1
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Kuper J, Hove T, Maidl S, Neitz H, Sauer F, Kempf M, Schroeder T, Greiter E, Höbartner C, Kisker C. XPD stalled on cross-linked DNA provides insight into damage verification. Nat Struct Mol Biol 2024:10.1038/s41594-024-01323-5. [PMID: 38806694 DOI: 10.1038/s41594-024-01323-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Accepted: 04/24/2024] [Indexed: 05/30/2024]
Abstract
The superfamily 2 helicase XPD is a central component of the general transcription factor II H (TFIIH), which is essential for transcription and nucleotide excision DNA repair (NER). Within these two processes, the helicase function of XPD is vital for NER but not for transcription initiation, where XPD acts only as a scaffold for other factors. Using cryo-EM, we deciphered one of the most enigmatic steps in XPD helicase action: the active separation of double-stranded DNA (dsDNA) and its stalling upon approaching a DNA interstrand cross-link, a highly toxic form of DNA damage. The structure shows how dsDNA is separated and reveals a highly unusual involvement of the Arch domain in active dsDNA separation. Combined with mutagenesis and biochemical analyses, we identified distinct functional regions important for helicase activity. Surprisingly, those areas also affect core TFIIH translocase activity, revealing a yet unencountered function of XPD within the TFIIH scaffold. In summary, our data provide a universal basis for NER bubble formation, XPD damage verification and XPG incision.
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Affiliation(s)
- Jochen Kuper
- Rudolf Virchow Center for Integrative and Translational Bioimaging, University of Würzburg, Würzburg, Germany.
| | - Tamsanqa Hove
- Rudolf Virchow Center for Integrative and Translational Bioimaging, University of Würzburg, Würzburg, Germany
| | - Sarah Maidl
- Rudolf Virchow Center for Integrative and Translational Bioimaging, University of Würzburg, Würzburg, Germany
| | - Hermann Neitz
- Institute of Organic Chemistry, University of Würzburg, Würzburg, Germany
| | - Florian Sauer
- Rudolf Virchow Center for Integrative and Translational Bioimaging, University of Würzburg, Würzburg, Germany
| | - Maximilian Kempf
- Rudolf Virchow Center for Integrative and Translational Bioimaging, University of Würzburg, Würzburg, Germany
| | - Till Schroeder
- Rudolf Virchow Center for Integrative and Translational Bioimaging, University of Würzburg, Würzburg, Germany
| | - Elke Greiter
- Rudolf Virchow Center for Integrative and Translational Bioimaging, University of Würzburg, Würzburg, Germany
| | - Claudia Höbartner
- Institute of Organic Chemistry, University of Würzburg, Würzburg, Germany
- Center for Nanosystems Chemistry (CNC), University of Würzburg, Würzburg, Germany
| | - Caroline Kisker
- Rudolf Virchow Center for Integrative and Translational Bioimaging, University of Würzburg, Würzburg, Germany.
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2
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Mao C, Mills M. Characterization of human XPD helicase activity with single-molecule magnetic tweezers. Biophys J 2024; 123:260-271. [PMID: 38111195 PMCID: PMC10808040 DOI: 10.1016/j.bpj.2023.12.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 06/02/2023] [Accepted: 12/13/2023] [Indexed: 12/20/2023] Open
Abstract
XPD helicase is a DNA-unwinding enzyme involved in DNA repair. As part of TFIIH, XPD opens a repair bubble in DNA for access by proteins in the nucleotide excision repair pathway. XPD uses the energy from ATP hydrolysis to translocate in the 5' to 3' direction on one strand of duplex DNA, displacing the opposite strand in the process. We used magnetic tweezers assays to measure the double-stranded DNA unwinding and single-stranded DNA translocation activities of human XPD in isolation. In our experimental setup, hXPD exhibited low unwinding processivity of ∼14 bp and slow unwinding rate of ∼0.3 bp/s. Measurements of the ssDNA translocation activity demonstrated that hXPD translocated on ssDNA at a similar rate as unwinding, revealing that slow rate was an intrinsic property of the hXPD translocation. Individual unwinding and translocation events were composed of pauses and runs with a distribution of lengths and rates. Analysis of these events unveiled similar mean run lengths and rates for unwinding and translocation, indicating that the unwinding behavior was a direct reflection of the translocation activity. The analysis also revealed that hXPD spent similar time stalling and unwinding/translocating. The detailed basal activity of hXPD reported here provides a baseline for future studies on how hXPD activity is regulated by other TFIIH components.
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Affiliation(s)
- Chunfeng Mao
- Department of Physics and Astronomy, University of Missouri, Columbia, Missouri
| | - Maria Mills
- Department of Physics and Astronomy, University of Missouri, Columbia, Missouri.
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3
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Loup-Forest J, Matuchet M, Schnitzler C, Pichard S, Poterszman A. A Time and Cost-Effective Pipeline for Expression Screening and Protein Production in Insect Cells Based on the HR-Bac Toolbox to Generate Recombinant Baculoviruses. Methods Mol Biol 2024; 2829:21-48. [PMID: 38951325 DOI: 10.1007/978-1-0716-3961-0_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/03/2024]
Abstract
The baculovirus expression vector system (BEVS) is recognized as a powerful platform for producing challenging proteins and multiprotein complexes both in academia and industry. Since a baculovirus was first used to produce heterologous human IFN-β protein in insect cells, the BEVS has continuously been developed and its applications expanded. We have recently established a multigene expression toolbox (HR-bac) composed of a set of engineered bacmids expressing a fluorescent marker to monitor virus propagation and a library of transfer vectors. Unlike platforms that rely on Tn7-medidated transposition for the construction of baculoviruses, HR-bac relies on homologous recombination, which allows to evaluate expression constructs in 2 weeks and is thus perfectly adapted to parallel expression screening. In this chapter, we detail our standard operating procedures for the preparation of the reagents, the construction and evaluation of baculoviruses, and the optimization of protein production for both intracellularly expressed and secreted proteins.
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Affiliation(s)
- Jules Loup-Forest
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Integrated Structural Biology Department, Center for Integrated Structural Biology (CBI), Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France
- Université de Strasbourg, Equipe labellisée Ligue Contre le Cancer, BP, Illkirch, France
| | - Manon Matuchet
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Integrated Structural Biology Department, Center for Integrated Structural Biology (CBI), Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France
- Université de Strasbourg, Equipe labellisée Ligue Contre le Cancer, BP, Illkirch, France
| | - Charlotte Schnitzler
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Integrated Structural Biology Department, Center for Integrated Structural Biology (CBI), Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France
- Université de Strasbourg, Equipe labellisée Ligue Contre le Cancer, BP, Illkirch, France
| | - Simon Pichard
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Integrated Structural Biology Department, Center for Integrated Structural Biology (CBI), Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France
- Université de Strasbourg, Equipe labellisée Ligue Contre le Cancer, BP, Illkirch, France
| | - Arnaud Poterszman
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Integrated Structural Biology Department, Center for Integrated Structural Biology (CBI), Illkirch, France.
- Centre National de la Recherche Scientifique, UMR7104, Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France.
- Université de Strasbourg, Equipe labellisée Ligue Contre le Cancer, BP, Illkirch, France.
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4
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Mao C, Mills M. Characterization of human XPD helicase activity with Single Molecule Magnetic Tweezers. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.07.527508. [PMID: 36798221 PMCID: PMC9934580 DOI: 10.1101/2023.02.07.527508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
XPD helicase is a DNA unwinding enzyme involved in multiple cellular processes. As part of TFIIH, XPD opens a repair bubble in DNA for access by proteins in the nucleotide excision repair pathway. XPD uses the energy from ATP hydrolysis to translocate in the 5-prime to 3-prime direction on one strand of duplex DNA, displacing the opposite strand in the process. We used magnetic tweezers assays to measure the double-stranded DNA (dsDNA) unwinding and single-stranded DNA (ssDNA) translocation activities of human XPD by itself. In our experimental setup, hXPD exhibits low unwinding processivity of ~14 bp and slow overall unwinding rate of ~0.3 bp/s. Individual unwinding and translocation events were composed of fast and slow runs and pauses. Analysis of these events gave similar mean run sizes and rates for unwinding and translocation, suggesting that unwinding is a reflection of translocation. The analysis also revealed that hXPD spent similar time stalling and unwinding. hXPD translocated on ssDNA at a similar overall rate as that of unwinding, pointing to an active helicase. However, we observed modest effects of DNA sequence on stalling and unwinding initiation position. Considering the slow unwinding rate, high probability of base pair separation at the ssDNA/dsDNA fork, and the observed DNA sequence dependences, we propose that hXPD is most likely a partially active helicase. Our results provide detailed information on the basal activity of hXPD which enhances our mechanistic understanding of hXPD activity.
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5
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Pichard S, Troffer-Charlier N, Kolb-Cheynel I, Poussin-Courmontagne P, Abdulrahman W, Birck C, Cura V, Poterszman A. Insect Cells-Baculovirus System for the Production of Difficult to Express Proteins: From Expression Screening for Soluble Constructs to Protein Quality Control. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2406:281-317. [PMID: 35089564 DOI: 10.1007/978-1-0716-1859-2_17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Rapid preparation of proteins for functional and structural analysis is a major challenge both in academia and industry. The number potential targets continuously increases and many are difficult to express proteins which, when produced in bacteria, result in insoluble and/or misfolded recombinant proteins, protein aggregates, or unusable low protein yield. We focus here on the baculovirus expression vector system which is now commonly used for heterologous production of human targets. This chapter describes simple and cost-effective protocols that enable iterative cycles of construct design, expression screening and optimization of protein production. We detail time- and cost-effective methods for generation of baculoviruses by homologous recombination and titer evaluation. Handling of insect cell cultures and preparation of bacmid for cotransfection are also presented.
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Affiliation(s)
- Simon Pichard
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Center for Integrated Structural Biology (CBI), Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), Université de Strasbourg, Illkirch, France
| | - Nathalie Troffer-Charlier
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Center for Integrated Structural Biology (CBI), Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), Université de Strasbourg, Illkirch, France
| | - Isabelle Kolb-Cheynel
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Center for Integrated Structural Biology (CBI), Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), Université de Strasbourg, Illkirch, France
| | - Pierre Poussin-Courmontagne
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Center for Integrated Structural Biology (CBI), Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), Université de Strasbourg, Illkirch, France
| | | | - Catherine Birck
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Center for Integrated Structural Biology (CBI), Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), Université de Strasbourg, Illkirch, France
| | - Vincent Cura
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Center for Integrated Structural Biology (CBI), Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), Université de Strasbourg, Illkirch, France
| | - Arnaud Poterszman
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Center for Integrated Structural Biology (CBI), Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), Université de Strasbourg, Illkirch, France.
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6
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Kolesnikova O, Zachayus A, Pichard S, Osz J, Rochel N, Rossolillo P, Kolb-Cheynel I, Troffer-Charlier N, Compe E, Bensaude O, Berger I, Poterszman A. HR-Bac, a toolbox based on homologous recombination for expression, screening and production of multiprotein complexes using the baculovirus expression system. Sci Rep 2022; 12:2030. [PMID: 35132103 PMCID: PMC8821708 DOI: 10.1038/s41598-021-04715-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Accepted: 11/25/2021] [Indexed: 11/09/2022] Open
Abstract
The Baculovirus/insect cell expression system is a powerful technology for reconstitution of eukaryotic macromolecular assemblies. Most multigene expression platforms rely on Tn7-mediated transposition for transferring the expression cassette into the baculoviral genome. This allows a rigorous characterization of recombinant bacmids but involves multiple steps, a limitation when many constructs are to be tested. For parallel expression screening and potential high throughput applications, we have established an open source multigene-expression toolbox exploiting homologous recombination, thus reducing the recombinant baculovirus generation to a single-step procedure and shortening the time from cloning to protein production to 2 weeks. The HR-bac toolbox is composed of a set of engineered bacmids expressing a fluorescent marker to monitor virus propagation and a library of transfer vectors. They contain single or dual expression cassettes bearing different affinity tags and their design facilitates the mix and match utilization of expression units from Multibac constructs. The overall cost of virus generation with HR-bac toolbox is relatively low as the preparation of linearized baculoviral DNA only requires standard reagents. Various multiprotein assemblies (nuclear hormone receptor heterodimers, the P-TEFb or the ternary CAK kinase complex associated with the XPD TFIIH subunit) are used as model systems to validate the toolbox presented.
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Affiliation(s)
- Olga Kolesnikova
- Institute of Genetics and of Molecular and Cellular Biology (IGBMC), 1 rue Laurent Fries, Illkirch, France.,Centre National de la Recherche Scientifique (CNRS), UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (Inserm), U964, Illkirch, France.,Université de Strasbourg, Illkirch, France.,EMBL, Heidelberg, Germany
| | - Amélie Zachayus
- Institute of Genetics and of Molecular and Cellular Biology (IGBMC), 1 rue Laurent Fries, Illkirch, France.,Centre National de la Recherche Scientifique (CNRS), UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (Inserm), U964, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Simon Pichard
- Institute of Genetics and of Molecular and Cellular Biology (IGBMC), 1 rue Laurent Fries, Illkirch, France.,Centre National de la Recherche Scientifique (CNRS), UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (Inserm), U964, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Judit Osz
- Institute of Genetics and of Molecular and Cellular Biology (IGBMC), 1 rue Laurent Fries, Illkirch, France.,Centre National de la Recherche Scientifique (CNRS), UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (Inserm), U964, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Natacha Rochel
- Institute of Genetics and of Molecular and Cellular Biology (IGBMC), 1 rue Laurent Fries, Illkirch, France.,Centre National de la Recherche Scientifique (CNRS), UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (Inserm), U964, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Paola Rossolillo
- Institute of Genetics and of Molecular and Cellular Biology (IGBMC), 1 rue Laurent Fries, Illkirch, France.,Centre National de la Recherche Scientifique (CNRS), UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (Inserm), U964, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Isabelle Kolb-Cheynel
- Institute of Genetics and of Molecular and Cellular Biology (IGBMC), 1 rue Laurent Fries, Illkirch, France.,Centre National de la Recherche Scientifique (CNRS), UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (Inserm), U964, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Nathalie Troffer-Charlier
- Institute of Genetics and of Molecular and Cellular Biology (IGBMC), 1 rue Laurent Fries, Illkirch, France.,Centre National de la Recherche Scientifique (CNRS), UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (Inserm), U964, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Emmanuel Compe
- Institute of Genetics and of Molecular and Cellular Biology (IGBMC), 1 rue Laurent Fries, Illkirch, France.,Centre National de la Recherche Scientifique (CNRS), UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (Inserm), U964, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Olivier Bensaude
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL Research University, 46 rue d'Ulm, 75005, Paris, France
| | - Imre Berger
- Max Planck Bristol Centre for Minimal Biology, Cantock's Close, University of Bristol, Bristol, BS8 1TS, UK.,Bristol Synthetic Biology Centre BrisSynBio, School of Biochemistry, 1 Tankard's Close, University of Bristol, Bristol, BS8 1TD, UK
| | - Arnaud Poterszman
- Institute of Genetics and of Molecular and Cellular Biology (IGBMC), 1 rue Laurent Fries, Illkirch, France. .,Centre National de la Recherche Scientifique (CNRS), UMR 7104, Illkirch, France. .,Institut National de la Santé et de la Recherche Médicale (Inserm), U964, Illkirch, France. .,Université de Strasbourg, Illkirch, France.
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7
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Kerchner KM, Mou TC, Sun Y, Rusnac DV, Sprang SR, Briknarová K. The structure of the cysteine-rich region from human histone-lysine N-methyltransferase EHMT2 (G9a). JOURNAL OF STRUCTURAL BIOLOGY-X 2021; 5:100050. [PMID: 34278292 PMCID: PMC8261083 DOI: 10.1016/j.yjsbx.2021.100050] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 06/21/2021] [Accepted: 06/22/2021] [Indexed: 11/28/2022]
Abstract
Euchromatic histone-lysine N-methyltransferase 1 (EHMT1; G9a-like protein; GLP) and euchromatic histone-lysine N-methyltransferase 2 (EHMT2; G9a) are protein lysine methyltransferases that regulate gene expression and are essential for development and the ability of organisms to change and adapt. In addition to ankyrin repeats and the catalytic SET domain, the EHMT proteins contain a unique cysteine-rich region (CRR) that mediates protein-protein interactions and recruitment of the methyltransferases to specific sites in chromatin. We have determined the structure of the CRR from human EHMT2 by X-ray crystallography and show that the CRR adopts an unusual compact fold with four bound zinc atoms. The structure consists of a RING domain preceded by a smaller zinc-binding motif and an N-terminal segment. The smaller zinc-binding motif straddles the N-terminal end of the RING domain, and the N-terminal segment runs in an extended conformation along one side of the structure and interacts with both the smaller zinc-binding motif and the RING domain. The interface between the N-terminal segment and the RING domain includes one of the zinc atoms. The RING domain is partially sequestered within the CRR and unlikely to function as a ubiquitin ligase.
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Affiliation(s)
- Keshia M Kerchner
- Department of Chemistry and Biochemistry, University of Montana, Missoula, MT 59812, USA
| | - Tung-Chung Mou
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA.,Center for Biomolecular Structure and Dynamics, University of Montana, Missoula, MT 59812, USA
| | - Yizhi Sun
- Department of Chemistry and Biochemistry, University of Montana, Missoula, MT 59812, USA
| | - Domniţa-Valeria Rusnac
- Department of Chemistry and Biochemistry, University of Montana, Missoula, MT 59812, USA
| | - Stephen R Sprang
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA.,Center for Biomolecular Structure and Dynamics, University of Montana, Missoula, MT 59812, USA
| | - Klára Briknarová
- Department of Chemistry and Biochemistry, University of Montana, Missoula, MT 59812, USA.,Center for Biomolecular Structure and Dynamics, University of Montana, Missoula, MT 59812, USA
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8
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Kuper J, Kisker C. Three targets in one complex: A molecular perspective of TFIIH in cancer therapy. DNA Repair (Amst) 2021; 105:103143. [PMID: 34144487 DOI: 10.1016/j.dnarep.2021.103143] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 05/26/2021] [Accepted: 05/31/2021] [Indexed: 12/21/2022]
Abstract
The general transcription factor II H (TFIIH) plays an essential role in transcription and nucleotide excision DNA repair (NER). TFIIH is a complex 10 subunit containing molecular machine that harbors three enzymatic activities while the remaining subunits assume regulatory and/or structural functions. Intriguingly, the three enzymatic activities of the CDK7 kinase, the XPB translocase, and the XPD helicase exert different impacts on the overall activities of TFIIH. While the enzymatic function of the XPD helicase is exclusively required in NER, the CDK7 kinase is deeply involved in transcription, whereas XPB is essential to both processes. Recent structural and biochemical endeavors enabled unprecedented details towards the molecular basis of these different TFIIH functions and how the enzymatic activities are regulated within the entire complex. Due to its involvement in two fundamental processes, TFIIH has become increasingly important as a target in cancer therapy and two of the three enzymes have already been addressed successfully. Here we explore the possibilities of recent high resolution structures in the context of TFIIH druggability and shed light on the functional consequences of the different approaches towards TFIIH inhibition.
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Affiliation(s)
- Jochen Kuper
- Rudolf Virchow Center for Integrative and Translational Bioimaging, University of Wuerzburg, Germany.
| | - Caroline Kisker
- Rudolf Virchow Center for Integrative and Translational Bioimaging, University of Wuerzburg, Germany.
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9
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Barnett JT, Kuper J, Koelmel W, Kisker C, Kad NM. The TFIIH subunits p44/p62 act as a damage sensor during nucleotide excision repair. Nucleic Acids Res 2021; 48:12689-12696. [PMID: 33166411 PMCID: PMC7736792 DOI: 10.1093/nar/gkaa973] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 09/17/2020] [Accepted: 10/13/2020] [Indexed: 01/09/2023] Open
Abstract
Nucleotide excision repair (NER) in eukaryotes is orchestrated by the core form of the general transcription factor TFIIH, containing the helicases XPB, XPD and five ‘structural’ subunits, p62, p44, p34, p52 and p8. Recent cryo-EM structures show that p62 makes extensive contacts with p44 and in part occupies XPD’s DNA binding site. While p44 is known to regulate the helicase activity of XPD during NER, p62 is thought to be purely structural. Here, using helicase and adenosine triphosphatase assays we show that a complex containing p44 and p62 enhances XPD’s affinity for dsDNA 3-fold over p44 alone. Remarkably, the relative affinity is further increased to 60-fold by dsDNA damage. Direct binding studies show this preference derives from p44/p62’s high affinity (20 nM) for damaged ssDNA. Single molecule imaging of p44/p62 complexes without XPD reveals they bind to and randomly diffuse on DNA, however, in the presence of UV-induced DNA lesions these complexes stall. Combined with the analysis of a recent cryo-EM structure, we suggest that p44/p62 acts as a novel DNA-binding entity that enhances damage recognition in TFIIH. This revises our understanding of TFIIH and prompts investigation into the core subunits for an active role during DNA repair and/or transcription.
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Affiliation(s)
- Jamie T Barnett
- School of Biological Sciences, University of Kent, Canterbury CT2 7NH, UK
| | - Jochen Kuper
- Rudolf Virchow Center for Integrative and Translational Bioimaging, Institute for Structural Biology, University of Würzburg, 97080 Würzburg, Germany
| | - Wolfgang Koelmel
- Rudolf Virchow Center for Integrative and Translational Bioimaging, Institute for Structural Biology, University of Würzburg, 97080 Würzburg, Germany
| | - Caroline Kisker
- Rudolf Virchow Center for Integrative and Translational Bioimaging, Institute for Structural Biology, University of Würzburg, 97080 Würzburg, Germany
| | - Neil M Kad
- School of Biological Sciences, University of Kent, Canterbury CT2 7NH, UK
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10
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Kappenberger J, Koelmel W, Schoenwetter E, Scheuer T, Woerner J, Kuper J, Kisker C. How to limit the speed of a motor: the intricate regulation of the XPB ATPase and translocase in TFIIH. Nucleic Acids Res 2020; 48:12282-12296. [PMID: 33196848 PMCID: PMC7708078 DOI: 10.1093/nar/gkaa911] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 09/28/2020] [Accepted: 11/13/2020] [Indexed: 12/24/2022] Open
Abstract
The superfamily 2 helicase XPB is an integral part of the general transcription factor TFIIH and assumes essential catalytic functions in transcription initiation and nucleotide excision repair. The ATPase activity of XPB is required in both processes. We investigated the interaction network that regulates XPB via the p52 and p8 subunits with functional mutagenesis based on our crystal structure of the p52/p8 complex and current cryo-EM structures. Importantly, we show that XPB’s ATPase can be activated either by DNA or by the interaction with the p52/p8 proteins. Intriguingly, we observe that the ATPase activation by p52/p8 is significantly weaker than the activation by DNA and when both p52/p8 and DNA are present, p52/p8 dominates the maximum activation. We therefore define p52/p8 as the master regulator of XPB acting as an activator and speed limiter at the same time. A correlative analysis of the ATPase and translocase activities of XPB shows that XPB only acts as a translocase within the context of complete core TFIIH and that XPA increases the processivity of the translocase complex without altering XPB’s ATPase activity. Our data define an intricate network that tightly controls the activity of XPB during transcription and nucleotide excision repair.
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Affiliation(s)
- Jeannette Kappenberger
- Rudolf Virchow Center for Integrative and Translational Bioimaging, Institute for Structural Biology, University of Würzburg, 97080 Würzburg, Germany
| | - Wolfgang Koelmel
- Rudolf Virchow Center for Integrative and Translational Bioimaging, Institute for Structural Biology, University of Würzburg, 97080 Würzburg, Germany
| | - Elisabeth Schoenwetter
- Rudolf Virchow Center for Integrative and Translational Bioimaging, Institute for Structural Biology, University of Würzburg, 97080 Würzburg, Germany
| | - Tobias Scheuer
- Rudolf Virchow Center for Integrative and Translational Bioimaging, Institute for Structural Biology, University of Würzburg, 97080 Würzburg, Germany
| | - Julia Woerner
- Rudolf Virchow Center for Integrative and Translational Bioimaging, Institute for Structural Biology, University of Würzburg, 97080 Würzburg, Germany
| | - Jochen Kuper
- Rudolf Virchow Center for Integrative and Translational Bioimaging, Institute for Structural Biology, University of Würzburg, 97080 Würzburg, Germany
| | - Caroline Kisker
- Rudolf Virchow Center for Integrative and Translational Bioimaging, Institute for Structural Biology, University of Würzburg, 97080 Würzburg, Germany
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11
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Hands on Native Mass Spectrometry Analysis of Multi-protein Complexes. Methods Mol Biol 2020. [PMID: 33301118 DOI: 10.1007/978-1-0716-1126-5_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/17/2023]
Abstract
By maintaining intact multi-protein complexes in the gas-phase, native mass spectrometry provides their molecular weight with very good accuracy compared to other methods (typically native PAGE or SEC-MALS) (Marcoux and Robinson, Structure 21:1541-1550, 2013). Besides, heterogeneous samples, in terms of both oligomeric states and ligand-bound species can be fully characterized. Here we thoroughly describe the analysis of several oligomeric protein complexes ranging from a 16 = kDa dimer to a 801-kDa tetradecameric complex on different instrumental setups.
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12
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Kokic G, Chernev A, Tegunov D, Dienemann C, Urlaub H, Cramer P. Structural basis of TFIIH activation for nucleotide excision repair. Nat Commun 2019; 10:2885. [PMID: 31253769 PMCID: PMC6599211 DOI: 10.1038/s41467-019-10745-5] [Citation(s) in RCA: 94] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 05/28/2019] [Indexed: 12/16/2022] Open
Abstract
Nucleotide excision repair (NER) is the major DNA repair pathway that removes UV-induced and bulky DNA lesions. There is currently no structure of NER intermediates, which form around the large multisubunit transcription factor IIH (TFIIH). Here we report the cryo-EM structure of an NER intermediate containing TFIIH and the NER factor XPA. Compared to its transcription conformation, the TFIIH structure is rearranged such that its ATPase subunits XPB and XPD bind double- and single-stranded DNA, consistent with their translocase and helicase activities, respectively. XPA releases the inhibitory kinase module of TFIIH, displaces a ‘plug’ element from the DNA-binding pore in XPD, and together with the NER factor XPG stimulates XPD activity. Our results explain how TFIIH is switched from a transcription to a repair factor, and provide the basis for a mechanistic analysis of the NER pathway. The NER machinery contains the multisubunit transcription factor IIH (TFIIH) that opens the DNA repair bubble, scans for the lesion, and coordinates excision of the damaged site. Here the authors resolve the cryo-electron microscopy structure of the human core TFIIH-XPA-DNA complex and provide insights into its activation.
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Affiliation(s)
- Goran Kokic
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
| | - Aleksandar Chernev
- Max Planck Institute for Biophysical Chemistry, Bioanalytical Mass Spectrometry, Am Fassberg 11, 37077, Göttingen, Germany.,University Medical Center Göttingen, Institute of Clinical Chemistry, Bioanalytics Group, Robert-Koch-Straße 40, 37075, Göttingen, Germany
| | - Dimitry Tegunov
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
| | - Christian Dienemann
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
| | - Henning Urlaub
- Max Planck Institute for Biophysical Chemistry, Bioanalytical Mass Spectrometry, Am Fassberg 11, 37077, Göttingen, Germany.,University Medical Center Göttingen, Institute of Clinical Chemistry, Bioanalytics Group, Robert-Koch-Straße 40, 37075, Göttingen, Germany
| | - Patrick Cramer
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany.
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13
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Yan C, Dodd T, He Y, Tainer JA, Tsutakawa SE, Ivanov I. Transcription preinitiation complex structure and dynamics provide insight into genetic diseases. Nat Struct Mol Biol 2019; 26:397-406. [PMID: 31110295 PMCID: PMC6642811 DOI: 10.1038/s41594-019-0220-3] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 03/29/2019] [Indexed: 12/11/2022]
Abstract
Transcription preinitiation complexes (PICs) are vital assemblies whose function underlies the expression of protein-encoding genes. Cryo-EM advances have begun to uncover their structural organization. Nevertheless, functional analyses are hindered by incompletely modeled regions. Here we integrate all available cryo-EM data to build a practically complete human PIC structural model. This enables simulations that reveal the assembly's global motions, define PIC partitioning into dynamic communities and delineate how structural modules function together to remodel DNA. We identify key TFIIE-p62 interactions that link core-PIC to TFIIH. p62 rigging interlaces p34, p44 and XPD while capping the DNA-binding and ATP-binding sites of XPD. PIC kinks and locks substrate DNA, creating negative supercoiling within the Pol II cleft to facilitate promoter opening. Mapping disease mutations associated with xeroderma pigmentosum, trichothiodystrophy and Cockayne syndrome onto defined communities reveals clustering into three mechanistic classes that affect TFIIH helicase functions, protein interactions and interface dynamics.
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Affiliation(s)
- Chunli Yan
- Department of Chemistry, Georgia State University, Atlanta, GA, USA
- Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, USA
| | - Thomas Dodd
- Department of Chemistry, Georgia State University, Atlanta, GA, USA
- Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, USA
| | - Yuan He
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, USA
| | - John A Tainer
- Department of Molecular and Cellular Oncology, The University of Texas M. D. Anderson Cancer Center, Houston, TX, USA
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Susan E Tsutakawa
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Ivaylo Ivanov
- Department of Chemistry, Georgia State University, Atlanta, GA, USA.
- Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, USA.
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14
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Greber BJ, Toso DB, Fang J, Nogales E. The complete structure of the human TFIIH core complex. eLife 2019; 8:e44771. [PMID: 30860024 PMCID: PMC6422496 DOI: 10.7554/elife.44771] [Citation(s) in RCA: 82] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Accepted: 03/03/2019] [Indexed: 01/26/2023] Open
Abstract
Transcription factor IIH (TFIIH) is a heterodecameric protein complex critical for transcription initiation by RNA polymerase II and nucleotide excision DNA repair. The TFIIH core complex is sufficient for its repair functions and harbors the XPB and XPD DNA-dependent ATPase/helicase subunits, which are affected by human disease mutations. Transcription initiation additionally requires the CdK activating kinase subcomplex. Previous structural work has provided only partial insight into the architecture of TFIIH and its interactions within transcription pre-initiation complexes. Here, we present the complete structure of the human TFIIH core complex, determined by phase-plate cryo-electron microscopy at 3.7 Å resolution. The structure uncovers the molecular basis of TFIIH assembly, revealing how the recruitment of XPB by p52 depends on a pseudo-symmetric dimer of homologous domains in these two proteins. The structure also suggests a function for p62 in the regulation of XPD, and allows the mapping of previously unresolved human disease mutations.
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Affiliation(s)
- Basil J Greber
- California Institute for Quantitative BiosciencesUniversity of CaliforniaBerkeleyUnited States
- Molecular Biophysics and Integrative Bio-Imaging DivisionLawrence Berkeley National LaboratoryBerkeleyUnited States
| | - Daniel B Toso
- California Institute for Quantitative BiosciencesUniversity of CaliforniaBerkeleyUnited States
| | - Jie Fang
- Howard Hughes Medical Institute, University of CaliforniaBerkeleyUnited States
| | - Eva Nogales
- California Institute for Quantitative BiosciencesUniversity of CaliforniaBerkeleyUnited States
- Molecular Biophysics and Integrative Bio-Imaging DivisionLawrence Berkeley National LaboratoryBerkeleyUnited States
- Howard Hughes Medical Institute, University of CaliforniaBerkeleyUnited States
- Department of Molecular and Cell BiologyUniversity of CaliforniaBerkeleyUnited States
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15
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Kolesnikova O, Radu L, Poterszman A. TFIIH: A multi-subunit complex at the cross-roads of transcription and DNA repair. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2019; 115:21-67. [PMID: 30798933 DOI: 10.1016/bs.apcsb.2019.01.003] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Transcription factor IIH (TFIIH) is a multiprotein complex involved in both eukaryotic transcription and DNA repair, revealing a tight connection between these two processes. Composed of 10 subunits, it can be resolved into a 7-subunits core complex with the XPB translocase and the XPD helicase, and the 3-subunits kinase complex CAK, which also exists as a free complex with a distinct function. Initially identified as basal transcription factor, TFIIH also participates in transcription regulation and plays a key role in nucleotide excision repair (NER) for opening DNA at damaged sites, lesion verification and recruitment of additional repair factors. Our understanding of TFIIH function in eukaryotic cells has greatly benefited from studies of the genetic rare diseases xeroderma pigmentosum (XP), Cockayne syndrome (CS) and trichothiodystrophy (TTD), that are not only characterized by cancer and aging predispositions but also by neurological and developmental defects. Although much remains unknown about TFIIH function, significant progresses have been done regarding the structure of the complex, the functions of its catalytic subunits and the multiple roles of the regulatory core-TFIIH subunits. This review provides a non-exhaustive survey of key discoveries on the structure and function of this pivotal factor, which can be considered as a promising target for therapeutic strategies.
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Affiliation(s)
- Olga Kolesnikova
- Institut de Génétique et de Biologie Moléculaire et Cellulaire Illkirch Cedex, C.U. Strasbourg, France; Centre National de la Recherche Scientifique, UMR7104, Illkirch, France; Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France; Université de Strasbourg, Illkirch, France
| | - Laura Radu
- Institut de Génétique et de Biologie Moléculaire et Cellulaire Illkirch Cedex, C.U. Strasbourg, France; Centre National de la Recherche Scientifique, UMR7104, Illkirch, France; Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France; Université de Strasbourg, Illkirch, France
| | - Arnaud Poterszman
- Institut de Génétique et de Biologie Moléculaire et Cellulaire Illkirch Cedex, C.U. Strasbourg, France; Centre National de la Recherche Scientifique, UMR7104, Illkirch, France; Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France; Université de Strasbourg, Illkirch, France.
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16
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Rimel JK, Taatjes DJ. The essential and multifunctional TFIIH complex. Protein Sci 2018; 27:1018-1037. [PMID: 29664212 PMCID: PMC5980561 DOI: 10.1002/pro.3424] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2018] [Revised: 04/04/2018] [Accepted: 04/05/2018] [Indexed: 12/19/2022]
Abstract
TFIIH is a 10‐subunit complex that regulates RNA polymerase II (pol II) transcription but also serves other important biological roles. Although much remains unknown about TFIIH function in eukaryotic cells, much progress has been made even in just the past few years, due in part to technological advances (e.g. cryoEM and single molecule methods) and the development of chemical inhibitors of TFIIH enzymes. This review focuses on the major cellular roles for TFIIH, with an emphasis on TFIIH function as a regulator of pol II transcription. We describe the structure of TFIIH and its roles in pol II initiation, promoter‐proximal pausing, elongation, and termination. We also discuss cellular roles for TFIIH beyond transcription (e.g. DNA repair, cell cycle regulation) and summarize small molecule inhibitors of TFIIH and diseases associated with defects in TFIIH structure and function.
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Affiliation(s)
- Jenna K Rimel
- Department of Chemistry & Biochemistry, University of Colorado, Boulder, Colorado, 80303
| | - Dylan J Taatjes
- Department of Chemistry & Biochemistry, University of Colorado, Boulder, Colorado, 80303
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