1
|
Odango RJ, Camberos J, Fregoso FE, Fischhaber PL. SAW1 is increasingly required to recruit Rad10 as SSA flap-length increases from 20 to 50 bases in single-strand annealing in S. cerevisiae. Biochem Biophys Rep 2021; 28:101125. [PMID: 34622036 PMCID: PMC8481969 DOI: 10.1016/j.bbrep.2021.101125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 08/27/2021] [Accepted: 08/30/2021] [Indexed: 11/16/2022] Open
Abstract
SAW1 is required by the Rad1-Rad10 nuclease for efficient removal of 3′ non-homologous DNA ends (flaps) formed as intermediates during two modes of double-strand break repair in S. cerevisiae, single-strand annealing (SSA) and synthesis-dependent strand annealing (SDSA). Saw1 was shown in vitro to exhibit increasing affinity for flap DNAs as flap lengths varied from 0 to 40 deoxynucleotides (nt) with almost no binding observed when flaps were shorter than 10 nt. Accordingly, our prior in vivo fluorescence microscopy investigation showed that SAW1 was not required for recruitment of Rad10-YFP to DNA double-strand breaks (DSBs) when flaps were ∼10 nt, but it was required when flaps were ∼500 nt in G1 phase of the cell cycle. We were curious whether we would also observe an increased requirement of SAW1 for Rad10 recruitment in vivo as flaps varied from ∼20 to 50 nt, as was shown in vitro. In this investigation, we utilized SSA substrates that generate 20, 30, and 50 nt flaps in vivo in fluorescence microscopy assays and determined that SAW1 becomes increasingly necessary for SSA starting at about ∼20 nt and is completely required at ∼50 nt. Quantitative PCR experiments corroborate these results by demonstrating that repair product formation decreases in the absence of SAW1 as flap length increases. Experiments with strains containing fluorescently labeled Saw1 (Saw1-CFP) show that Saw1 localizes with Rad10 at SSA foci and that about half of the foci containing Rad10 at DSBs do not contain Saw1. Colocalization patterns of Saw1-CFP are consistent regardless of the flap length of the substrate and are roughly similar in all phases of the cell cycle. Together, these data show that Saw1 becomes increasingly important for Rad1-Rad10 recruitment and SSA repair in the ∼20–50 nt flap range, and Saw1 is present at repair sites even when not required and may depart the repair site ahead of Rad1-Rad10. There is an increasing dependence on Saw1 to recruit Rad1-Rad10 as DNA flaps increase The flap length range causing the increasing dependence is 20–50 deoxynucleotides Saw1 is found at single-strand annealing foci even when not required to recruit Rad1-Rad10 Saw1 is found in only about half of the single-strand annealing foci containing Rad1-Rad10
Collapse
Affiliation(s)
- Rowen Jane Odango
- Department of Chemistry and Biochemistry, California State University Northridge, 18111 Nordhoff St, Northridge, CA, 91330-8262, United States
| | - Juan Camberos
- Department of Chemistry and Biochemistry, California State University Northridge, 18111 Nordhoff St, Northridge, CA, 91330-8262, United States
| | - Fred Erick Fregoso
- Department of Chemistry and Biochemistry, California State University Northridge, 18111 Nordhoff St, Northridge, CA, 91330-8262, United States
| | - Paula L Fischhaber
- Department of Chemistry and Biochemistry, California State University Northridge, 18111 Nordhoff St, Northridge, CA, 91330-8262, United States
| |
Collapse
|
2
|
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: 1.2] [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.
Collapse
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
| |
Collapse
|
3
|
Distinct roles of XPF-ERCC1 and Rad1-Rad10-Saw1 in replication-coupled and uncoupled inter-strand crosslink repair. Nat Commun 2018; 9:2025. [PMID: 29795289 PMCID: PMC5966407 DOI: 10.1038/s41467-018-04327-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 04/20/2018] [Indexed: 01/17/2023] Open
Abstract
Yeast Rad1-Rad10 (XPF-ERCC1 in mammals) incises UV, oxidation, and cross-linking agent-induced DNA lesions, and contributes to multiple DNA repair pathways. To determine how Rad1-Rad10 catalyzes inter-strand crosslink repair (ICLR), we examined sensitivity to ICLs from yeast deleted for SAW1 and SLX4, which encode proteins that interact physically with Rad1-Rad10 and bind stalled replication forks. Saw1, Slx1, and Slx4 are critical for replication-coupled ICLR in mus81 deficient cells. Two rad1 mutations that disrupt interactions between Rpa1 and Rad1-Rad10 selectively disable non-nucleotide excision repair (NER) function, but retain UV lesion repair. Mutations in the analogous region of XPF also compromised XPF interactions with Rpa1 and Slx4, and are proficient in NER but deficient in ICLR and direct repeat recombination. We propose that Rad1-Rad10 makes distinct contributions to ICLR depending on cell cycle phase: in G1, Rad1-Rad10 removes ICL via NER, whereas in S/G2, Rad1-Rad10 facilitates NER-independent replication-coupled ICLR.
Collapse
|
4
|
Saw1 localizes to repair sites but is not required for recruitment of Rad10 to repair intermediates bearing short non-homologous 3' flaps during single-strand annealing in S. cerevisiae. Mol Cell Biochem 2015; 412:131-9. [PMID: 26699908 DOI: 10.1007/s11010-015-2616-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Accepted: 12/08/2015] [Indexed: 10/22/2022]
Abstract
SAW1 is required for efficient removal by the Rad1-Rad10 nuclease of 3' non-homologous DNA ends (flaps) formed as intermediates during two modes of double-strand break (DSB) repair in S. cerevisiae, single-strand annealing (SSA) and synthesis-dependent strand annealing. Saw1 was shown in vitro to bind flaps with high affinity, but displayed diminished affinity when flaps were short (<30 deoxynucleotides [nt]), consistent with it not being required for short flap cleavage. Accordingly, this study, using in vivo fluorescence microscopy showed that SAW1 was not required for recruitment of Rad10-YFP to DNA DSBs during their repair by SSA when the flaps were ~10 nt. In contrast, recruitment of Rad10-YFP to DSBs when flaps were ~500 nt did require SAW1 in G1 phase of cell cycle. Interestingly, we observed a substantial increase in colocalization of Saw1-CFP and Rad10-YFP at DSBs when short flaps were formed during repair, especially in G1, indicating significant recruitment of Saw1 despite there being no requirement for Saw1 to recruit Rad10. Saw1-CFP was seldom observed at DSBs without Rad10-YFP. Together, these results support a model in which Saw1 and Rad1-Rad10 are recruited as a complex to short and long flaps in all phases of cell cycle, but that Saw1 is only required for recruitment of Rad1-Rad10 to DSBs when long flaps are formed in G1.
Collapse
|
5
|
Abstract
Homologous recombination provides high-fidelity DNA repair throughout all domains of life. Live cell fluorescence microscopy offers the opportunity to image individual recombination events in real time providing insight into the in vivo biochemistry of the involved proteins and DNA molecules as well as the cellular organization of the process of homologous recombination. Herein we review the cell biological aspects of mitotic homologous recombination with a focus on Saccharomyces cerevisiae and mammalian cells, but will also draw on findings from other experimental systems. Key topics of this review include the stoichiometry and dynamics of recombination complexes in vivo, the choreography of assembly and disassembly of recombination proteins at sites of DNA damage, the mobilization of damaged DNA during homology search, and the functional compartmentalization of the nucleus with respect to capacity of homologous recombination.
Collapse
Affiliation(s)
- Michael Lisby
- Department of Biology, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Rodney Rothstein
- Department of Genetics and Development, Columbia University Medical Center, New York, New York 10032
| |
Collapse
|
6
|
Sarangi P, Altmannova V, Holland C, Bartosova Z, Hao F, Anrather D, Ammerer G, Lee SE, Krejci L, Zhao X. A versatile scaffold contributes to damage survival via sumoylation and nuclease interactions. Cell Rep 2014; 9:143-152. [PMID: 25263559 PMCID: PMC4280569 DOI: 10.1016/j.celrep.2014.08.054] [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] [Received: 06/16/2014] [Revised: 07/23/2014] [Accepted: 08/22/2014] [Indexed: 11/30/2022] Open
Abstract
DNA repair scaffolds mediate specific DNA and protein interactions in order to assist repair enzymes in recognizing and removing damaged sequences. Many scaffold proteins are dedicated to repairing a particular type of lesion. Here, we show that the budding yeast Saw1 scaffold is more versatile. It helps cells cope with base lesions and protein-DNA adducts through its known function of recruiting the Rad1-Rad10 nuclease to DNA. In addition, it promotes UV survival via a mechanism mediated by its sumoylation. Saw1 sumoylation favors its interaction with another nuclease Slx1-Slx4, and this SUMO-mediated role is genetically separable from two main UV lesion repair processes. These effects of Saw1 and its sumoylation suggest that Saw1 is a multifunctional scaffold that can facilitate diverse types of DNA repair through its modification and nuclease interactions.
Collapse
Affiliation(s)
- Prabha Sarangi
- Molecular Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA; Programs in Biochemistry, Cell, and Molecular Biology, Weill Cornell Graduate School of Medical Sciences, New York, NY 10065, USA
| | | | - Cory Holland
- Department of Molecular Medicine, Institute of Biotechnology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Zdenka Bartosova
- Department of Biology, Masaryk University, Brno 62500, Czech Republic
| | - Fanfan Hao
- Molecular Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Dorothea Anrather
- Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories, University of Vienna, Vienna 1030, Austria
| | - Gustav Ammerer
- Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories, University of Vienna, Vienna 1030, Austria
| | - Sang Eun Lee
- Department of Molecular Medicine, Institute of Biotechnology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA; Division of Radiation Biology, Department of Radiation Oncology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Lumir Krejci
- Department of Biology, Masaryk University, Brno 62500, Czech Republic; National Centre for Biomolecular Research, Masaryk University, Brno 62500, Czech Republic; International Clinical Research Center, St. Anne's University Hospital in Brno, Brno 60200, Czech Republic.
| | - Xiaolan Zhao
- Molecular Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA; Programs in Biochemistry, Cell, and Molecular Biology, Weill Cornell Graduate School of Medical Sciences, New York, NY 10065, USA.
| |
Collapse
|