1
|
Muniesa-Vargas A, Davó-Martínez C, Ribeiro-Silva C, van der Woude M, Thijssen KL, Haspels B, Häckes D, Kaynak ÜU, Kanaar R, Marteijn JA, Theil AF, Kuijten MMP, Vermeulen W, Lans H. Persistent TFIIH binding to non-excised DNA damage causes cell and developmental failure. Nat Commun 2024; 15:3490. [PMID: 38664429 PMCID: PMC11045817 DOI: 10.1038/s41467-024-47935-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Accepted: 04/12/2024] [Indexed: 04/28/2024] Open
Abstract
Congenital nucleotide excision repair (NER) deficiency gives rise to several cancer-prone and/or progeroid disorders. It is not understood how defects in the same DNA repair pathway cause different disease features and severity. Here, we show that the absence of functional ERCC1-XPF or XPG endonucleases leads to stable and prolonged binding of the transcription/DNA repair factor TFIIH to DNA damage, which correlates with disease severity and induces senescence features in human cells. In vivo, in C. elegans, this prolonged TFIIH binding to non-excised DNA damage causes developmental arrest and neuronal dysfunction, in a manner dependent on transcription-coupled NER. NER factors XPA and TTDA both promote stable TFIIH DNA binding and their depletion therefore suppresses these severe phenotypical consequences. These results identify stalled NER intermediates as pathogenic to cell functionality and organismal development, which can in part explain why mutations in XPF or XPG cause different disease features than mutations in XPA or TTDA.
Collapse
Affiliation(s)
- Alba Muniesa-Vargas
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 GD, Rotterdam, The Netherlands
| | - Carlota Davó-Martínez
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 GD, Rotterdam, The Netherlands
| | - Cristina Ribeiro-Silva
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 GD, Rotterdam, The Netherlands
| | - Melanie van der Woude
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 GD, Rotterdam, The Netherlands
| | - Karen L Thijssen
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 GD, Rotterdam, The Netherlands
| | - Ben Haspels
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Oncode Institute, Erasmus University Medical Center, 3015 GD, Rotterdam, The Netherlands
| | - David Häckes
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 GD, Rotterdam, The Netherlands
| | - Ülkem U Kaynak
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 GD, Rotterdam, The Netherlands
| | - Roland Kanaar
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Oncode Institute, Erasmus University Medical Center, 3015 GD, Rotterdam, The Netherlands
| | - Jurgen A Marteijn
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Oncode Institute, Erasmus University Medical Center, 3015 GD, Rotterdam, The Netherlands
| | - Arjan F Theil
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 GD, Rotterdam, The Netherlands
| | - Maayke M P Kuijten
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Oncode Institute, Erasmus University Medical Center, 3015 GD, Rotterdam, The Netherlands
| | - Wim Vermeulen
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 GD, Rotterdam, The Netherlands
| | - Hannes Lans
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 GD, Rotterdam, The Netherlands.
| |
Collapse
|
2
|
Kuppa S, Corless E, Caldwell CC, Spies M, Antony E. Generation of site-specifically labelled fluorescent human XPA to investigate DNA binding dynamics during nucleotide excision repair. Methods 2024; 224:47-53. [PMID: 38387709 PMCID: PMC10960328 DOI: 10.1016/j.ymeth.2024.02.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Revised: 02/16/2024] [Accepted: 02/19/2024] [Indexed: 02/24/2024] Open
Abstract
Nucleotide excision repair (NER) promotes genomic integrity by removing bulky DNA adducts introduced by external factors such as ultraviolet light. Defects in NER enzymes are associated with pathological conditions such as Xeroderma Pigmentosum, trichothiodystrophy, and Cockayne syndrome. A critical step in NER is the binding of the Xeroderma Pigmentosum group A protein (XPA) to the ss/ds DNA junction. To better capture the dynamics of XPA interactions with DNA during NER we have utilized the fluorescence enhancement through non-canonical amino acids (FEncAA) approach. 4-azido-L-phenylalanine (4AZP or pAzF) was incorporated at Arg-158 in human XPA and conjugated to Cy3 using strain-promoted azide-alkyne cycloaddition. The resulting fluorescent XPA protein (XPACy3) shows no loss in DNA binding activity and generates a robust change in fluorescence upon binding to DNA. Here we describe methods to generate XPACy3 and detail in vitro experimental conditions required to stably maintain the protein during biochemical and biophysical studies.
Collapse
Affiliation(s)
- Sahiti Kuppa
- Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO 63104, USA
| | - Elliot Corless
- Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO 63104, USA
| | - Colleen C Caldwell
- Department of Biochemistry and Molecular Biology, University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
| | - Maria Spies
- Department of Biochemistry and Molecular Biology, University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
| | - Edwin Antony
- Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO 63104, USA.
| |
Collapse
|
3
|
Blee AM, Gallagher K, Kim HS, Kim M, Kharat S, Troll C, D’Souza A, Park J, Neufer P, Schärer O, Chazin W. XPA tumor variant leads to defects in NER that sensitize cells to cisplatin. NAR Cancer 2024; 6:zcae013. [PMID: 38500596 PMCID: PMC10946055 DOI: 10.1093/narcan/zcae013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 01/27/2024] [Accepted: 02/29/2024] [Indexed: 03/20/2024] Open
Abstract
Nucleotide excision repair (NER) reduces efficacy of treatment with platinum (Pt)-based chemotherapy by removing Pt lesions from DNA. Previous study has identified that missense mutation or loss of the NER genes Excision Repair Cross Complementation Group 1 and 2 (ERCC1 and ERCC2) leads to improved patient outcomes after treatment with Pt-based chemotherapies. Although most NER gene alterations found in patient tumors are missense mutations, the impact of mutations in the remaining nearly 20 NER genes is unknown. Towards this goal, we previously developed a machine learning strategy to predict genetic variants in an essential NER protein, Xeroderma Pigmentosum Complementation Group A (XPA), that disrupt repair. In this study, we report in-depth analyses of a subset of the predicted variants, including in vitro analyses of purified recombinant protein and cell-based assays to test Pt agent sensitivity in cells and determine mechanisms of NER dysfunction. The most NER deficient variant Y148D had reduced protein stability, weaker DNA binding, disrupted recruitment to damage, and degradation. Our findings demonstrate that tumor mutations in XPA impact cell survival after cisplatin treatment and provide valuable mechanistic insights to improve variant effect prediction. Broadly, these findings suggest XPA tumor variants should be considered when predicting chemotherapy response.
Collapse
Affiliation(s)
- Alexandra M Blee
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37205, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37240, USA
| | - Kaitlyn S Gallagher
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37205, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37240, USA
| | - Hyun-Suk Kim
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Republic of Korea
| | - Mihyun Kim
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Republic of Korea
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Suhas S Kharat
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37205, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37240, USA
| | - Christina R Troll
- Department of Chemistry, Vanderbilt University, Nashville, TN 37240, USA
| | - Areetha D’Souza
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37205, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37240, USA
| | - Jiyoung Park
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Republic of Korea
| | - P Drew Neufer
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37205, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37240, USA
| | - Orlando D Schärer
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37205, USA
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Republic of Korea
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Walter J Chazin
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37205, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37240, USA
- Department of Chemistry, Vanderbilt University, Nashville, TN 37240, USA
| |
Collapse
|
4
|
Dao HM, AboulFotouh K, Hussain AF, Marras AE, Johnston KP, Cui Z, Williams RO. Characterization of mRNA Lipid Nanoparticles by Electron Density Mapping Reconstruction: X-ray Scattering with Density from Solution Scattering (DENSS) Algorithm. Pharm Res 2024; 41:501-512. [PMID: 38326530 DOI: 10.1007/s11095-024-03671-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 01/28/2024] [Indexed: 02/09/2024]
Abstract
PURPOSE This study aimed to test the feasibility of using Small Angle X-ray Scattering (SAXS) coupled with Density from Solution Scattering (DENSS) algorithm to characterize the internal architecture of messenger RNA-containing lipid nanoparticles (mRNA-LNPs). METHODS The DENSS algorithm was employed to construct a three-dimensional model of average individual mRNA-LNP. The reconstructed models were cross validated with cryogenic transmission electron microscopy (cryo-TEM), and dynamic light scattering (DLS) to assess size, morphology, and internal structure. RESULTS Cryo-TEM and DLS complemented SAXS, revealed a core-shell mRNA-LNP structure with electron-rich mRNA-rich region at the core, surrounded by lipids. The reconstructed model, utilizing the DENSS algorithm, effectively distinguishes mRNA and lipids via electron density mapping. Notably, DENSS accurately models the morphology of the mRNA-LNPs as an ellipsoidal shape with a "bleb" architecture or a two-compartment structure with contrasting electron densities, corresponding to mRNA-filled and empty lipid compartments, respectively. Finally, subtle changes in the LNP structure after three freeze-thaw cycles were detected by SAXS, demonstrating an increase in radius of gyration (Rg) associated with mRNA leakage. CONCLUSION Analyzing SAXS profiles based on DENSS algorithm to yield a reconstructed electron density based three-dimensional model can be a useful physicochemical characterization method in the toolbox to study mRNA-LNPs and facilitate their development.
Collapse
Affiliation(s)
- Huy M Dao
- Division of Molecular Pharmaceutics and Drug Delivery, College of Pharmacy, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Khaled AboulFotouh
- Division of Molecular Pharmaceutics and Drug Delivery, College of Pharmacy, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Aasim Faheem Hussain
- Department of Biomedical Engineering, Cockrell School of Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Alexander E Marras
- Department of Biomedical Engineering, Cockrell School of Engineering, The University of Texas at Austin, Austin, TX, USA
- Materials Science and Engineering Graduate Program, Texas Materials Institute, The University of Texas at Austin, Austin, TX, USA
- Walker Department of Mechanical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Keith P Johnston
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Zhengrong Cui
- Division of Molecular Pharmaceutics and Drug Delivery, College of Pharmacy, The University of Texas at Austin, Austin, TX, 78712, USA.
| | - Robert O Williams
- Division of Molecular Pharmaceutics and Drug Delivery, College of Pharmacy, The University of Texas at Austin, Austin, TX, 78712, USA.
| |
Collapse
|
5
|
Morledge-Hampton B, Kalyanaraman A, Wyrick JJ. Analysis of cytosine deamination events in excision repair sequencing reads reveals mechanisms of incision site selection in NER. Nucleic Acids Res 2024; 52:1720-1735. [PMID: 38109317 PMCID: PMC10899786 DOI: 10.1093/nar/gkad1195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 11/28/2023] [Accepted: 12/01/2023] [Indexed: 12/20/2023] Open
Abstract
Nucleotide excision repair (NER) removes helix-distorting DNA lesions and is therefore critical for genome stability. During NER, DNA is unwound on either side of the lesion and excised, but the rules governing incision site selection, particularly in eukaryotic cells, are unclear. Excision repair-sequencing (XR-seq) sequences excised NER fragments, but analysis has been limited because the lesion location is unknown. Here, we exploit accelerated cytosine deamination rates in UV-induced CPD (cyclobutane pyrimidine dimer) lesions to precisely map their locations at C to T mismatches in XR-seq reads, revealing general and species-specific patterns of incision site selection during NER. Our data indicate that the 5' incision site occurs preferentially in HYV (i.e. not G; C/T; not T) sequence motifs, a pattern that can be explained by sequence preferences of the XPF-ERCC1 endonuclease. In contrast, the 3' incision site does not show strong sequence preferences, once truncated reads arising from mispriming events are excluded. Instead, the 3' incision is partially determined by the 5' incision site distance, indicating that the two incision events are coupled. Finally, our data reveal unique and coupled NER incision patterns at nucleosome boundaries. These findings reveal key principles governing NER incision site selection in eukaryotic cells.
Collapse
Affiliation(s)
| | - Ananth Kalyanaraman
- School of Electrical Engineering and Computer Science, Washington State University, Pullman, WA 99164, USA
| | - John J Wyrick
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164, USA
| |
Collapse
|
6
|
Son K, Takhaveev V, Mor V, Yu H, Dillier E, Zilio N, Püllen NJL, Ivanov D, Ulrich HD, Sturla SJ, Schärer OD. Trabectedin derails transcription-coupled nucleotide excision repair to induce DNA breaks in highly transcribed genes. Nat Commun 2024; 15:1388. [PMID: 38360910 PMCID: PMC10869700 DOI: 10.1038/s41467-024-45664-7] [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: 08/04/2023] [Accepted: 01/30/2024] [Indexed: 02/17/2024] Open
Abstract
Most genotoxic anticancer agents fail in tumors with intact DNA repair. Therefore, trabectedin, anagent more toxic to cells with active DNA repair, specifically transcription-coupled nucleotide excision repair (TC-NER), provides therapeutic opportunities. To unlock the potential of trabectedin and inform its application in precision oncology, an understanding of the mechanism of the drug's TC-NER-dependent toxicity is needed. Here, we determine that abortive TC-NER of trabectedin-DNA adducts forms persistent single-strand breaks (SSBs) as the adducts block the second of the two sequential NER incisions. We map the 3'-hydroxyl groups of SSBs originating from the first NER incision at trabectedin lesions, recording TC-NER on a genome-wide scale. Trabectedin-induced SSBs primarily occur in transcribed strands of active genes and peak near transcription start sites. Frequent SSBs are also found outside gene bodies, connecting TC-NER to divergent transcription from promoters. This work advances the use of trabectedin for precision oncology and for studying TC-NER and transcription.
Collapse
Affiliation(s)
- Kook Son
- Center for Genomic Integrity, Institute for Basic Science (IBS), 44919, Ulsan, Republic of Korea
| | - Vakil Takhaveev
- Department of Health Sciences and Technology, ETH Zürich, 8092, Zürich, Switzerland
| | - Visesato Mor
- Center for Genomic Integrity, Institute for Basic Science (IBS), 44919, Ulsan, Republic of Korea
| | - Hobin Yu
- Center for Genomic Integrity, Institute for Basic Science (IBS), 44919, Ulsan, Republic of Korea
- Department of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), 44919, Ulsan, Republic of Korea
| | - Emma Dillier
- Department of Health Sciences and Technology, ETH Zürich, 8092, Zürich, Switzerland
| | - Nicola Zilio
- Institute of Molecular Biology (IMB), 55128, Mainz, Germany
| | - Nikolai J L Püllen
- Department of Health Sciences and Technology, ETH Zürich, 8092, Zürich, Switzerland
| | - Dmitri Ivanov
- Center for Genomic Integrity, Institute for Basic Science (IBS), 44919, Ulsan, Republic of Korea
| | - Helle D Ulrich
- Institute of Molecular Biology (IMB), 55128, Mainz, Germany
| | - Shana J Sturla
- Department of Health Sciences and Technology, ETH Zürich, 8092, Zürich, Switzerland.
| | - Orlando D Schärer
- Center for Genomic Integrity, Institute for Basic Science (IBS), 44919, Ulsan, Republic of Korea.
- Department of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), 44919, Ulsan, Republic of Korea.
| |
Collapse
|
7
|
Kumar N, Taneja A, Ghosh M, Rothweiler U, Sundaresan N, Singh M. Harmonin homology domain-mediated interaction of RTEL1 helicase with RPA and DNA provides insights into its recruitment to DNA repair sites. Nucleic Acids Res 2024; 52:1450-1470. [PMID: 38153196 PMCID: PMC10853778 DOI: 10.1093/nar/gkad1208] [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: 11/03/2022] [Revised: 12/04/2023] [Accepted: 12/06/2023] [Indexed: 12/29/2023] Open
Abstract
The regulator of telomere elongation helicase 1 (RTEL1) plays roles in telomere DNA maintenance, DNA repair, and genome stability by dismantling D-loops and unwinding G-quadruplex structures. RTEL1 comprises a helicase domain, two tandem harmonin homology domains 1&2 (HHD1 and HHD2), and a Zn2+-binding RING domain. In vitro D-loop disassembly by RTEL1 is enhanced in the presence of replication protein A (RPA). However, the mechanism of RTEL1 recruitment at non-telomeric D-loops remains unknown. In this study, we have unravelled a direct physical interaction between RTEL1 and RPA. Under DNA damage conditions, we showed that RTEL1 and RPA colocalise in the cell. Coimmunoprecipitation showed that RTEL1 and RPA interact, and the deletion of HHDs of RTEL1 significantly reduced this interaction. NMR chemical shift perturbations (CSPs) showed that RPA uses its 32C domain to interact with the HHD2 of RTEL1. Interestingly, HHD2 also interacted with DNA in the in vitro experiments. HHD2 structure was determined using X-ray crystallography, and NMR CSPs mapping revealed that both RPA 32C and DNA competitively bind to HHD2 on an overlapping surface. These results establish novel roles of accessory HHDs in RTEL1's functions and provide mechanistic insights into the RPA-mediated recruitment of RTEL1 to DNA repair sites.
Collapse
Affiliation(s)
- Niranjan Kumar
- Molecular Biophysics Unit, Indian Institute of Science, Bengaluru 560012, India
| | - Arushi Taneja
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru 560012, India
| | - Meenakshi Ghosh
- Molecular Biophysics Unit, Indian Institute of Science, Bengaluru 560012, India
| | - Ulli Rothweiler
- The Norwegian Structural Biology Centre, Department of Chemistry, The Arctic University of Norway, N-9037, Tromsø, Norway
| | | | - Mahavir Singh
- Molecular Biophysics Unit, Indian Institute of Science, Bengaluru 560012, India
| |
Collapse
|
8
|
Fu I, Geacintov NE, Broyde S. Differing structures and dynamics of two photolesions portray verification differences by the human XPD helicase. Nucleic Acids Res 2023; 51:12261-12274. [PMID: 37933861 PMCID: PMC10711554 DOI: 10.1093/nar/gkad974] [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: 08/03/2023] [Revised: 09/28/2023] [Accepted: 10/16/2023] [Indexed: 11/08/2023] Open
Abstract
Ultraviolet light generates cyclobutane pyrimidine dimer (CPD) and pyrimidine 6-4 pyrimidone (6-4PP) photoproducts that cause skin malignancies if not repaired by nucleotide excision repair (NER). While the faster repair of the more distorting 6-4PPs is attributed mainly to more efficient recognition by XPC, the XPD lesion verification helicase may play a role, as it directly scans the damaged DNA strand. With extensive molecular dynamics simulations of XPD-bound single-strand DNA containing each lesion outside the entry pore of XPD, we elucidate strikingly different verification processes for these two lesions that have very different topologies. The open book-like CPD thymines are sterically blocked from pore entry and preferably entrapped by sensors that are outside the pore; however, the near-perpendicular 6-4PP thymines can enter, accompanied by a displacement of the Arch domain toward the lesion, which is thereby tightly accommodated within the pore. This trapped 6-4PP may inhibit XPD helicase activity to foster lesion verification by locking the Arch to other domains. Furthermore, the movement of the Arch domain, only in the case of 6-4PP, may trigger signaling to the XPG nuclease for subsequent lesion incision by fostering direct contact between the Arch domain and XPG, and thereby facilitating repair of 6-4PP.
Collapse
Affiliation(s)
- Iwen Fu
- Department of Biology, New York University, 24 Waverly Place, 6th Floor, New York, NY 10003, USA
| | - Nicholas E Geacintov
- Department of Chemistry, New York University, 100 Washington Square East, New York, NY 10003, USA
| | - Suse Broyde
- Department of Biology, New York University, 24 Waverly Place, 6th Floor, New York, NY 10003, USA
| |
Collapse
|
9
|
Theil AF, Häckes D, Lans H. TFIIH central activity in nucleotide excision repair to prevent disease. DNA Repair (Amst) 2023; 132:103568. [PMID: 37977600 DOI: 10.1016/j.dnarep.2023.103568] [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] [Received: 04/28/2023] [Revised: 08/22/2023] [Accepted: 09/03/2023] [Indexed: 11/19/2023]
Abstract
The heterodecameric transcription factor IIH (TFIIH) functions in multiple cellular processes, foremost in nucleotide excision repair (NER) and transcription initiation by RNA polymerase II. TFIIH is essential for life and hereditary mutations in TFIIH cause the devastating human syndromes xeroderma pigmentosum, Cockayne syndrome or trichothiodystrophy, or combinations of these. In NER, TFIIH binds to DNA after DNA damage is detected and, using its translocase and helicase subunits XPB and XPD, opens up the DNA and checks for the presence of DNA damage. This central activity leads to dual incision and removal of the DNA strand containing the damage, after which the resulting DNA gap is restored. In this review, we discuss new structural and mechanistic insights into the central function of TFIIH in NER. Moreover, we provide an elaborate overview of all currently known patients and diseases associated with inherited TFIIH mutations and describe how our understanding of TFIIH function in NER and transcription can explain the different disease features caused by TFIIH deficiency.
Collapse
Affiliation(s)
- Arjan F Theil
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 GD Rotterdam, the Netherlands
| | - David Häckes
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 GD Rotterdam, the Netherlands
| | - Hannes Lans
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 GD Rotterdam, the Netherlands.
| |
Collapse
|
10
|
Popov AA, Petruseva IO, Naumenko NV, Lavrik OI. Methods for Assessment of Nucleotide Excision Repair Efficiency. BIOCHEMISTRY. BIOKHIMIIA 2023; 88:1844-1856. [PMID: 38105203 DOI: 10.1134/s0006297923110147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 08/30/2023] [Accepted: 08/31/2023] [Indexed: 12/19/2023]
Abstract
Nucleotide excision repair (NER) is responsible for removing a wide variety of bulky adducts from DNA, thus contributing to the maintenance of genome stability. The efficiency with which proteins of the NER system recognize and remove bulky adducts depends on many factors and is of great clinical and diagnostic significance. The review examines current concepts of the NER system molecular basis in eukaryotic cells and analyzes methods for the assessment of the NER-mediated DNA repair efficiency both in vitro and ex vivo.
Collapse
Affiliation(s)
- Aleksei A Popov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | - Irina O Petruseva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | - Natalya V Naumenko
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | - Olga I Lavrik
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia.
- Novosibirsk National Research State University, Novosibirsk, 630090, Russia
| |
Collapse
|
11
|
Wie M, Khim K, Groehler IV A, Heo S, Woo J, Son K, Lee E, Ra J, Hong S, Schärer O, Choi J, Myung K. Alkylation of nucleobases by 2-chloro- N,N-diethylethanamine hydrochloride (CDEAH) sensitizes PARP1-deficient tumors. NAR Cancer 2023; 5:zcad042. [PMID: 37554969 PMCID: PMC10405566 DOI: 10.1093/narcan/zcad042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 06/16/2023] [Accepted: 07/26/2023] [Indexed: 08/10/2023] Open
Abstract
Targeting BRCA1- and BRCA2-deficient tumors through synthetic lethality using poly(ADP-ribose) polymerase inhibitors (PARPi) has emerged as a successful strategy for cancer therapy. PARPi monotherapy has shown excellent efficacy and safety profiles in clinical practice but is limited by the need for tumor genome mutations in BRCA or other homologous recombination genes as well as the rapid emergence of resistance. In this study, we identified 2-chloro-N,N-diethylethanamine hydrochloride (CDEAH) as a small molecule that selectively kills PARP1- and xeroderma pigmentosum A-deficient cells. CDEAH is a monofunctional alkylating agent that preferentially alkylates guanine nucleobases, forming DNA adducts that can be removed from DNA by either a PARP1-dependent base excision repair or nucleotide excision repair. Treatment of PARP1-deficient cells leads to the formation of strand breaks, an accumulation of cells in S phase and activation of the DNA damage response. Furthermore, CDEAH selectively inhibits PARP1-deficient xenograft tumor growth compared to isogenic PARP1-proficient tumors. Collectively, we report the discovery of an alkylating agent inducing DNA damage that requires PARP1 activity for repair and acts synergistically with PARPi.
Collapse
Affiliation(s)
- Minwoo Wie
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Republic of Korea
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Keon Woo Khim
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Republic of Korea
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Arnold S Groehler IV
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Republic of Korea
| | - Soomin Heo
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Republic of Korea
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Junhyeok Woo
- Department of Chemistry, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Kook Son
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Republic of Korea
| | - Eun A Lee
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Republic of Korea
| | - Jae Sun Ra
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Republic of Korea
| | - Sung You Hong
- Department of Chemistry, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Orlando D Schärer
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Republic of Korea
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Jang Hyun Choi
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Republic of Korea
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Kyungjae Myung
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Republic of Korea
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| |
Collapse
|
12
|
Kang Y, Han YG, Khim KW, Choi WG, Ju MK, Park K, Shin KJ, Chae YC, Choi JH, Kim H, Lee JY. Alteration of replication protein A binding mode on single-stranded DNA by NSMF potentiates RPA phosphorylation by ATR kinase. Nucleic Acids Res 2023; 51:7936-7950. [PMID: 37378431 PMCID: PMC10450186 DOI: 10.1093/nar/gkad543] [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: 12/03/2022] [Revised: 06/07/2023] [Accepted: 06/13/2023] [Indexed: 06/29/2023] Open
Abstract
Replication protein A (RPA), a eukaryotic single-stranded DNA (ssDNA) binding protein, dynamically interacts with ssDNA in different binding modes and plays essential roles in DNA metabolism such as replication, repair, and recombination. RPA accumulation on ssDNA due to replication stress triggers the DNA damage response (DDR) by activating the ataxia telangiectasia and RAD3-related (ATR) kinase, which phosphorylates itself and downstream DDR factors, including RPA. We recently reported that the N-methyl-D-aspartate receptor synaptonuclear signaling and neuronal migration factor (NSMF), a neuronal protein associated with Kallmann syndrome, promotes RPA32 phosphorylation via ATR upon replication stress. However, how NSMF enhances ATR-mediated RPA32 phosphorylation remains elusive. Here, we demonstrate that NSMF colocalizes and physically interacts with RPA at DNA damage sites in vivo and in vitro. Using purified RPA and NSMF in biochemical and single-molecule assays, we find that NSMF selectively displaces RPA in the more weakly bound 8- and 20-nucleotide binding modes from ssDNA, allowing the retention of more stable RPA molecules in the 30-nt binding mode. The 30-nt binding mode of RPA enhances RPA32 phosphorylation by ATR, and phosphorylated RPA becomes stabilized on ssDNA. Our findings provide new mechanistic insight into how NSMF facilitates the role of RPA in the ATR pathway.
Collapse
Affiliation(s)
- Yujin Kang
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Ye Gi Han
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Keon Woo Khim
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Woo Gyun Choi
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Min Kyung Ju
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Kibeom Park
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Kyeong Jin Shin
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Young Chan Chae
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Jang Hyun Choi
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
- Institute of Basic Science Center for Genomic Integrity, Ulsan 44919, Republic of Korea
| | - Hongtae Kim
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
- Institute of Basic Science Center for Genomic Integrity, Ulsan 44919, Republic of Korea
| | - Ja Yil Lee
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
- Institute of Basic Science Center for Genomic Integrity, Ulsan 44919, Republic of Korea
| |
Collapse
|
13
|
Blee AM, Gallagher KS, Kim HS, Kim M, Troll CR, D'Souza A, Park J, Neufer PD, Schärer OD, Chazin WJ. XPA tumor variants lead to defects in NER that sensitize cells to cisplatin. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.29.547124. [PMID: 37425789 PMCID: PMC10327148 DOI: 10.1101/2023.06.29.547124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Nucleotide excision repair (NER) neutralizes treatment with platinum (Pt)-based chemotherapy by removing Pt lesions from DNA. Previous study has identified that missense mutation or loss of either of the NER genes Excision Repair Cross Complementation Group 1 and 2 ( ERCC1 and ERCC2 ) leads to improved patient outcomes after treatment with Pt-based chemotherapies. Although most NER gene alterations found in patient tumors are missense mutations, the impact of such mutations in the remaining nearly 20 NER genes is unknown. Towards this goal, we previously developed a machine learning strategy to predict genetic variants in an essential NER scaffold protein, Xeroderma Pigmentosum Complementation Group A (XPA), that disrupt repair activity on a UV-damaged substrate. In this study, we report in-depth analyses of a subset of the predicted NER-deficient XPA variants, including in vitro analyses of purified recombinant protein and cell-based assays to test Pt agent sensitivity in cells and determine mechanisms of NER dysfunction. The most NER deficient variant Y148D had reduced protein stability, weaker DNA binding, disrupted recruitment to damage, and degradation resulting from tumor missense mutation. Our findings demonstrate that tumor mutations in XPA impact cell survival after cisplatin treatment and provide valuable mechanistic insights to further improve variant effect prediction efforts. More broadly, these findings suggest XPA tumor variants should be considered when predicting patient response to Pt-based chemotherapy. Significance A destabilized, readily degraded tumor variant identified in the NER scaffold protein XPA sensitizes cells to cisplatin, suggesting that XPA variants can be used to predict response to chemotherapy.
Collapse
|
14
|
Kuper J, Kisker C. At the core of nucleotide excision repair. Curr Opin Struct Biol 2023; 80:102605. [PMID: 37150041 DOI: 10.1016/j.sbi.2023.102605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 04/04/2023] [Accepted: 04/06/2023] [Indexed: 05/09/2023]
Abstract
Nucleotide excision repair (NER) is unique in its ability to identify and remove vastly different lesions from DNA. Recent advances in the structural characterization of complexes involved in detection, verification, and excision of damaged DNA have reshaped our understanding of the molecular architecture of this efficient and accurate machinery. Initial damage recognition achieved through transcription coupled repair (TC-NER) or global genome repair (GG-NER) has been addressed by complexes of RNA Pol II with different TC-NER factors and XPC/RAD23B/Centrin-2 with TFIIH, respectively. Moreover, transcription factor IIH (TFIIH), one of the core repair factors and a central NER hub was resolved in different states, providing important insights how this complex facilitates DNA opening and damage verification. Combined, these recent advances led to a highly improved understanding of the molecular landscape of NER core processes, sharpening our view on how NER is successfully achieved.
Collapse
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.
| |
Collapse
|
15
|
van den Heuvel D, Kim M, Wondergem AP, van der Meer PJ, Witkamp M, Lambregtse F, Kim HS, Kan F, Apelt K, Kragten A, González-Prieto R, Vertegaal ACO, Yeo JE, Kim BG, van Doorn R, Schärer OD, Luijsterburg MS. A disease-associated XPA allele interferes with TFIIH binding and primarily affects transcription-coupled nucleotide excision repair. Proc Natl Acad Sci U S A 2023; 120:e2208860120. [PMID: 36893274 PMCID: PMC10089173 DOI: 10.1073/pnas.2208860120] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 01/30/2023] [Indexed: 03/11/2023] Open
Abstract
XPA is a central scaffold protein that coordinates the assembly of repair complexes in the global genome (GG-NER) and transcription-coupled nucleotide excision repair (TC-NER) subpathways. Inactivating mutations in XPA cause xeroderma pigmentosum (XP), which is characterized by extreme UV sensitivity and a highly elevated skin cancer risk. Here, we describe two Dutch siblings in their late forties carrying a homozygous H244R substitution in the C-terminus of XPA. They present with mild cutaneous manifestations of XP without skin cancer but suffer from marked neurological features, including cerebellar ataxia. We show that the mutant XPA protein has a severely weakened interaction with the transcription factor IIH (TFIIH) complex leading to an impaired association of the mutant XPA and the downstream endonuclease ERCC1-XPF with NER complexes. Despite these defects, the patient-derived fibroblasts and reconstituted knockout cells carrying the XPA-H244R substitution show intermediate UV sensitivity and considerable levels of residual GG-NER (~50%), in line with the intrinsic properties and activities of the purified protein. By contrast, XPA-H244R cells are exquisitely sensitive to transcription-blocking DNA damage, show no detectable recovery of transcription after UV irradiation, and display a severe deficiency in TC-NER-associated unscheduled DNA synthesis. Our characterization of a new case of XPA deficiency that interferes with TFIIH binding and primarily affects the transcription-coupled subpathway of nucleotide excision repair, provides an explanation of the dominant neurological features in these patients, and reveals a specific role for the C-terminus of XPA in TC-NER.
Collapse
Affiliation(s)
- Diana van den Heuvel
- Department of Human Genetics, Leiden University Medical Center, 2333 ZCLeiden, The Netherlands
| | - Mihyun Kim
- Center for Genomic Integrity, Institute for Basic Science, 44919Ulsan, Republic of Korea
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, 44919Ulsan, Republic of Korea
| | - Annelotte P. Wondergem
- Department of Human Genetics, Leiden University Medical Center, 2333 ZCLeiden, The Netherlands
| | - Paula J. van der Meer
- Department of Human Genetics, Leiden University Medical Center, 2333 ZCLeiden, The Netherlands
| | - Myrèse Witkamp
- Department of Human Genetics, Leiden University Medical Center, 2333 ZCLeiden, The Netherlands
| | - Ferdy Lambregtse
- Department of Human Genetics, Leiden University Medical Center, 2333 ZCLeiden, The Netherlands
| | - Hyun-Suk Kim
- Center for Genomic Integrity, Institute for Basic Science, 44919Ulsan, Republic of Korea
| | - Folkert Kan
- Department of Human Genetics, Leiden University Medical Center, 2333 ZCLeiden, The Netherlands
| | - Katja Apelt
- Department of Human Genetics, Leiden University Medical Center, 2333 ZCLeiden, The Netherlands
| | - Angela Kragten
- Department of Human Genetics, Leiden University Medical Center, 2333 ZCLeiden, The Netherlands
| | - Román González-Prieto
- Department of Cell and Chemical Biology, Leiden University Medical Center, 2333 ZCLeiden, The Netherlands
- Andalusian Center for Molecular Biology and Regenerative Medicine, University of Sevilla, 41092Seville, Spain
- Department of Cell Biology, University of Seville, 41012Seville, Spain
| | - Alfred C. O. Vertegaal
- Department of Cell and Chemical Biology, Leiden University Medical Center, 2333 ZCLeiden, The Netherlands
| | - Jung-Eun Yeo
- Center for Genomic Integrity, Institute for Basic Science, 44919Ulsan, Republic of Korea
| | - Byung-Gyu Kim
- Center for Genomic Integrity, Institute for Basic Science, 44919Ulsan, Republic of Korea
| | - Remco van Doorn
- Department of Dermatology, Leiden University Medical Center, 2333 ZALeiden, The Netherlands
| | - Orlando D. Schärer
- Center for Genomic Integrity, Institute for Basic Science, 44919Ulsan, Republic of Korea
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, 44919Ulsan, Republic of Korea
| | - Martijn S. Luijsterburg
- Department of Human Genetics, Leiden University Medical Center, 2333 ZCLeiden, The Netherlands
| |
Collapse
|
16
|
Bralić A, Tehseen M, Sobhy MA, Tsai CL, Alhudhali L, Yi G, Yu J, Yan C, Ivanov I, Tsutakawa SE, Tainer J, Hamdan S. A scanning-to-incision switch in TFIIH-XPG induced by DNA damage licenses nucleotide excision repair. Nucleic Acids Res 2022; 51:1019-1033. [PMID: 36477609 PMCID: PMC9943652 DOI: 10.1093/nar/gkac1095] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 10/21/2022] [Accepted: 11/26/2022] [Indexed: 12/12/2022] Open
Abstract
Nucleotide excision repair (NER) is critical for removing bulky DNA base lesions and avoiding diseases. NER couples lesion recognition by XPC to strand separation by XPB and XPD ATPases, followed by lesion excision by XPF and XPG nucleases. Here, we describe key regulatory mechanisms and roles of XPG for and beyond its cleavage activity. Strikingly, by combing single-molecule imaging and bulk cleavage assays, we found that XPG binding to the 7-subunit TFIIH core (coreTFIIH) stimulates coreTFIIH-dependent double-strand (ds)DNA unwinding 10-fold, and XPG-dependent DNA cleavage by up to 700-fold. Simultaneous monitoring of rates for coreTFIIH single-stranded (ss)DNA translocation and dsDNA unwinding showed XPG acts by switching ssDNA translocation to dsDNA unwinding as a likely committed step. Pertinent to the NER pathway regulation, XPG incision activity is suppressed during coreTFIIH translocation on DNA but is licensed when coreTFIIH stalls at the lesion or when ATP hydrolysis is blocked. Moreover, ≥15 nucleotides of 5'-ssDNA is a prerequisite for efficient translocation and incision. Our results unveil a paired coordination mechanism in which key lesion scanning and DNA incision steps are sequentially coordinated, and damaged patch removal is only licensed after generation of ≥15 nucleotides of 5'-ssDNA, ensuring the correct ssDNA bubble size before cleavage.
Collapse
Affiliation(s)
- Amer Bralić
- Bioscience Program, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Muhammad Tehseen
- Bioscience Program, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Mohamed A Sobhy
- Bioscience Program, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Chi-Lin Tsai
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Lubna Alhudhali
- Bioscience Program, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Gang Yi
- Bioscience Program, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Jina Yu
- Department of Chemistry, Georgia State University, Atlanta, GA 30302 USA; Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, 30302, USA
| | - Chunli Yan
- Department of Chemistry, Georgia State University, Atlanta, GA 30302 USA; Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, 30302, USA
| | - Ivaylo Ivanov
- Department of Chemistry, Georgia State University, Atlanta, GA 30302 USA; Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, 30302, USA
| | - Susan E Tsutakawa
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - John A Tainer
- Correspondence may also be addressed to John A. Tainer. Tel: +1 713 563 7725; Fax: +1 713 794 3270;
| | - Samir M Hamdan
- To whom correspondence should be addressed. Tel: +96 628082384; Cell: +96 6544700031;
| |
Collapse
|
17
|
Krasikova YS, Lavrik OI, Rechkunova NI. The XPA Protein-Life under Precise Control. Cells 2022; 11:cells11233723. [PMID: 36496984 PMCID: PMC9739396 DOI: 10.3390/cells11233723] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 11/15/2022] [Accepted: 11/16/2022] [Indexed: 11/24/2022] Open
Abstract
Nucleotide excision repair (NER) is a central DNA repair pathway responsible for removing a wide variety of DNA-distorting lesions from the genome. The highly choreographed cascade of core NER reactions requires more than 30 polypeptides. The xeroderma pigmentosum group A (XPA) protein plays an essential role in the NER process. XPA interacts with almost all NER participants and organizes the correct NER repair complex. In the absence of XPA's scaffolding function, no repair process occurs. In this review, we briefly summarize our current knowledge about the XPA protein structure and analyze the formation of contact with its protein partners during NER complex assembling. We focus on different ways of regulation of the XPA protein's activity and expression and pay special attention to the network of post-translational modifications. We also discuss the data that is not in line with the currently accepted hypothesis about the functioning of the XPA protein.
Collapse
Affiliation(s)
- Yuliya S. Krasikova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Olga I. Lavrik
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Nadejda I. Rechkunova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
- Correspondence:
| |
Collapse
|
18
|
Kim M, Kim HS, D’Souza A, Gallagher K, Jeong E, Topolska-Woś A, Ogorodnik Le Meur K, Tsai CL, Tsai MS, Kee M, Tainer JA, Yeo JE, Chazin WJ, Schärer OD. Two interaction surfaces between XPA and RPA organize the preincision complex in nucleotide excision repair. Proc Natl Acad Sci U S A 2022; 119:e2207408119. [PMID: 35969784 PMCID: PMC9407234 DOI: 10.1073/pnas.2207408119] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 07/04/2022] [Indexed: 12/15/2022] Open
Abstract
The xeroderma pigmentosum protein A (XPA) and replication protein A (RPA) proteins fulfill essential roles in the assembly of the preincision complex in the nucleotide excision repair (NER) pathway. We have previously characterized the two interaction sites, one between the XPA N-terminal (XPA-N) disordered domain and the RPA32 C-terminal domain (RPA32C), and the other with the XPA DNA binding domain (DBD) and the RPA70AB DBDs. Here, we show that XPA mutations that inhibit the physical interaction in either site reduce NER activity in biochemical and cellular systems. Combining mutations in the two sites leads to an additive inhibition of NER, implying that they fulfill distinct roles. Our data suggest a model in which the interaction between XPA-N and RPA32C is important for the initial association of XPA with NER complexes, while the interaction between XPA DBD and RPA70AB is needed for structural organization of the complex to license the dual incision reaction. Integrative structural models of complexes of XPA and RPA bound to single-stranded/double-stranded DNA (ss/dsDNA) junction substrates that mimic the NER bubble reveal key features of the architecture of XPA and RPA in the preincision complex. Most critical among these is that the shape of the NER bubble is far from colinear as depicted in current models, but rather the two strands of unwound DNA must assume a U-shape with the two ss/dsDNA junctions localized in close proximity. Our data suggest that the interaction between XPA and RPA70 is key for the organization of the NER preincision complex.
Collapse
Affiliation(s)
- Mihyun Kim
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Republic of Korea
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Hyun-Suk Kim
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Republic of Korea
| | - Areetha D’Souza
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232-7917
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37232-7917
| | - Kaitlyn Gallagher
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232-7917
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37232-7917
| | - Eunwoo Jeong
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Republic of Korea
| | - Agnieszka Topolska-Woś
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232-7917
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37232-7917
| | - Kateryna Ogorodnik Le Meur
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232-7917
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37232-7917
| | - Chi-Lin Tsai
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030
| | - Miaw-Sheue Tsai
- Biological and Systems Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Minyong Kee
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Republic of Korea
| | - John A. Tainer
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030
| | - Jung-Eun Yeo
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Republic of Korea
| | - Walter J. Chazin
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232-7917
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37232-7917
- Department of Chemistry, Vanderbilt University, Nashville, TN 37232-7917
| | - Orlando D. Schärer
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Republic of Korea
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232-7917
| |
Collapse
|