1
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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.
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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
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2
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Manguinhas R, Serra PA, Soares RB, Rosell R, Gil N, Oliveira NG, Guedes RC. Unveiling Novel ERCC1-XPF Complex Inhibitors: Bridging the Gap from In Silico Exploration to Experimental Design. Int J Mol Sci 2024; 25:1246. [PMID: 38279246 PMCID: PMC10816628 DOI: 10.3390/ijms25021246] [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: 12/04/2023] [Revised: 01/09/2024] [Accepted: 01/10/2024] [Indexed: 01/28/2024] Open
Abstract
Modifications in DNA repair pathways are recognized as prognostic markers and potential therapeutic targets in various cancers, including non-small cell lung cancer (NSCLC). Overexpression of ERCC1 correlates with poorer prognosis and response to platinum-based chemotherapy. As a result, there is a pressing need to discover new inhibitors of the ERCC1-XPF complex that can potentiate the efficacy of cisplatin in NSCLC. In this study, we developed a structure-based virtual screening strategy targeting the inhibition of ERCC1 and XPF interaction. Analysis of crystal structures and a library of small molecules known to act against the complex highlighted the pivotal role of Phe293 (ERCC1) in maintaining complex stability. This residue was chosen as the primary binding site for virtual screening. Using an optimized docking protocol, we screened compounds from various databases, ultimately identifying more than one hundred potential inhibitors. Their capability to amplify cisplatin-induced cytotoxicity was assessed in NSCLC H1299 cells, which exhibited the highest ERCC1 expression of all the cell lines tested. Of these, 22 compounds emerged as promising enhancers of cisplatin efficacy. Our results underscore the value of pinpointing crucial molecular characteristics in the pursuit of novel modulators of the ERCC1-XPF interaction, which could be combined with cisplatin to treat NSCLC more effectively.
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Affiliation(s)
- Rita Manguinhas
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, 1649-003 Lisboa, Portugal; (R.M.); (P.A.S.); (R.B.S.)
| | - Patrícia A. Serra
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, 1649-003 Lisboa, Portugal; (R.M.); (P.A.S.); (R.B.S.)
- Lung Unit, Champalimaud Clinical Centre (CCC), Champalimaud Foundation, 1400-038 Lisboa, Portugal;
- Egas Moniz Interdisciplinary Research Center, Instituto Universitário Egas Moniz, 2829-511 Caparica, Portugal
| | - Rita B. Soares
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, 1649-003 Lisboa, Portugal; (R.M.); (P.A.S.); (R.B.S.)
- Lung Unit, Champalimaud Clinical Centre (CCC), Champalimaud Foundation, 1400-038 Lisboa, Portugal;
| | - Rafael Rosell
- Dr. Rosell Oncology Institute, 08028 Barcelona, Spain;
- Catalan Institute of Oncology, 08916 Barcelona, Spain
| | - Nuno Gil
- Lung Unit, Champalimaud Clinical Centre (CCC), Champalimaud Foundation, 1400-038 Lisboa, Portugal;
| | - Nuno G. Oliveira
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, 1649-003 Lisboa, Portugal; (R.M.); (P.A.S.); (R.B.S.)
| | - Rita C. Guedes
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, 1649-003 Lisboa, Portugal; (R.M.); (P.A.S.); (R.B.S.)
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3
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Sun J, Wang J, Chen X. Functionalization of Mesoporous Silica with a G-A-Mismatched dsDNA Chain for Efficient Identification and Selective Capturing of the MutY Protein. ACS APPLIED MATERIALS & INTERFACES 2023; 15:8884-8894. [PMID: 36757327 DOI: 10.1021/acsami.2c19257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
MUTYH adenine DNA glycosylase and its homologous protein (collectively MutY) are typical DNA glycosylases with a [4Fe4S] cluster and a helix-hairpin-helix (HhH) motif in its structure. In the present work, the binding behaviors of the MutY protein to dsDNA containing different base mismatches were investigated. The type and distribution of base mismatch in the dsDNA chain were found to influence the DNA-protein binding interaction greatly. The [4Fe4S] cluster of the MutY protein is able to identify a G-A mismatch in the dsDNA chain specifically by monitoring the anomalies of charge transport in the dsDNA chain, allowing the entrance of the identified dsDNA chain into the internal cavity of the MutY protein and the strong DNA-protein binding at the HhH motif of the protein through multiple H-bonds. The dsDNA chain with a centrally located G-A mismatch is thus functionalized on mesoporous silica (MSN) via amination reaction, and the obtained dsDNA(G-A)@MSN is used as a powerful sorbent for the selective capturing of the MutY protein from complex samples. By using 0.5% NH3·H2O (m/v) as a stripping reagent, efficient isolation of the MutY protein from different cell lines and bacteria is achieved and the recovered MutY protein is demonstrated to maintain favorable DNA adenine glycosylase activity.
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Affiliation(s)
- Jingqi Sun
- Research Center for Analytical Sciences, Department of Chemistry, College of Sciences, Northeastern University, Box 332, Shenyang, Liaoning 110819, China
| | - Jianhua Wang
- Research Center for Analytical Sciences, Department of Chemistry, College of Sciences, Northeastern University, Box 332, Shenyang, Liaoning 110819, China
| | - Xuwei Chen
- Research Center for Analytical Sciences, Department of Chemistry, College of Sciences, Northeastern University, Box 332, Shenyang, Liaoning 110819, China
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4
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XPF -673C>T variation is associated with the susceptibility to breast cancer. Cancer Epidemiol 2021; 74:102007. [PMID: 34416547 DOI: 10.1016/j.canep.2021.102007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 08/02/2021] [Accepted: 08/08/2021] [Indexed: 11/22/2022]
Abstract
PURPOSE XPF variations might decrease the DNA repair capacity and further contribute to cancer development. This study aimed to investigate the association of XPF polymorphisms with risk of developing breast cancer. METHODS TCGA, the Human Protein Atlas and Kaplan-Meier plotter were used to analyze the expression of XPF in breast cancer tissues and its effect on the survival of breast cancer patients. The expression of XPF in breast cancer tissues was detected by qRT-PCR. This case-control study included 467 breast cancer patients and 467 healthy controls. The genotype of genetic variation was detected by polymerase chain reaction restriction fragment length polymorphism. Odds ratios and 95 % confidence intervals were calculated. Correlations between XPF variation and clinicopathological parameters were assessed through Kendall's Tau-b test. The relationship between XPF gene function variation and XPF gene expression was analyzed by GTEx. RESULTS The expression of XPF in breast cancer tissues is higher than that in normal tissues. Breast cancer patients with high XPF expression have a higher relapse free survival rate (HR = 0.88, 95 % CI = 0.80-0.97), but have no effect on the overall survival rate (logrank P = 0.28). XPF -673C > T variant can reduce the risk of breast cancer patients (OR = 0.35, 95 %CI = 0.20-0.63 for codominant mode; OR = 0.66, 95 %CI = 0.51-0.85 for dominant model; OR = 0.40, 95 %CI = 0.23-0.70 for recessive model). The XPF 11985 GG genotype reduced the risk of early breast cancer (OR = 0.49, 95 %CI = 0.24-0.97), but not the risk of advanced breast cancer (OR = 1.20, 95 % CI = 0.58-2.48). XPF 11985A > G variant can also reduce the risk of ERBB2 expression in patients (OR = 0.50, 95 %CI = 0.27-0.94). There is no correlation between XPF -673C > T/XPF11985A > G variants and ER and PR. XPF -673C > T variant can reduce XPF expression (P < 0.05). CONCLUSIONS Genetic variations of XPF gene may affect its expression and the risk of breast cancer in the Chinese population.
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5
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Liu W, Palovcak A, Li F, Zafar A, Yuan F, Zhang Y. Fanconi anemia pathway as a prospective target for cancer intervention. Cell Biosci 2020; 10:39. [PMID: 32190289 PMCID: PMC7075017 DOI: 10.1186/s13578-020-00401-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 03/06/2020] [Indexed: 12/13/2022] Open
Abstract
Fanconi anemia (FA) is a recessive genetic disorder caused by biallelic mutations in at least one of 22 FA genes. Beyond its pathological presentation of bone marrow failure and congenital abnormalities, FA is associated with chromosomal abnormality and genomic instability, and thus represents a genetic vulnerability for cancer predisposition. The cancer relevance of the FA pathway is further established with the pervasive occurrence of FA gene alterations in somatic cancers and observations of FA pathway activation-associated chemotherapy resistance. In this article we describe the role of the FA pathway in canonical interstrand crosslink (ICL) repair and possible contributions of FA gene alterations to cancer development. We also discuss the perspectives and potential of targeting the FA pathway for cancer intervention.
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Affiliation(s)
- Wenjun Liu
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Gautier Building Room 311, 1011 NW 15th Street, Miami, FL 33136 USA
| | - Anna Palovcak
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Gautier Building Room 311, 1011 NW 15th Street, Miami, FL 33136 USA
| | - Fang Li
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Gautier Building Room 311, 1011 NW 15th Street, Miami, FL 33136 USA
| | - Alyan Zafar
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Gautier Building Room 311, 1011 NW 15th Street, Miami, FL 33136 USA
| | - Fenghua Yuan
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Gautier Building Room 311, 1011 NW 15th Street, Miami, FL 33136 USA
| | - Yanbin Zhang
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Gautier Building Room 311, 1011 NW 15th Street, Miami, FL 33136 USA
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136 USA
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6
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Arora K, Corbett KD. The conserved XPF:ERCC1-like Zip2:Spo16 complex controls meiotic crossover formation through structure-specific DNA binding. Nucleic Acids Res 2019; 47:2365-2376. [PMID: 30566683 PMCID: PMC6411835 DOI: 10.1093/nar/gky1273] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 12/06/2018] [Accepted: 12/11/2018] [Indexed: 01/24/2023] Open
Abstract
In eukaryotic meiosis, generation of haploid gametes depends on the formation of inter-homolog crossovers, which enable the pairing, physical linkage, and eventual segregation of homologs in the meiosis I division. A class of conserved meiosis-specific proteins, collectively termed ZMMs, are required for formation and spatial control of crossovers throughout eukaryotes. Here, we show that three Saccharomyces cerevisiae ZMM proteins-Zip2, Zip4 and Spo16-interact with one another and form a DNA-binding complex critical for crossover formation and control. We determined the crystal structure of a Zip2:Spo16 subcomplex, revealing a heterodimer structurally related to the XPF:ERCC1 endonuclease complex. Zip2:Spo16 lacks an endonuclease active site, but binds specific DNA structures found in early meiotic recombination intermediates. Mutations in multiple DNA-binding surfaces on Zip2:Spo16 severely compromise DNA binding, supporting a model in which the complex's central and HhH domains cooperate to bind DNA. Overall, our data support a model in which the Zip2:Zip4:Spo16 complex binds and stabilizes early meiotic recombination intermediates, then coordinates additional factors to promote crossover formation and license downstream events including synaptonemal complex assembly.
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Affiliation(s)
- Kanika Arora
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Kevin D Corbett
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA.,Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
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7
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Eichmiller R, Medina-Rivera M, DeSanto R, Minca E, Kim C, Holland C, Seol JH, Schmit M, Oramus D, Smith J, Gallardo IF, Finkelstein IJ, Lee SE, Surtees JA. Coordination of Rad1-Rad10 interactions with Msh2-Msh3, Saw1 and RPA is essential for functional 3' non-homologous tail removal. Nucleic Acids Res 2019; 46:5075-5096. [PMID: 29660012 PMCID: PMC6007489 DOI: 10.1093/nar/gky254] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2017] [Accepted: 03/28/2018] [Indexed: 12/19/2022] Open
Abstract
Double strand DNA break repair (DSBR) comprises multiple pathways. A subset of DSBR pathways, including single strand annealing, involve intermediates with 3' non-homologous tails that must be removed to complete repair. In Saccharomyces cerevisiae, Rad1-Rad10 is the structure-specific endonuclease that cleaves the tails in 3' non-homologous tail removal (3' NHTR). Rad1-Rad10 is also an essential component of the nucleotide excision repair (NER) pathway. In both cases, Rad1-Rad10 requires protein partners for recruitment to the relevant DNA intermediate. Msh2-Msh3 and Saw1 recruit Rad1-Rad10 in 3' NHTR; Rad14 recruits Rad1-Rad10 in NER. We created two rad1 separation-of-function alleles, rad1R203A,K205A and rad1R218A; both are defective in 3' NHTR but functional in NER. In vitro, rad1R203A,K205A was impaired at multiple steps in 3' NHTR. The rad1R218A in vivo phenotype resembles that of msh2- or msh3-deleted cells; recruitment of rad1R218A-Rad10 to recombination intermediates is defective. Interactions among rad1R218A-Rad10 and Msh2-Msh3 and Saw1 are altered and rad1R218A-Rad10 interactions with RPA are compromised. We propose a model in which Rad1-Rad10 is recruited and positioned at the recombination intermediate through interactions, between Saw1 and DNA, Rad1-Rad10 and Msh2-Msh3, Saw1 and Msh2-Msh3 and Rad1-Rad10 and RPA. When any of these interactions is altered, 3' NHTR is impaired.
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Affiliation(s)
- Robin Eichmiller
- Department of Biochemistry, University at Buffalo (SUNY), Buffalo, NY 14214, USA
| | - Melisa Medina-Rivera
- Department of Biochemistry, University at Buffalo (SUNY), Buffalo, NY 14214, USA
| | - Rachel DeSanto
- Department of Biochemistry, University at Buffalo (SUNY), Buffalo, NY 14214, USA
| | - Eugen Minca
- Department of Biochemistry, University at Buffalo (SUNY), Buffalo, NY 14214, USA
| | - Christopher Kim
- Department of Molecular Medicine, Institute of Biotechnology, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229-3900, USA
| | - Cory Holland
- Department of Molecular Medicine, Institute of Biotechnology, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229-3900, USA
| | - Ja-Hwan Seol
- Department of Molecular Medicine, Institute of Biotechnology, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229-3900, USA
| | - Megan Schmit
- Department of Biochemistry, University at Buffalo (SUNY), Buffalo, NY 14214, USA
| | - Diane Oramus
- Department of Biochemistry, University at Buffalo (SUNY), Buffalo, NY 14214, USA
| | - Jessica Smith
- Department of Biochemistry, University at Buffalo (SUNY), Buffalo, NY 14214, USA
| | - Ignacio F Gallardo
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Ilya J Finkelstein
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Sang Eun Lee
- Department of Molecular Medicine, Institute of Biotechnology, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229-3900, USA.,Department of Radiation Oncology, Institute of Biotechnology, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229-3900, USA
| | - Jennifer A Surtees
- Department of Biochemistry, University at Buffalo (SUNY), Buffalo, NY 14214, USA.,Genetics, Genomics and Bioinformatics Graduate Program, University at Buffalo (SUNY), Buffalo, NY 14214, USA
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8
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Faridounnia M, Folkers GE, Boelens R. Function and Interactions of ERCC1-XPF in DNA Damage Response. Molecules 2018; 23:E3205. [PMID: 30563071 PMCID: PMC6320978 DOI: 10.3390/molecules23123205] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Revised: 11/27/2018] [Accepted: 12/01/2018] [Indexed: 12/28/2022] Open
Abstract
Numerous proteins are involved in the multiple pathways of the DNA damage response network and play a key role to protect the genome from the wide variety of damages that can occur to DNA. An example of this is the structure-specific endonuclease ERCC1-XPF. This heterodimeric complex is in particular involved in nucleotide excision repair (NER), but also in double strand break repair and interstrand cross-link repair pathways. Here we review the function of ERCC1-XPF in various DNA repair pathways and discuss human disorders associated with ERCC1-XPF deficiency. We also overview our molecular and structural understanding of XPF-ERCC1.
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Affiliation(s)
- Maryam Faridounnia
- Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.
| | - Gert E Folkers
- Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.
| | - Rolf Boelens
- Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.
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9
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Mori T, Yousefzadeh MJ, Faridounnia M, Chong JX, Hisama FM, Hudgins L, Mercado G, Wade EA, Barghouthy AS, Lee L, Martin GM, Nickerson DA, Bamshad MJ, Niedernhofer LJ, Oshima J. ERCC4 variants identified in a cohort of patients with segmental progeroid syndromes. Hum Mutat 2017; 39:255-265. [PMID: 29105242 DOI: 10.1002/humu.23367] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 09/26/2017] [Accepted: 10/29/2017] [Indexed: 12/30/2022]
Abstract
Pathogenic variants in genes, which encode DNA repair and damage response proteins, result in a number of genomic instability syndromes with features of accelerated aging. ERCC4 (XPF) encodes a protein that forms a complex with ERCC1 and is required for the 5' incision during nucleotide excision repair. ERCC4 is also FANCQ, illustrating a critical role in interstrand crosslink repair. Pathogenic variants in this gene cause xeroderma pigmentosum, XFE progeroid syndrome, Cockayne syndrome (CS), and Fanconi anemia. We performed massive parallel sequencing for 42 unsolved cases submitted to the International Registry of Werner Syndrome. Two cases, each carrying two novel heterozygous ERCC4 variants, were identified. The first case was a compound heterozygote for: c.2395C > T (p.Arg799Trp) and c.388+1164_792+795del (p.Gly130Aspfs*18). Further molecular and cellular studies indicated that the ERCC4 variants in this patient are responsible for a phenotype consistent with a variant of CS. The second case was heterozygous for two variants in cis: c.[1488A > T; c.2579C > A] (p.[Gln496His; Ala860Asp]). While the second case also had several phenotypic features of accelerated aging, we were unable to provide biological evidence supporting the pathogenic roles of the associated ERCC4 variants. Precise genetic causes and disease mechanism of the second case remains to be determined.
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Affiliation(s)
- Takayasu Mori
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, Washington
| | - Matthew J Yousefzadeh
- Department of Molecular Medicine, Center on Aging, The Scripps Research Institute, Jupiter, Florida
| | - Maryam Faridounnia
- Department of Molecular Medicine, Center on Aging, The Scripps Research Institute, Jupiter, Florida
| | - Jessica X Chong
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, Washington
| | - Fuki M Hisama
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, Washington
| | - Louanne Hudgins
- Division of Medical Genetics, Stanford University School of Medicine, Stanford, California
| | | | - Erin A Wade
- Department of Molecular Medicine, Center on Aging, The Scripps Research Institute, Jupiter, Florida
| | - Amira S Barghouthy
- Department of Molecular Medicine, Center on Aging, The Scripps Research Institute, Jupiter, Florida
| | - Lin Lee
- Department of Pathology, University of Washington, Seattle, Washington
| | - George M Martin
- Department of Pathology, University of Washington, Seattle, Washington
| | - Deborah A Nickerson
- Department of Genome Sciences, University of Washington, Seattle, Washington
| | - Michael J Bamshad
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, Washington.,Department of Genome Sciences, University of Washington, Seattle, Washington.,Division of Genetic Medicine, Seattle Children's Hospital, Seattle, Washington
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- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, Washington
| | - Laura J Niedernhofer
- Department of Molecular Medicine, Center on Aging, The Scripps Research Institute, Jupiter, Florida
| | - Junko Oshima
- Department of Pathology, University of Washington, Seattle, Washington.,Department of Clinical Cell Biology and Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan
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10
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Das D, Faridounnia M, Kovacic L, Kaptein R, Boelens R, Folkers GE. Single-stranded DNA Binding by the Helix-Hairpin-Helix Domain of XPF Protein Contributes to the Substrate Specificity of the ERCC1-XPF Protein Complex. J Biol Chem 2016; 292:2842-2853. [PMID: 28028171 DOI: 10.1074/jbc.m116.747857] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Revised: 12/24/2016] [Indexed: 11/06/2022] Open
Abstract
The nucleotide excision repair protein complex ERCC1-XPF is required for incision of DNA upstream of DNA damage. Functional studies have provided insights into the binding of ERCC1-XPF to various DNA substrates. However, because no structure for the ERCC1-XPF-DNA complex has been determined, the mechanism of substrate recognition remains elusive. Here we biochemically characterize the substrate preferences of the helix-hairpin-helix (HhH) domains of XPF and ERCC-XPF and show that the binding to single-stranded DNA (ssDNA)/dsDNA junctions is dependent on joint binding to the DNA binding domain of ERCC1 and XPF. We reveal that the homodimeric XPF is able to bind various ssDNA sequences but with a clear preference for guanine-containing substrates. NMR titration experiments and in vitro DNA binding assays also show that, within the heterodimeric ERCC1-XPF complex, XPF specifically recognizes ssDNA. On the other hand, the HhH domain of ERCC1 preferentially binds dsDNA through the hairpin region. The two separate non-overlapping DNA binding domains in the ERCC1-XPF heterodimer jointly bind to an ssDNA/dsDNA substrate and, thereby, at least partially dictate the incision position during damage removal. Based on structural models, NMR titrations, DNA-binding studies, site-directed mutagenesis, charge distribution, and sequence conservation, we propose that the HhH domain of ERCC1 binds to dsDNA upstream of the damage, and XPF binds to the non-damaged strand within a repair bubble.
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Affiliation(s)
- Devashish Das
- From the Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands and
| | - Maryam Faridounnia
- From the Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands and
| | - Lidija Kovacic
- the Department of Molecular and Biomedical Sciences, Jožef Stefan Institute, Jamova cesta 39, 1000 Ljubljana, Slovenia
| | - Robert Kaptein
- From the Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands and
| | - Rolf Boelens
- From the Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands and
| | - Gert E Folkers
- From the Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands and
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11
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Abstract
Nucleotide excision repair (NER) is a highly versatile and efficient DNA repair process, which is responsible for the removal of a large number of structurally diverse DNA lesions. Its extreme broad substrate specificity ranges from DNA damages formed upon exposure to ultraviolet radiation to numerous bulky DNA adducts induced by mutagenic environmental chemicals and cytotoxic drugs used in chemotherapy. Defective NER leads to serious diseases, such as xeroderma pigmentosum (XP). Eight XP complementation groups are known of which seven (XPA-XPG) are caused by mutations in genes involved in the NER process. The eighth gene, XPV, codes for the DNA polymerase ɳ, which replicates through DNA lesions in a process called translesion synthesis (TLS). Over the past decade, detailed structural information of these DNA repair proteins involved in eukaryotic NER and TLS have emerged. These structures allow us now to understand the molecular mechanism of the NER and TLS processes in quite some detail and we have begun to understand the broad substrate specificity of NER. In this review, we aim to highlight recent advances in the process of damage recognition and repair as well as damage tolerance by the XP proteins.
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12
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Nowotny M, Gaur V. Structure and mechanism of nucleases regulated by SLX4. Curr Opin Struct Biol 2016; 36:97-105. [PMID: 26827285 DOI: 10.1016/j.sbi.2016.01.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 01/06/2016] [Accepted: 01/07/2016] [Indexed: 01/08/2023]
Abstract
SLX4 is a multidomain platform that regulates various proteins that are involved in genome maintenance and stability. Among these proteins are three structure-selective nucleases (SSEs). XPF-ERCC1 and MUS81-EME1 are structurally similar and function as heterodimers of highly similar subunits, in which only one is active. Two independent modules are formed from subunits of the heterodimers - a dimer of nuclease and nuclease-like domains and a dimer of tandem helix-hairpin-helix HhH2 domains. Both modules are responsible for substrate recognition. The third SSE, SLX1, contains GIY-YIG and RING domains and is a promiscuous nuclease. Structural data imply that SLX1 exists in free form as an autoinhibited homodimer. Association with SLX4 platform disrupts the homodimer and activates SLX1. This review discusses the available structural and mechanistic information on SLX4-regulated SSEs.
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Affiliation(s)
- Marcin Nowotny
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, Warsaw, Poland.
| | - Vineet Gaur
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, Warsaw, Poland.
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13
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Fadda E. Role of the XPA protein in the NER pathway: A perspective on the function of structural disorder in macromolecular assembly. Comput Struct Biotechnol J 2015; 14:78-85. [PMID: 26865925 PMCID: PMC4710682 DOI: 10.1016/j.csbj.2015.11.007] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 11/25/2015] [Accepted: 11/26/2015] [Indexed: 12/23/2022] Open
Abstract
Lack of structure is often an essential functional feature of protein domains. The coordination of macromolecular assemblies in DNA repair pathways is yet another task disordered protein regions are highly implicated in. Here I review the available experimental and computational data and within this context discuss the functional role of structure and disorder in one of the essential scaffolding proteins in the nucleotide excision repair (NER) pathway, namely Xeroderma pigmentosum complementation group A (XPA). From the analysis of the current knowledge, in addition to protein–protein docking and secondary structure prediction results presented for the first time herein, a mechanistic framework emerges, where XPA builds the NER pre-incision complex in a modular fashion, as “beads on a string”, where the protein–protein interaction “beads”, or modules, are interconnected by disordered link regions. This architecture is ideal to avoid the expected steric hindrance constraints of the DNA expanded bubble. Finally, the role of the XPA structural disorder in binding affinity modulation and in the sequential binding of NER core factors in the pre-incision complex is also discussed.
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Affiliation(s)
- Elisa Fadda
- Department of Chemistry, Maynooth University, Maynooth, Kildare, Ireland
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14
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Faridounnia M, Wienk H, Kovačič L, Folkers GE, Jaspers NGJ, Kaptein R, Hoeijmakers JHJ, Boelens R. The Cerebro-oculo-facio-skeletal Syndrome Point Mutation F231L in the ERCC1 DNA Repair Protein Causes Dissociation of the ERCC1-XPF Complex. J Biol Chem 2015; 290:20541-55. [PMID: 26085086 DOI: 10.1074/jbc.m114.635169] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Indexed: 12/15/2022] Open
Abstract
The ERCC1-XPF heterodimer, a structure-specific DNA endonuclease, is best known for its function in the nucleotide excision repair (NER) pathway. The ERCC1 point mutation F231L, located at the hydrophobic interaction interface of ERCC1 (excision repair cross-complementation group 1) and XPF (xeroderma pigmentosum complementation group F), leads to severe NER pathway deficiencies. Here, we analyze biophysical properties and report the NMR structure of the complex of the C-terminal tandem helix-hairpin-helix domains of ERCC1-XPF that contains this mutation. The structures of wild type and the F231L mutant are very similar. The F231L mutation results in only a small disturbance of the ERCC1-XPF interface, where, in contrast to Phe(231), Leu(231) lacks interactions stabilizing the ERCC1-XPF complex. One of the two anchor points is severely distorted, and this results in a more dynamic complex, causing reduced stability and an increased dissociation rate of the mutant complex as compared with wild type. These data provide a biophysical explanation for the severe NER deficiencies caused by this mutation.
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Affiliation(s)
- Maryam Faridounnia
- From the Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Hans Wienk
- From the Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Lidija Kovačič
- the Department of Molecular and Biomedical Sciences, Jožef Stefan Institute, Jamova cesta 39, SI-1000 Ljubljana, Slovenia, and
| | - Gert E Folkers
- From the Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Nicolaas G J Jaspers
- the Department of Genetics, Erasmus Medical Center, PO Box 2040, 3000 CA Rotterdam, The Netherlands
| | - Robert Kaptein
- From the Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Jan H J Hoeijmakers
- the Department of Genetics, Erasmus Medical Center, PO Box 2040, 3000 CA Rotterdam, The Netherlands
| | - Rolf Boelens
- From the Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands,
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15
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Manandhar M, Boulware KS, Wood RD. The ERCC1 and ERCC4 (XPF) genes and gene products. Gene 2015; 569:153-61. [PMID: 26074087 DOI: 10.1016/j.gene.2015.06.026] [Citation(s) in RCA: 93] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Revised: 05/01/2015] [Accepted: 06/09/2015] [Indexed: 12/22/2022]
Abstract
The ERCC1 and ERCC4 genes encode the two subunits of the ERCC1-XPF nuclease. This enzyme plays an important role in repair of DNA damage and in maintaining genomic stability. ERCC1-XPF nuclease nicks DNA specifically at junctions between double-stranded and single-stranded DNA, when the single-strand is oriented 5' to 3' away from a junction. ERCC1-XPF is a core component of nucleotide excision repair and also plays a role in interstrand crosslink repair, some pathways of double-strand break repair by homologous recombination and end-joining, as a backup enzyme in base excision repair, and in telomere length regulation. In many of these activities, ERCC1-XPF complex cleaves the 3' tails of DNA intermediates in preparation for further processing. ERCC1-XPF interacts with other proteins including XPA, RPA, SLX4 and TRF2 to perform its functions. Disruption of these interactions or direct targeting of ERCC1-XPF to decrease its DNA repair function might be a useful strategy to increase the sensitivity of cancer cells to some DNA damaging agents. Complete deletion of either ERCC1 or ERCC4 is not compatible with viability in mice or humans. However, mutations in the ERCC1 or ERCC4 genes cause a remarkable array of rare inherited human disorders. These include specific forms of xeroderma pigmentosum, Cockayne syndrome, Fanconi anemia, XFE progeria and cerebro-oculo-facio-skeletal syndrome.
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Affiliation(s)
- Mandira Manandhar
- Department of Epigenetics & Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA; The University of Texas Graduate School of Biomedical Sciences at Houston, Houston, TX 77030, USA
| | - Karen S Boulware
- The University of Texas Graduate School of Biomedical Sciences at Houston, Houston, TX 77030, USA
| | - Richard D Wood
- Department of Epigenetics & Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA; The University of Texas Graduate School of Biomedical Sciences at Houston, Houston, TX 77030, USA.
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16
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Feltes BC, Bonatto D. Overview of xeroderma pigmentosum proteins architecture, mutations and post-translational modifications. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2014; 763:306-20. [PMID: 25795128 DOI: 10.1016/j.mrrev.2014.12.002] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Revised: 12/08/2014] [Accepted: 12/09/2014] [Indexed: 12/15/2022]
Abstract
The xeroderma pigmentosum complementation group proteins (XPs), which include XPA through XPG, play a critical role in coordinating and promoting global genome and transcription-coupled nucleotide excision repair (GG-NER and TC-NER, respectively) pathways in eukaryotic cells. GG-NER and TC-NER are both required for the repair of bulky DNA lesions, such as those induced by UV radiation. Mutations in genes that encode XPs lead to the clinical condition xeroderma pigmentosum (XP). Although the roles of XPs in the GG-NER/TC-NER subpathways have been extensively studied, complete knowledge of their three-dimensional structure is only beginning to emerge. Hence, this review aims to summarize the current knowledge of mapped mutations and other structural information on XP proteins that influence their function and protein-protein interactions. We also review the possible post-translational modifications for each protein and the impact of these modifications on XP protein functions.
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Affiliation(s)
- Bruno César Feltes
- Biotechnology Center of the Federal University of Rio Grande do Sul, Department of Molecular Biology and Biotechnology, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Diego Bonatto
- Biotechnology Center of the Federal University of Rio Grande do Sul, Department of Molecular Biology and Biotechnology, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil.
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17
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Liu Y, Cao L, Chang J, Lin J, He B, Rao J, Zhang Z, Zhang X. XPF-673C>T polymorphism effect on the susceptibility to esophageal cancer in Chinese population. PLoS One 2014; 9:e94136. [PMID: 24709955 PMCID: PMC3978021 DOI: 10.1371/journal.pone.0094136] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Accepted: 03/12/2014] [Indexed: 12/12/2022] Open
Abstract
Purpose Xeroderma pigmentsum group F (XPF) plays a pivotal role in DNA nucleotide excision repair and has been linked to the development of various cancers. This study aims to assess the association of XPF genetic variants with the susceptibility to esophageal squamous cell carcinoma (ESCC) in Chinese population. Methods This two-stage case-control study was conducted in a total of 1524 patients with ESCC and 1524 controls. Genotype of XPF -673C>T and 11985A>G variants were determined by polymerase chain reaction-based restriction fragment length polymorphism (PCR-RFLP). Logistic regression analysis was performed to estimate odd ratios (ORs) and 95% confidence intervals (95% CI). Results Our case-control study showed that XPF -673TT genotype was associated with a decreased risk of ESCC compared with CC genotype in both case-control sets (Tangshan set: OR = 0.58; 95%CI = 0.34–0.99, P = 0.040; Beijing set: OR = 0.66; 95%CI = 0.46–0.95, P = 0.027). Stratified analyses revealed that a multiplicative interaction between -673C>T variant and age, sex or smoking status was evident (Gene-age: Pinteraction = 0.002; Gene-sex: Pinteraction = 0.002; Gene-smoking: Pinteraction = 0.002). For XPF 11985A>G polymorphism, there was no significant difference of genotype distribution between ESCC cases and controls. Conclusion These findings indicated that genetic variants in XPF might contribute to the susceptibility to ESCC.
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Affiliation(s)
- Yingwen Liu
- Department of Molecular Genetics, College of Life Science, Hebei United University, Tangshan, China
- Department of Epidemiology, College of Public Health, Hebei United University, Tangshan, China
| | - Lei Cao
- Department of Molecular Genetics, College of Life Science, Hebei United University, Tangshan, China
| | - Jiang Chang
- Department of Etiology and Carcinogenesis, Cancer Institute and Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Jia Lin
- Department of Molecular Genetics, College of Life Science, Hebei United University, Tangshan, China
| | - Bing He
- Department of Molecular Genetics, College of Life Science, Hebei United University, Tangshan, China
| | - Juan Rao
- Department of Molecular Genetics, College of Life Science, Hebei United University, Tangshan, China
| | - Zhi Zhang
- Hebei United University Affiliated Tangshan Gongren Hospital, Tangshan, China
| | - Xuemei Zhang
- Department of Molecular Genetics, College of Life Science, Hebei United University, Tangshan, China
- * E-mail:
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18
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Wang W, Ding J, Zhang Y, Hu Y, Wang DC. Structural insights into the unique single-stranded DNA-binding mode of Helicobacter pylori DprA. Nucleic Acids Res 2013; 42:3478-91. [PMID: 24369431 PMCID: PMC3950713 DOI: 10.1093/nar/gkt1334] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Natural transformation (NT) in bacteria is a complex process, including binding, uptake, transport and recombination of exogenous DNA into the chromosome, consequently generating genetic diversity and driving evolution. DNA processing protein A (DprA), which is distributed among virtually all bacterial species, is involved in binding to the internalized single-stranded DNA (ssDNA) and promoting the loading of RecA on ssDNA during NTs. Here we present the structures of DNA_processg_A (DprA) domain of the Helicobacter pylori DprA (HpDprA) and its complex with an ssDNA at 2.20 and 1.80 Å resolutions, respectively. The complex structure revealed for the first time how the conserved DprA domain binds to ssDNA. Based on structural comparisons and binding assays, a unique ssDNA-binding mode is proposed: the dimer of HpDprA binds to ssDNA through two small, positively charged binding pockets of the DprA domains with classical Rossmann folds and the key residue Arg52 is re-oriented to ‘open’ the pocket in order to accommodate one of the bases of ssDNA, thus enabling HpDprA to grasp substrate with high affinity. This mode is consistent with the oligomeric composition of the complex as shown by electrophoretic mobility-shift assays and static light scattering measurements, but differs from the direct polymeric complex of Streptococcus pneumoniae DprA–ssDNA.
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Affiliation(s)
- Wei Wang
- The National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China
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Yang H, Zhang T, Tao Y, Wang F, Tong L, Ding J. Structural insights into the functions of the FANCM-FAAP24 complex in DNA repair. Nucleic Acids Res 2013; 41:10573-83. [PMID: 24003026 PMCID: PMC3905867 DOI: 10.1093/nar/gkt788] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Fanconi anemia (FA) is a genetically heterogeneous disorder associated with deficiencies in the FA complementation group network. FA complementation group M (FANCM) and FA-associated protein 24 kDa (FAAP24) form a stable complex to anchor the FA core complex to chromatin in repairing DNA interstrand crosslinks. Here, we report the first crystal structure of the C-terminal segment of FANCM in complex with FAAP24. The C-terminal segment of FANCM and FAAP24 both consist of a nuclease domain at the N-terminus and a tandem helix-hairpin-helix (HhH)2 domain at the C-terminus. The FANCM-FAAP24 complex exhibits a similar architecture as that of ApXPF. However, the variations of several key residues and the electrostatic property at the active-site region render a catalytically inactive nuclease domain of FANCM, accounting for the lack of nuclease activity. We also show that the first HhH motif of FAAP24 is a potential binding site for DNA, which plays a critical role in targeting FANCM-FAAP24 to chromatin. These results reveal the mechanistic insights into the functions of FANCM-FAAP24 in DNA repair.
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Affiliation(s)
- Hui Yang
- State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai 200031, China, Graduate School of Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai 200031, China and Department of Biological Sciences, Columbia University, New York, NY 10027, USA
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Wienk H, Slootweg JC, Speerstra S, Kaptein R, Boelens R, Folkers GE. The Fanconi anemia associated protein FAAP24 uses two substrate specific binding surfaces for DNA recognition. Nucleic Acids Res 2013; 41:6739-49. [PMID: 23661679 PMCID: PMC3711432 DOI: 10.1093/nar/gkt354] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
To maintain the integrity of the genome, multiple DNA repair systems exist to repair damaged DNA. Recognition of altered DNA, including bulky adducts, pyrimidine dimers and interstrand crosslinks (ICL), partially depends on proteins containing helix-hairpin-helix (HhH) domains. To understand how ICL is specifically recognized by the Fanconi anemia proteins FANCM and FAAP24, we determined the structure of the HhH domain of FAAP24. Although it resembles other HhH domains, the FAAP24 domain contains a canonical hairpin motif followed by distorted motif. The HhH domain can bind various DNA substrates; using nuclear magnetic resonance titration experiments, we demonstrate that the canonical HhH motif is required for double-stranded DNA (dsDNA) binding, whereas the unstructured N-terminus can interact with single-stranded DNA. Both DNA binding surfaces are used for binding to ICL-like single/double-strand junction-containing DNA substrates. A structural model for FAAP24 bound to dsDNA has been made based on homology with the translesion polymerase iota. Site-directed mutagenesis, sequence conservation and charge distribution support the dsDNA-binding model. Analogous to other HhH domain-containing proteins, we suggest that multiple FAAP24 regions together contribute to binding to single/double-strand junction, which could contribute to specificity in ICL DNA recognition.
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Affiliation(s)
- Hans Wienk
- Bijvoet Center For Biomolecular Research, NMR Spectroscopy, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
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21
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McNeil EM, Melton DW. DNA repair endonuclease ERCC1-XPF as a novel therapeutic target to overcome chemoresistance in cancer therapy. Nucleic Acids Res 2012; 40:9990-10004. [PMID: 22941649 PMCID: PMC3488251 DOI: 10.1093/nar/gks818] [Citation(s) in RCA: 138] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The ERCC1–XPF complex is a structure-specific endonuclease essential for the repair of DNA damage by the nucleotide excision repair pathway. It is also involved in other key cellular processes, including DNA interstrand crosslink (ICL) repair and DNA double-strand break (DSB) repair. New evidence has recently emerged, increasing our understanding of its requirement in these additional roles. In this review, we focus on the protein–protein and protein–DNA interactions made by the ERCC1 and XPF proteins and discuss how these coordinate ERCC1–XPF in its various roles. In a number of different cancers, high expression of ERCC1 has been linked to a poor response to platinum-based chemotherapy. We discuss prospects for the development of DNA repair inhibitors that target the activity, stability or protein interactions of the ERCC1–XPF complex as a novel therapeutic strategy to overcome chemoresistance.
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Affiliation(s)
- Ewan M McNeil
- MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, MRC Human Genetics Unit, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK
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Abstract
In this issue of Structure, Das et al. report the structure of the helix-hairpin-helix dimerization domain of XPF bound to ssDNA. These results provide insight into the architecture of nucleotide excision repair machinery and how it interacts with damaged DNA substrates.
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Affiliation(s)
- Steven M Shell
- Department of Biochemistry, Center for Structural Biology, 5140 Biological Sciences/MRB III, Vanderbilt University, Nashville, TN 37232-8725, USA.
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