for Genomic Instability and Carcinogenesis (NRGIC), Nagasaki, Japan. Department of Molecular Medicine, Atomic Bomb Disease Institute, Nagasaki University, Nagasaki, Japan. SW Thames Regional Genetics Service, St. George’s Healthcare NHS Trust, London, United Kingdom. Department of Neuroradiology, St. George’s Hospital, London, United Kingdom. Windows of Hope Genetic Study, Walnut Creek, Ohio, USA. SUNY Upstate Medical University, Syracuse, New York, USA. School of Cancer Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom. MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom. Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
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Binder JK, Douma LG, Ranjit S, Kanno DM, Chakraborty M, Bloom LB, Levitus M. Intrinsic stability and oligomerization dynamics of DNA processivity clamps. Nucleic Acids Res 2014; 42:6476-86. [PMID: 24728995 PMCID: PMC4041429 DOI: 10.1093/nar/gku255] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Revised: 03/14/2014] [Accepted: 03/17/2014] [Indexed: 11/29/2022] Open
Abstract
Sliding clamps are ring-shaped oligomeric proteins that are essential for processive deoxyribonucleic acid replication. Although crystallographic structures of several clamps have been determined, much less is known about clamp structure and dynamics in solution. Here, we characterized the intrinsic solution stability and oligomerization dynamics of the homodimeric Escherichia coli β and the homotrimeric Saccharomyces cerevisiae proliferating cell nuclear antigen (PCNA) clamps using single-molecule approaches. We show that E. coli β is stable in solution as a closed ring at concentrations three orders of magnitude lower than PCNA. The trimeric structure of PCNA results in slow subunit association rates and is largely responsible for the lower solution stability. Despite this large difference, the intrinsic lifetimes of the rings differ by only one order of magnitude. Our results show that the longer lifetime of the E. coli β dimer is due to more prominent electrostatic interactions that stabilize the subunit interfaces.
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Affiliation(s)
- Jennifer K Binder
- Department of Chemistry and Biochemistry and Biodesign Institute, Arizona State University, Tempe, AZ 85287-5601, USA
| | - Lauren G Douma
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610-0245, USA
| | - Suman Ranjit
- Department of Chemistry and Biochemistry and Biodesign Institute, Arizona State University, Tempe, AZ 85287-5601, USA
| | - David M Kanno
- Department of Chemistry and Biochemistry and Biodesign Institute, Arizona State University, Tempe, AZ 85287-5601, USA
| | - Manas Chakraborty
- Department of Chemistry and Biochemistry and Biodesign Institute, Arizona State University, Tempe, AZ 85287-5601, USA
| | - Linda B Bloom
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610-0245, USA
| | - Marcia Levitus
- Department of Chemistry and Biochemistry and Biodesign Institute, Arizona State University, Tempe, AZ 85287-5601, USA
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Carrasco-Miranda JS, Lopez-Zavala AA, Arvizu-Flores AA, Garcia-Orozco KD, Stojanoff V, Rudiño-Piñera E, Brieba LG, Sotelo-Mundo RR. Crystal structure of the shrimp proliferating cell nuclear antigen: structural complementarity with WSSV DNA polymerase PIP-box. PLoS One 2014; 9:e94369. [PMID: 24728082 PMCID: PMC3984155 DOI: 10.1371/journal.pone.0094369] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Accepted: 03/14/2014] [Indexed: 12/23/2022] Open
Abstract
DNA replication requires processivity factors that allow replicative DNA polymerases to extend long stretches of DNA. Some DNA viruses encode their own replicative DNA polymerase, such as the white spot syndrome virus (WSSV) that infects decapod crustaceans but still require host replication accessory factors. We have determined by X-ray diffraction the three-dimensional structure of the Pacific white leg shrimp Litopenaeus vannamei Proliferating Cell Nuclear Antigen (LvPCNA). This protein is a member of the sliding clamp family of proteins, that binds DNA replication and DNA repair proteins through a motif called PIP-box (PCNA-Interacting Protein). The crystal structure of LvPCNA was refined to a resolution of 3 Å, and allowed us to determine the trimeric protein assembly and details of the interactions between PCNA and the DNA. To address the possible interaction between LvPCNA and the viral DNA polymerase, we docked a theoretical model of a PIP-box peptide from the WSSV DNA polymerase within LvPCNA crystal structure. The theoretical model depicts a feasible model of interaction between both proteins. The crystal structure of shrimp PCNA allows us to further understand the mechanisms of DNA replication processivity factors in non-model systems.
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Affiliation(s)
| | | | - Aldo A. Arvizu-Flores
- Departamento de Ciencias Químico Biológicas, Universidad de Sonora, Hermosillo, Sonora, México
| | | | - Vivian Stojanoff
- National Synchrotron Light Source, Brookhaven National Laboratory, Upton, New York, United States of America
| | - Enrique Rudiño-Piñera
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología-Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Luis G. Brieba
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y Estudios Avanzados, Irapuato, Guanajuato, México
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Abstract
Proliferating cell nuclear antigen (PCNA) is known as a molecular marker for proliferation given its role in replication. Three identical molecules of PCNA form a molecular sliding clamp around the DNA double helix. This provides an essential platform on which multiple proteins are dynamically recruited and coordinately regulated. Over the past decade, new research has provided a deeper comprehension of PCNA as a coordinator of essential cellular functions for cell growth, death, and maintenance. Although the biology of PCNA in proliferation has been comprehensively reviewed, research progress in unveiling the potential of targeting PCNA for disease treatment has not been systematically discussed. Here we briefly summarize the basic structural and functional characteristics of PCNA, and then discuss new developments in its protein interactions, trimer formation, and signaling regulation that open the door to possible therapeutic targeting of PCNA.
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Affiliation(s)
- Shao-Chun Wang
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA.
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34
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Craggs TD, Hutton RD, Brenlla A, White MF, Penedo JC. Single-molecule characterization of Fen1 and Fen1/PCNA complexes acting on flap substrates. Nucleic Acids Res 2014; 42:1857-72. [PMID: 24234453 PMCID: PMC3919604 DOI: 10.1093/nar/gkt1116] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2013] [Revised: 10/21/2013] [Accepted: 10/22/2013] [Indexed: 11/21/2022] Open
Abstract
Flap endonuclease 1 (Fen1) is a highly conserved structure-specific nuclease that catalyses a specific incision to remove 5' flaps in double-stranded DNA substrates. Fen1 plays an essential role in key cellular processes, such as DNA replication and repair, and mutations that compromise Fen1 expression levels or activity have severe health implications in humans. The nuclease activity of Fen1 and other FEN family members can be stimulated by processivity clamps such as proliferating cell nuclear antigen (PCNA); however, the exact mechanism of PCNA activation is currently unknown. Here, we have used a combination of ensemble and single-molecule Förster resonance energy transfer together with protein-induced fluorescence enhancement to uncouple and investigate the substrate recognition and catalytic steps of Fen1 and Fen1/PCNA complexes. We propose a model in which upon Fen1 binding, a highly dynamic substrate is bent and locked into an open flap conformation where specific Fen1/DNA interactions can be established. PCNA enhances Fen1 recognition of the DNA substrate by further promoting the open flap conformation in a step that may involve facilitated threading of the 5' ssDNA flap. Merging our data with existing crystallographic and molecular dynamics simulations we provide a solution-based model for the Fen1/PCNA/DNA ternary complex.
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Affiliation(s)
- Timothy D. Craggs
- SUPA, School of Physics and Astronomy, University of St Andrews, St Andrews, Fife, KY16 9SS, UK and Biomedical Sciences Research Complex, University of St Andrews, St Andrews, Fife KY16 9SS, UK
| | - Richard D. Hutton
- SUPA, School of Physics and Astronomy, University of St Andrews, St Andrews, Fife, KY16 9SS, UK and Biomedical Sciences Research Complex, University of St Andrews, St Andrews, Fife KY16 9SS, UK
| | - Alfonso Brenlla
- SUPA, School of Physics and Astronomy, University of St Andrews, St Andrews, Fife, KY16 9SS, UK and Biomedical Sciences Research Complex, University of St Andrews, St Andrews, Fife KY16 9SS, UK
| | - Malcolm F. White
- SUPA, School of Physics and Astronomy, University of St Andrews, St Andrews, Fife, KY16 9SS, UK and Biomedical Sciences Research Complex, University of St Andrews, St Andrews, Fife KY16 9SS, UK
| | - J. Carlos Penedo
- SUPA, School of Physics and Astronomy, University of St Andrews, St Andrews, Fife, KY16 9SS, UK and Biomedical Sciences Research Complex, University of St Andrews, St Andrews, Fife KY16 9SS, UK
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35
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Yu YL, Chou RH, Liang JH, Chang WJ, Su KJ, Tseng YJ, Huang WC, Wang SC, Hung MC. Targeting the EGFR/PCNA signaling suppresses tumor growth of triple-negative breast cancer cells with cell-penetrating PCNA peptides. PLoS One 2013; 8:e61362. [PMID: 23593472 PMCID: PMC3620387 DOI: 10.1371/journal.pone.0061362] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2012] [Accepted: 03/07/2013] [Indexed: 12/20/2022] Open
Abstract
Tyrosine 211 (Y211) phosphorylation of proliferation cell nuclear antigen (PCNA) coincides with pronounced cancer cell proliferation and correlates with poor survival of breast cancer patients. In epidermal growth factor receptor (EGFR) tyrosine kinase inhibitor (TKI)-resistant cells, both nuclear EGFR (nEGFR) expression and PCNA Y211 phosphorylation are increased. Moreover, the resistance to EGFR TKI is a major clinical problem in treating EGFR-overexpressing triple-negative breast cancer (TNBC). Thus, effective treatment to combat resistance is urgently needed. Here, we show that treatment of cell-penetrating PCNA peptide (CPPP) inhibits growth and induces apoptosis of human TNBC cells. The Y211F CPPP specifically targets EGFR and competes directly for PCNA tyrosine Y211 phosphorylation and prevents nEGFR from binding PCNA in vivo; it also suppresses tumor growth by sensitizing EGFR TKI resistant cells, which have enhanced nEGFR function and abrogated classical EGFR membrane signaling. Furthermore, we identify an active motif of CPPP, RFLNFF (RF6 CPPP), which is necessary and sufficient to inhibit TKI-resistant TNBC cell growth of orthotopic implanted tumor in mice. Finally, the activity of its synthetic retro-inverted derivative, D-RF6 CPPP, on an equimolar basis, is more potent than RF6 CPPP. Our study reveals a drug candidate with translational potential for the future development of safe and effective therapeutic for EGFR TKI resistance in TNBC.
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Affiliation(s)
- Yung-Luen Yu
- Graduate Institute of Cancer Biology and Center for Molecular Medicine, China Medical University, Taichung, Taiwan
- Department of Biotechnology, Asia University, Taichung, Taiwan
- * E-mail: (YLY); (MCH)
| | - Ruey-Hwang Chou
- Graduate Institute of Cancer Biology and Center for Molecular Medicine, China Medical University, Taichung, Taiwan
- Department of Biotechnology, Asia University, Taichung, Taiwan
| | - Jia-Hong Liang
- Graduate Institute of Cancer Biology and Center for Molecular Medicine, China Medical University, Taichung, Taiwan
| | - Wei-Jung Chang
- Graduate Institute of Cancer Biology and Center for Molecular Medicine, China Medical University, Taichung, Taiwan
| | - Kuo-Jung Su
- Graduate Institute of Cancer Biology and Center for Molecular Medicine, China Medical University, Taichung, Taiwan
- The Ph.D. Program for Cancer Biology and Drug Discovery, China Medical University, Taichung, Taiwan
| | - Yen-Ju Tseng
- Graduate Institute of Cancer Biology and Center for Molecular Medicine, China Medical University, Taichung, Taiwan
| | - Wei-Chien Huang
- Graduate Institute of Cancer Biology and Center for Molecular Medicine, China Medical University, Taichung, Taiwan
| | - Shao-Chun Wang
- Department of Cancer and Cell Biology, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
| | - Mien-Chie Hung
- Graduate Institute of Cancer Biology and Center for Molecular Medicine, China Medical University, Taichung, Taiwan
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
- * E-mail: (YLY); (MCH)
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36
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Chernikov VA, Gorokhovets NV, Savvateeva LV, Severin SE. [Analysis of complex formation of human recombinant HSP70 with tumor-associated peptides]. Biomed Khim 2013; 58:651-61. [PMID: 23350197 DOI: 10.18097/pbmc20125806651] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Molecular chaperones of HSP70 family assists presentation of exogenous antigenic peptides by antigen-presenting cells (APC). HSP70-peptide complexes are powerful immunotherapeutic agents, which enhance cross-presentation of captured antigen in dendritic cells and macrophages. Several clinical trials have shown that HSP-based cancer vaccines possess good efficacy and safety. However, sometime it is impossible to isolate sufficient amount of vaccine. These make us to pay attention for recombinant HSP70-based vaccines and to optimize in vitro complex formation mechanism. Here we have investigated two human recombinant proteins HSP70(HYB) and HSC70. Optimal values of ADP concentration, pH, temperature and peptides excess are determined in this work. We have also shown that proposed complex formation method enriches eluted from HSP70-complexes peptide repertoire compared to in vivo assembled ones.
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37
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Hibbert RG, Sixma TK. Intrinsic flexibility of ubiquitin on proliferating cell nuclear antigen (PCNA) in translesion synthesis. J Biol Chem 2012; 287:39216-23. [PMID: 22989887 PMCID: PMC3493961 DOI: 10.1074/jbc.m112.389890] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2012] [Revised: 08/29/2012] [Indexed: 12/22/2022] Open
Abstract
Ubiquitin conjugation provides a crucial signaling role in hundreds of cellular pathways; however, a structural understanding of ubiquitinated substrates is lacking. One important substrate is monoubiquitinated PCNA (PCNA-Ub), which signals for recruitment of damage-tolerant polymerases in the translesion synthesis (TLS) pathway of DNA damage avoidance. We use a novel and efficient enzymatic method to produce PCNA-Ub at high yield with a native isopeptide bond and study its Usp1/UAF1-dependent deconjugation. In solution we find that the ubiquitin moiety is flexible relative to the PCNA, with its hydrophobic patch mostly accessible for recruitment of TLS polymerases, which promotes the interaction with polymerase η. The studies are a prototype for the nature of the ubiquitin modification.
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Affiliation(s)
- Richard G. Hibbert
- From the Division of Biochemistry and Center for Biomedical Genetics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Titia K. Sixma
- From the Division of Biochemistry and Center for Biomedical Genetics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
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38
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Carrasco-Miranda JS, Cardona-Felix CS, Lopez-Zavala AA, de-la-Re-Vega E, De la Mora E, Rudiño-Piñera E, Sotelo-Mundo RR, Brieba LG. Crystallization and X-ray diffraction studies of crustacean proliferating cell nuclear antigen. Acta Crystallogr Sect F Struct Biol Cryst Commun 2012; 68:1367-70. [PMID: 23143251 PMCID: PMC3515383 DOI: 10.1107/s1744309112040444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2012] [Accepted: 09/25/2012] [Indexed: 11/10/2022]
Abstract
Proliferating cell nuclear antigen (PCNA), a member of the sliding clamp family of proteins, interacts specifically with DNA replication and repair proteins through a small peptide motif called the PCNA-interacting protein or PIP box. PCNA is recognized as one of the key proteins involved in DNA metabolism. In the present study, the recombinant PCNA from Litopenaeus vannamei (LvPCNA) was heterologously overexpressed and purified using metal ion-affinity chromatography. Crystals suitable for diffraction grew overnight using the hanging-drop vapour-diffusion method. LvPCNA crystals belong to space group C2 with unit-cell parameters a=144.6, b=83.4, c=74.3 Å, β=117.6°. One data set was processed to 3 Å resolution, with an overall Rmeas of 0.09 and a completeness of 93.3%. Initial phases were obtained by molecular replacement using a homology model of LvPCNA as the search model. Refinement and structural analysis are underway. This report is the first successful crystallographic analysis of a marine crustacean decapod shrimp (L. vannamei) proliferating cell nuclear antigen.
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Affiliation(s)
- Jesus S. Carrasco-Miranda
- Centro de Investigación en Alimentación y Desarrollo, A.C. (CIAD), Carretera a Ejido La Victoria Km 0.6, Apartado Postal 1735, Hermosillo, Sonora 83304, Mexico
| | - Cesar S. Cardona-Felix
- Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), Centro de Investigación y Estudios Avanzados-Unidad Irapuato, Km 9.6 Libramiento Norte Carretera Irapuato-León, Apartado Postal 629, Irapuato, Guanajuato 36500, Mexico
| | - Alonso A. Lopez-Zavala
- Centro de Investigación en Alimentación y Desarrollo, A.C. (CIAD), Carretera a Ejido La Victoria Km 0.6, Apartado Postal 1735, Hermosillo, Sonora 83304, Mexico
| | - Enrique de-la-Re-Vega
- Departamento de Investigaciones Científicas y Tecnológicas (DICTUS), Universidad de Sonora, Blvd. Luis Encinas y Rosales S/N, Col. Centro, Hermosillo, Sonora 83000, Mexico
| | - Eugenio De la Mora
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología (IBT), Universidad Nacional Autónoma de México (UNAM), Av. Universidad 2001, Col. Chamilpa, Cuernavaca, Morelos 62210, Mexico
| | - Enrique Rudiño-Piñera
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología (IBT), Universidad Nacional Autónoma de México (UNAM), Av. Universidad 2001, Col. Chamilpa, Cuernavaca, Morelos 62210, Mexico
| | - Rogerio R. Sotelo-Mundo
- Centro de Investigación en Alimentación y Desarrollo, A.C. (CIAD), Carretera a Ejido La Victoria Km 0.6, Apartado Postal 1735, Hermosillo, Sonora 83304, Mexico
| | - Luis G. Brieba
- Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), Centro de Investigación y Estudios Avanzados-Unidad Irapuato, Km 9.6 Libramiento Norte Carretera Irapuato-León, Apartado Postal 629, Irapuato, Guanajuato 36500, Mexico
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39
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Loveland AB, Habuchi S, Walter JC, van Oijen AM. A general approach to break the concentration barrier in single-molecule imaging. Nat Methods 2012; 9:987-92. [PMID: 22961247 PMCID: PMC3610324 DOI: 10.1038/nmeth.2174] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2012] [Accepted: 08/09/2012] [Indexed: 02/04/2023]
Abstract
Single-molecule fluorescence imaging is often incompatible with physiological protein concentrations, as fluorescence background overwhelms an individual molecule's signal. We solve this problem with a new imaging approach called PhADE (PhotoActivation, Diffusion and Excitation). A protein of interest is fused to a photoactivatable protein (mKikGR) and introduced to its surface-immobilized substrate. After photoactivation of mKikGR near the surface, rapid diffusion of the unbound mKikGR fusion out of the detection volume eliminates background fluorescence, whereupon the bound molecules are imaged. We labeled the eukaryotic DNA replication protein flap endonuclease 1 with mKikGR and added it to replication-competent Xenopus laevis egg extracts. PhADE imaging of high concentrations of the fusion construct revealed its dynamics and micrometer-scale movements on individual, replicating DNA molecules. Because PhADE imaging is in principle compatible with any photoactivatable fluorophore, it should have broad applicability in revealing single-molecule dynamics and stoichiometry of macromolecular protein complexes at previously inaccessible fluorophore concentrations.
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Affiliation(s)
- Anna B. Loveland
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
- Graduate Program in Biophysics, Harvard University, Cambridge, MA 02138, USA
| | - Satoshi Habuchi
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Johannes C. Walter
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Antoine M. van Oijen
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
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40
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Bouayad D, Pederzoli-Ribeil M, Mocek J, Candalh C, Arlet JB, Hermine O, Reuter N, Davezac N, Witko-Sarsat V. Nuclear-to-cytoplasmic relocalization of the proliferating cell nuclear antigen (PCNA) during differentiation involves a chromosome region maintenance 1 (CRM1)-dependent export and is a prerequisite for PCNA antiapoptotic activity in mature neutrophils. J Biol Chem 2012; 287:33812-25. [PMID: 22846997 PMCID: PMC3460476 DOI: 10.1074/jbc.m112.367839] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2012] [Revised: 07/24/2012] [Indexed: 01/03/2023] Open
Abstract
Neutrophils are deprived of proliferative capacity and have a tightly controlled lifespan to avoid their persistence at the site of injury. We have recently described that the proliferating cell nuclear antigen (PCNA), a nuclear factor involved in DNA replication and repair of proliferating cells, is a key regulator of neutrophil survival. In neutrophils, PCNA was localized exclusively in the cytoplasm due to its nuclear-to-cytoplasmic relocalization during granulocytic differentiation. We showed here that leptomycin B, an inhibitor of the chromosome region maintenance 1 (CRM1) exportin, inhibited PCNA relocalization during granulocytic differentiation of HL-60 and NB4 promyelocytic cell lines and of human CD34(+) primary cells. Using enhanced green fluorescent protein fusion constructs, we have demonstrated that PCNA relocalization involved a nuclear export signal (NES) located from Ile-11 to Ile-23 in the PCNA sequence. However, this NES, located at the inner face of the PCNA trimer, was not functional in wild-type PCNA, but instead, was fully active and leptomycin B-sensitive in the monomeric PCNAY114A mutant. To test whether a defect in PCNA cytoplasmic relocalization would affect its antiapoptotic activity in mature neutrophils, a chimeric PCNA fused with the SV40 nuclear localization sequence (NLS) was generated to preclude its cytoplasmic localization. As expected, neutrophil-differentiated PLB985 cells expressing ectopic SV40NLS-PCNA had an increased nuclear PCNA as compared with cells expressing wild-type PCNA. Accordingly, the nuclear PCNA mutant did not show any antiapoptotic activity as compared with wild-type PCNA. Nuclear-to-cytoplasmic relocalization that occurred during myeloid differentiation is essential for PCNA antiapoptotic activity in mature neutrophils and is dependent on the newly identified monomerization-dependent PCNA NES.
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Affiliation(s)
- Dikra Bouayad
- From the INSERM U1016, 75014 Paris, France
- the Institut Cochin, Université Paris Descartes, Cochin Hospital, 75015 Paris, France
- the CNRS UMR8104, 75014 Paris, France
| | - Magali Pederzoli-Ribeil
- From the INSERM U1016, 75014 Paris, France
- the Institut Cochin, Université Paris Descartes, Cochin Hospital, 75015 Paris, France
- the CNRS UMR8104, 75014 Paris, France
| | - Julie Mocek
- From the INSERM U1016, 75014 Paris, France
- the Institut Cochin, Université Paris Descartes, Cochin Hospital, 75015 Paris, France
- the CNRS UMR8104, 75014 Paris, France
| | - Céline Candalh
- From the INSERM U1016, 75014 Paris, France
- the Institut Cochin, Université Paris Descartes, Cochin Hospital, 75015 Paris, France
- the CNRS UMR8104, 75014 Paris, France
| | | | - Olivier Hermine
- the CNRS UMR8147 and
- Hematology Department, Université Paris Descartes, Necker Hospital, 75015 Paris, France
| | - Nathalie Reuter
- the Computational Biology Unit, University of Bergen, N-5008 Bergen, Norway, and
| | - Noélie Davezac
- CNRS UMR5547, Université Toulouse III, 31400 Toulouse, France
| | - Véronique Witko-Sarsat
- From the INSERM U1016, 75014 Paris, France
- the Institut Cochin, Université Paris Descartes, Cochin Hospital, 75015 Paris, France
- the CNRS UMR8104, 75014 Paris, France
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41
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Takawa M, Cho HS, Hayami S, Toyokawa G, Kogure M, Yamane Y, Iwai Y, Maejima K, Ueda K, Masuda A, Dohmae N, Field HI, Tsunoda T, Kobayashi T, Akasu T, Sugiyama M, Ohnuma SI, Atomi Y, Ponder BAJ, Nakamura Y, Hamamoto R. Histone lysine methyltransferase SETD8 promotes carcinogenesis by deregulating PCNA expression. Cancer Res 2012; 72:3217-27. [PMID: 22556262 DOI: 10.1158/0008-5472.can-11-3701] [Citation(s) in RCA: 139] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Although the physiologic significance of lysine methylation of histones is well known, whether lysine methylation plays a role in the regulation of nonhistone proteins has not yet been examined. The histone lysine methyltransferase SETD8 is overexpressed in various types of cancer and seems to play a crucial role in S-phase progression. Here, we show that SETD8 regulates the function of proliferating cell nuclear antigen (PCNA) protein through lysine methylation. We found that SETD8 methylated PCNA on lysine 248, and either depletion of SETD8 or substitution of lysine 248 destabilized PCNA expression. Mechanistically, lysine methylation significantly enhanced the interaction between PCNA and the flap endonuclease FEN1. Loss of PCNA methylation retarded the maturation of Okazaki fragments, slowed DNA replication, and induced DNA damage, and cells expressing a methylation-inactive PCNA mutant were more susceptible to DNA damage. An increase of methylated PCNA was found in cancer cells, and the expression levels of SETD8 and PCNA were correlated in cancer tissue samples. Together, our findings reveal a function for lysine methylation on a nonhistone protein and suggest that aberrant lysine methylation of PCNA may play a role in human carcinogenesis.
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Affiliation(s)
- Masashi Takawa
- Laboratory of Molecular Medicine, Human Genome Center, Institute of Medical Science, The University of Tokyo, and National Cancer Center Hospital, Chuo-ku, Tokyo, Japan
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42
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Yardimci H, Loveland AB, van Oijen AM, Walter JC. Single-molecule analysis of DNA replication in Xenopus egg extracts. Methods 2012; 57:179-86. [PMID: 22503776 PMCID: PMC3427465 DOI: 10.1016/j.ymeth.2012.03.033] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2011] [Revised: 03/29/2012] [Accepted: 03/31/2012] [Indexed: 11/18/2022] Open
Abstract
The recent advent in single-molecule imaging and manipulation methods has made a significant impact on the understanding of molecular mechanisms underlying many essential cellular processes. Single-molecule techniques such as electron microscopy and DNA fiber assays have been employed to study the duplication of genome in eukaryotes. Here, we describe a single-molecule assay that allows replication of DNA attached to the functionalized surface of a microfluidic flow cell in a soluble Xenopus leavis egg extract replication system and subsequent visualization of replication products via fluorescence microscopy. We also explain a method for detection of replication proteins, through fluorescently labeled antibodies, on partially replicated DNA immobilized at both ends to the surface.
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Affiliation(s)
- Hasan Yardimci
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Anna B. Loveland
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Antoine M. van Oijen
- The Zernike Institute for Advanced Materials, University of Groningen, Groningen, The Netherlands
| | - Johannes C. Walter
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
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43
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Strzalka W, Labecki P, Bartnicki F, Aggarwal C, Rapala-Kozik M, Tani C, Tanaka K, Gabrys H. Arabidopsis thaliana proliferating cell nuclear antigen has several potential sumoylation sites. J Exp Bot 2012; 63:2971-83. [PMID: 22330895 DOI: 10.1093/jxb/ers002] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Proliferating cell nuclear antigen (PCNA) is post-translationally modified in yeast and animal cells. Major studies carried out in the last decade have focused on the role of sumoylated and ubiquitinated PCNA. Using different approaches, an interaction between plant PCNA and SUMO both in vivo and in bacteria has been demonstrated for the first time. In addition, identical sumoylation patterns for both AtPCNA1 and 2 were observed in bacteria. The plant PCNA sumoylation pattern has been shown to differ significantly from that of Saccharomyces cerevisiae. This result contrasts with a common opinion based on previous structural analysis of yeast, human, and plant PCNAs, which treats PCNA as a highly conserved protein even between species. Analyses of AtPCNA post-translational modifications using different SUMO proteins (SUMO1, 2, 3, and 5) revealed similar modification patterns for each tested SUMO protein. Potential target lysine residues that might be sumoylated in vivo were identified on the basis of in bacteria AtPCNA mutational analyses. Taken together, these results clearly show that plant PCNA is post-translationally modified in bacteria and may be sumoylated in a plant cell at various sites. These data open up important new perspectives for further detailed studies on the role of PCNA sumoylation in plant cells.
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Affiliation(s)
- Wojciech Strzalka
- Department of Plant Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland.
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44
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Zhao H, Ho PC, Lo YH, Espejo A, Bedford MT, Hung MC, Wang SC. Interaction of proliferation cell nuclear antigen (PCNA) with c-Abl in cell proliferation and response to DNA damages in breast cancer. PLoS One 2012; 7:e29416. [PMID: 22238610 PMCID: PMC3251568 DOI: 10.1371/journal.pone.0029416] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2011] [Accepted: 11/28/2011] [Indexed: 01/09/2023] Open
Abstract
Cell proliferation in primary and metastatic tumors is a fundamental characteristic of advanced breast cancer. Further understanding of the mechanism underlying enhanced cell growth will be important in identifying novel prognostic markers and therapeutic targets. Here we demonstrated that tyrosine phosphorylation of the proliferating cell nuclear antigen (PCNA) is a critical event in growth regulation of breast cancer cells. We found that phosphorylation of PCNA at tyrosine 211 (Y211) enhanced its association with the non-receptor tyrosine kinase c-Abl. We further demonstrated that c-Abl facilitates chromatin association of PCNA and is required for nuclear foci formation of PCNA in cells stressed by DNA damage as well as in unperturbed cells. Targeting Y211 phosphorylation of PCNA with a cell-permeable peptide inhibited the phosphorylation and reduced the PCNA-Abl interaction. These results show that PCNA signal transduction has an important impact on the growth regulation of breast cancer cells.
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Affiliation(s)
- Huajun Zhao
- Department of Cancer and Cell Biology, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
| | - Po-Chun Ho
- Department of Cancer and Cell Biology, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
| | - Yuan-Hung Lo
- Department of Cancer and Cell Biology, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
| | - Alexsandra Espejo
- Department of Molecular Carcinogenesis, M. D. Anderson Cancer Center, University of Texas, Smithville, Texas, United States of America
| | - Mark T. Bedford
- Department of Molecular Carcinogenesis, M. D. Anderson Cancer Center, University of Texas, Smithville, Texas, United States of America
| | - Mien-Chie Hung
- Department of Molecular and Cellular Oncology, M. D. Anderson Cancer Center, University of Texas, Houston, Texas, United States of America
- Center for Molecular Medicine, China Medical University and Hospital, Taichung, Taiwan
- Graduate Institute of Cancer Biology, China Medical University and Hospital, Taichung, Taiwan
| | - Shao-Chun Wang
- Department of Cancer and Cell Biology, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
- * E-mail: .
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45
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Wang Y, Zhang Q, Chen H, Li X, Mai W, Chen K, Zhang S, Lee EYC, Lee MYWT, Zhou Y. P50, the small subunit of DNA polymerase delta, is required for mediation of the interaction of polymerase delta subassemblies with PCNA. PLoS One 2011; 6:e27092. [PMID: 22073260 PMCID: PMC3206906 DOI: 10.1371/journal.pone.0027092] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2011] [Accepted: 10/10/2011] [Indexed: 11/18/2022] Open
Abstract
Mammalian DNA polymerase δ (pol δ), a four-subunit enzyme, plays a crucial and versatile role in DNA replication and various DNA repair processes. Its function as a chromosomal DNA polymerase is dependent on the association with proliferating cell nuclear antigen (PCNA) which functions as a molecular sliding clamp. All four of the pol δ subunits (p125, p50, p68, and p12) have been reported to bind to PCNA. However, the identity of the subunit of pol δ that directly interacts with PCNA and is therefore primarily responsible for the processivity of the enzyme still remains controversial. Previous model for the network of protein-protein interactions of the pol δ-PCNA complex showed that pol δ might be able to interact with a single molecule of PCNA homotrimer through its three subunits, p125, p68, and p12 in which the p50 was not included in. Here, we have confirmed that the small subunit p50 of human pol δ truthfully interacts with PCNA by the use of far-Western analysis, quantitative ELISA assay, and subcellular co-localization. P50 is required for mediation of the interaction between pol δ subassemblies and PCNA homotrimer. Thus, pol δ interacts with PCNA via its four subunits.
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Affiliation(s)
- Yujue Wang
- Institute of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu, People's Republic of China
| | - Qian Zhang
- Institute of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu, People's Republic of China
| | - Huiqing Chen
- Institute of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu, People's Republic of China
| | - Xiao Li
- Institute of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu, People's Republic of China
| | - Weijun Mai
- Institute of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu, People's Republic of China
| | - Keping Chen
- Institute of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu, People's Republic of China
| | - Sufang Zhang
- Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla, New York, United States of America
| | - Ernest Y. C. Lee
- Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla, New York, United States of America
| | - Marietta Y. W. T. Lee
- Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla, New York, United States of America
| | - Yajing Zhou
- Institute of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu, People's Republic of China
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Abstract
BACKGROUND PCNA (proliferating cell nuclear antigen) has been found in the nuclei of yeast, plant and animal cells that undergo cell division, suggesting a function in cell cycle regulation and/or DNA replication. It subsequently became clear that PCNA also played a role in other processes involving the cell genome. SCOPE This review discusses eukaryotic PCNA, with an emphasis on plant PCNA, in terms of the protein structure and its biochemical properties as well as gene structure, organization, expression and function. PCNA exerts a tripartite function by operating as (1) a sliding clamp during DNA synthesis, (2) a polymerase switch factor and (3) a recruitment factor. Most of its functions are mediated by its interactions with various proteins involved in DNA synthesis, repair and recombination as well as in regulation of the cell cycle and chromatid cohesion. Moreover, post-translational modifications of PCNA play a key role in regulation of its functions. Finally, a phylogenetic comparison of PCNA genes suggests that the multi-functionality observed in most species is a product of evolution. CONCLUSIONS Most plant PCNAs exhibit features similar to those found for PCNAs of other eukaryotes. Similarities include: (1) a trimeric ring structure of the PCNA sliding clamp, (2) the involvement of PCNA in DNA replication and repair, (3) the ability to stimulate the activity of DNA polymerase δ and (4) the ability to interact with p21, a regulator of the cell cycle. However, many plant genomes seem to contain the second, probably functional, copy of the PCNA gene, in contrast to PCNA pseudogenes that are found in mammalian genomes.
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Affiliation(s)
- Wojciech Strzalka
- Department of Plant Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland
| | - Alicja Ziemienowicz
- Department of Biological Sciences, University of Lethbridge, 4401 University Drive, Lethbridge, AB T1K 3M4, Canada
- For correspondence. E-mail
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47
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Strzalka W, Ziemienowicz A. Proliferating cell nuclear antigen (PCNA): a key factor in DNA replication and cell cycle regulation. Ann Bot 2011. [PMID: 21169293 DOI: 10.1093/aob/mcq43] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
BACKGROUND PCNA (proliferating cell nuclear antigen) has been found in the nuclei of yeast, plant and animal cells that undergo cell division, suggesting a function in cell cycle regulation and/or DNA replication. It subsequently became clear that PCNA also played a role in other processes involving the cell genome. SCOPE This review discusses eukaryotic PCNA, with an emphasis on plant PCNA, in terms of the protein structure and its biochemical properties as well as gene structure, organization, expression and function. PCNA exerts a tripartite function by operating as (1) a sliding clamp during DNA synthesis, (2) a polymerase switch factor and (3) a recruitment factor. Most of its functions are mediated by its interactions with various proteins involved in DNA synthesis, repair and recombination as well as in regulation of the cell cycle and chromatid cohesion. Moreover, post-translational modifications of PCNA play a key role in regulation of its functions. Finally, a phylogenetic comparison of PCNA genes suggests that the multi-functionality observed in most species is a product of evolution. CONCLUSIONS Most plant PCNAs exhibit features similar to those found for PCNAs of other eukaryotes. Similarities include: (1) a trimeric ring structure of the PCNA sliding clamp, (2) the involvement of PCNA in DNA replication and repair, (3) the ability to stimulate the activity of DNA polymerase δ and (4) the ability to interact with p21, a regulator of the cell cycle. However, many plant genomes seem to contain the second, probably functional, copy of the PCNA gene, in contrast to PCNA pseudogenes that are found in mammalian genomes.
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Affiliation(s)
- Wojciech Strzalka
- Department of Plant Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, Krakow, Poland
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De Biasio A, Sánchez R, Prieto J, Villate M, Campos-Olivas R, Blanco FJ. Reduced stability and increased dynamics in the human proliferating cell nuclear antigen (PCNA) relative to the yeast homolog. PLoS One 2011; 6:e16600. [PMID: 21364740 PMCID: PMC3041752 DOI: 10.1371/journal.pone.0016600] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2010] [Accepted: 01/05/2011] [Indexed: 11/18/2022] Open
Abstract
Proliferating Cell Nuclear Antigen (PCNA) is an essential factor for DNA replication and repair. PCNA forms a toroidal, ring shaped structure of 90 kDa by the symmetric association of three identical monomers. The ring encircles the DNA and acts as a platform where polymerases and other proteins dock to carry out different DNA metabolic processes. The amino acid sequence of human PCNA is 35% identical to the yeast homolog, and the two proteins have the same 3D crystal structure. In this report, we give evidence that the budding yeast (sc) and human (h) PCNAs have highly similar structures in solution but differ substantially in their stability and dynamics. hPCNA is less resistant to chemical and thermal denaturation and displays lower cooperativity of unfolding as compared to scPCNA. Solvent exchange rates measurements show that the slowest exchanging backbone amides are at the β-sheet, in the structure core, and not at the helices, which line the central channel. However, all the backbone amides of hPCNA exchange fast, becoming undetectable within hours, while the signals from the core amides of scPCNA persist for longer times. The high dynamics of the α-helices, which face the DNA in the PCNA-loaded form, is likely to have functional implications for the sliding of the PCNA ring on the DNA since a large hole with a flexible wall facilitates the establishment of protein-DNA interactions that are transient and easily broken. The increased dynamics of hPCNA relative to scPCNA may allow it to acquire multiple induced conformations upon binding to its substrates enlarging its binding diversity.
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Affiliation(s)
| | | | - Jesús Prieto
- Structural and Computational Biology Programme, Centro Nacional de Investigaciones Oncológicas (CNIO), Madrid, Spain
| | | | - Ramón Campos-Olivas
- Structural and Computational Biology Programme, Centro Nacional de Investigaciones Oncológicas (CNIO), Madrid, Spain
| | - Francisco J. Blanco
- Structural Biology Unit, CIC bioGUNE, Derio, Spain
- IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
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Fridman Y, Palgi N, Dovrat D, Ben-Aroya S, Hieter P, Aharoni A. Subtle alterations in PCNA-partner interactions severely impair DNA replication and repair. PLoS Biol 2010; 8:e1000507. [PMID: 20967232 PMCID: PMC2953525 DOI: 10.1371/journal.pbio.1000507] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2010] [Accepted: 08/24/2010] [Indexed: 11/24/2022] Open
Abstract
Dynamic switching of PCNA-partner interactions is essential for normal DNA replication and repair in yeast. The robustness of complex biological processes in the face of environmental and genetic perturbations is a key biological trait. However, while robustness has been extensively studied, little is known regarding the fragility of biological processes. Here, we have examined the susceptibility of DNA replication and repair processes mediated by the proliferating cell nuclear antigen (PCNA). Using protein directed evolution, biochemical, and genetic approaches, we have generated and characterized PCNA mutants with increased affinity for several key partners of the PCNA-partner network. We found that increases in PCNA-partner interaction affinities led to severe in vivo phenotypic defects. Surprisingly, such defects are much more severe than those induced by complete abolishment of the respective interactions. Thus, the subtle and tunable nature of these affinity perturbations produced different phenotypic effects than realized with traditional “on-off” analysis using gene knockouts. Our findings indicate that biological systems can be robust to one set of perturbations yet fragile to others. Many biological processes are mediated by complex protein-protein interaction networks. The most highly connected proteins in such networks, termed hub proteins, precisely regulate biological processes by the regulated and sequential binding and releasing of partner proteins. In the case of DNA replication and repair, proliferating cell nuclear antigen (PCNA) is a hub protein that encircles the DNA to dynamically bind and release a variety of DNA-modifying enzymes. In this work, we explored the impact of subtle alterations of PCNA-partner interaction affinities on DNA replication and repair in yeast. Using directed evolution approaches, we generated a large library of PCNA mutants and selected for those with enhanced affinity for five different PCNA partners. In vivo analysis of such mutants indicated the high sensitivity of DNA replication and repair processes to minor alterations in PCNA-partner interaction affinities. Importantly, we discovered that some of the defects observed in the strains with increased PCNA-partner protein interaction far exceed the defects observed when the same partner protein is deleted altogether. Our analysis suggests that the cost of misregulating biological processes through disruption of the carefully orchestrated action of hub-interacting proteins can be much higher than the cost of deleting parts of the network altogether, demonstrating both the fragility and robustness of biological processes.
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Affiliation(s)
- Yearit Fridman
- Departments of Life Sciences and the National Institute for Biotechnology in the Negev (NIBN), Ben-Gurion University of the Negev, Be'er Sheva, Israel
| | - Niv Palgi
- Departments of Life Sciences and the National Institute for Biotechnology in the Negev (NIBN), Ben-Gurion University of the Negev, Be'er Sheva, Israel
| | - Daniel Dovrat
- Departments of Life Sciences and the National Institute for Biotechnology in the Negev (NIBN), Ben-Gurion University of the Negev, Be'er Sheva, Israel
| | - Shay Ben-Aroya
- The Nano Center, The Mina and Everard Goodman Faculty of Life Sciences Bar-Ilan University, Ramat-Gan, Israel
| | - Philip Hieter
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Amir Aharoni
- Departments of Life Sciences and the National Institute for Biotechnology in the Negev (NIBN), Ben-Gurion University of the Negev, Be'er Sheva, Israel
- * E-mail:
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Xu H, Chen C, Peng J, Tang HW, Liu CM, He Y, Chen ZZ, Li Y, Zhang ZL, Pang DW. Evaluation of the bioconjugation efficiency of different quantum dots as probes for immunostaining tumor-marker proteins. Appl Spectrosc 2010; 64:847-852. [PMID: 20719046 DOI: 10.1366/000370210792081154] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
The differing bioconjugation efficiencies of quantum dots (QDs) are a practical obstacle to their popularization. Differences in bioconjugation efficiency based on immunostaining the same targeted molecules using different batches of QDs need to be evaluated prior to their application. In this paper, a quantitative method for evaluating the efficiency of QDs in staining tissues has been developed based on Hadamard transform (HT) spectral imaging. Proliferating cell nuclear antigens (PCNA) in breast cancer tissues were labeled with bioconjugated QD bioprobes using a 454 nm laser as the light source for fluorescence spectral imaging. Four-dimensional (4D) spectral imaging analysis of PCNA in cell nuclei was carried out using HT spectral microscopy based on immunostaining with different batches of QDs. The fluorescence intensity distributions in the cell nuclei were collected from the 4D images. Based on the information obtained from microscopic spectra and 4D images, differences in the bioconjugation efficiency among different batches of QDs were evaluated. The results demonstrate that it is possible to maintain uniform bioconjugation efficiencies with different QD bioconjugation processes in order to obtain accurate and reliable results in biomedical analysis and cancer diagnosis.
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Affiliation(s)
- Hao Xu
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, PR China
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