{"gene":"SWI5","run_date":"2026-06-10T10:51:54","timeline":{"discoveries":[{"year":1991,"finding":"CDC28 kinase (Cdk1) directly phosphorylates three serine residues located within or adjacent to the nuclear localization signal (NLS) of S. cerevisiae SWI5, and this phosphorylation is responsible for cell cycle-dependent cytoplasmic retention. Mutation of all three serines results in constitutive nuclear entry; all three are phosphorylated by purified CDC28-dependent H1 kinase activity in vitro.","method":"In vitro phosphorylation by purified CDC28-H1 kinase, site-directed mutagenesis of NLS serines, cell fractionation/localization, heterologous NLS fusion","journal":"Cell","confidence":"High","confidence_rationale":"Tier 1 / Strong — in vitro kinase reconstitution plus mutagenesis plus cell localization, replicated conceptually across multiple experiments in one rigorous study","pmids":["1652372"],"is_preprint":false},{"year":1992,"finding":"SWI5 encodes a zinc finger DNA-binding protein that functions as a transcriptional activator of the HO endonuclease gene. SWI5 and its homolog ACE2 have nearly identical zinc finger regions, bind the same DNA sequences, but activate different gene sets (SWI5→HO; ACE2→CTS1); chimeric fusion experiments show that promoter specificity resides in a domain distinct from the zinc finger domain.","method":"Gene disruption/deletion, promoter-reporter assays, chimeric SWI5/ACE2 protein fusions","journal":"Genes & development","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal genetic and biochemical approaches, replicated across labs","pmids":["1730413"],"is_preprint":false},{"year":1992,"finding":"NMR structural analysis of two SWI5 zinc-finger domains reveals that finger 2 adopts a classical C2H2 fold, while finger 1 has an additional N-terminal beta strand not seen in other zinc fingers, which stabilizes the folded structure of finger 1.","method":"2D 1H NMR spectroscopy, structure calculation with simulated annealing","journal":"Journal of molecular biology","confidence":"High","confidence_rationale":"Tier 1 / Strong — NMR structure determination with detailed three-dimensional coordinates for two zinc-finger domains","pmids":["1453468"],"is_preprint":false},{"year":1992,"finding":"NMR analysis of SWI5 zinc-finger peptides shows that adjacent zinc-finger domains are structurally independent (flexibly linked); the N-terminal two fingers (fingers 1+2) bind to the 5' end of the DNA binding site, establishing binding polarity.","method":"2D NMR, limited proteolysis, DNA binding assays with one-, two-, and three-finger peptides","journal":"Journal of molecular biology","confidence":"High","confidence_rationale":"Tier 1 / Strong — NMR structure determination combined with functional DNA binding assays in the same study","pmids":["1453467"],"is_preprint":false},{"year":1993,"finding":"SWI5 binds the HO promoter cooperatively with the homeodomain protein GRF10 (PHO2/BAS2). The two proteins bind adjacent DNA sites and make unique contacts; the cooperative complex has a longer half-life than either protein alone. GRF10 was purified via cooperative interaction-based DNA affinity chromatography with GST-SWI5.","method":"Purification of GST-SWI5 fusion protein; DNA affinity chromatography; methylation interference; missing-nucleoside analysis; in vitro DNA binding/cooperative binding assays","journal":"Molecular and cellular biology","confidence":"High","confidence_rationale":"Tier 1 / Moderate — in vitro reconstitution of cooperative DNA binding, multiple orthogonal footprinting methods, confirmed in vivo by genetic requirement for GRF10","pmids":["8355698","7902583"],"is_preprint":false},{"year":1993,"finding":"Rapid proteolytic degradation of SWI5 during early G1 is necessary to prevent HO expression in daughter cells; more stable mutant SWI5 proteins cause daughter cells to switch mating type, demonstrating that SWI5 instability is required for asymmetric HO expression.","method":"Stable SWI5 mutant expression, mating-type switching assays, pulse-chase protein stability analysis","journal":"Genes & development","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic approach with defined phenotypic readout (daughter-cell switching), single lab","pmids":["8449406"],"is_preprint":false},{"year":1996,"finding":"Swi5 directly activates transcription of SIC1 (the Cdk inhibitor p40SIC1) at late M phase/early G1 by entering the nucleus at the end of anaphase. Cell cycle-regulated nuclear entry of Swi5 generates the burst of SIC1 transcription required for inactivation of Clb/Cdk1 kinase.","method":"SWI5 deletion/mutation analysis, SIC1 mRNA and protein expression assays, genetic suppression (sic1Δ suppresses cdc4 arrest), cell synchronization","journal":"Molecular and cellular biology","confidence":"High","confidence_rationale":"Tier 2 / Strong — replicated across two independent studies (PMID 8816483 and 9017392), multiple genetic and molecular approaches","pmids":["8816483","9017392"],"is_preprint":false},{"year":1996,"finding":"The N-terminal additional beta strand and helix in SWI5 zinc finger 1 (identified by NMR) increase DNA-binding affinity, representing a structural extension that enhances DNA recognition beyond the canonical C2H2 fold.","method":"NMR structural analysis, biochemical DNA-binding studies","journal":"Structure","confidence":"Medium","confidence_rationale":"Tier 1 / Moderate — NMR structure plus biochemical DNA binding, single lab","pmids":["8736557"],"is_preprint":false},{"year":1996,"finding":"Swi5 activates EGT2 transcription immediately upon nuclear entry at the end of mitosis in a concentration-dependent manner; as Swi5 is unstable in the nucleus, its rapid degradation terminates EGT2 transcription before the next cell cycle commitment.","method":"Cell cycle synchronization, promoter-reporter assays, SWI5 deletion analysis","journal":"Molecular and cellular biology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic and molecular analysis with defined transcriptional readout, single lab","pmids":["8668141"],"is_preprint":false},{"year":1997,"finding":"SAE3 (budding yeast, also called SWI5 in fission yeast context) is a meiosis-specific gene; sae3 mutants produce persistent hyper-resected meiotic DSBs and severely fail to form recombinants, phenotypically similar to dmc1 mutants, indicating SAE3/SWI5 and DMC1 act at the same step of chromosome metabolism.","method":"Genetic screen, spore viability, physical monitoring of DSBs and recombinants","journal":"Genetics","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic epistasis with defined molecular (DSB resection/repair) readout, single lab","pmids":["9215889"],"is_preprint":false},{"year":1998,"finding":"A 24-amino-acid region of Swi5, upstream of the DNA-binding domain (residues 471–513), is necessary and sufficient for interaction with Pho2 and for cooperative DNA binding at the HO promoter; specific point mutations in this region specifically abolish Pho2-dependent (but not Pho2-independent) gene activation without affecting DNA binding.","method":"Two-hybrid assay, in vitro DNA binding, reporter assays, site-directed mutagenesis","journal":"Molecular and cellular biology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — two-hybrid plus in vitro binding plus mutagenesis, single lab","pmids":["9774660"],"is_preprint":false},{"year":1998,"finding":"Swi5 controls transcription of PCL9 and PCL2 in late M phase/telophase; these Pho85-associated cyclins represent the only cyclins expressed at this cell cycle stage. The Swi5 transcription factor thus drives a wave of Pcl-type cyclin synthesis at the end of mitosis.","method":"PCL9/PCL2 promoter-reporter assays, SWI5 deletion, Pho85 kinase activity assays, genetic synthetic lethality","journal":"Molecular biology of the cell","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — defined transcriptional and kinase activity readouts, single lab","pmids":["9529390"],"is_preprint":false},{"year":1999,"finding":"Chimeric SWI5/ACE2 fusion analysis identifies distinct, separable regions of Swi5 required for HO-specific activation; the Swi5 HO-specificity region coincides with the Pho2-interaction region, demonstrating that promoter specificity is encoded outside the zinc finger DNA-binding domain.","method":"Chimeric protein fusions, promoter-reporter assays, in vitro DNA binding","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple chimeric constructs and reporter assays, single lab","pmids":["10409653"],"is_preprint":false},{"year":2000,"finding":"Swi5 interacts physically with Pho85 cyclins (Pcl2 and Pho80) and is phosphorylated in vitro by the Pho80-Pho85 kinase; in pho85 deletion strains, Swi5 activity is misregulated in vivo (overexpression of SWI5 is lethal in pho85Δ), implicating Swi5 as a Pho85 substrate.","method":"Two-hybrid screen, in vitro kinase assay with Pho80-Pho85 complex, genetic epistasis/lethality assays","journal":"Molecular microbiology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — two-hybrid plus in vitro kinase plus genetic analysis, single lab","pmids":["10692159"],"is_preprint":false},{"year":2001,"finding":"Swi5 recruits the Mediator complex to the HO promoter (1.5 kb upstream of TSS) through specific interaction with the Gal11 module of Mediator, independently of SBF and prior to RNA Pol II binding; Swi/Snf is required for Mediator binding and acts in the same genetic pathway as Mediator for HO activation.","method":"Chromatin immunoprecipitation (ChIP) of Mediator and Pol II components, genetic suppression epistasis analysis, kinetic binding experiments","journal":"Genes & development","confidence":"High","confidence_rationale":"Tier 2 / Moderate — ChIP plus genetic epistasis plus kinetic binding, multiple orthogonal methods, single lab","pmids":["11562354"],"is_preprint":false},{"year":2003,"finding":"Fission yeast Swi5 (sp) forms two distinct protein complexes: Swi5-Sfr1 (involved in Rhp51-dependent recombination repair) and Swi5-Swi2 (involved in mating-type switching together with Swi6). Protein interactions with Rhp51 are mediated by a domain common to Swi2 and Sfr1. Genetic epistasis shows these two complexes function in distinct pathways.","method":"Co-immunoprecipitation, two-hybrid assays, genetic epistasis analysis","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal Co-IP/two-hybrid plus genetic epistasis, confirmed in multiple analyses","pmids":["14663140"],"is_preprint":false},{"year":2004,"finding":"Budding yeast Mei5 (SWI5 ortholog context) and Sae3 form a ternary complex with Dmc1 and are required for Dmc1 (but not Rad51) assembly on chromosomes. Mei5, Sae3, and Dmc1 are mutually dependent for chromosome association; their absence prevents disassembly of Rad51 filaments. Rad51 is required for recruitment of the Mei5-Sae3-Dmc1 complex to chromosomes.","method":"Chromatin immunoprecipitation, immunofluorescence on meiotic chromosomes, sporulation/spore viability assays, overexpression suppression","journal":"Cell","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal in vivo methods (ChIP, IF, genetics), replicated in parallel study (PMID 15579681)","pmids":["15620352","15579681"],"is_preprint":false},{"year":2004,"finding":"Fission yeast Swi5 (sp) encodes an 85-amino-acid polypeptide with an N-terminal predicted coiled-coil domain. swi5Δ reduces meiotic recombinant frequencies ~10-fold, is hypersensitive to DNA-damaging agents, and acts in a branched pathway of joint molecule formation; swi5Δ suppresses the low spore viability of mus81Δ eme1Δ (joint molecule resolution mutant), placing Swi5 in joint molecule formation.","method":"Gene identification/deletion, recombination frequency assays, epistasis analysis with mus81Δ/eme1Δ and rhp55Δ/rhp57Δ","journal":"Genetics","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic epistasis plus defined molecular phenotype, single lab","pmids":["15466419"],"is_preprint":false},{"year":2006,"finding":"The fission yeast Swi5-Sfr1 complex stimulates Rhp51 (Rad51) and Dmc1-mediated DNA strand exchange at substoichiometric concentrations on long DNA substrates; stimulation is completely dependent on RPA and ATP. Swi5-Sfr1 overcomes the inhibitory effect of RPA on recombinase loading and preferentially stimulates the ssDNA-dependent ATPase activity of Rhp51, and increases Dmc1 binding to ssDNA.","method":"In vitro strand exchange assay, ATPase assay, ssDNA binding assay with purified proteins","journal":"Nature structural & molecular biology","confidence":"High","confidence_rationale":"Tier 1 / Strong — in vitro reconstitution with purified proteins, multiple enzymatic assays, replicated and extended by subsequent studies","pmids":["16921379"],"is_preprint":false},{"year":2007,"finding":"In fission yeast, Swi5-GFP localizes to the nucleus forming diffuse staining with foci; spontaneous foci require Swi2. Upon UV irradiation, Swi5 foci form in swi2Δ mutants (depending on Sfr1); Sfr1 foci colocalize with damage-induced Rhp51 foci. An HO endonuclease-induced DSB assay showed Rhp51 and Rhp57 (but not Swi5/Sfr1) are essential for crossover production, distinguishing Swi5-Sfr1 from Rhp55/57 in recombination outcome.","method":"Live fluorescence microscopy (GFP), UV irradiation-induced focus formation, HO endonuclease DSB assay, genetic analysis","journal":"The EMBO journal","confidence":"High","confidence_rationale":"Tier 2 / Moderate — direct localization with functional epistasis and quantitative recombination outcomes, single lab but multiple orthogonal methods","pmids":["17304215"],"is_preprint":false},{"year":2008,"finding":"Swi5 is a substrate of the SCF(Cdc4) ubiquitin ligase complex. Swi5 is ubiquitinated and degraded through SCF(Cdc4), and this degradation is required to terminate SIC1 transcription at early G1, ensuring efficient S-phase entry. Stabilized Swi5 causes hyperaccumulation of Sic1 and delays S-phase entry in a manner suppressed by SIC1 deletion.","method":"Refined two-hybrid screen under substrate-stabilizing conditions, ubiquitination assay, cell synchronization, S-phase entry assays, SIC1 deletion suppression","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — two-hybrid identification plus ubiquitination assay plus genetic suppression, single lab","pmids":["18787112"],"is_preprint":false},{"year":2009,"finding":"Budding yeast Mei5-Sae3 complex preferentially binds ssDNA and relieves RPA-imposed inhibition of Dmc1 strand assimilation and DNA binding; Mei5-Sae3 physically interacts with RPA. These results establish Mei5-Sae3 as a mediator (loader) of Dmc1 onto RPA-coated ssDNA.","method":"Purified protein in vitro binding assays, strand assimilation assay, Co-IP with RPA","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 / Moderate — in vitro reconstitution with purified components, multiple functional assays, single lab","pmids":["19270307"],"is_preprint":false},{"year":2010,"finding":"Mammalian (mouse) Swi5 and Sfr1 are nuclear proteins that form a complex in vivo and in vitro; Swi5 interacts in vitro with Rad51. Both proteins are mutually interdependent for their stability. Loss of either (Swi5−/− or Sfr1−/−) sensitizes ES cells to ionizing radiation, camptothecin, and PARP inhibitor, attenuates SCE induction, and increases chromosome aberrations, demonstrating a role for the mammalian Swi5-Sfr1 complex in homologous recombination.","method":"Co-IP, in vitro pulldown with Rad51, ES cell knockout, colony survival assays, SCE assay, chromosomal aberration analysis","journal":"PLoS genetics","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal Co-IP, in vitro binding, KO cells with multiple orthogonal phenotypic readouts, replication of fission yeast findings in mammals","pmids":["20976249"],"is_preprint":false},{"year":2011,"finding":"The fission yeast Swi5-Sfr1 complex has a 1:1 stoichiometry and displays an extremely elongated dogleg-shaped structure (frictional ratio f/f0 = 2.0) in solution as determined by SAXS and analytical ultracentrifugation; topology mapping with Fab fragments places Sfr1 subdomains at defined positions, suggesting the complex fits into the groove of the Rad51 filament.","method":"Analytical ultracentrifugation, ESI-MS, SAXS, Fab-fragment mapping","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 / Moderate — multiple biophysical methods (AUC, MS, SAXS) in one study, single lab","pmids":["22033972"],"is_preprint":false},{"year":2011,"finding":"The budding yeast Mei5-Sae3 complex preferentially binds a fork-like DNA substrate; Mei5 (not Sae3) confers DNA binding activity; Mei5-Sae3 interacts with Rad51 through the N-terminal domain of Mei5. Mei5-Sae3 lacks recombination mediator activity for Rad51 and lacks ssDNA annealing activity, distinguishing it from Rad52.","method":"Purified protein biochemical assays (DNA binding, ssDNA annealing, strand exchange), domain deletion/interaction mapping","journal":"DNA repair","confidence":"Medium","confidence_rationale":"Tier 1 / Moderate — multiple in vitro assays with purified proteins, single lab","pmids":["21543267"],"is_preprint":false},{"year":2012,"finding":"Crystal structure of the Swi5-Sfr1 complex reveals that Swi5 and the C-terminal core domain of Sfr1 form a parallel coiled-coil heterodimer joined by two leucine-zipper motifs and a bundle; the coiled coil is sharply kinked creating a crescent-shaped structure for binding within the Rad51 filament groove. The N-terminal region of Sfr1 provides the Rad51-binding interface.","method":"X-ray crystallography, functional mutagenesis","journal":"Structure","confidence":"High","confidence_rationale":"Tier 1 / Strong — crystal structure with functional mutagenesis, defining atomic-level mechanism","pmids":["22405003"],"is_preprint":false},{"year":2012,"finding":"Mouse Swi5-Sfr1 complex has 1:1 stoichiometry; the intact complex (not Swi5 or Sfr1 alone) physically interacts with Rad51 and stimulates Rad51-mediated homologous DNA pairing by stabilizing the Rad51-ssDNA presynaptic filament. The RSfp (rodent Sfr1 proline-rich) motif in Sfr1 functions as a negative regulatory element.","method":"Biophysical stoichiometry determination, Co-IP, in vitro strand exchange assay, presynaptic filament stability assay, mutagenesis of RSfp motif","journal":"Nucleic acids research","confidence":"High","confidence_rationale":"Tier 1 / Moderate — biophysical, biochemical, and mutagenesis methods in one study with defined mechanism","pmids":["22492707"],"is_preprint":false},{"year":2012,"finding":"Karyopherin Msn5 is required for nuclear export of Swi5 in S. cerevisiae and physically interacts with the N-terminal end of Swi5. Inactivation of Msn5 reduces cellular Swi5 protein levels by a post-transcriptional defect in Swi5 synthesis (not increased degradation). High Swi5 nuclear accumulation in msn5 cells is toxic.","method":"GFP localization, Co-IP, mRNA level analysis, protein stability (cycloheximide chase), genetic toxicity assay","journal":"Biochimica et biophysica acta","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct localization experiment (GFP), Co-IP, and multiple mechanistic assays, single lab","pmids":["22374135"],"is_preprint":false},{"year":2013,"finding":"Human SWI5-SFR1 complex enhances ADP release from the RAD51 presynaptic filament (measured by optical tweezers and biochemical assay), thereby stimulating ATP hydrolysis by ssDNA-bound RAD51 and maintaining the catalytically active state of the presynaptic filament.","method":"Optical tweezers single-molecule assay, biochemical ATPase/ADP release assay","journal":"Nucleic acids research","confidence":"High","confidence_rationale":"Tier 1 / Moderate — single-molecule biophysics plus biochemical reconstitution, mechanistic clarity, single lab","pmids":["24078249"],"is_preprint":false},{"year":2013,"finding":"Swi5-Sfr1 promotes more perpendicular alignment of nucleobases in the Rad51/ssDNA presynaptic filament (measured by flow linear dichroism); this structural change is mediated through interaction with the Rad51 filament (not directly with DNA), as deletion of the DNA-binding N-terminal Sfr1 domain does not abolish the effect.","method":"Flow linear dichroism spectroscopy, deletion mutagenesis of Sfr1 N-terminus","journal":"Nucleic acids research","confidence":"Medium","confidence_rationale":"Tier 1 / Moderate — specialized biophysical method on purified proteins, single lab","pmids":["24304898"],"is_preprint":false},{"year":2013,"finding":"Fission yeast Swi5-Sfr1 acts as both a mediator (loads Dmc1 onto RPA-coated ssDNA) and a direct activator of Dmc1 strand exchange; in contrast, Rad22 (fission yeast Rad52) inhibits Dmc1 activity by competing for binding to RPA-coated ssDNA, demonstrating dual opposing regulation of meiotic recombination.","method":"In vitro strand exchange assays, mediator assay, competition assays with purified proteins","journal":"Genes & development","confidence":"High","confidence_rationale":"Tier 1 / Moderate — in vitro reconstitution with purified proteins demonstrating both mediator and activator functions, single lab","pmids":["24186976"],"is_preprint":false},{"year":2016,"finding":"A C-terminal domain within mammalian (mouse) SWI5 contributes to RAD51 interaction; SWI5-SFR1 preferentially associates with the oligomeric form of RAD51. RAD51-interaction-defective mutants of SWI5-SFR1 fail to stimulate Rad51 recombinase activity, establishing that physical interaction is indispensable for functional stimulation.","method":"Co-IP, pulldown, mutagenesis, in vitro strand exchange assay","journal":"Nucleic acids research","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP plus mutagenesis plus functional assay, single lab","pmids":["27131790"],"is_preprint":false},{"year":2018,"finding":"Mouse Swi5-Sfr1 stimulates Rad51 filament assembly by reducing Rad51 dissociation from filaments (both at nucleation and filament maintenance stages), demonstrated at single-molecule level; this reduces the nucleus size from three Rad51 molecules to two. Fission yeast Swi5-Sfr1 similarly specifically reduces SpRad51 disassembly.","method":"Single-molecule tethered particle motion (TPM), single-molecule FRET (smFRET)","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"High","confidence_rationale":"Tier 1 / Moderate — single-molecule biophysics with two orthogonal methods, conservation demonstrated in two organisms","pmids":["30297419"],"is_preprint":false},{"year":2020,"finding":"Two distinct sites within the intrinsically disordered N-terminus of Sfr1 (Sfr1N) cooperatively bind Rad51; deletion of Sfr1N impairs Rad51 stimulation in vitro and causes DNA damage sensitivity. Swi5-Sfr1 and Rad55-Rad57 form a higher-order complex and can collaboratively stimulate Rad51, suggesting they are not fully independent.","method":"NMR, in vitro pull-down, strand exchange assay, DNA damage sensitivity assay, mutagenesis","journal":"eLife","confidence":"High","confidence_rationale":"Tier 1 / Moderate — NMR plus biochemical reconstitution plus mutagenesis plus cellular assay, single lab","pmids":["32204793"],"is_preprint":false},{"year":2021,"finding":"Mass spectrometry of Swi5-Sfr1 complex purified from fission yeast meiotic cells identified multiple phosphorylation sites on both Swi5 and Sfr1; phosphomimetic (aspartate) mutants at identified sites are only partially functional, while phospho-null mutants do not impair function, suggesting phosphorylation can negatively modulate but is not required for Swi5-Sfr1 activity.","method":"Mass spectrometry of purified meiotic complex, phosphomimetic/phospho-null mutagenesis, functional assays","journal":"Genes","confidence":"Low","confidence_rationale":"Tier 3 / Weak — MS identification of phosphosites plus partial mutagenesis, functional significance unclear from abstract alone","pmids":["34208949"],"is_preprint":false},{"year":2023,"finding":"Phosphorylation of five residues within the intrinsically disordered domain of Sfr1 regulates interaction of Swi5-Sfr1 with Rad51; phosphomimetic Swi5-Sfr1 is defective in both physical and functional interaction with Rad51 and causes DNA repair deficiency. Blocking Sfr1 phosphorylation also causes DNA damage sensitivity, suggesting controlled phosphorylation cycles are important for Rad51-dependent DNA repair.","method":"Biochemical reconstitution with phosphomimetic/phospho-null mutants, Co-IP, DNA damage sensitivity assays","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 1 / Moderate — biochemical reconstitution plus mutagenesis plus cellular phenotype, single lab","pmids":["37330173"],"is_preprint":false},{"year":2023,"finding":"Hop2-Mnd1 and Swi5-Sfr1 stimulate Dmc1 filament assembly by distinct mechanisms: Hop2-Mnd1 increases the Dmc1 binding rate (recruits Dmc1 at ssDNA/dsDNA junctions via direct DNA binding), while Swi5-Sfr1 specifically reduces the Dmc1 dissociation rate during nucleation (~2-fold). Together they provide additive stimulation.","method":"Single-molecule FRET (smFRET), tethered particle motion (TPM), order-of-addition experiments","journal":"Nucleic acids research","confidence":"High","confidence_rationale":"Tier 1 / Moderate — two orthogonal single-molecule methods clearly distinguishing mechanistic steps, single lab","pmids":["37395447"],"is_preprint":false},{"year":2024,"finding":"Mei5-Sae3 stabilizes Dmc1 nucleating clusters (2–3 molecules) on naked ssDNA by preferentially reducing Dmc1 dissociation rates; it also stimulates Dmc1 assembly on RPA-coated ssDNA by stabilizing early clusters, which promotes RPA displacement. Coexistence of an intermediate containing both Dmc1 and RPA was directly observed.","method":"Single-molecule FRET (smFRET), colocalization single-molecule spectroscopy (CoSMoS), GFP-labeled RPA","journal":"Nucleic acids research","confidence":"High","confidence_rationale":"Tier 1 / Moderate — single-molecule reconstitution with multiple orthogonal methods directly observing molecular intermediates, single lab","pmids":["39275989"],"is_preprint":false},{"year":2024,"finding":"Swi5-Sfr1 stimulates Dmc1-driven strand exchange by acting as a mediator (promotes filament nucleus formation/association with ssDNA) rather than as an activator of the C1-C2 intermediate transition used for Rad51; this mechanistic distinction from Rad51 regulation was established by kinetic real-time analysis identifying three-stranded intermediates.","method":"Real-time strand exchange assay with kinetic intermediate analysis, comparison of Dmc1 and Rad51 reactions","journal":"Nucleic acids research","confidence":"High","confidence_rationale":"Tier 1 / Moderate — detailed kinetic reconstitution resolving mechanistic differences, single lab","pmids":["39340300"],"is_preprint":false},{"year":2025,"finding":"Mouse SWI5-SFR1 reduces the dissociation probability of RAD51 during filament extension and shifts the oligomeric assembly unit from octamers to tetramers, promoting more uniform filament growth; this modulation of RAD51 oligomeric state facilitates extension and stabilizes DNA binding.","method":"Single-molecule tethered particle motion (TPM), step-size analysis of RAD51 assembly","journal":"Nucleic acids research","confidence":"Medium","confidence_rationale":"Tier 1 / Weak — single-molecule reconstitution, single lab, single study (0 citations, very recent)","pmids":["40682818"],"is_preprint":false},{"year":2025,"finding":"Mei5-Sae3 stabilizes Dmc1 filaments in both the active (ATP-bound) and inactive (ADP-bound) allosteric conformations; unlike calcium, AMP-PNP, or the E157D mutation, Mei5-Sae3 stabilizes the active filament without inhibiting ATP hydrolysis (and may enhance ATP hydrolysis). Filament stabilization activity of Mei5-Sae3 does not depend on alteration of the hydrolytic cycle.","method":"Dmc1 filament conformation assays, ATPase assays, comparison with known ATP hydrolysis inhibitors, single-molecule approaches","journal":"Nucleic acids research","confidence":"Medium","confidence_rationale":"Tier 1 / Weak — biochemical reconstitution with mechanistic precision, very recent single study with 0 citations","pmids":["41206037"],"is_preprint":false}],"current_model":"SWI5/SAE3 encodes a conserved protein with two distinct functional identities depending on organism: in S. cerevisiae, SWI5 is a CDC28-phosphorylated, SCF(Cdc4)-degraded zinc-finger transcription factor that enters the nucleus at late mitosis to activate HO, SIC1, EGT2, PCL9, and other G1 genes through cooperative DNA binding with Pho2 and recruitment of Swi/Snf, SAGA, and Mediator complexes; in fission yeast and mammals, the small Swi5 polypeptide (orthologous to budding yeast Sae3/Mei5-Sae3 complex components) forms the Swi5-Sfr1 heterodimeric complex that acts as a Rad51/Dmc1 recombination mediator and activator—physically docking within the Rad51 filament groove via a crescent-shaped coiled-coil structure, reducing recombinase dissociation to stabilize presynaptic filaments, enhancing ADP release to maintain ATP-bound active filament states, and enabling Dmc1 loading onto RPA-coated ssDNA, with this activity regulated by controlled phosphorylation of the intrinsically disordered Sfr1 subunit."},"narrative":{"mechanistic_narrative":"The SWI5 symbol resolves to two mechanistically distinct, organism-dependent proteins within this corpus. In budding yeast, Swi5 is a C2H2 zinc-finger transcriptional activator that drives a wave of late-mitotic/early-G1 gene expression, including HO, SIC1, EGT2, and the Pho85 cyclins PCL9/PCL2 [PMID:1730413, PMID:8816483, PMID:9017392, PMID:8668141, PMID:9529390]. Its DNA-binding zinc fingers are structurally independent modules in which finger 1 carries an N-terminal beta-strand extension that augments the canonical fold and DNA affinity [PMID:1453468, PMID:1453467, PMID:8736557], while promoter specificity (e.g. for HO) is encoded in a separate region that mediates cooperative DNA binding with the homeodomain protein Pho2/Grf10 [PMID:8355698, PMID:7902583, PMID:9774660, PMID:10409653]. Once nuclear, Swi5 recruits the Mediator complex via its Gal11 module, with Swi/Snf required for Mediator binding, to activate transcription ahead of Pol II [PMID:11562354]. Swi5 activity is tightly gated by the cell cycle: CDC28/Cdk1 phosphorylates serines in its NLS to enforce cytoplasmic retention until anaphase [PMID:1652372], Msn5 controls its nuclear export and synthesis [PMID:22374135], and SCF(Cdc4)-mediated ubiquitination degrades it in early G1 to terminate SIC1 transcription and permit S-phase entry [PMID:8449406, PMID:18787112]. Separately, the small fission-yeast/mammalian Swi5 polypeptide (orthologous to budding-yeast Sae3 of the Mei5-Sae3 complex) forms a 1:1 heterodimer with Sfr1 that functions as a Rad51/Dmc1 recombination mediator and activator in homologous recombination [PMID:14663140, PMID:15466419, PMID:20976249, PMID:22033972]. Crystallographic and biophysical work shows the complex adopts an elongated, sharply kinked crescent-shaped coiled-coil that docks within the Rad51 filament groove, with the Sfr1 N-terminus providing the recombinase interface [PMID:22033972, PMID:22405003, PMID:32204793]. Functionally, Swi5-Sfr1 stabilizes the presynaptic filament by reducing recombinase dissociation, enhances ADP release to maintain the ATP-bound active filament state, overcomes RPA-imposed inhibition to load Dmc1 onto ssDNA, and stimulates strand exchange — activities conserved from fission yeast to mammals and regulated by phosphorylation of the intrinsically disordered Sfr1 subunit [PMID:16921379, PMID:19270307, PMID:22492707, PMID:24078249, PMID:30297419, PMID:37330173].","teleology":[{"year":1991,"claim":"Established how Swi5 nuclear access is gated to the cell cycle, answering why a constitutive transcription factor only acts at a specific phase.","evidence":"In vitro CDC28-H1 kinase phosphorylation, NLS serine mutagenesis, and localization in S. cerevisiae","pmids":["1652372"],"confidence":"High","gaps":["Did not identify the phosphatase or trigger for late-mitotic dephosphorylation/entry","In vitro kinase specificity vs in vivo timing not fully resolved"]},{"year":1992,"claim":"Defined Swi5 as a zinc-finger transcriptional activator and showed that target-gene specificity is separable from the DNA-binding module, framing how a shared DNA-recognition fold can drive distinct programs.","evidence":"Gene disruption, promoter-reporter assays, SWI5/ACE2 chimeras, and NMR structures of the zinc fingers in budding yeast","pmids":["1730413","1453468","1453467"],"confidence":"High","gaps":["Did not identify the molecular basis of the specificity-conferring region","Full-length DNA-bound complex not structurally defined"]},{"year":1993,"claim":"Showed cooperative DNA binding with Pho2/Grf10 and that proteolytic instability enforces asymmetric, daughter-cell-restricted HO expression, linking Swi5 abundance control to a developmental outcome.","evidence":"DNA affinity purification, footprinting, cooperative binding assays, and stable-mutant mating-type switching assays","pmids":["8355698","7902583","8449406"],"confidence":"High","gaps":["Degradation machinery not identified at this stage","Mechanism of cooperativity at atomic level not resolved"]},{"year":1996,"claim":"Connected Swi5 nuclear entry to the cell cycle engine by showing it triggers the SIC1 burst that inactivates Clb/Cdk1, and identified EGT2 and Pho85-cyclin targets, establishing Swi5 as the driver of a coordinated M/G1 transcriptional wave.","evidence":"Deletion analysis, mRNA/protein assays, genetic suppression, synchronization, and promoter-reporter assays in S. cerevisiae","pmids":["8816483","9017392","8668141","9529390"],"confidence":"High","gaps":["How concentration thresholds set sharp on/off transcription not mechanistically defined","Direct vs indirect target distinctions for some genes incomplete"]},{"year":1998,"claim":"Mapped a discrete 24-residue Swi5 region required for Pho2 interaction and cooperative binding, demonstrating that HO promoter specificity coincides with the Pho2-interaction surface rather than the zinc fingers.","evidence":"Two-hybrid, in vitro DNA binding, reporter assays, mutagenesis, and chimeric analysis","pmids":["9774660","10409653"],"confidence":"Medium","gaps":["Structure of the Swi5-Pho2-DNA cooperative complex not determined","Single-lab mapping"]},{"year":2000,"claim":"Identified Swi5 as a Pho85-cyclin substrate, adding a second kinase input to Swi5 regulation beyond Cdc28.","evidence":"Two-hybrid, in vitro Pho80-Pho85 kinase assay, and genetic lethality in S. cerevisiae","pmids":["10692159"],"confidence":"Medium","gaps":["Functional consequence of Pho85 phosphorylation sites in vivo not pinpointed","Single lab"]},{"year":2001,"claim":"Showed Swi5 recruits the Mediator Gal11 module to the HO promoter prior to Pol II, with Swi/Snf required, defining the coactivator-recruitment step of Swi5-driven activation.","evidence":"ChIP of Mediator/Pol II, genetic epistasis, and kinetic binding in budding yeast","pmids":["11562354"],"confidence":"High","gaps":["Direct Swi5-Gal11 contact surface not mapped structurally","Generality across other Swi5 targets not established"]},{"year":2003,"claim":"Revealed that fission-yeast Swi5 partitions into two functionally distinct complexes — Swi5-Sfr1 (recombination repair) and Swi5-Swi2 (mating-type switching) — separating its roles via shared partner domains.","evidence":"Co-IP, two-hybrid, and genetic epistasis in S. pombe","pmids":["14663140"],"confidence":"High","gaps":["Switch governing complex choice not defined","Stoichiometry/structure of complexes not resolved here"]},{"year":2004,"claim":"Established the meiotic recombination identity of the small Swi5/Sae3 protein, showing Mei5-Sae3 is required for Dmc1 (not Rad51) chromosome loading and that fission-yeast Swi5 promotes joint-molecule formation.","evidence":"ChIP, immunofluorescence on meiotic chromosomes, sporulation assays, and recombination/epistasis analysis in budding and fission yeast","pmids":["15620352","15579681","15466419","9215889"],"confidence":"High","gaps":["Biochemical mechanism of Dmc1 loading not yet defined","Relationship between transcription-factor Swi5 and recombination Swi5 across species reflects orthology rather than one protein"]},{"year":2006,"claim":"Demonstrated biochemically that Swi5-Sfr1 stimulates Rhp51/Dmc1 strand exchange substoichiometrically, overcoming RPA inhibition in an ATP-dependent manner, establishing it as a recombination mediator/activator.","evidence":"In vitro strand exchange, ATPase, and ssDNA binding assays with purified S. pombe proteins","pmids":["16921379"],"confidence":"High","gaps":["Molecular step targeted within the filament cycle not yet resolved","Single lab"]},{"year":2009,"claim":"Showed budding-yeast Mei5-Sae3 binds ssDNA, interacts with RPA, and relieves RPA inhibition to load Dmc1, defining a mediator activity even though Mei5-Sae3 lacks Rad51-mediator and annealing functions.","evidence":"Purified-protein binding, strand assimilation, Co-IP with RPA, and domain mapping","pmids":["19270307","21543267"],"confidence":"High","gaps":["Why Mei5-Sae3 mediates Dmc1 but not Rad51 not fully explained","Single lab"]},{"year":2007,"claim":"Placed Swi5-Sfr1 in DNA-damage-induced repair foci dependent on Sfr1 and distinguished it from the Rhp55/57 pathway in crossover outcome, defining its in vivo localization and pathway position.","evidence":"Live GFP microscopy, UV-induced focus formation, and HO-DSB recombination assays in S. pombe","pmids":["17304215"],"confidence":"High","gaps":["Recruitment hierarchy to damage sites only partially defined","Single lab"]},{"year":2010,"claim":"Demonstrated conservation in mammals: mouse Swi5-Sfr1 forms a mutually stabilizing complex that interacts with Rad51 and is required for homologous recombination and genome stability.","evidence":"Co-IP, in vitro Rad51 pulldown, ES-cell knockouts, survival, SCE, and chromosomal aberration assays","pmids":["20976249"],"confidence":"High","gaps":["In vivo loading sites and kinetics in mammals not defined","Physiological role in meiosis vs somatic HR not separated"]},{"year":2012,"claim":"Solved the architecture of the complex, showing an elongated crescent-shaped parallel coiled-coil heterodimer that fits the Rad51 filament groove, with Sfr1's N-terminus as the recombinase interface and the rodent RSfp motif as a negative regulator.","evidence":"Crystallography, SAXS, AUC, Fab mapping, and mutagenesis across fission yeast and mouse proteins","pmids":["22405003","22033972","22492707"],"confidence":"High","gaps":["Atomic structure of the Swi5-Sfr1-Rad51 filament complex not determined","How the disordered Sfr1 N-terminus engages Rad51 not resolved here"]},{"year":2013,"claim":"Resolved the mechanistic action on the filament: Swi5-Sfr1 enhances ADP release to sustain the ATP-bound active state, reorients nucleobases via the Rad51 interface, and acts as a dual mediator/activator for Dmc1 opposed by Rad22/Rad52.","evidence":"Optical tweezers, ATPase/ADP-release assays, flow linear dichroism, and competition strand-exchange assays in human and fission yeast systems","pmids":["24078249","24304898","24186976"],"confidence":"High","gaps":["Coupling between ADP release and filament stability not fully quantified","Single lab for each measurement"]},{"year":2016,"claim":"Identified a C-terminal SWI5 contribution to RAD51 binding, showed preference for oligomeric RAD51, and proved physical interaction is indispensable for functional stimulation.","evidence":"Co-IP, pulldown, interaction-defective mutagenesis, and strand exchange assays in mouse","pmids":["27131790"],"confidence":"Medium","gaps":["Relative contributions of Swi5 C-terminus vs Sfr1 N-terminus to the interface not fully partitioned","Single lab"]},{"year":2018,"claim":"Established at single-molecule resolution that Swi5-Sfr1 reduces recombinase dissociation at both nucleation and maintenance, lowering the nucleation threshold — a mechanism conserved between mouse and fission yeast.","evidence":"Single-molecule TPM and smFRET on Rad51/SpRad51 filaments","pmids":["30297419"],"confidence":"High","gaps":["How dissociation reduction translates to in vivo HR efficiency not quantified","Single lab"]},{"year":2020,"claim":"Showed the intrinsically disordered Sfr1 N-terminus uses two cooperative Rad51-binding sites and that Swi5-Sfr1 collaborates with Rad55-Rad57 in a higher-order complex, refining the recombinase interface and inter-mediator coordination.","evidence":"NMR, pull-downs, strand exchange, DNA-damage sensitivity, and mutagenesis","pmids":["32204793"],"confidence":"High","gaps":["Structure of the Swi5-Sfr1/Rad55-Rad57 super-complex not determined","Single lab"]},{"year":2023,"claim":"Established that controlled phosphorylation cycles of the disordered Sfr1 domain tune Swi5-Sfr1 binding to Rad51, with both phosphomimetic and phospho-blocked states impairing repair, defining a regulatory layer over recombinase activation.","evidence":"Phosphomimetic/phospho-null reconstitution, Co-IP, and DNA-damage sensitivity assays; complemented by mechanistic dissection vs Hop2-Mnd1","pmids":["37330173","37395447"],"confidence":"High","gaps":["The kinase/phosphatase pair controlling Sfr1 phosphorylation cycles not identified","In vivo timing of phospho-regulation not mapped"]},{"year":2024,"claim":"Refined the mediator mechanism for Dmc1, showing Mei5-Sae3/Swi5-Sfr1 stabilizes early Dmc1 clusters to promote RPA displacement and acts as a nucleation-promoting mediator distinct from the activator mechanism used for Rad51.","evidence":"smFRET, CoSMoS, and real-time kinetic strand-exchange analysis with purified proteins","pmids":["39275989","39340300"],"confidence":"High","gaps":["Structural basis of the Dmc1/RPA intermediate not resolved","Quantitative link to meiotic crossover control incomplete"]},{"year":2025,"claim":"Extended the stabilization mechanism by showing the complex shifts recombinase oligomeric assembly units (octamer-to-tetramer for RAD51) and stabilizes both ATP- and ADP-bound Dmc1 conformations without inhibiting hydrolysis, defining how it sustains active filaments.","evidence":"Single-molecule TPM step-size analysis (mouse) and Dmc1 conformation/ATPase assays (budding yeast)","pmids":["40682818","41206037"],"confidence":"Medium","gaps":["Very recent, single-study findings not yet independently replicated","Physiological relevance of oligomeric-state switching not established in vivo"]},{"year":null,"claim":"How the two Swi5 identities — a CDK/SCF-regulated zinc-finger transcription factor in budding yeast and the conserved Swi5-Sfr1 recombination mediator in fission yeast/mammals — relate at the level of evolutionary origin and whether any single organism uses both functions remains unresolved in this corpus.","evidence":"","pmids":[],"confidence":"Low","gaps":["No timeline study reconciles the transcription-factor and recombination-mediator orthology groups under one molecular framework","Kinase/phosphatase identity for Sfr1 regulation unknown","No atomic structure of the recombinase-bound complex"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0003677","term_label":"DNA binding","supporting_discovery_ids":[1,2,3,4,7]},{"term_id":"GO:0140110","term_label":"transcription regulator activity","supporting_discovery_ids":[1,6,8,11,14]},{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[16,18,21,26,28,30,32]},{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[14,25,33]},{"term_id":"GO:0003723","term_label":"RNA binding","supporting_discovery_ids":[18,21,24]}],"localization":[{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[0,6,19,22,27]},{"term_id":"GO:0000228","term_label":"nuclear 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recombination","subcellular_location":"Nucleus","url":"https://www.uniprot.org/uniprotkb/Q1ZZU3/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/SWI5","classification":"Not Classified","n_dependent_lines":35,"n_total_lines":1090,"dependency_fraction":0.03211009174311927},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/SWI5","total_profiled":1310},"omim":[{"mim_id":"616528","title":"SWI5 HOMOLOGOUS RECOMBINATION REPAIR PROTEIN; SWI5","url":"https://www.omim.org/entry/616528"},{"mim_id":"616527","title":"SWI5-DEPENDENT HOMOLOGOUS RECOMBINATION REPAIR PROTEIN 1; 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genetics","url":"https://pubmed.ncbi.nlm.nih.gov/31790385","citation_count":12,"is_preprint":false},{"pmid":"27329041","id":"PMC_27329041","title":"Hop2 and Sae3 Are Required for Dmc1-Mediated Double-Strand Break Repair via Homolog Bias during Meiosis.","date":"2016","source":"Molecules and cells","url":"https://pubmed.ncbi.nlm.nih.gov/27329041","citation_count":12,"is_preprint":false},{"pmid":"26975390","id":"PMC_26975390","title":"The transcription factor Ace2 and its paralog Swi5 regulate ethanol production during static fermentation through their targets Cts1 and Rps4a in Saccharomyces cerevisiae.","date":"2016","source":"FEMS yeast research","url":"https://pubmed.ncbi.nlm.nih.gov/26975390","citation_count":11,"is_preprint":false},{"pmid":"32204793","id":"PMC_32204793","title":"Cooperative interactions facilitate stimulation of Rad51 by the Swi5-Sfr1 auxiliary factor 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Section F, Structural biology and crystallization communications","url":"https://pubmed.ncbi.nlm.nih.gov/20823543","citation_count":7,"is_preprint":false},{"pmid":"22374135","id":"PMC_22374135","title":"Regulation of cell cycle transcription factor Swi5 by karyopherin Msn5.","date":"2012","source":"Biochimica et biophysica acta","url":"https://pubmed.ncbi.nlm.nih.gov/22374135","citation_count":5,"is_preprint":false},{"pmid":"34208949","id":"PMC_34208949","title":"Mapping and Analysis of Swi5 and Sfr1 Phosphorylation Sites.","date":"2021","source":"Genes","url":"https://pubmed.ncbi.nlm.nih.gov/34208949","citation_count":4,"is_preprint":false},{"pmid":"37330173","id":"PMC_37330173","title":"Phosphoregulation of DNA repair via the Rad51 auxiliary factor Swi5-Sfr1.","date":"2023","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/37330173","citation_count":3,"is_preprint":false},{"pmid":"39275989","id":"PMC_39275989","title":"Mei5-Sae3 stabilizes Dmc1 nucleating clusters for efficient Dmc1 assembly on RPA-coated single-stranded DNA.","date":"2024","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/39275989","citation_count":3,"is_preprint":false},{"pmid":"38924305","id":"PMC_38924305","title":"Mutational analysis of Mei5, a subunit of Mei5-Sae3 complex, in Dmc1-mediated recombination during yeast meiosis.","date":"2024","source":"Genes to cells : devoted to molecular & cellular mechanisms","url":"https://pubmed.ncbi.nlm.nih.gov/38924305","citation_count":2,"is_preprint":false},{"pmid":"37225456","id":"PMC_37225456","title":"The role of conserved amino acid residues of Sae3 in Mei5-Sae3 complex for Dmc1 assembly in meiotic recombination.","date":"2023","source":"Genes & genetic systems","url":"https://pubmed.ncbi.nlm.nih.gov/37225456","citation_count":2,"is_preprint":false},{"pmid":"30739521","id":"PMC_30739521","title":"Karyopherin Msn5 is involved in a novel mechanism controlling the cellular level of cell cycle regulators Cln2 and Swi5.","date":"2019","source":"Cell cycle (Georgetown, Tex.)","url":"https://pubmed.ncbi.nlm.nih.gov/30739521","citation_count":2,"is_preprint":false},{"pmid":"27265469","id":"PMC_27265469","title":"Downregulation of SWI5 and CTC1 genes: hepatitis B virus DNA polymerase transactivated protein 1-mediated inhibition of DNA repair.","date":"2016","source":"Acta virologica","url":"https://pubmed.ncbi.nlm.nih.gov/27265469","citation_count":2,"is_preprint":false},{"pmid":"39340300","id":"PMC_39340300","title":"The Swi5-Sfr1 complex regulates Dmc1- and Rad51-driven DNA strand exchange proceeding through two distinct three-stranded intermediates by different mechanisms.","date":"2024","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/39340300","citation_count":1,"is_preprint":false},{"pmid":"41206037","id":"PMC_41206037","title":"Mei5-Sae3 stabilizes both active and inactive forms of Dmc1 filaments independently of its impact on ATP hydrolysis.","date":"2025","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/41206037","citation_count":0,"is_preprint":false},{"pmid":"40682818","id":"PMC_40682818","title":"SWI5-SFR1 reduces RAD51 recombinase extending units during filament assembly.","date":"2025","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/40682818","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":28338,"output_tokens":9867,"usd":0.11651,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":20221,"output_tokens":6790,"usd":0.135428,"stage2_stop_reason":"end_turn"},"total_usd":0.251938,"stage1_batch_id":"msgbatch_017qqVz33Ga63SCDwzb35XPb","stage2_batch_id":"msgbatch_01Scr2Ei9x4HJMiRGxwrmvLK","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 1991,\n      \"finding\": \"CDC28 kinase (Cdk1) directly phosphorylates three serine residues located within or adjacent to the nuclear localization signal (NLS) of S. cerevisiae SWI5, and this phosphorylation is responsible for cell cycle-dependent cytoplasmic retention. Mutation of all three serines results in constitutive nuclear entry; all three are phosphorylated by purified CDC28-dependent H1 kinase activity in vitro.\",\n      \"method\": \"In vitro phosphorylation by purified CDC28-H1 kinase, site-directed mutagenesis of NLS serines, cell fractionation/localization, heterologous NLS fusion\",\n      \"journal\": \"Cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — in vitro kinase reconstitution plus mutagenesis plus cell localization, replicated conceptually across multiple experiments in one rigorous study\",\n      \"pmids\": [\"1652372\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1992,\n      \"finding\": \"SWI5 encodes a zinc finger DNA-binding protein that functions as a transcriptional activator of the HO endonuclease gene. SWI5 and its homolog ACE2 have nearly identical zinc finger regions, bind the same DNA sequences, but activate different gene sets (SWI5→HO; ACE2→CTS1); chimeric fusion experiments show that promoter specificity resides in a domain distinct from the zinc finger domain.\",\n      \"method\": \"Gene disruption/deletion, promoter-reporter assays, chimeric SWI5/ACE2 protein fusions\",\n      \"journal\": \"Genes & development\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal genetic and biochemical approaches, replicated across labs\",\n      \"pmids\": [\"1730413\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1992,\n      \"finding\": \"NMR structural analysis of two SWI5 zinc-finger domains reveals that finger 2 adopts a classical C2H2 fold, while finger 1 has an additional N-terminal beta strand not seen in other zinc fingers, which stabilizes the folded structure of finger 1.\",\n      \"method\": \"2D 1H NMR spectroscopy, structure calculation with simulated annealing\",\n      \"journal\": \"Journal of molecular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — NMR structure determination with detailed three-dimensional coordinates for two zinc-finger domains\",\n      \"pmids\": [\"1453468\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1992,\n      \"finding\": \"NMR analysis of SWI5 zinc-finger peptides shows that adjacent zinc-finger domains are structurally independent (flexibly linked); the N-terminal two fingers (fingers 1+2) bind to the 5' end of the DNA binding site, establishing binding polarity.\",\n      \"method\": \"2D NMR, limited proteolysis, DNA binding assays with one-, two-, and three-finger peptides\",\n      \"journal\": \"Journal of molecular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — NMR structure determination combined with functional DNA binding assays in the same study\",\n      \"pmids\": [\"1453467\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1993,\n      \"finding\": \"SWI5 binds the HO promoter cooperatively with the homeodomain protein GRF10 (PHO2/BAS2). The two proteins bind adjacent DNA sites and make unique contacts; the cooperative complex has a longer half-life than either protein alone. GRF10 was purified via cooperative interaction-based DNA affinity chromatography with GST-SWI5.\",\n      \"method\": \"Purification of GST-SWI5 fusion protein; DNA affinity chromatography; methylation interference; missing-nucleoside analysis; in vitro DNA binding/cooperative binding assays\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — in vitro reconstitution of cooperative DNA binding, multiple orthogonal footprinting methods, confirmed in vivo by genetic requirement for GRF10\",\n      \"pmids\": [\"8355698\", \"7902583\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1993,\n      \"finding\": \"Rapid proteolytic degradation of SWI5 during early G1 is necessary to prevent HO expression in daughter cells; more stable mutant SWI5 proteins cause daughter cells to switch mating type, demonstrating that SWI5 instability is required for asymmetric HO expression.\",\n      \"method\": \"Stable SWI5 mutant expression, mating-type switching assays, pulse-chase protein stability analysis\",\n      \"journal\": \"Genes & development\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic approach with defined phenotypic readout (daughter-cell switching), single lab\",\n      \"pmids\": [\"8449406\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1996,\n      \"finding\": \"Swi5 directly activates transcription of SIC1 (the Cdk inhibitor p40SIC1) at late M phase/early G1 by entering the nucleus at the end of anaphase. Cell cycle-regulated nuclear entry of Swi5 generates the burst of SIC1 transcription required for inactivation of Clb/Cdk1 kinase.\",\n      \"method\": \"SWI5 deletion/mutation analysis, SIC1 mRNA and protein expression assays, genetic suppression (sic1Δ suppresses cdc4 arrest), cell synchronization\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — replicated across two independent studies (PMID 8816483 and 9017392), multiple genetic and molecular approaches\",\n      \"pmids\": [\"8816483\", \"9017392\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1996,\n      \"finding\": \"The N-terminal additional beta strand and helix in SWI5 zinc finger 1 (identified by NMR) increase DNA-binding affinity, representing a structural extension that enhances DNA recognition beyond the canonical C2H2 fold.\",\n      \"method\": \"NMR structural analysis, biochemical DNA-binding studies\",\n      \"journal\": \"Structure\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — NMR structure plus biochemical DNA binding, single lab\",\n      \"pmids\": [\"8736557\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1996,\n      \"finding\": \"Swi5 activates EGT2 transcription immediately upon nuclear entry at the end of mitosis in a concentration-dependent manner; as Swi5 is unstable in the nucleus, its rapid degradation terminates EGT2 transcription before the next cell cycle commitment.\",\n      \"method\": \"Cell cycle synchronization, promoter-reporter assays, SWI5 deletion analysis\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic and molecular analysis with defined transcriptional readout, single lab\",\n      \"pmids\": [\"8668141\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1997,\n      \"finding\": \"SAE3 (budding yeast, also called SWI5 in fission yeast context) is a meiosis-specific gene; sae3 mutants produce persistent hyper-resected meiotic DSBs and severely fail to form recombinants, phenotypically similar to dmc1 mutants, indicating SAE3/SWI5 and DMC1 act at the same step of chromosome metabolism.\",\n      \"method\": \"Genetic screen, spore viability, physical monitoring of DSBs and recombinants\",\n      \"journal\": \"Genetics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic epistasis with defined molecular (DSB resection/repair) readout, single lab\",\n      \"pmids\": [\"9215889\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1998,\n      \"finding\": \"A 24-amino-acid region of Swi5, upstream of the DNA-binding domain (residues 471–513), is necessary and sufficient for interaction with Pho2 and for cooperative DNA binding at the HO promoter; specific point mutations in this region specifically abolish Pho2-dependent (but not Pho2-independent) gene activation without affecting DNA binding.\",\n      \"method\": \"Two-hybrid assay, in vitro DNA binding, reporter assays, site-directed mutagenesis\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — two-hybrid plus in vitro binding plus mutagenesis, single lab\",\n      \"pmids\": [\"9774660\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1998,\n      \"finding\": \"Swi5 controls transcription of PCL9 and PCL2 in late M phase/telophase; these Pho85-associated cyclins represent the only cyclins expressed at this cell cycle stage. The Swi5 transcription factor thus drives a wave of Pcl-type cyclin synthesis at the end of mitosis.\",\n      \"method\": \"PCL9/PCL2 promoter-reporter assays, SWI5 deletion, Pho85 kinase activity assays, genetic synthetic lethality\",\n      \"journal\": \"Molecular biology of the cell\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — defined transcriptional and kinase activity readouts, single lab\",\n      \"pmids\": [\"9529390\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1999,\n      \"finding\": \"Chimeric SWI5/ACE2 fusion analysis identifies distinct, separable regions of Swi5 required for HO-specific activation; the Swi5 HO-specificity region coincides with the Pho2-interaction region, demonstrating that promoter specificity is encoded outside the zinc finger DNA-binding domain.\",\n      \"method\": \"Chimeric protein fusions, promoter-reporter assays, in vitro DNA binding\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple chimeric constructs and reporter assays, single lab\",\n      \"pmids\": [\"10409653\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2000,\n      \"finding\": \"Swi5 interacts physically with Pho85 cyclins (Pcl2 and Pho80) and is phosphorylated in vitro by the Pho80-Pho85 kinase; in pho85 deletion strains, Swi5 activity is misregulated in vivo (overexpression of SWI5 is lethal in pho85Δ), implicating Swi5 as a Pho85 substrate.\",\n      \"method\": \"Two-hybrid screen, in vitro kinase assay with Pho80-Pho85 complex, genetic epistasis/lethality assays\",\n      \"journal\": \"Molecular microbiology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — two-hybrid plus in vitro kinase plus genetic analysis, single lab\",\n      \"pmids\": [\"10692159\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2001,\n      \"finding\": \"Swi5 recruits the Mediator complex to the HO promoter (1.5 kb upstream of TSS) through specific interaction with the Gal11 module of Mediator, independently of SBF and prior to RNA Pol II binding; Swi/Snf is required for Mediator binding and acts in the same genetic pathway as Mediator for HO activation.\",\n      \"method\": \"Chromatin immunoprecipitation (ChIP) of Mediator and Pol II components, genetic suppression epistasis analysis, kinetic binding experiments\",\n      \"journal\": \"Genes & development\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — ChIP plus genetic epistasis plus kinetic binding, multiple orthogonal methods, single lab\",\n      \"pmids\": [\"11562354\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2003,\n      \"finding\": \"Fission yeast Swi5 (sp) forms two distinct protein complexes: Swi5-Sfr1 (involved in Rhp51-dependent recombination repair) and Swi5-Swi2 (involved in mating-type switching together with Swi6). Protein interactions with Rhp51 are mediated by a domain common to Swi2 and Sfr1. Genetic epistasis shows these two complexes function in distinct pathways.\",\n      \"method\": \"Co-immunoprecipitation, two-hybrid assays, genetic epistasis analysis\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal Co-IP/two-hybrid plus genetic epistasis, confirmed in multiple analyses\",\n      \"pmids\": [\"14663140\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2004,\n      \"finding\": \"Budding yeast Mei5 (SWI5 ortholog context) and Sae3 form a ternary complex with Dmc1 and are required for Dmc1 (but not Rad51) assembly on chromosomes. Mei5, Sae3, and Dmc1 are mutually dependent for chromosome association; their absence prevents disassembly of Rad51 filaments. Rad51 is required for recruitment of the Mei5-Sae3-Dmc1 complex to chromosomes.\",\n      \"method\": \"Chromatin immunoprecipitation, immunofluorescence on meiotic chromosomes, sporulation/spore viability assays, overexpression suppression\",\n      \"journal\": \"Cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal in vivo methods (ChIP, IF, genetics), replicated in parallel study (PMID 15579681)\",\n      \"pmids\": [\"15620352\", \"15579681\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2004,\n      \"finding\": \"Fission yeast Swi5 (sp) encodes an 85-amino-acid polypeptide with an N-terminal predicted coiled-coil domain. swi5Δ reduces meiotic recombinant frequencies ~10-fold, is hypersensitive to DNA-damaging agents, and acts in a branched pathway of joint molecule formation; swi5Δ suppresses the low spore viability of mus81Δ eme1Δ (joint molecule resolution mutant), placing Swi5 in joint molecule formation.\",\n      \"method\": \"Gene identification/deletion, recombination frequency assays, epistasis analysis with mus81Δ/eme1Δ and rhp55Δ/rhp57Δ\",\n      \"journal\": \"Genetics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic epistasis plus defined molecular phenotype, single lab\",\n      \"pmids\": [\"15466419\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2006,\n      \"finding\": \"The fission yeast Swi5-Sfr1 complex stimulates Rhp51 (Rad51) and Dmc1-mediated DNA strand exchange at substoichiometric concentrations on long DNA substrates; stimulation is completely dependent on RPA and ATP. Swi5-Sfr1 overcomes the inhibitory effect of RPA on recombinase loading and preferentially stimulates the ssDNA-dependent ATPase activity of Rhp51, and increases Dmc1 binding to ssDNA.\",\n      \"method\": \"In vitro strand exchange assay, ATPase assay, ssDNA binding assay with purified proteins\",\n      \"journal\": \"Nature structural & molecular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — in vitro reconstitution with purified proteins, multiple enzymatic assays, replicated and extended by subsequent studies\",\n      \"pmids\": [\"16921379\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2007,\n      \"finding\": \"In fission yeast, Swi5-GFP localizes to the nucleus forming diffuse staining with foci; spontaneous foci require Swi2. Upon UV irradiation, Swi5 foci form in swi2Δ mutants (depending on Sfr1); Sfr1 foci colocalize with damage-induced Rhp51 foci. An HO endonuclease-induced DSB assay showed Rhp51 and Rhp57 (but not Swi5/Sfr1) are essential for crossover production, distinguishing Swi5-Sfr1 from Rhp55/57 in recombination outcome.\",\n      \"method\": \"Live fluorescence microscopy (GFP), UV irradiation-induced focus formation, HO endonuclease DSB assay, genetic analysis\",\n      \"journal\": \"The EMBO journal\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct localization with functional epistasis and quantitative recombination outcomes, single lab but multiple orthogonal methods\",\n      \"pmids\": [\"17304215\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"Swi5 is a substrate of the SCF(Cdc4) ubiquitin ligase complex. Swi5 is ubiquitinated and degraded through SCF(Cdc4), and this degradation is required to terminate SIC1 transcription at early G1, ensuring efficient S-phase entry. Stabilized Swi5 causes hyperaccumulation of Sic1 and delays S-phase entry in a manner suppressed by SIC1 deletion.\",\n      \"method\": \"Refined two-hybrid screen under substrate-stabilizing conditions, ubiquitination assay, cell synchronization, S-phase entry assays, SIC1 deletion suppression\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — two-hybrid identification plus ubiquitination assay plus genetic suppression, single lab\",\n      \"pmids\": [\"18787112\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"Budding yeast Mei5-Sae3 complex preferentially binds ssDNA and relieves RPA-imposed inhibition of Dmc1 strand assimilation and DNA binding; Mei5-Sae3 physically interacts with RPA. These results establish Mei5-Sae3 as a mediator (loader) of Dmc1 onto RPA-coated ssDNA.\",\n      \"method\": \"Purified protein in vitro binding assays, strand assimilation assay, Co-IP with RPA\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — in vitro reconstitution with purified components, multiple functional assays, single lab\",\n      \"pmids\": [\"19270307\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"Mammalian (mouse) Swi5 and Sfr1 are nuclear proteins that form a complex in vivo and in vitro; Swi5 interacts in vitro with Rad51. Both proteins are mutually interdependent for their stability. Loss of either (Swi5−/− or Sfr1−/−) sensitizes ES cells to ionizing radiation, camptothecin, and PARP inhibitor, attenuates SCE induction, and increases chromosome aberrations, demonstrating a role for the mammalian Swi5-Sfr1 complex in homologous recombination.\",\n      \"method\": \"Co-IP, in vitro pulldown with Rad51, ES cell knockout, colony survival assays, SCE assay, chromosomal aberration analysis\",\n      \"journal\": \"PLoS genetics\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal Co-IP, in vitro binding, KO cells with multiple orthogonal phenotypic readouts, replication of fission yeast findings in mammals\",\n      \"pmids\": [\"20976249\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"The fission yeast Swi5-Sfr1 complex has a 1:1 stoichiometry and displays an extremely elongated dogleg-shaped structure (frictional ratio f/f0 = 2.0) in solution as determined by SAXS and analytical ultracentrifugation; topology mapping with Fab fragments places Sfr1 subdomains at defined positions, suggesting the complex fits into the groove of the Rad51 filament.\",\n      \"method\": \"Analytical ultracentrifugation, ESI-MS, SAXS, Fab-fragment mapping\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — multiple biophysical methods (AUC, MS, SAXS) in one study, single lab\",\n      \"pmids\": [\"22033972\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"The budding yeast Mei5-Sae3 complex preferentially binds a fork-like DNA substrate; Mei5 (not Sae3) confers DNA binding activity; Mei5-Sae3 interacts with Rad51 through the N-terminal domain of Mei5. Mei5-Sae3 lacks recombination mediator activity for Rad51 and lacks ssDNA annealing activity, distinguishing it from Rad52.\",\n      \"method\": \"Purified protein biochemical assays (DNA binding, ssDNA annealing, strand exchange), domain deletion/interaction mapping\",\n      \"journal\": \"DNA repair\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — multiple in vitro assays with purified proteins, single lab\",\n      \"pmids\": [\"21543267\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"Crystal structure of the Swi5-Sfr1 complex reveals that Swi5 and the C-terminal core domain of Sfr1 form a parallel coiled-coil heterodimer joined by two leucine-zipper motifs and a bundle; the coiled coil is sharply kinked creating a crescent-shaped structure for binding within the Rad51 filament groove. The N-terminal region of Sfr1 provides the Rad51-binding interface.\",\n      \"method\": \"X-ray crystallography, functional mutagenesis\",\n      \"journal\": \"Structure\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — crystal structure with functional mutagenesis, defining atomic-level mechanism\",\n      \"pmids\": [\"22405003\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"Mouse Swi5-Sfr1 complex has 1:1 stoichiometry; the intact complex (not Swi5 or Sfr1 alone) physically interacts with Rad51 and stimulates Rad51-mediated homologous DNA pairing by stabilizing the Rad51-ssDNA presynaptic filament. The RSfp (rodent Sfr1 proline-rich) motif in Sfr1 functions as a negative regulatory element.\",\n      \"method\": \"Biophysical stoichiometry determination, Co-IP, in vitro strand exchange assay, presynaptic filament stability assay, mutagenesis of RSfp motif\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — biophysical, biochemical, and mutagenesis methods in one study with defined mechanism\",\n      \"pmids\": [\"22492707\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"Karyopherin Msn5 is required for nuclear export of Swi5 in S. cerevisiae and physically interacts with the N-terminal end of Swi5. Inactivation of Msn5 reduces cellular Swi5 protein levels by a post-transcriptional defect in Swi5 synthesis (not increased degradation). High Swi5 nuclear accumulation in msn5 cells is toxic.\",\n      \"method\": \"GFP localization, Co-IP, mRNA level analysis, protein stability (cycloheximide chase), genetic toxicity assay\",\n      \"journal\": \"Biochimica et biophysica acta\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct localization experiment (GFP), Co-IP, and multiple mechanistic assays, single lab\",\n      \"pmids\": [\"22374135\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"Human SWI5-SFR1 complex enhances ADP release from the RAD51 presynaptic filament (measured by optical tweezers and biochemical assay), thereby stimulating ATP hydrolysis by ssDNA-bound RAD51 and maintaining the catalytically active state of the presynaptic filament.\",\n      \"method\": \"Optical tweezers single-molecule assay, biochemical ATPase/ADP release assay\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — single-molecule biophysics plus biochemical reconstitution, mechanistic clarity, single lab\",\n      \"pmids\": [\"24078249\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"Swi5-Sfr1 promotes more perpendicular alignment of nucleobases in the Rad51/ssDNA presynaptic filament (measured by flow linear dichroism); this structural change is mediated through interaction with the Rad51 filament (not directly with DNA), as deletion of the DNA-binding N-terminal Sfr1 domain does not abolish the effect.\",\n      \"method\": \"Flow linear dichroism spectroscopy, deletion mutagenesis of Sfr1 N-terminus\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — specialized biophysical method on purified proteins, single lab\",\n      \"pmids\": [\"24304898\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"Fission yeast Swi5-Sfr1 acts as both a mediator (loads Dmc1 onto RPA-coated ssDNA) and a direct activator of Dmc1 strand exchange; in contrast, Rad22 (fission yeast Rad52) inhibits Dmc1 activity by competing for binding to RPA-coated ssDNA, demonstrating dual opposing regulation of meiotic recombination.\",\n      \"method\": \"In vitro strand exchange assays, mediator assay, competition assays with purified proteins\",\n      \"journal\": \"Genes & development\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — in vitro reconstitution with purified proteins demonstrating both mediator and activator functions, single lab\",\n      \"pmids\": [\"24186976\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"A C-terminal domain within mammalian (mouse) SWI5 contributes to RAD51 interaction; SWI5-SFR1 preferentially associates with the oligomeric form of RAD51. RAD51-interaction-defective mutants of SWI5-SFR1 fail to stimulate Rad51 recombinase activity, establishing that physical interaction is indispensable for functional stimulation.\",\n      \"method\": \"Co-IP, pulldown, mutagenesis, in vitro strand exchange assay\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP plus mutagenesis plus functional assay, single lab\",\n      \"pmids\": [\"27131790\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"Mouse Swi5-Sfr1 stimulates Rad51 filament assembly by reducing Rad51 dissociation from filaments (both at nucleation and filament maintenance stages), demonstrated at single-molecule level; this reduces the nucleus size from three Rad51 molecules to two. Fission yeast Swi5-Sfr1 similarly specifically reduces SpRad51 disassembly.\",\n      \"method\": \"Single-molecule tethered particle motion (TPM), single-molecule FRET (smFRET)\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — single-molecule biophysics with two orthogonal methods, conservation demonstrated in two organisms\",\n      \"pmids\": [\"30297419\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"Two distinct sites within the intrinsically disordered N-terminus of Sfr1 (Sfr1N) cooperatively bind Rad51; deletion of Sfr1N impairs Rad51 stimulation in vitro and causes DNA damage sensitivity. Swi5-Sfr1 and Rad55-Rad57 form a higher-order complex and can collaboratively stimulate Rad51, suggesting they are not fully independent.\",\n      \"method\": \"NMR, in vitro pull-down, strand exchange assay, DNA damage sensitivity assay, mutagenesis\",\n      \"journal\": \"eLife\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — NMR plus biochemical reconstitution plus mutagenesis plus cellular assay, single lab\",\n      \"pmids\": [\"32204793\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"Mass spectrometry of Swi5-Sfr1 complex purified from fission yeast meiotic cells identified multiple phosphorylation sites on both Swi5 and Sfr1; phosphomimetic (aspartate) mutants at identified sites are only partially functional, while phospho-null mutants do not impair function, suggesting phosphorylation can negatively modulate but is not required for Swi5-Sfr1 activity.\",\n      \"method\": \"Mass spectrometry of purified meiotic complex, phosphomimetic/phospho-null mutagenesis, functional assays\",\n      \"journal\": \"Genes\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — MS identification of phosphosites plus partial mutagenesis, functional significance unclear from abstract alone\",\n      \"pmids\": [\"34208949\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"Phosphorylation of five residues within the intrinsically disordered domain of Sfr1 regulates interaction of Swi5-Sfr1 with Rad51; phosphomimetic Swi5-Sfr1 is defective in both physical and functional interaction with Rad51 and causes DNA repair deficiency. Blocking Sfr1 phosphorylation also causes DNA damage sensitivity, suggesting controlled phosphorylation cycles are important for Rad51-dependent DNA repair.\",\n      \"method\": \"Biochemical reconstitution with phosphomimetic/phospho-null mutants, Co-IP, DNA damage sensitivity assays\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — biochemical reconstitution plus mutagenesis plus cellular phenotype, single lab\",\n      \"pmids\": [\"37330173\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"Hop2-Mnd1 and Swi5-Sfr1 stimulate Dmc1 filament assembly by distinct mechanisms: Hop2-Mnd1 increases the Dmc1 binding rate (recruits Dmc1 at ssDNA/dsDNA junctions via direct DNA binding), while Swi5-Sfr1 specifically reduces the Dmc1 dissociation rate during nucleation (~2-fold). Together they provide additive stimulation.\",\n      \"method\": \"Single-molecule FRET (smFRET), tethered particle motion (TPM), order-of-addition experiments\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — two orthogonal single-molecule methods clearly distinguishing mechanistic steps, single lab\",\n      \"pmids\": [\"37395447\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"Mei5-Sae3 stabilizes Dmc1 nucleating clusters (2–3 molecules) on naked ssDNA by preferentially reducing Dmc1 dissociation rates; it also stimulates Dmc1 assembly on RPA-coated ssDNA by stabilizing early clusters, which promotes RPA displacement. Coexistence of an intermediate containing both Dmc1 and RPA was directly observed.\",\n      \"method\": \"Single-molecule FRET (smFRET), colocalization single-molecule spectroscopy (CoSMoS), GFP-labeled RPA\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — single-molecule reconstitution with multiple orthogonal methods directly observing molecular intermediates, single lab\",\n      \"pmids\": [\"39275989\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"Swi5-Sfr1 stimulates Dmc1-driven strand exchange by acting as a mediator (promotes filament nucleus formation/association with ssDNA) rather than as an activator of the C1-C2 intermediate transition used for Rad51; this mechanistic distinction from Rad51 regulation was established by kinetic real-time analysis identifying three-stranded intermediates.\",\n      \"method\": \"Real-time strand exchange assay with kinetic intermediate analysis, comparison of Dmc1 and Rad51 reactions\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — detailed kinetic reconstitution resolving mechanistic differences, single lab\",\n      \"pmids\": [\"39340300\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"Mouse SWI5-SFR1 reduces the dissociation probability of RAD51 during filament extension and shifts the oligomeric assembly unit from octamers to tetramers, promoting more uniform filament growth; this modulation of RAD51 oligomeric state facilitates extension and stabilizes DNA binding.\",\n      \"method\": \"Single-molecule tethered particle motion (TPM), step-size analysis of RAD51 assembly\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Weak — single-molecule reconstitution, single lab, single study (0 citations, very recent)\",\n      \"pmids\": [\"40682818\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"Mei5-Sae3 stabilizes Dmc1 filaments in both the active (ATP-bound) and inactive (ADP-bound) allosteric conformations; unlike calcium, AMP-PNP, or the E157D mutation, Mei5-Sae3 stabilizes the active filament without inhibiting ATP hydrolysis (and may enhance ATP hydrolysis). Filament stabilization activity of Mei5-Sae3 does not depend on alteration of the hydrolytic cycle.\",\n      \"method\": \"Dmc1 filament conformation assays, ATPase assays, comparison with known ATP hydrolysis inhibitors, single-molecule approaches\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Weak — biochemical reconstitution with mechanistic precision, very recent single study with 0 citations\",\n      \"pmids\": [\"41206037\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"SWI5/SAE3 encodes a conserved protein with two distinct functional identities depending on organism: in S. cerevisiae, SWI5 is a CDC28-phosphorylated, SCF(Cdc4)-degraded zinc-finger transcription factor that enters the nucleus at late mitosis to activate HO, SIC1, EGT2, PCL9, and other G1 genes through cooperative DNA binding with Pho2 and recruitment of Swi/Snf, SAGA, and Mediator complexes; in fission yeast and mammals, the small Swi5 polypeptide (orthologous to budding yeast Sae3/Mei5-Sae3 complex components) forms the Swi5-Sfr1 heterodimeric complex that acts as a Rad51/Dmc1 recombination mediator and activator—physically docking within the Rad51 filament groove via a crescent-shaped coiled-coil structure, reducing recombinase dissociation to stabilize presynaptic filaments, enhancing ADP release to maintain ATP-bound active filament states, and enabling Dmc1 loading onto RPA-coated ssDNA, with this activity regulated by controlled phosphorylation of the intrinsically disordered Sfr1 subunit.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"The SWI5 symbol resolves to two mechanistically distinct, organism-dependent proteins within this corpus. In budding yeast, Swi5 is a C2H2 zinc-finger transcriptional activator that drives a wave of late-mitotic/early-G1 gene expression, including HO, SIC1, EGT2, and the Pho85 cyclins PCL9/PCL2 [#1, #6, #8, #11]. Its DNA-binding zinc fingers are structurally independent modules in which finger 1 carries an N-terminal beta-strand extension that augments the canonical fold and DNA affinity [#2, #3, #7], while promoter specificity (e.g. for HO) is encoded in a separate region that mediates cooperative DNA binding with the homeodomain protein Pho2/Grf10 [#4, #10, #12]. Once nuclear, Swi5 recruits the Mediator complex via its Gal11 module, with Swi/Snf required for Mediator binding, to activate transcription ahead of Pol II [#14]. Swi5 activity is tightly gated by the cell cycle: CDC28/Cdk1 phosphorylates serines in its NLS to enforce cytoplasmic retention until anaphase [#0], Msn5 controls its nuclear export and synthesis [#27], and SCF(Cdc4)-mediated ubiquitination degrades it in early G1 to terminate SIC1 transcription and permit S-phase entry [#5, #20]. Separately, the small fission-yeast/mammalian Swi5 polypeptide (orthologous to budding-yeast Sae3 of the Mei5-Sae3 complex) forms a 1:1 heterodimer with Sfr1 that functions as a Rad51/Dmc1 recombination mediator and activator in homologous recombination [#15, #17, #22, #23]. Crystallographic and biophysical work shows the complex adopts an elongated, sharply kinked crescent-shaped coiled-coil that docks within the Rad51 filament groove, with the Sfr1 N-terminus providing the recombinase interface [#23, #25, #33]. Functionally, Swi5-Sfr1 stabilizes the presynaptic filament by reducing recombinase dissociation, enhances ADP release to maintain the ATP-bound active filament state, overcomes RPA-imposed inhibition to load Dmc1 onto ssDNA, and stimulates strand exchange — activities conserved from fission yeast to mammals and regulated by phosphorylation of the intrinsically disordered Sfr1 subunit [#18, #21, #26, #28, #32, #35].\",\n  \"teleology\": [\n    {\n      \"year\": 1991,\n      \"claim\": \"Established how Swi5 nuclear access is gated to the cell cycle, answering why a constitutive transcription factor only acts at a specific phase.\",\n      \"evidence\": \"In vitro CDC28-H1 kinase phosphorylation, NLS serine mutagenesis, and localization in S. cerevisiae\",\n      \"pmids\": [\"1652372\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not identify the phosphatase or trigger for late-mitotic dephosphorylation/entry\", \"In vitro kinase specificity vs in vivo timing not fully resolved\"]\n    },\n    {\n      \"year\": 1992,\n      \"claim\": \"Defined Swi5 as a zinc-finger transcriptional activator and showed that target-gene specificity is separable from the DNA-binding module, framing how a shared DNA-recognition fold can drive distinct programs.\",\n      \"evidence\": \"Gene disruption, promoter-reporter assays, SWI5/ACE2 chimeras, and NMR structures of the zinc fingers in budding yeast\",\n      \"pmids\": [\"1730413\", \"1453468\", \"1453467\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not identify the molecular basis of the specificity-conferring region\", \"Full-length DNA-bound complex not structurally defined\"]\n    },\n    {\n      \"year\": 1993,\n      \"claim\": \"Showed cooperative DNA binding with Pho2/Grf10 and that proteolytic instability enforces asymmetric, daughter-cell-restricted HO expression, linking Swi5 abundance control to a developmental outcome.\",\n      \"evidence\": \"DNA affinity purification, footprinting, cooperative binding assays, and stable-mutant mating-type switching assays\",\n      \"pmids\": [\"8355698\", \"7902583\", \"8449406\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Degradation machinery not identified at this stage\", \"Mechanism of cooperativity at atomic level not resolved\"]\n    },\n    {\n      \"year\": 1996,\n      \"claim\": \"Connected Swi5 nuclear entry to the cell cycle engine by showing it triggers the SIC1 burst that inactivates Clb/Cdk1, and identified EGT2 and Pho85-cyclin targets, establishing Swi5 as the driver of a coordinated M/G1 transcriptional wave.\",\n      \"evidence\": \"Deletion analysis, mRNA/protein assays, genetic suppression, synchronization, and promoter-reporter assays in S. cerevisiae\",\n      \"pmids\": [\"8816483\", \"9017392\", \"8668141\", \"9529390\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How concentration thresholds set sharp on/off transcription not mechanistically defined\", \"Direct vs indirect target distinctions for some genes incomplete\"]\n    },\n    {\n      \"year\": 1998,\n      \"claim\": \"Mapped a discrete 24-residue Swi5 region required for Pho2 interaction and cooperative binding, demonstrating that HO promoter specificity coincides with the Pho2-interaction surface rather than the zinc fingers.\",\n      \"evidence\": \"Two-hybrid, in vitro DNA binding, reporter assays, mutagenesis, and chimeric analysis\",\n      \"pmids\": [\"9774660\", \"10409653\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Structure of the Swi5-Pho2-DNA cooperative complex not determined\", \"Single-lab mapping\"]\n    },\n    {\n      \"year\": 2000,\n      \"claim\": \"Identified Swi5 as a Pho85-cyclin substrate, adding a second kinase input to Swi5 regulation beyond Cdc28.\",\n      \"evidence\": \"Two-hybrid, in vitro Pho80-Pho85 kinase assay, and genetic lethality in S. cerevisiae\",\n      \"pmids\": [\"10692159\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Functional consequence of Pho85 phosphorylation sites in vivo not pinpointed\", \"Single lab\"]\n    },\n    {\n      \"year\": 2001,\n      \"claim\": \"Showed Swi5 recruits the Mediator Gal11 module to the HO promoter prior to Pol II, with Swi/Snf required, defining the coactivator-recruitment step of Swi5-driven activation.\",\n      \"evidence\": \"ChIP of Mediator/Pol II, genetic epistasis, and kinetic binding in budding yeast\",\n      \"pmids\": [\"11562354\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Direct Swi5-Gal11 contact surface not mapped structurally\", \"Generality across other Swi5 targets not established\"]\n    },\n    {\n      \"year\": 2003,\n      \"claim\": \"Revealed that fission-yeast Swi5 partitions into two functionally distinct complexes — Swi5-Sfr1 (recombination repair) and Swi5-Swi2 (mating-type switching) — separating its roles via shared partner domains.\",\n      \"evidence\": \"Co-IP, two-hybrid, and genetic epistasis in S. pombe\",\n      \"pmids\": [\"14663140\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Switch governing complex choice not defined\", \"Stoichiometry/structure of complexes not resolved here\"]\n    },\n    {\n      \"year\": 2004,\n      \"claim\": \"Established the meiotic recombination identity of the small Swi5/Sae3 protein, showing Mei5-Sae3 is required for Dmc1 (not Rad51) chromosome loading and that fission-yeast Swi5 promotes joint-molecule formation.\",\n      \"evidence\": \"ChIP, immunofluorescence on meiotic chromosomes, sporulation assays, and recombination/epistasis analysis in budding and fission yeast\",\n      \"pmids\": [\"15620352\", \"15579681\", \"15466419\", \"9215889\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Biochemical mechanism of Dmc1 loading not yet defined\", \"Relationship between transcription-factor Swi5 and recombination Swi5 across species reflects orthology rather than one protein\"]\n    },\n    {\n      \"year\": 2006,\n      \"claim\": \"Demonstrated biochemically that Swi5-Sfr1 stimulates Rhp51/Dmc1 strand exchange substoichiometrically, overcoming RPA inhibition in an ATP-dependent manner, establishing it as a recombination mediator/activator.\",\n      \"evidence\": \"In vitro strand exchange, ATPase, and ssDNA binding assays with purified S. pombe proteins\",\n      \"pmids\": [\"16921379\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Molecular step targeted within the filament cycle not yet resolved\", \"Single lab\"]\n    },\n    {\n      \"year\": 2009,\n      \"claim\": \"Showed budding-yeast Mei5-Sae3 binds ssDNA, interacts with RPA, and relieves RPA inhibition to load Dmc1, defining a mediator activity even though Mei5-Sae3 lacks Rad51-mediator and annealing functions.\",\n      \"evidence\": \"Purified-protein binding, strand assimilation, Co-IP with RPA, and domain mapping\",\n      \"pmids\": [\"19270307\", \"21543267\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Why Mei5-Sae3 mediates Dmc1 but not Rad51 not fully explained\", \"Single lab\"]\n    },\n    {\n      \"year\": 2007,\n      \"claim\": \"Placed Swi5-Sfr1 in DNA-damage-induced repair foci dependent on Sfr1 and distinguished it from the Rhp55/57 pathway in crossover outcome, defining its in vivo localization and pathway position.\",\n      \"evidence\": \"Live GFP microscopy, UV-induced focus formation, and HO-DSB recombination assays in S. pombe\",\n      \"pmids\": [\"17304215\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Recruitment hierarchy to damage sites only partially defined\", \"Single lab\"]\n    },\n    {\n      \"year\": 2010,\n      \"claim\": \"Demonstrated conservation in mammals: mouse Swi5-Sfr1 forms a mutually stabilizing complex that interacts with Rad51 and is required for homologous recombination and genome stability.\",\n      \"evidence\": \"Co-IP, in vitro Rad51 pulldown, ES-cell knockouts, survival, SCE, and chromosomal aberration assays\",\n      \"pmids\": [\"20976249\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"In vivo loading sites and kinetics in mammals not defined\", \"Physiological role in meiosis vs somatic HR not separated\"]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"Solved the architecture of the complex, showing an elongated crescent-shaped parallel coiled-coil heterodimer that fits the Rad51 filament groove, with Sfr1's N-terminus as the recombinase interface and the rodent RSfp motif as a negative regulator.\",\n      \"evidence\": \"Crystallography, SAXS, AUC, Fab mapping, and mutagenesis across fission yeast and mouse proteins\",\n      \"pmids\": [\"22405003\", \"22033972\", \"22492707\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Atomic structure of the Swi5-Sfr1-Rad51 filament complex not determined\", \"How the disordered Sfr1 N-terminus engages Rad51 not resolved here\"]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"Resolved the mechanistic action on the filament: Swi5-Sfr1 enhances ADP release to sustain the ATP-bound active state, reorients nucleobases via the Rad51 interface, and acts as a dual mediator/activator for Dmc1 opposed by Rad22/Rad52.\",\n      \"evidence\": \"Optical tweezers, ATPase/ADP-release assays, flow linear dichroism, and competition strand-exchange assays in human and fission yeast systems\",\n      \"pmids\": [\"24078249\", \"24304898\", \"24186976\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Coupling between ADP release and filament stability not fully quantified\", \"Single lab for each measurement\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Identified a C-terminal SWI5 contribution to RAD51 binding, showed preference for oligomeric RAD51, and proved physical interaction is indispensable for functional stimulation.\",\n      \"evidence\": \"Co-IP, pulldown, interaction-defective mutagenesis, and strand exchange assays in mouse\",\n      \"pmids\": [\"27131790\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Relative contributions of Swi5 C-terminus vs Sfr1 N-terminus to the interface not fully partitioned\", \"Single lab\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Established at single-molecule resolution that Swi5-Sfr1 reduces recombinase dissociation at both nucleation and maintenance, lowering the nucleation threshold — a mechanism conserved between mouse and fission yeast.\",\n      \"evidence\": \"Single-molecule TPM and smFRET on Rad51/SpRad51 filaments\",\n      \"pmids\": [\"30297419\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How dissociation reduction translates to in vivo HR efficiency not quantified\", \"Single lab\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Showed the intrinsically disordered Sfr1 N-terminus uses two cooperative Rad51-binding sites and that Swi5-Sfr1 collaborates with Rad55-Rad57 in a higher-order complex, refining the recombinase interface and inter-mediator coordination.\",\n      \"evidence\": \"NMR, pull-downs, strand exchange, DNA-damage sensitivity, and mutagenesis\",\n      \"pmids\": [\"32204793\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structure of the Swi5-Sfr1/Rad55-Rad57 super-complex not determined\", \"Single lab\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Established that controlled phosphorylation cycles of the disordered Sfr1 domain tune Swi5-Sfr1 binding to Rad51, with both phosphomimetic and phospho-blocked states impairing repair, defining a regulatory layer over recombinase activation.\",\n      \"evidence\": \"Phosphomimetic/phospho-null reconstitution, Co-IP, and DNA-damage sensitivity assays; complemented by mechanistic dissection vs Hop2-Mnd1\",\n      \"pmids\": [\"37330173\", \"37395447\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"The kinase/phosphatase pair controlling Sfr1 phosphorylation cycles not identified\", \"In vivo timing of phospho-regulation not mapped\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Refined the mediator mechanism for Dmc1, showing Mei5-Sae3/Swi5-Sfr1 stabilizes early Dmc1 clusters to promote RPA displacement and acts as a nucleation-promoting mediator distinct from the activator mechanism used for Rad51.\",\n      \"evidence\": \"smFRET, CoSMoS, and real-time kinetic strand-exchange analysis with purified proteins\",\n      \"pmids\": [\"39275989\", \"39340300\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structural basis of the Dmc1/RPA intermediate not resolved\", \"Quantitative link to meiotic crossover control incomplete\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Extended the stabilization mechanism by showing the complex shifts recombinase oligomeric assembly units (octamer-to-tetramer for RAD51) and stabilizes both ATP- and ADP-bound Dmc1 conformations without inhibiting hydrolysis, defining how it sustains active filaments.\",\n      \"evidence\": \"Single-molecule TPM step-size analysis (mouse) and Dmc1 conformation/ATPase assays (budding yeast)\",\n      \"pmids\": [\"40682818\", \"41206037\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Very recent, single-study findings not yet independently replicated\", \"Physiological relevance of oligomeric-state switching not established in vivo\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How the two Swi5 identities — a CDK/SCF-regulated zinc-finger transcription factor in budding yeast and the conserved Swi5-Sfr1 recombination mediator in fission yeast/mammals — relate at the level of evolutionary origin and whether any single organism uses both functions remains unresolved in this corpus.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No timeline study reconciles the transcription-factor and recombination-mediator orthology groups under one molecular framework\", \"Kinase/phosphatase identity for Sfr1 regulation unknown\", \"No atomic structure of the recombinase-bound complex\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0003677\", \"supporting_discovery_ids\": [1, 2, 3, 4, 7]},\n      {\"term_id\": \"GO:0140110\", \"supporting_discovery_ids\": [1, 6, 8, 11, 14]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [16, 18, 21, 26, 28, 30, 32]},\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [14, 25, 33]},\n      {\"term_id\": \"GO:0003723\", \"supporting_discovery_ids\": [18, 21, 24]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [0, 6, 19, 22, 27]},\n      {\"term_id\": \"GO:0000228\", \"supporting_discovery_ids\": [16, 19]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-73894\", \"supporting_discovery_ids\": [18, 22, 30, 33]},\n      {\"term_id\": \"R-HSA-74160\", \"supporting_discovery_ids\": [1, 6, 14]},\n      {\"term_id\": \"R-HSA-1640170\", \"supporting_discovery_ids\": [0, 6, 20]},\n      {\"term_id\": \"R-HSA-1474165\", \"supporting_discovery_ids\": [9, 16, 17]}\n    ],\n    \"complexes\": [\n      \"Swi5-Sfr1\",\n      \"Mei5-Sae3\",\n      \"Swi5-Swi2\"\n    ],\n    \"partners\": [\n      \"SFR1\",\n      \"RAD51\",\n      \"DMC1\",\n      \"PHO2\",\n      \"RPA\",\n      \"CDC4\",\n      \"MSN5\",\n      \"PHO85\"\n    ],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"tie","faith_supported":7,"faith_total":7,"faith_pct":100.0}}