1
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Hardebeck S, Schreiber S, Adick A, Langer K, Jose J. A FRET-Based Assay for the Identification of PCNA Inhibitors. Int J Mol Sci 2023; 24:11858. [PMID: 37511614 PMCID: PMC10380293 DOI: 10.3390/ijms241411858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 07/19/2023] [Accepted: 07/20/2023] [Indexed: 07/30/2023] Open
Abstract
Proliferating cell nuclear antigen (PCNA) is the key regulator of human DNA metabolism. One important interaction partner is p15, involved in DNA replication and repair. Targeting the PCNA-p15 interaction is a promising therapeutic strategy against cancer. Here, a Förster resonance energy transfer (FRET)-based assay for the analysis of the PCNA-p15 interaction was developed. Next to the application as screening tool for the identification and characterization of PCNA-p15 interaction inhibitors, the assay is also suitable for the investigation of mutation-induced changes in their affinity. This is particularly useful for analyzing disease associated PCNA or p15 variants at the molecular level. Recently, the PCNA variant C148S has been associated with Ataxia-telangiectasia-like disorder type 2 (ATLD2). ATLD2 is a neurodegenerative disease based on defects in DNA repair due to an impaired PCNA. Incubation time dependent FRET measurements indicated no effect on PCNAC148S-p15 affinity, but on PCNA stability. The impaired stability and increased aggregation behavior of PCNAC148S was confirmed by intrinsic tryptophan fluorescence, differential scanning fluorimetry (DSF) and asymmetrical flow field-flow fractionation (AF4) measurements. The analysis of the disease associated PCNA variant demonstrated the versatility of the interaction assay as developed.
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Affiliation(s)
- Sarah Hardebeck
- University of Münster, Institute of Pharmaceutical and Medicinal Chemistry, Pharmacampus, 48149 Münster, Germany
| | - Sebastian Schreiber
- University of Münster, Institute of Pharmaceutical and Medicinal Chemistry, Pharmacampus, 48149 Münster, Germany
| | - Annika Adick
- University of Münster, Institute for Pharmaceutical Technology and Biopharmacy, Pharmacampus, 48149 Münster, Germany
| | - Klaus Langer
- University of Münster, Institute for Pharmaceutical Technology and Biopharmacy, Pharmacampus, 48149 Münster, Germany
| | - Joachim Jose
- University of Münster, Institute of Pharmaceutical and Medicinal Chemistry, Pharmacampus, 48149 Münster, Germany
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2
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Kibler RD, Lee S, Kennedy MA, Wicky BIM, Lai SM, Kostelic MM, Li X, Chow CM, Carter L, Wysocki VH, Stoddard BL, Baker D. Stepwise design of pseudosymmetric protein hetero-oligomers. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.07.535760. [PMID: 37066191 PMCID: PMC10104133 DOI: 10.1101/2023.04.07.535760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Pseudosymmetric hetero-oligomers with three or more unique subunits with overall structural (but not sequence) symmetry play key roles in biology, and systematic approaches for generating such proteins de novo would provide new routes to controlling cell signaling and designing complex protein materials. However, the de novo design of protein hetero-oligomers with three or more distinct chains with nearly identical structures is a challenging problem because it requires the accurate design of multiple protein-protein interfaces simultaneously. Here, we describe a divide-and-conquer approach that breaks the multiple-interface design challenge into a set of more tractable symmetric single-interface redesign problems, followed by structural recombination of the validated homo-oligomers into pseudosymmetric hetero-oligomers. Starting from de novo designed circular homo-oligomers composed of 9 or 24 tandemly repeated units, we redesigned the inter-subunit interfaces to generate 15 new homo-oligomers and recombined them to make 17 new hetero-oligomers, including ABC heterotrimers, A2B2 heterotetramers, and A3B3 and A2B2C2 heterohexamers which assemble with high structural specificity. The symmetric homo-oligomers and pseudosymmetric hetero-oligomers generated for each system share a common backbone, and hence are ideal building blocks for generating and functionalizing larger symmetric assemblies.
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Affiliation(s)
- Ryan D. Kibler
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Sangmin Lee
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Madison A. Kennedy
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Division of Basic Sciences, Fred Hutchinson Cancer Center, Seattle, WA 98006, USA
| | - Basile I. M. Wicky
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Stella M. Lai
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
- Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Marius M. Kostelic
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
- Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Xinting Li
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Cameron M. Chow
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Lauren Carter
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Vicki H. Wysocki
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
- Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Barry L. Stoddard
- Division of Basic Sciences, Fred Hutchinson Cancer Center, Seattle, WA 98006, USA
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
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3
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Acharya S, Dahal A, Bhattarai HK. Evolution and origin of sliding clamp in bacteria, archaea and eukarya. PLoS One 2021; 16:e0241093. [PMID: 34379636 PMCID: PMC8357120 DOI: 10.1371/journal.pone.0241093] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Accepted: 07/07/2021] [Indexed: 11/18/2022] Open
Abstract
The replication of DNA is an essential process in all domains of life. A protein often involved in replication is the sliding clamp. The sliding clamp encircles the DNA and helps replicative polymerase stay attached to the replication machinery increasing the processivity of the polymerase. In eukaryotes and archaea, the sliding clamp is called the Proliferating Cell Nuclear Antigen (PCNA) and consists of two domains. This PCNA forms a trimer encircling the DNA as a hexamer. In bacteria, the structure of the sliding clamp is highly conserved, but the protein itself, called beta clamp, contains three domains, which dimerize to form a hexamer. The bulk of literature touts a conservation of the structure of the sliding clamp, but fails to recognize the conservation of protein sequence among sliding clamps. In this paper, we have used PSI blast to the second iteration in NCBI to show a statistically significant sequence homology between Pyrococcus furiosus PCNA and Kallipyga gabonensis beta clamp. The last two domains of beta clamp align with the two domains of PCNA. This homology data demonstrates that PCNA and beta clamp arose from a common ancestor. In this paper, we have further used beta clamp and PCNA sequences from diverse bacteria, archaea and eukarya to build maximum likelihood phylogenetic tree. Most, but not all, species in different domains of life harbor one sliding clamp from vertical inheritance. Some of these species that have two or more sliding clamps have acquired them from gene duplication or horizontal gene transfer events.
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Affiliation(s)
- Sandesh Acharya
- Department of Biotechnology, Kathmandu University, Dhulikhel, Nepal
| | - Amol Dahal
- Department of Biotechnology, Kathmandu University, Dhulikhel, Nepal
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4
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Abstract
Significant advances in enzyme discovery, protein and reaction engineering have transformed biocatalysis into a viable technology for the industrial scale manufacturing of chemicals. Multi-enzyme catalysis has emerged as a new frontier for the synthesis of complex chemicals. However, the in vitro operation of multiple enzymes simultaneously in one vessel poses challenges that require new strategies for increasing the operational performance of enzymatic cascade reactions. Chief among those strategies is enzyme co-immobilization. This review will explore how advances in synthetic biology and protein engineering have led to bioinspired co-localization strategies for the scaffolding and compartmentalization of enzymes. Emphasis will be placed on genetically encoded co-localization mechanisms as platforms for future autonomously self-organizing biocatalytic systems. Such genetically programmable systems could be produced by cell factories or emerging cell-free systems. Challenges and opportunities towards self-assembling, multifunctional biocatalytic materials will be discussed.
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5
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Sundaram R, Manohar K, Patel SK, Acharya N, Vasudevan D. Structural analyses of PCNA from the fungal pathogen Candida albicans identify three regions with species-specific conformations. FEBS Lett 2021; 595:1328-1349. [PMID: 33544878 DOI: 10.1002/1873-3468.14055] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 01/29/2021] [Accepted: 02/01/2021] [Indexed: 01/11/2023]
Abstract
An assembly of multiprotein complexes achieves chromosomal DNA replication at the replication fork. In eukaryotes, proliferating cell nuclear antigen (PCNA) plays a vital role in the assembly of multiprotein complexes at the replication fork and is essential for cell viability. PCNA from several organisms, including Saccharomyces cerevisiae, has been structurally characterised. However, the structural analyses of PCNA from fungal pathogens are limited. Recently, we have reported that PCNA from the opportunistic fungal pathogen Candida albicans complements the essential functions of ScPCNA in S. cerevisiae. Still, it only partially rescues the loss of ScPCNA when the yeast cells are under genotoxic stress. To understand this further, herein, we have determined the crystal structure of CaPCNA and compared that with the existing structures of other fungal and human PCNA. Our comparative structural and in-solution small-angle X-ray scattering (SAXS) analyses reveal that CaPCNA forms a stable homotrimer, both in crystal and in solution. It displays noticeable structural alterations in the oligomerisation interface, P-loop and hydrophobic pocket regions, suggesting its differential function in a heterologous system and avenues for developing specific therapeutics. DATABASES: The PDB and SASBDB accession codes for CaPCNA are 7BUP and SASDHQ9, respectively.
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Affiliation(s)
- Rajivgandhi Sundaram
- Laboratory of Macromolecular Crystallography, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, India.,Manipal Academy of Higher Education, India
| | - Kodavati Manohar
- Laboratory of Genomic Instability and Diseases, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, India
| | - Shraddheya Kumar Patel
- Laboratory of Genomic Instability and Diseases, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, India
| | - Narottam Acharya
- Laboratory of Genomic Instability and Diseases, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, India
| | - Dileep Vasudevan
- Laboratory of Macromolecular Crystallography, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, India
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6
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Cranford MT, Kaszubowski JD, Trakselis MA. A hand-off of DNA between archaeal polymerases allows high-fidelity replication to resume at a discrete intermediate three bases past 8-oxoguanine. Nucleic Acids Res 2020; 48:10986-10997. [PMID: 32997110 PMCID: PMC7641752 DOI: 10.1093/nar/gkaa803] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 08/22/2020] [Accepted: 09/16/2020] [Indexed: 01/12/2023] Open
Abstract
During DNA replication, the presence of 8-oxoguanine (8-oxoG) lesions in the template strand cause the high-fidelity (HiFi) DNA polymerase (Pol) to stall. An early response to 8-oxoG lesions involves ‘on-the-fly’ translesion synthesis (TLS), in which a specialized TLS Pol is recruited and replaces the stalled HiFi Pol for lesion bypass. The length of TLS must be long enough for effective bypass, but it must also be regulated to minimize replication errors by the TLS Pol. The exact position where the TLS Pol ends and the HiFi Pol resumes (i.e. the length of the TLS patch) has not been described. We use steady-state and pre-steady-state kinetic assays to characterize lesion bypass intermediates formed by different archaeal polymerase holoenzyme complexes that include PCNA123 and RFC. After bypass of 8-oxoG by TLS PolY, products accumulate at the template position three base pairs beyond the lesion. PolY is catalytically poor for subsequent extension from this +3 position beyond 8-oxoG, but this inefficiency is overcome by rapid extension of HiFi PolB1. The reciprocation of Pol activities at this intermediate indicates a defined position where TLS Pol extension is limited and where the DNA substrate is handed back to the HiFi Pol after bypass of 8-oxoG.
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Affiliation(s)
- Matthew T Cranford
- Baylor University, Department of Chemistry and Biochemistry, One Bear Place, #97348, Waco, TX 76798, USA
| | - Joseph D Kaszubowski
- Baylor University, Department of Chemistry and Biochemistry, One Bear Place, #97348, Waco, TX 76798, USA
| | - Michael A Trakselis
- Baylor University, Department of Chemistry and Biochemistry, One Bear Place, #97348, Waco, TX 76798, USA
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7
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Dynamics of the E. coli β-Clamp Dimer Interface and Its Influence on DNA Loading. Biophys J 2019; 117:587-601. [PMID: 31349986 DOI: 10.1016/j.bpj.2019.06.035] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 06/21/2019] [Accepted: 06/27/2019] [Indexed: 01/17/2023] Open
Abstract
The ring-shaped sliding clamp proteins have crucial roles in the regulation of DNA replication, recombination, and repair in all organisms. We previously showed that the Escherichia coli β-clamp is dynamic in solution, transiently visiting conformational states in which Domain 1 at the dimer interface is more flexible and prone to unfolding. This work aims to understand how the stability of the dimer interface influences clamp-opening dynamics and clamp loading by designing and characterizing stabilizing and destabilizing mutations in the clamp. The variants with stabilizing mutations conferred similar or increased thermostability and had similar quaternary structure as compared to the wild type. These variants stimulated the ATPase function of the clamp loader, complemented cell growth of a temperature-sensitive strain, and were successfully loaded onto a DNA substrate. The L82D and L82E I272A variants with purported destabilizing mutations had decreased thermostability, did not complement the growth of a temperature-sensitive strain, and had weakened dimerization as determined by native trapped ion mobility spectrometry-mass spectrometry. The β L82E variant had a reduced melting temperature but dimerized and complemented growth of a temperature-sensitive strain. All three clamps with destabilizing mutations had perturbed loading on DNA. Molecular dynamics simulations indicate altered hydrogen-bonding patterns at the dimer interface, and cross-correlation analysis showed the largest perturbations in the destabilized variants, consistent with the observed change in the conformations and functions of these clamps.
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8
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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] [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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9
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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: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [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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10
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Cranford MT, Chu AM, Baguley JK, Bauer RJ, Trakselis MA. Characterization of a coupled DNA replication and translesion synthesis polymerase supraholoenzyme from archaea. Nucleic Acids Res 2017; 45:8329-8340. [PMID: 28655184 PMCID: PMC5737361 DOI: 10.1093/nar/gkx539] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 06/12/2017] [Indexed: 02/04/2023] Open
Abstract
The ability of the replisome to seamlessly coordinate both high fidelity and translesion DNA synthesis requires a means to regulate recruitment and binding of enzymes from solution. Co-occupancy of multiple DNA polymerases within the replisome has been observed primarily in bacteria and is regulated by posttranslational modifications in eukaryotes, and both cases are coordinated by the processivity clamp. Because of the heterotrimeric nature of the PCNA clamp in some archaea, there is potential to occupy and regulate specific polymerases at defined subunits. In addition to specific PCNA and polymerase interactions (PIP site), we have now identified and characterized a novel protein contact between the Y-family DNA polymerase and the B-family replication polymerase (YB site) bound to PCNA and DNA from Sulfolobus solfataricus. These YB contacts are essential in forming and stabilizing a supraholoenzyme (SHE) complex on DNA, effectively increasing processivity of DNA synthesis. The SHE complex can not only coordinate polymerase exchange within the complex but also provides a mechanism for recruitment of polymerases from solution based on multiequilibrium processes. Our results provide evidence for an archaeal PCNA 'tool-belt' recruitment model of multienzyme function that can facilitate both high fidelity and translesion synthesis within the replisome during DNA replication.
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Affiliation(s)
- Matthew T Cranford
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX 76798, USA
| | - Aurea M Chu
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX 76798, USA
| | - Joshua K Baguley
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX 76798, USA
| | - Robert J Bauer
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Michael A Trakselis
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX 76798, USA
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11
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Trakselis MA, Cranford MT, Chu AM. Coordination and Substitution of DNA Polymerases in Response to Genomic Obstacles. Chem Res Toxicol 2017; 30:1956-1971. [PMID: 28881136 DOI: 10.1021/acs.chemrestox.7b00190] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The ability for DNA polymerases (Pols) to overcome a variety of obstacles in its path to maintain genomic stability during replication is a complex endeavor. It requires the coordination of multiple Pols with differing specificities through molecular control and access to the replisome. Although a number of contacts directly between Pols and accessory proteins have been identified, forming the basis of a variety of holoenzyme complexes, the dynamics of Pol active site substitutions remain uncharacterized. Substitutions can occur externally by recruiting new Pols to replisome complexes through an "exchange" of enzyme binding or internally through a "switch" in the engagement of DNA from preformed associated enzymes contained within supraholoenzyme complexes. Models for how high fidelity (HiFi) replication Pols can be substituted by translesion synthesis (TLS) Pols at sites of damage during active replication will be discussed. These substitution mechanisms may be as diverse as the number of Pol families and types of damage; however, common themes can be recognized across species. Overall, Pol substitutions will be controlled by explicit protein contacts, complex multiequilibrium processes, and specific kinetic activities. Insight into how these dynamic processes take place and are regulated will be of utmost importance for our greater understanding of the specifics of TLS as well as providing for future novel chemotherapeutic and antimicrobial strategies.
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Affiliation(s)
- Michael A Trakselis
- Department of Chemistry and Biochemistry, Baylor University , Waco, Texas 76798, United States
| | - Matthew T Cranford
- Department of Chemistry and Biochemistry, Baylor University , Waco, Texas 76798, United States
| | - Aurea M Chu
- Department of Chemistry and Biochemistry, Baylor University , Waco, Texas 76798, United States
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12
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Koç I, Caetano-Anollés G. The natural history of molecular functions inferred from an extensive phylogenomic analysis of gene ontology data. PLoS One 2017; 12:e0176129. [PMID: 28467492 PMCID: PMC5414959 DOI: 10.1371/journal.pone.0176129] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 04/05/2017] [Indexed: 11/18/2022] Open
Abstract
The origin and natural history of molecular functions hold the key to the emergence of cellular organization and modern biochemistry. Here we use a genomic census of Gene Ontology (GO) terms to reconstruct phylogenies at the three highest (1, 2 and 3) and the lowest (terminal) levels of the hierarchy of molecular functions, which reflect the broadest and the most specific GO definitions, respectively. These phylogenies define evolutionary timelines of functional innovation. We analyzed 249 free-living organisms comprising the three superkingdoms of life, Archaea, Bacteria, and Eukarya. Phylogenies indicate catalytic, binding and transport functions were the oldest, suggesting a 'metabolism-first' origin scenario for biochemistry. Metabolism made use of increasingly complicated organic chemistry. Primordial features of ancient molecular functions and functional recruitments were further distilled by studying the oldest child terms of the oldest level 1 GO definitions. Network analyses showed the existence of an hourglass pattern of enzyme recruitment in the molecular functions of the directed acyclic graph of molecular functions. Older high-level molecular functions were thoroughly recruited at younger lower levels, while very young high-level functions were used throughout the timeline. This pattern repeated in every one of the three mappings, which gave a criss-cross pattern. The timelines and their mappings were remarkable. They revealed the progressive evolutionary development of functional toolkits, starting with the early rise of metabolic activities, followed chronologically by the rise of macromolecular biosynthesis, the establishment of controlled interactions with the environment and self, adaptation to oxygen, and enzyme coordinated regulation, and ending with the rise of structural and cellular complexity. This historical account holds important clues for dissection of the emergence of biomcomplexity and life.
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Affiliation(s)
- Ibrahim Koç
- Molecular Biology and Genetics, Gebze Technical University, Kocaeli, Turkey
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, United States of America
| | - Gustavo Caetano-Anollés
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, United States of America
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13
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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] [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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14
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Wegrzyn KE, Gross M, Uciechowska U, Konieczny I. Replisome Assembly at Bacterial Chromosomes and Iteron Plasmids. Front Mol Biosci 2016; 3:39. [PMID: 27563644 PMCID: PMC4980987 DOI: 10.3389/fmolb.2016.00039] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 07/25/2016] [Indexed: 11/13/2022] Open
Abstract
The proper initiation and occurrence of DNA synthesis depends on the formation and rearrangements of nucleoprotein complexes within the origin of DNA replication. In this review article, we present the current knowledge on the molecular mechanism of replication complex assembly at the origin of bacterial chromosome and plasmid replicon containing direct repeats (iterons) within the origin sequence. We describe recent findings on chromosomal and plasmid replication initiators, DnaA and Rep proteins, respectively, and their sequence-specific interactions with double- and single-stranded DNA. Also, we discuss the current understanding of the activities of DnaA and Rep proteins required for replisome assembly that is fundamental to the duplication and stability of genetic information in bacterial cells.
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Affiliation(s)
- Katarzyna E Wegrzyn
- Department of Molecular and Cellular Biology, Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk Gdansk, Poland
| | - Marta Gross
- Department of Molecular and Cellular Biology, Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk Gdansk, Poland
| | - Urszula Uciechowska
- Department of Molecular and Cellular Biology, Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk Gdansk, Poland
| | - Igor Konieczny
- Department of Molecular and Cellular Biology, Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk Gdansk, Poland
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15
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Iwata F, Hirakawa H, Nagamune T. Three proliferating cell nuclear antigen homologues from Metallosphaera sedula form a head-to-tail heterotrimer. Sci Rep 2016; 6:26588. [PMID: 27228945 PMCID: PMC4894655 DOI: 10.1038/srep26588] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Accepted: 05/04/2016] [Indexed: 11/28/2022] Open
Abstract
Proliferating cell nuclear antigen (PCNA) is a sliding clamp that plays a key role in
DNA metabolism. Genome sequence analysis has revealed that some crenarchaea possess
three PCNA genes in their genome, but it has been reported that three PCNAs
do not always form a unique heterotrimer composed of one of each molecule. The
thermoacidophilic archaeon, Metallosphaera sedula, has three PCNA
homologue genes. Here, we demonstrated that the three PCNA homologues, MsePCNA1,
MsePCNA2 and MsePCNA3, exclusively form a heterotrimer in a stepwise fashion;
MsePCNA1 and MsePCNA2 form a heterodimer, and then MsePCNA3 binds to the
heterodimer. We determined that the dissociation constants between MsePCNA1 and
MsePCNA2, and between MsePCNA3 and the MsePCNA1:MsePCNA2 heterodimer are 0.29 and
43 nM, respectively. Moreover, the MsePCNA1, MsePCNA2 and MsePCNA3
heterotrimer stimulated M. sedula DNA ligase 1 activity, suggesting that the
heterotrimer works as a DNA sliding clamp in the organism. The stable and stepwise
heterotrimerization of M. sedula PCNA homologues would be useful to generate
functional protein-based materials such as artificial multi-enzyme complexes,
functional hydrogels and protein fibres, which have recently been achieved by
protein self-assembly.
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Affiliation(s)
- Fumiya Iwata
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Hidehiko Hirakawa
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Teruyuki Nagamune
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan.,Department of Bioengineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
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16
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PCNA-binding proteins in the archaea: novel functionality beyond the conserved core. Curr Genet 2016; 62:527-32. [PMID: 26886233 PMCID: PMC4929162 DOI: 10.1007/s00294-016-0577-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 02/06/2016] [Indexed: 11/30/2022]
Abstract
Sliding clamps play an essential role in coordinating protein activity in DNA metabolism in all three domains of life. In eukaryotes and archaea, the sliding clamp is PCNA (proliferating cell nuclear antigen). Across the diversity of the archaea PCNA interacts with a highly conserved set of proteins with key roles in DNA replication and repair, including DNA polymerases B and D, replication factor C, the Fen1 nuclease and RNAseH2, but this core set of factors is likely to represent a fraction of the PCNA interactome only. Here, I review three recently characterised non-core archaeal PCNA-binding proteins NusS, NreA/NreB and TIP, highlighting what is known of their interactions with PCNA and their functions in vivo and in vitro. Gaining a detailed understanding of the non-core PCNA interactome will provide significant insights into key aspects of chromosome biology in divergent archaeal lineages.
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17
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Abstract
DNA replication is essential for all life forms. Although the process is fundamentally conserved in the three domains of life, bioinformatic, biochemical, structural, and genetic studies have demonstrated that the process and the proteins involved in archaeal DNA replication are more similar to those in eukaryal DNA replication than in bacterial DNA replication, but have some archaeal-specific features. The archaeal replication system, however, is not monolithic, and there are some differences in the replication process between different species. In this review, the current knowledge of the mechanisms governing DNA replication in Archaea is summarized. The general features of the replication process as well as some of the differences are discussed.
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Affiliation(s)
- Lori M Kelman
- Program in Biotechnology, Montgomery College, Germantown, Maryland 20876;
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18
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Niiranen L, Lian K, Johnson KA, Moe E. Crystal structure of the DNA polymerase III β subunit (β-clamp) from the extremophile Deinococcus radiodurans. BMC STRUCTURAL BIOLOGY 2015; 15:5. [PMID: 25886944 PMCID: PMC4350885 DOI: 10.1186/s12900-015-0032-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Accepted: 02/13/2015] [Indexed: 02/08/2023]
Abstract
BACKGROUND Deinococcus radiodurans is an extremely radiation and desiccation resistant bacterium which can tolerate radiation doses up to 5,000 Grays without losing viability. We are studying the role of DNA repair and replication proteins for this unusual phenotype by a structural biology approach. The DNA polymerase III β subunit (β-clamp) acts as a sliding clamp on DNA, promoting the binding and processivity of many DNA-acting proteins, and here we report the crystal structure of D. radiodurans β-clamp (Drβ-clamp) at 2.0 Å resolution. RESULTS The sequence verification process revealed that at the time of the study the gene encoding Drβ-clamp was wrongly annotated in the genome database, encoding a protein of 393 instead of 362 amino acids. The short protein was successfully expressed, purified and used for crystallisation purposes in complex with Cy5-labeled DNA. The structure, which was obtained from blue crystals, shows a typical ring-shaped bacterial β-clamp formed of two monomers, each with three domains of identical topology, but with no visible DNA in electron density. A visualisation of the electrostatic surface potential reveals a highly negatively charged outer surface while the inner surface and the dimer forming interface have a more even charge distribution. CONCLUSIONS The structure of Drβ-clamp was determined to 2.0 Å resolution and shows an evenly distributed electrostatic surface charge on the DNA interacting side. We hypothesise that this charge distribution may facilitate efficient movement on encircled DNA and help ensure efficient DNA metabolism in D. radiodurans upon exposure to high doses of ionizing irradiation or desiccation.
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Affiliation(s)
- Laila Niiranen
- The Norwegian Structural Biology Center (NorStruct), Department of Chemistry, UIT - the Arctic University of Norway, N-9037, Tromsø, Norway.
| | - Kjersti Lian
- The Norwegian Structural Biology Center (NorStruct), Department of Chemistry, UIT - the Arctic University of Norway, N-9037, Tromsø, Norway.
| | - Kenneth A Johnson
- The Norwegian Structural Biology Center (NorStruct), Department of Chemistry, UIT - the Arctic University of Norway, N-9037, Tromsø, Norway.
| | - Elin Moe
- The Norwegian Structural Biology Center (NorStruct), Department of Chemistry, UIT - the Arctic University of Norway, N-9037, Tromsø, Norway. .,The Macromolecular Crystallography Unit, Instituto de Tecnologia Química e Biológica (ITQB), Universidade Nova de Lisboa, Oeiras, 2780-157, Portugal.
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19
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Protein-protein interactions leading to recruitment of the host DNA sliding clamp by the hyperthermophilic Sulfolobus islandicus rod-shaped virus 2. J Virol 2014; 88:7105-8. [PMID: 24696494 DOI: 10.1128/jvi.00636-14] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Viruses infecting hyperthermophilic archaea typically do not encode DNA polymerases, raising questions regarding their genome replication. Here, using a yeast two-hybrid approach, we have assessed interactions between proteins of Sulfolobus islandicus rod-shaped virus 2 (SIRV2) and the host-encoded proliferating cell nuclear antigen (PCNA), a key DNA replication protein in archaea. Five SIRV2 proteins were found to interact with PCNA, providing insights into the recruitment of host replisome for viral DNA replication.
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20
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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] [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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21
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Bauer RJ, Wolff ID, Zuo X, Lin HK, Trakselis MA. Assembly and distributive action of an archaeal DNA polymerase holoenzyme. J Mol Biol 2013; 425:4820-36. [PMID: 24035812 DOI: 10.1016/j.jmb.2013.09.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Revised: 09/03/2013] [Accepted: 09/04/2013] [Indexed: 11/25/2022]
Abstract
The assembly and enzymatic ability of the replication DNA polymerase holoenzyme from Sulfolobus solfataricus (Sso) was investigated using presteady-state fluorescence resonance energy transfer assays coupled with functional and structural studies. Kinetic experiments reveal that ATP binding to replication factor C (RFC) is sufficient for loading the heterotrimeric PCNA123 [proliferating cell nuclear antigen (PCNA)] clamp onto DNA that includes a rate-limiting conformational rearrangement of the complex. ATP hydrolysis is required for favorable recruitment and interactions with the replication polymerase (PolB1) that most likely include clamp closing and RFC dissociation. Surprisingly, the assembled holoenzyme complex synthesizes DNA distributively and with low processivity, unlike most other well-characterized DNA polymerase holoenzyme complexes. We show that PolB1 repeatedly disengages from the DNA template, leaving PCNA123 behind. Interactions with a newly identified C-terminal PCNA-interacting peptide (PIP) motif on PolB1 specifically with PCNA2 are required for holoenzyme formation and continuous re-recruitment during synthesis. The extended tail-like structure of the C-terminal PIP motif in PolB1 is revealed alone and when bound to DNA using small-angle X-ray scattering allowing us to develop a model for the holoenzyme complex. This is the first detailed kinetic description of clamp loading and holoenzyme assembly in crenarchaea and has revealed a novel mode for dynamic processivity that occurs by a polymerase exchange mechanism. This work has important implications for processive DNA replication synthesis and also suggests a potential mechanism for polymerase switching to bypass lesions.
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Affiliation(s)
- Robert J Bauer
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA
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22
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23
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Abstract
To achieve the high degree of processivity required for DNA replication, DNA polymerases associate with ring-shaped sliding clamps that encircle the template DNA and slide freely along it. The closed circular structure of sliding clamps necessitates an enzyme-catalyzed mechanism, which not only opens them for assembly and closes them around DNA, but specifically targets them to sites where DNA synthesis is initiated and orients them correctly for replication. Such a feat is performed by multisubunit complexes known as clamp loaders, which use ATP to open sliding clamp rings and place them around the 3' end of primer-template (PT) junctions. Here we discuss the structure and composition of sliding clamps and clamp loaders from the three domains of life as well as T4 bacteriophage, and provide our current understanding of the clamp-loading process.
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Affiliation(s)
- Mark Hedglin
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
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24
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Wang K, Shi Z, Zhang M, Cheng D. Structure of PCNA from Drosophila melanogaster. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:387-92. [PMID: 23545643 PMCID: PMC3614162 DOI: 10.1107/s1744309113004971] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2013] [Accepted: 02/20/2013] [Indexed: 11/10/2022]
Abstract
Proliferating cell nuclear antigen (PCNA) plays essential roles in DNA replication, DNA repair, cell-cycle regulation and chromatin metabolism. The PCNA from Drosophila melanogaster (DmPCNA) was purified and crystallized. The crystal of DmPCNA diffracted to 2.0 Å resolution and belonged to space group H3, with unit-cell parameters a = b = 151.16, c = 38.28 Å. The structure of DmPCNA was determined by molecular replacement. DmPCNA forms a symmetric homotrimer in a head-to-tail manner. An interdomain connector loop (IDCL) links the N- and C-terminal domains. Additionally, the N-terminal and C-terminal domains contact each other through hydrophobic associations. Compared with human PCNA, the IDCL of DmPCNA has conformational changes, which may explain their difference in function. This work provides a structural basis for further functional and evolutionary studies of PCNA.
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Affiliation(s)
- Ke Wang
- Department of Biology, Qingdao University, Qingdao, Shandong 266021, People’s Republic of China
| | - Zhubing Shi
- Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, People’s Republic of China
| | - Min Zhang
- School of Life Sciences, Anhui University, Hefei, Anhui 230039, People’s Republic of China
| | - Dianlin Cheng
- Department of Biology, Qingdao University, Qingdao, Shandong 266021, People’s Republic of China
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25
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Hirakawa H, Kakitani A, Nagamune T. Introduction of selective intersubunit disulfide bonds into self-assembly protein scaffold to enhance an artificial multienzyme complex's activity. Biotechnol Bioeng 2013; 110:1858-64. [DOI: 10.1002/bit.24861] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Revised: 01/24/2013] [Accepted: 01/28/2013] [Indexed: 11/09/2022]
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26
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XIE LIQUN, ZHENG YANMIN, LI XUAN, ZHAO JUNYAN, CHEN XIAOYI, CHEN LI, ZHOU JING, HAI OU, LI FEI. Enhanced proliferation of human hepatoma cells by PAR-2 agonists via the ERK/AP-1 pathway. Oncol Rep 2012; 28:1665-72. [DOI: 10.3892/or.2012.2007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2012] [Accepted: 07/13/2012] [Indexed: 11/06/2022] Open
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27
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Ishino Y, Ishino S. Rapid progress of DNA replication studies in Archaea, the third domain of life. SCIENCE CHINA-LIFE SCIENCES 2012; 55:386-403. [PMID: 22645083 DOI: 10.1007/s11427-012-4324-9] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2012] [Accepted: 04/20/2012] [Indexed: 02/04/2023]
Abstract
Archaea, the third domain of life, are interesting organisms to study from the aspects of molecular and evolutionary biology. Archaeal cells have a unicellular ultrastructure without a nucleus, resembling bacterial cells, but the proteins involved in genetic information processing pathways, including DNA replication, transcription, and translation, share strong similarities with those of Eukaryota. Therefore, archaea provide useful model systems to understand the more complex mechanisms of genetic information processing in eukaryotic cells. Moreover, the hyperthermophilic archaea provide very stable proteins, which are especially useful for the isolation of replisomal multicomplexes, to analyze their structures and functions. This review focuses on the history, current status, and future directions of archaeal DNA replication studies.
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Affiliation(s)
- Yoshizumi Ishino
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, Japan.
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28
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Beattie TR, Bell SD. Coordination of multiple enzyme activities by a single PCNA in archaeal Okazaki fragment maturation. EMBO J 2012; 31:1556-67. [PMID: 22307085 PMCID: PMC3321178 DOI: 10.1038/emboj.2012.12] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2011] [Accepted: 01/09/2012] [Indexed: 11/16/2022] Open
Abstract
In vitro reconstitution of Okazaki fragment processing shows that DNA polymerase, flap endonuclease and DNA ligase need to simultaneously bind to the same PCNA-sliding clamp molecule during DNA lagging strand replication. Chromosomal DNA replication requires one daughter strand—the lagging strand—to be synthesised as a series of discontinuous, RNA-primed Okazaki fragments, which must subsequently be matured into a single covalent DNA strand. Here, we describe the reconstitution of Okazaki fragment maturation in vitro using proteins derived from the archaeon Sulfolobus solfataricus. Six proteins are necessary and sufficient for coupled DNA synthesis, RNA primer removal and DNA ligation. PolB1, Fen1 and Lig1 provide the required catalytic activities, with coordination of their activities dependent upon the DNA sliding clamp, proliferating cell nuclear antigen (PCNA). S. solfataricus PCNA is a heterotrimer, with each subunit having a distinct specificity for binding PolB1, Fen1 or Lig1. Our data demonstrate that the most efficient coupling of activities occurs when a single PCNA ring organises PolB1, Fen1 and Lig1 into a complex.
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Affiliation(s)
- Thomas R Beattie
- Sir William Dunn School of Pathology, Oxford University, Oxford, UK
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29
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Dieckman LM, Freudenthal BD, Washington MT. PCNA structure and function: insights from structures of PCNA complexes and post-translationally modified PCNA. Subcell Biochem 2012; 62:281-99. [PMID: 22918591 DOI: 10.1007/978-94-007-4572-8_15] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Proliferating cell nuclear antigen (PCNA), the eukaryotic DNA sliding clamp, forms a ring-shaped homo-trimer that encircles double-stranded DNA. This protein is best known for its ability to confer high processivity to replicative DNA polymerases. However, it does far more than this, because it forms a mobile platform on the DNA that recruits many of the proteins involved in DNA replication, repair, and recombination to replication forks. X-ray crystal structures of PCNA bound to PCNA-binding proteins have provided insights into how PCNA recognizes its binding partners and recruits them to replication forks. More recently, X-ray crystal structures of ubiquitin-modified and SUMO-modified PCNA have provided insights into how these post-translational modifications alter the specificity of PCNA for some of its binding partners. This article focuses on the insights gained from structural studies of PCNA complexes and post-translationally modified PCNA.
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Affiliation(s)
- Lynne M Dieckman
- Department of Biochemistry, University of Iowa College of Medicine, Iowa City, IA, 52242-1109, USA
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30
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Kazlauskas D, Venclovas C. Computational analysis of DNA replicases in double-stranded DNA viruses: relationship with the genome size. Nucleic Acids Res 2011; 39:8291-305. [PMID: 21742758 PMCID: PMC3201878 DOI: 10.1093/nar/gkr564] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Genome duplication in free-living cellular organisms is performed by DNA replicases that always include a DNA polymerase, a DNA sliding clamp and a clamp loader. What are the evolutionary solutions for DNA replicases associated with smaller genomes? Are there some general principles? To address these questions we analyzed DNA replicases of double-stranded (ds) DNA viruses. In the process we discovered highly divergent B-family DNA polymerases in phiKZ-like phages and remote sliding clamp homologs in Ascoviridae family and Ma-LMM01 phage. The analysis revealed a clear dependency between DNA replicase components and the viral genome size. As the genome size increases, viruses universally encode their own DNA polymerases and frequently have homologs of DNA sliding clamps, which sometimes are accompanied by clamp loader subunits. This pattern is highly non-random. The absence of sliding clamps in large viral genomes usually coincides with the presence of atypical polymerases. Meanwhile, sliding clamp homologs, not accompanied by clamp loaders, have an elevated positive electrostatic potential, characteristic of non-ring viral processivity factors that bind the DNA directly. Unexpectedly, we found that similar electrostatic properties are shared by the eukaryotic 9-1-1 clamp subunits, Hus1 and, to a lesser extent, Rad9, also suggesting the possibility of direct DNA binding.
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Affiliation(s)
- Darius Kazlauskas
- Institute of Biotechnology, Vilnius University, Graičiūno 8, LT-02241 Vilnius, Lithuania
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31
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Kawai A, Hashimoto H, Higuchi S, Tsunoda M, Sato M, Nakamura KT, Miyamoto S. A novel heterotetrameric structure of the crenarchaeal PCNA2–PCNA3 complex. J Struct Biol 2011; 174:443-50. [PMID: 21352919 DOI: 10.1016/j.jsb.2011.02.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2010] [Revised: 02/02/2011] [Accepted: 02/17/2011] [Indexed: 11/27/2022]
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32
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Cardona-Felix CS, Lara-Gonzalez S, Brieba LG. Structure and biochemical characterization of proliferating cellular nuclear antigen from a parasitic protozoon. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2011; 67:497-505. [PMID: 21636889 DOI: 10.1107/s0907444911010547] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2011] [Accepted: 03/21/2011] [Indexed: 11/10/2022]
Abstract
Proliferating cellular nuclear antigen (PCNA) is a toroidal-shaped protein that is involved in cell-cycle control, DNA replication and DNA repair. Parasitic protozoa are early-diverged eukaryotes that are responsible for neglected diseases. In this work, a PCNA from a parasitic protozoon was identified, cloned and biochemically characterized and its crystal structure was determined. Structural and biochemical studies demonstrate that PCNA from Entamoeba histolytica assembles as a homotrimer that is able to interact with and stimulate the activity of a PCNA-interacting peptide-motif protein from E. histolytica, EhDNAligI. The data indicate a conservation of the biochemical mechanisms of PCNA-mediated interactions between metazoa, yeast and parasitic protozoa.
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Affiliation(s)
- Cesar S Cardona-Felix
- Grupo de Bioquímica Estructural, Laboratorio Nacional de Genomica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Km 9.6 Libramiento Norte, Carretera Irapuato-León, 36821 Irapuato, Guanajuato, México
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Abstract
PCNA (proliferating-cell nuclear antigen) is a ring-shaped protein that encircles duplex DNA and plays an essential role in many DNA metabolic processes. The PCNA protein interacts with a large number of cellular factors and modulates their enzymatic activities. In the present paper, we summarize the structures, functions and interactions of the archaeal PCNA proteins.
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Abstract
Most of the core components of the archaeal chromosomal DNA replication apparatus share significant protein sequence similarity with eukaryotic replication factors, making the Archaea an excellent model system for understanding the biology of chromosome replication in eukaryotes. The present review summarizes current knowledge of how the core components of the archaeal chromosome replication apparatus interact with one another to perform their essential functions.
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Capes MD, Coker JA, Gessler R, Grinblat-Huse V, DasSarma SL, Jacob CG, Kim JM, DasSarma P, DasSarma S. The information transfer system of halophilic archaea. Plasmid 2010; 65:77-101. [PMID: 21094181 DOI: 10.1016/j.plasmid.2010.11.005] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2010] [Revised: 11/08/2010] [Accepted: 11/15/2010] [Indexed: 10/18/2022]
Abstract
Information transfer is fundamental to all life forms. In the third domain of life, the archaea, many of the genes functioning in these processes are similar to their eukaryotic counterparts, including DNA replication and repair, basal transcription, and translation genes, while many transcriptional regulators and the overall genome structure are more bacterial-like. Among halophilic (salt-loving) archaea, the genomes commonly include extrachromosomal elements, many of which are large megaplasmids or minichromosomes. With the sequencing of genomes representing ten different genera of halophilic archaea and the availability of genetic systems in two diverse models, Halobacterium sp. NRC-1 and Haloferax volcanii, a large number of genes have now been annotated, classified, and studied. Here, we review the comparative genomic, genetic, and biochemical work primarily aimed at the information transfer system of halophilic archaea, highlighting gene conservation and differences in the chromosomes and the large extrachromosomal elements among these organisms.
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Affiliation(s)
- Melinda D Capes
- Department of Microbiology & Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
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36
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Hirakawa H, Nagamune T. Molecular assembly of P450 with ferredoxin and ferredoxin reductase by fusion to PCNA. Chembiochem 2010; 11:1517-20. [PMID: 20607777 DOI: 10.1002/cbic.201000226] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Hidehiko Hirakawa
- Department of Bioengineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
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37
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Oke M, Carter LG, Johnson KA, Liu H, McMahon SA, Yan X, Kerou M, Weikart ND, Kadi N, Sheikh MA, Schmelz S, Dorward M, Zawadzki M, Cozens C, Falconer H, Powers H, Overton IM, van Niekerk CAJ, Peng X, Patel P, Garrett RA, Prangishvili D, Botting CH, Coote PJ, Dryden DTF, Barton GJ, Schwarz-Linek U, Challis GL, Taylor GL, White MF, Naismith JH. The Scottish Structural Proteomics Facility: targets, methods and outputs. ACTA ACUST UNITED AC 2010; 11:167-80. [PMID: 20419351 PMCID: PMC2883930 DOI: 10.1007/s10969-010-9090-y] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2010] [Accepted: 04/06/2010] [Indexed: 12/19/2022]
Abstract
The Scottish Structural Proteomics Facility was funded to develop a laboratory scale approach to high throughput structure determination. The effort was successful in that over 40 structures were determined. These structures and the methods harnessed to obtain them are reported here. This report reflects on the value of automation but also on the continued requirement for a high degree of scientific and technical expertise. The efficiency of the process poses challenges to the current paradigm of structural analysis and publication. In the 5 year period we published ten peer-reviewed papers reporting structural data arising from the pipeline. Nevertheless, the number of structures solved exceeded our ability to analyse and publish each new finding. By reporting the experimental details and depositing the structures we hope to maximize the impact of the project by allowing others to follow up the relevant biology.
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Affiliation(s)
- Muse Oke
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST UK
| | - Lester G. Carter
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST UK
- Present Address: Stanford Synchrotron Radiation Light Source, 2575 Sand Hill Road, MS 69, Menlo Park, CA 94025 USA
| | - Kenneth A. Johnson
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST UK
- Present Address: The Norwegian Structural Biology Centre, University of Tromsø, 9037 Tromsø, Norway
| | - Huanting Liu
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST UK
| | - Stephen A. McMahon
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST UK
| | - Xuan Yan
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST UK
| | - Melina Kerou
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST UK
| | - Nadine D. Weikart
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST UK
- Present Address: Faculty of Chemistry, Technische Universität Dortmund, Otto-Hahn-Str. 6, 44227 Dortmund, Germany
| | - Nadia Kadi
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL UK
- Present Address: Institute of Cancer Research, 15 Cotswold Road, Belmont, Sutton, Surrey, SM2 5NG UK
| | - Md. Arif Sheikh
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST UK
| | - Stefan Schmelz
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST UK
| | - Mark Dorward
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST UK
- Present Address: Division of Signal Transduction Therapy, College of Life Sciences, University of Dundee, Dundee, DD1 5EH Scotland, UK
| | - Michal Zawadzki
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST UK
- Present Address: Syngenta Ltd, Jealott’s Hill International Research Centre, Bracknell, Berkshire, RG42 6EY UK
| | - Christopher Cozens
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST UK
- Present Address: Medical Research Council Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 0QH UK
| | - Helen Falconer
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST UK
- Present Address: Institute of Structural and Molecular Biology, Edinburgh University, Kings Buildings, Edinburgh, EH9 3JR UK
| | - Helen Powers
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST UK
| | - Ian M. Overton
- Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee, DD1 5EH Scotland, UK
- Present Address: MRC Human Genetics Unit, Crewe Road South, Edinburgh, EH4 2XU UK
| | - C. A. Johannes van Niekerk
- Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee, DD1 5EH Scotland, UK
| | - Xu Peng
- Department of Biology, Archaea Centre, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark
| | - Prakash Patel
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL UK
| | - Roger A. Garrett
- Department of Biology, Archaea Centre, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark
| | | | - Catherine H. Botting
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST UK
| | - Peter J. Coote
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST UK
| | - David T. F. Dryden
- EaStChem School of Chemistry, University of Edinburgh, The King’s Buildings, Edinburgh, EH9 3JJ UK
| | - Geoffrey J. Barton
- Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee, DD1 5EH Scotland, UK
| | - Ulrich Schwarz-Linek
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST UK
| | | | - Garry L. Taylor
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST UK
| | - Malcolm F. White
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST UK
| | - James H. Naismith
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST UK
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Hutton RD, Craggs TD, White MF, Penedo JC. PCNA and XPF cooperate to distort DNA substrates. Nucleic Acids Res 2009; 38:1664-75. [PMID: 20008103 PMCID: PMC2836553 DOI: 10.1093/nar/gkp1104] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
XPF is a structure-specific endonuclease that preferentially cleaves 3′ DNA flaps during a variety of repair processes. The crystal structure of a crenarchaeal XPF protein bound to a DNA duplex yielded insights into how XPF might recognise branched DNA structures, and recent kinetic data have demonstrated that the sliding clamp PCNA acts as an essential cofactor, possibly by allowing XPF to distort the DNA structure into a proper conformation for efficient cleavage to occur. Here, we investigate the solution structure of the 3′-flap substrate bound to XPF in the presence and absence of PCNA using intramolecular Förster resonance energy transfer (FRET). We demonstrate that recognition of the flap substrate by XPF involves major conformational changes of the DNA, including a 90° kink of the DNA duplex and organization of the single-stranded flap. In the presence of PCNA, there is a further substantial reorganization of the flap substrate bound to XPF, providing a structural basis for the observation that PCNA has an essential catalytic role in this system. The wider implications of these observations for the plethora of PCNA-dependent enzymes are discussed.
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Affiliation(s)
- Richard D Hutton
- Centre for Biomolecular Sciences and School of Physics and Astronomy, University of St Andrews, North Haugh, St Andrews, KY16 9SS, UK
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39
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Kawai A, Higuchi S, Tsunoda M, Nakamura KT, Miyamoto S. Purification, crystallization and preliminary X-ray analysis of the PCNA2-PCNA3 complex from Sulfolobus tokodaii strain 7. Acta Crystallogr Sect F Struct Biol Cryst Commun 2009; 65:1282-4. [PMID: 20054129 PMCID: PMC2802881 DOI: 10.1107/s1744309109044479] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2009] [Accepted: 10/26/2009] [Indexed: 11/10/2022]
Abstract
Crenarchaeal PCNA is known to consist of three subunits (PCNA1, PCNA2 and PCNA3) that form a heterotrimer (PCNA123). Recently, another heterotrimeric PCNA composed of only PCNA2 and PCNA3 was identified in Sulfolobus tokodaii strain 7 (stoPCNAs). In this study, the purified stoPCNA2-stoPCNA3 complex was crystallized by hanging-drop vapour diffusion. The crystals obtained belonged to the orthorhombic space groups I222 and P2(1)2(1)2, with unit-cell parameters a = 91.1, b = 111.8, c = 170.9 A and a = 91.1, b = 160.6, c = 116.6 A, respectively. X-ray diffraction data sets were collected to 2.90 A resolution for the I222 crystals and to 2.80 A resolution for the P2(1)2(1)2 crystals.
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Affiliation(s)
- Akito Kawai
- Faculty of Pharmaceutical Sciences, Sojo University, 4-22-1 Ikeda, Kumamoto 860-0082, Japan
| | - Shigesada Higuchi
- Faculty of Pharmaceutical Sciences, Sojo University, 4-22-1 Ikeda, Kumamoto 860-0082, Japan
| | - Masaru Tsunoda
- School of Pharmacy, Showa University, 1-5-8 Hatanodai, Shinagawa-ku, Tokyo 142-8555, Japan
- Faculty of Pharmacy, Iwaki Meisei University, Chuodai-iino, Iwaki 970-8551, Japan
| | - Kazuo T. Nakamura
- School of Pharmacy, Showa University, 1-5-8 Hatanodai, Shinagawa-ku, Tokyo 142-8555, Japan
| | - Shuichi Miyamoto
- Faculty of Pharmaceutical Sciences, Sojo University, 4-22-1 Ikeda, Kumamoto 860-0082, Japan
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40
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Byrne-Steele ML, Hughes RC, Ng JD. Recombinant production, crystallization and preliminary X-ray analysis of PCNA from the psychrophilic archaeon Methanococcoides burtonii DSM 6242. Acta Crystallogr Sect F Struct Biol Cryst Commun 2009; 65:1131-5. [PMID: 19923734 PMCID: PMC2777042 DOI: 10.1107/s1744309109037075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2009] [Accepted: 09/13/2009] [Indexed: 11/10/2022]
Abstract
Proliferating cell nuclear antigen (PCNA) is a DNA-clamping protein that is responsible for increasing the processivity of the replicative polymerases during DNA replication and repair. The PCNA from the eurypsychrophilic archaeon Methanococcoides burtonii DSM 6242 (MbPCNA) has been targeted for protein structural studies. A recombinant expression system has been created that overproduces MbPCNA with an N-terminal hexahistidine affinity tag in Escherichia coli. As a result, recombinant MbPCNA with a molecular mass of 28.3 kDa has been purified to at least 95% homogeneity and crystallized by vapor-diffusion equilibration. Preliminary X-ray analysis revealed a trigonal hexagonal R3 space group, with unit-cell parameters a = b = 102.5, c = 97.5 angstrom. A singleMbPCNA crystal was subjected to complete diffraction data-set collection using synchrotron radiation and reflections were measured to 2.40 angstrom resolution. The diffraction data were of suitable quality for indexing and scaling and an unrefined molecular-replacement solution has been obtained.
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41
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Morgunova E, Gray FC, Macneill SA, Ladenstein R. Structural insights into the adaptation of proliferating cell nuclear antigen (PCNA) from Haloferax volcanii to a high-salt environment. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2009; 65:1081-8. [PMID: 19770505 PMCID: PMC2756170 DOI: 10.1107/s0907444909029321] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2009] [Accepted: 07/23/2009] [Indexed: 11/10/2022]
Abstract
The sliding clamp proliferating cell nuclear antigen (PCNA) plays vital roles in many aspects of DNA replication and repair in eukaryotic cells and in archaea. Realising the full potential of archaea as a model for PCNA function requires a combination of biochemical and genetic approaches. In order to provide a platform for subsequent reverse genetic analysis, PCNA from the halophilic archaeon Haloferax volcanii was subjected to crystallographic analysis. The gene was cloned and expressed in Escherichia coli and the protein was purified by affinity chromatography and crystallized by the vapour-diffusion technique. The structure was determined by molecular replacement and refined at 3.5 A resolution to a final R factor of 23.7% (R(free) = 25%). PCNA from H. volcanii was found to be homotrimeric and to resemble other homotrimeric PCNA clamps but with several differences that appear to be associated with adaptation of the protein to the high intracellular salt concentrations found in H. volcanii cells.
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Affiliation(s)
- Ekaterina Morgunova
- Karolinska Institutet, NOVUM, Centre of Structural Biochemistry, S-14157 Huddinge, Sweden.
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42
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Byrne-Steele ML, Ng JD. Expression, purification and preliminary X-ray analysis of proliferating cell nuclear antigen from the archaeon Thermococcus thioreducens. Acta Crystallogr Sect F Struct Biol Cryst Commun 2009; 65:906-9. [PMID: 19724129 PMCID: PMC2795597 DOI: 10.1107/s174430910903036x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2009] [Accepted: 07/30/2009] [Indexed: 11/10/2022]
Abstract
Proliferating cell nuclear antigen (PCNA) is a DNA sliding clamp which confers processivity on replicative DNA polymerases. PCNA also acts as a sliding platform that enables the association of many DNA-processing proteins with DNA in a non-sequence-specific manner. In this investigation, the PCNA from the hyperthermophilic archaeon Thermococcus thioreducens (TtPCNA) was cloned, overexpressed in Escherichia coli and purified to greater than 90% homogeneity. TtPCNA crystals were obtained by sitting-drop vapor-diffusion methods and the best ordered crystal diffracted to 1.86 A resolution using synchrotron radiation. The crystals belonged to the hexagonal space group P6(3), with unit-cell parameters a = b = 89.0, c = 62.8 A. Crystals of TtPCNA proved to be amenable to complete X-ray analysis and future structure determination.
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Affiliation(s)
- Miranda L. Byrne-Steele
- Laboratory for Structural Biology, Department of Biological Sciences, University of Alabama in Huntsville, Huntsville, AL 35899, USA
| | - Joseph D. Ng
- Laboratory for Structural Biology, Department of Biological Sciences, University of Alabama in Huntsville, Huntsville, AL 35899, USA
- ExtremoZyme Inc., HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL 35806, USA
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43
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Zhuang Z, Ai Y. Processivity factor of DNA polymerase and its expanding role in normal and translesion DNA synthesis. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2009; 1804:1081-93. [PMID: 19576301 DOI: 10.1016/j.bbapap.2009.06.018] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2009] [Revised: 06/16/2009] [Accepted: 06/22/2009] [Indexed: 11/30/2022]
Abstract
Clamp protein or clamp, initially identified as the processivity factor of the replicative DNA polymerase, is indispensable for the timely and faithful replication of DNA genome. Clamp encircles duplex DNA and physically interacts with DNA polymerase. Clamps from different organisms share remarkable similarities in both structure and function. Loading of clamp onto DNA requires the activity of clamp loader. Although all clamp loaders act by converting the chemical energy derived from ATP hydrolysis to mechanical force, intriguing differences exist in the mechanistic details of clamp loading. The structure and function of clamp in normal and translesion DNA synthesis has been subjected to extensive investigations. This review summarizes the current understanding of clamps from three kingdoms of life and the mechanism of loading by their cognate clamp loaders. We also discuss the recent findings on the interactions between clamp and DNA, as well as between clamp and DNA polymerase (both the replicative and specialized DNA polymerases). Lastly the role of clamp in modulating polymerase exchange is discussed in the context of translesion DNA synthesis.
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Affiliation(s)
- Zhihao Zhuang
- Department of Chemistry and Biochemistry, 214A Drake Hall, University of Delaware, Newark, DE, 19716, USA.
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44
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Bloom LB. Loading clamps for DNA replication and repair. DNA Repair (Amst) 2009; 8:570-8. [PMID: 19213612 DOI: 10.1016/j.dnarep.2008.12.014] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2008] [Accepted: 12/19/2008] [Indexed: 01/25/2023]
Abstract
Sliding clamps and clamp loaders were initially identified as DNA polymerase processivity factors. Sliding clamps are ring-shaped protein complexes that encircle and slide along duplex DNA, and clamp loaders are enzymes that load these clamps onto DNA. When bound to a sliding clamp, DNA polymerases remain tightly associated with the template being copied, but are able to translocate along DNA at rates limited by rates of nucleotide incorporation. Many different enzymes required for DNA replication and repair use sliding clamps. Clamps not only increase the processivity of these enzymes, but may also serve as an attachment point to coordinate the activities of enzymes required for a given process. Clamp loaders are members of the AAA+ family of ATPases and use energy from ATP binding and hydrolysis to catalyze the mechanical reaction of loading clamps onto DNA. Many structural and functional features of clamps and clamp loaders are conserved across all domains of life. Here, the mechanism of clamp loading is reviewed by comparing features of prokaryotic and eukaryotic clamps and clamp loaders.
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Affiliation(s)
- Linda B Bloom
- Department of Biochemistry & Molecular Biology, University of Florida, Gainesville, FL 32610-0245, United States.
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45
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Lu S, Li Z, Wang Z, Ma X, Sheng D, Ni J, Shen Y. Spatial subunit distribution and in vitro functions of the novel trimeric PCNA complex from Sulfolobus tokodaii. Biochem Biophys Res Commun 2008; 376:369-74. [DOI: 10.1016/j.bbrc.2008.08.150] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2008] [Accepted: 08/29/2008] [Indexed: 10/21/2022]
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46
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Hutton RD, Roberts JA, Penedo JC, White MF. PCNA stimulates catalysis by structure-specific nucleases using two distinct mechanisms: substrate targeting and catalytic step. Nucleic Acids Res 2008; 36:6720-7. [PMID: 18948279 PMCID: PMC2588518 DOI: 10.1093/nar/gkn745] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The sliding clamp Proliferating Cell Nuclear Antigen (PCNA) functions as a recruiter and organizer of a wide variety of DNA modifying enzymes including nucleases, helicases, polymerases and glycosylases. The 5'-flap endonuclease Fen-1 is essential for Okazaki fragment processing in eukaryotes and archaea, and is targeted to the replication fork by PCNA. Crenarchaeal XPF, a 3'-flap endonuclease, is also stimulated by PCNA in vitro. Using a novel continuous fluorimetric assay, we demonstrate that PCNA activates these two nucleases by fundamentally different mechanisms. PCNA stimulates Fen-1 by increasing the enzyme's binding affinity for substrates, as suggested previously. However, PCNA activates XPF by increasing the catalytic rate constant by four orders of magnitude without affecting the K(M). PCNA may function as a platform upon which XPF exerts force to distort DNA substrates, destabilizing the substrate and/or stabilizing the transition state structure. This suggests that PCNA can function directly in supporting catalysis as an essential cofactor in some circumstances, a new role for a protein that is generally assumed to perform a passive targeting and organizing function in molecular biology. This could provide a mechanism for the exquisite control of nuclease activity targeted to specific circumstances, such as replication forks or damaged DNA with pre-loaded PCNA.
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Affiliation(s)
- Richard D Hutton
- Centre for Biomolecular Sciences and School of Physics, University of St Andrews, Fife, UK
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47
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Hlinkova V, Xing G, Bauer J, Shin YJ, Dionne I, Rajashankar KR, Bell SD, Ling H. Structures of monomeric, dimeric and trimeric PCNA: PCNA-ring assembly and opening. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2008; 64:941-9. [PMID: 18703842 PMCID: PMC3606083 DOI: 10.1107/s0907444908021665] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2008] [Accepted: 07/11/2008] [Indexed: 11/10/2022]
Abstract
DNA sliding clamps form an oligomeric ring encircling DNA and serve as a moving platform for DNA-processing proteins. The opening and closing of a sliding-clamp ring is essential to load the clamp onto DNA in order to perform its functions. The molecular details of how clamp rings open and enclose DNA are still not clear. Three PCNA homologues have been found in Sulfolobus solfataricus which form a heterotrimer. Taking advantage of their hetero-oligomeric nature, the structures of the PCNAs in monomeric PCNA3, dimeric PCNA1-PCNA2 and trimeric PCNA1-PCNA2-PCNA3 forms were determined at resolutions of 2.6-1.9 A. The distinct oligomeric structures represent different stages in ring formation, which were verified in solution by ultracentrifugation analysis. The heterodimer opens in a V-shape of 130 degrees , while the heterotrimers form a ring with a 120 degrees rotation between monomers. The association of a rigid PCNA3 monomer with an opened PCNA1-PCNA2 heterodimer closes the ring and introduces a spring tension in the PCNA1-PCNA2 interface, thus bending the nine-stranded intermolecular beta-sheet to fit the 120 degrees rotation. The release of the spring tension as PCNA3 dissociates from the ring may facilitate ring opening. The structural features in different assemblies present a molecular model for clamp ring assembly and opening.
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Affiliation(s)
- Vladena Hlinkova
- Department of Biochemistry, University of Western Ontario, London, Ontario N6A 5C1, Canada
| | - Guangxin Xing
- Department of Biochemistry, University of Western Ontario, London, Ontario N6A 5C1, Canada
| | - Jacob Bauer
- Department of Biochemistry, University of Western Ontario, London, Ontario N6A 5C1, Canada
| | - Yoon Jung Shin
- Department of Biochemistry, University of Western Ontario, London, Ontario N6A 5C1, Canada
| | - Isabelle Dionne
- The Medical Research Council Cancer Cell Unit, Hutchison MRC Centre, Hills Road, Cambridge CB2 2XZ, England
| | | | - Stephen D. Bell
- The Medical Research Council Cancer Cell Unit, Hutchison MRC Centre, Hills Road, Cambridge CB2 2XZ, England
| | - Hong Ling
- Department of Biochemistry, University of Western Ontario, London, Ontario N6A 5C1, Canada
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48
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Deletion of dnaN1 generates a mutator phenotype in Bacillus anthracis. DNA Repair (Amst) 2008; 7:507-14. [PMID: 18242150 DOI: 10.1016/j.dnarep.2007.10.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2007] [Revised: 10/05/2007] [Accepted: 10/15/2007] [Indexed: 11/22/2022]
Abstract
The dnaN gene in eubacteria is an essential gene that encodes the beta subunit of replicative DNA polymerase. Nearly all eubacterial genomes sequenced to date predict a single copy of the dnaN gene in a well-conserved neighboring gene context. However, 19 genomes out of 348 scanned, including Bacillus anthracis, Bacillus cereus, Bacillus thuringiensis, and Bacillus weihenstephanensis, predict more than one dnaN gene. In most cases, these genomes appear to maintain a copy of the dnaN homolog in its usual neighboring gene context (designated as dnaN1) in addition to a second copy (designated as dnaN2) in an entirely different gene context. We used B. anthracis as our model system to investigate the role of these DnaNs. We constructed a single knockout mutant of dnaN1 and of dnaN2; however, we could not make a viable double knockout mutant of dnaN1 and dnaN2. The dnaN1 knockout mutant displays a markedly reduced colony size. It also displays a significantly increased mutation rate, which is similar to that of a mismatch repair deficient strain and to a strain deficient both in dnaN1 and mismatch repair. The dnaN2 knockout mutant, however, has a similar growth rate and a comparable mutation rate to that of the wild type. This is the first study demonstrating the existence of two functional DnaN homologs in the B. anthracis genome, with DnaN1 appearing to be more crucial than DnaN2. Our results also suggest the direct involvement of DnaN1 in the DNA mismatch repair process, which is consistent with previous findings.
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Crystal structure of vaccinia virus uracil-DNA glycosylase reveals dimeric assembly. BMC STRUCTURAL BIOLOGY 2007; 7:45. [PMID: 17605817 PMCID: PMC1936997 DOI: 10.1186/1472-6807-7-45] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/03/2007] [Accepted: 07/02/2007] [Indexed: 11/13/2022]
Abstract
Background Uracil-DNA glycosylases (UDGs) catalyze excision of uracil from DNA. Vaccinia virus, which is the prototype of poxviruses, encodes a UDG (vvUDG) that is significantly different from the UDGs of other organisms in primary, secondary and tertiary structure and characteristic motifs. It adopted a novel catalysis-independent role in DNA replication that involves interaction with a viral protein, A20, to form the processivity factor. UDG:A20 association is essential for assembling of the processive DNA polymerase complex. The structure of the protein must have provisions for such interactions with A20. This paper provides the first glimpse into the structure of a poxvirus UDG. Results Results of dynamic light scattering experiments and native size exclusion chromatography showed that vvUDG is a dimer in solution. The dimeric assembly is also maintained in two crystal forms. The core of vvUDG is reasonably well conserved but the structure contains one additional β-sheet at each terminus. A glycerol molecule is found in the active site of the enzyme in both crystal forms. Interaction of this glycerol molecule with the protein possibly mimics the enzyme-substrate (uracil) interactions. Conclusion The crystal structures reveal several distinctive features of vvUDG. The new structural features may have evolved for adopting novel functions in the replication machinery of poxviruses. The mode of interaction between the subunits in the dimers suggests a possible model for binding to its partner and the nature of the processivity factor in the polymerase complex.
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Imamura K, Fukunaga K, Kawarabayasi Y, Ishino Y. Specific interactions of three proliferating cell nuclear antigens with replication-related proteins in Aeropyrum pernix. Mol Microbiol 2007; 64:308-18. [PMID: 17493121 DOI: 10.1111/j.1365-2958.2007.05645.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Proliferating cell nuclear antigen (PCNA) is a well-known multifunctional protein involved in eukaryotic and archaeal DNA transactions. The homotrimeric PCNA ring encircles double-stranded DNA within its central hole and tethers many proteins on DNA. Plural genes encoding PCNA-like proteins have been found in the genome sequence of crenarchaeal organisms. We describe here the biochemical properties of the three PCNAs, PCNA1, PCNA2 and PCNA3, from the hyperthermophilic archaeon, Aeropyrum pernix. PCNA2 can form a trimeric structure by itself, and it also forms heterotrimeric structures with PCNA1 and PCNA3. However, neither PCNA1 nor PCNA3 can form homotrimers. The DNA synthesis activity of DNA polymerase I and II, the endonuclease activity of FEN1, and the nick-sealing activity of DNA ligase were stimulated by the complex of PCNA2 and 3 or PCNA1, 2 and 3. These results suggest that the heterotrimeric PCNA at least including PCNA2 and 3 function as the clamp in the replisome. However, PCNA2 is the most abundant in the cells throughout the growth stages among the three PCNAs, and therefore, PCNA2 may perform multitasks by changing complex composition.
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Affiliation(s)
- Kaori Imamura
- Department of Genetic Resources Technology, Faculty of Agriculture, Kyushu University, 6-10-1 Hakozaki, Fukuoka-shi, Fukuoka 812-8581, Japan
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