The structure-specific endonuclease complex SLX4–XPF regulates Tus–Ter-induced homologous recombination

Elango, Rajula; Panday, Arvind; Lach, Francis P.; Willis, Nicholas A.; Nicholson, Kaitlin; Duffey, Erin E.; Smogorzewska, Agata; Scully, Ralph

doi:10.1038/s41594-022-00812-9

Cited by 16 publications

(11 citation statements)

References 92 publications

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“…For example, SLX1 is catalytically inactive until it binds the conserved C-terminal domain (CCD) domain of SLX4, after which it is competent to cleave many types of branched DNA structures [10,[12][13][14]. Similarly, SLX4 stimulates XPF-ERCC1 to cleave replication forks that stall at protein-DNA adducts or interstrand crosslinks [18,19]. When cells enter mitosis, phosphorylation of the SLX4 scaffold triggers the recruitment of MUS81-EME1, leading to the formation of a tri-nuclease complex called SMX (for SLX1-SLX4, MUS81-EME1, and XPF-ERCC1) [10,15].…”

Section: Introductionmentioning

confidence: 99%

Comprehensive Interactome Mapping of the DNA Repair Scaffold SLX4 using Proximity Labeling and Affinity Purification

Aprosoff

Dyakov

Cheung

et al. 2022

Preprint

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The DNA repair scaffold SLX4 has pivotal roles in cellular processes that maintain genome stability, most notably homologous recombination. Germline mutations in SLX4 are associated with Fanconi anemia, a disease characterized by chromosome instability and cancer susceptibility. The role of mammalian SLX4 in homologous recombination depends critically on binding and activating structure-selective endonucleases, namely SLX1, MUS81-EME1, and XPF-ERCC1. Increasing evidence indicates that cells rely on distinct SLX4-dependent complexes to remove DNA lesions in specific regions of the genome. Despite our understanding of SLX4 as a scaffold for DNA repair proteins, a detailed repertoire of SLX4 interactors has never been reported. Here, we provide the first comprehensive map of the human SLX4 interactome using proximity-dependent biotin identification (BioID) and affinity purification coupled to mass spectrometry (AP-MS). We identified 237 high-confidence interactors, of which the vast majority represent novel SLX4 binding proteins. Network analysis of these hits revealed pathways with known involvement of SLX4, such as DNA repair, and novel or emerging pathways of interest, including RNA metabolism and chromatin remodeling. In summary, the comprehensive SLX4 interactome we report here provides a deeper understanding of how SLX4 functions in DNA repair while revealing new cellular processes that may involve SLX4.

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Section: Introductionmentioning

confidence: 99%

Comprehensive Interactome Mapping of the DNA Repair Scaffold SLX4 using Proximity Labeling and Affinity Purification

Aprosoff

Dyakov

Cheung

et al. 2022

Preprint

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“…Early clues about the scaffold function of mammalian SLX4 came from bioinformatics and affinity purification coupled to mass spectrometry (AP-MS) experiments, which revealed that SLX1, MUS81-EME1, and XPF-ERCC1 bind distinct regions of SLX4 (Figure A). − Subsequent biochemical studies revealed that SLX4 activates and regulates its endonuclease partners. For example, SLX1 is catalytically inactive until it binds the conserved C-terminal domain (CCD) of SLX4, after which it is competent to cleave many types of branched DNA structures. ,− Similarly, SLX4 stimulates XPF-ERCC1 to cleave replication forks that stall at protein–DNA adducts or interstrand crosslinks. , When cells enter mitosis, phosphorylation of the SLX4 scaffold triggers the recruitment of MUS81-EME1, leading to the formation of a tri-nuclease complex called SMX (for S LX1-SLX4, M US81-EME1, and X PF-ERCC1). , Notably, SLX4 binding to MUS81-EME1 stimulates the cleavage of branched DNA structures that represent replication and recombination intermediates . The current model is that SMX provides cells with a multifunctional nuclease that removes joint molecules prior to cytokinesis.…”

Section: Introductionmentioning

confidence: 99%

Comprehensive Interactome Mapping of the DNA Repair Scaffold SLX4 Using Proximity Labeling and Affinity Purification

et al. 2023

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The DNA repair scaffold SLX4 has pivotal roles in cellular processes that maintain genome stability, most notably homologous recombination. Germline mutations in SLX4 are associated with Fanconi anemia, a disease characterized by chromosome instability and cancer susceptibility. The role of mammalian SLX4 in homologous recombination depends critically on binding and activating structure-selective endonucleases, namely SLX1, MUS81-EME1, and XPF-ERCC1. Increasing evidence indicates that cells rely on distinct SLX4-dependent complexes to remove DNA lesions in specific regions of the genome. Despite our understanding of SLX4 as a scaffold for DNA repair proteins, a detailed repertoire of SLX4 interactors has never been reported. Here, we provide a comprehensive map of the human SLX4 interactome using proximity-dependent biotin identification (BioID) and affinity purification coupled to mass spectrometry (AP-MS). We identified 221 unique high-confidence interactors, of which the vast majority represent novel SLX4-binding proteins. Network analysis of these hits revealed pathways with known involvement of SLX4, such as DNA repair, and several emerging pathways of interest, including RNA metabolism and chromatin remodeling. In summary, the comprehensive SLX4 interactome we report here provides a deeper understanding of how SLX4 functions in DNA repair while revealing new cellular processes that may involve SLX4.

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“…Biallelic inactivation of SLX4 underlies complementation group P of Fanconi anemia (27, 28 ), an inherited disease associated with congenital abnormalities, pancytopenia and cancer proneness ( 29 ). SLX4 associates with multiple DNA repair factors including the structure-specific endonucleases (SSEs) XPF-ERCC1, MUS81-EME1, and SLX1 to repair interstrand DNA crosslinks, drive the resolution of Holliday junctions, promote DNA repair synthesis at common fragile sites and/or ensure telomere maintenance ( 30–40 ). Furthermore, SLX4-XPF promotes homologous recombination at a replication fork barrier caused by tightly DNA-bound proteins ( 41 ).…”

Section: Introductionmentioning

confidence: 99%

“…SLX4 associates with several DNA repair factors including the structure-specific endonucleases (SSEs) XPF-ERCC1, MUS81-EME1, and SLX1 to repair DNA interstrand crosslinks, resolve Holliday junctions, ensure telomere maintenance, and maintain stability of common fragile sites [42][43][44][45][46][47][48][49][50][51][52][53] . Recent evidence indicates that at a replication fork barrier caused by tightly DNA-bound proteins, SLX4-XPF promotes the recruitment of DNA damage response factors and DNA repair by homologous recombination 54,55 . SLX4 and XPF deficient cells are hypersensitive to DNA methyltransferases and topoisomerase 1 DNAprotein crosslinks (DPCs) 54,56,57 , but how SLX4-XPF mechanistically promotes the processing of DPCs remains incompletely understood.…”

Section: Introductionmentioning

confidence: 99%

“…Recent evidence indicates that at a replication fork barrier caused by tightly DNA-bound proteins, SLX4-XPF promotes the recruitment of DNA damage response factors and DNA repair by homologous recombination 54, 55 . SLX4 and XPF deficient cells are hypersensitive to DNA methyltransferases and topoisomerase 1 DNA-protein crosslinks (DPCs) 54, 56, 57 , but how SLX4-XPF mechanistically promotes the processing of DPCs remains incompletely understood.…”

Section: Introductionmentioning

confidence: 99%

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Compartmentalization of the SUMO/RNF4 pathway by SLX4 drives DNA repair

Alghoul

Paloni

Takedachi

et al. 2022

Preprint

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SLX4 disabled in Fanconi anemia group P is a multifunctional scaffold protein that coordinates the action of structure-specific endonucleases and other DNA repair proteins to ensure genome stability. We show here that SLX4 drives the regulated assembly of an extensive protein network cross-linked by SLX4 dimerization and SUMO-SIM interactions that yield liquid-like nuclear condensates. SLX4 condensates compartmentalize the SUMO system and the STUbL RNF4 to enhance selectively the modification of substrate proteins by SUMO and ubiquitin. Specifically, we find that the assembly of SLX4 condensates induces the processing of topoisomerase 1 - DNA protein crosslinks (TOP1cc), as well as the resection of newly synthesized DNA. This unanticipated function of SLX4 emerges from the collective behavior of proteins that compose SLX4 condensates in live cells. We conclude that SLX4 foci are functional compartments maintained by site-specific protein-protein interactions that control key biochemical reactions in DNA repair.

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The structure-specific endonuclease complex SLX4–XPF regulates Tus–Ter-induced homologous recombination

Cited by 16 publications

References 92 publications

Comprehensive Interactome Mapping of the DNA Repair Scaffold SLX4 using Proximity Labeling and Affinity Purification

Comprehensive Interactome Mapping of the DNA Repair Scaffold SLX4 using Proximity Labeling and Affinity Purification

Comprehensive Interactome Mapping of the DNA Repair Scaffold SLX4 Using Proximity Labeling and Affinity Purification

Compartmentalization of the SUMO/RNF4 pathway by SLX4 drives DNA repair

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