OsEME1 (Q0J9J6) is the rice ortholog of the EME1/MMS4-family DNA structure-specific endonuclease subunit. EME1 partners with MUS81 to form a heterodimeric (heterotetrameric) endonuclease that binds and cleaves branched DNA intermediates - nicked Holliday junctions, 3'-flaps, D-loops and replication-fork structures - generated during homologous recombination (HR) repair and replication. Unlike yeast Mms4/Eme1 and human EME1, which are non-catalytic regulatory subunits, recombinant OsEME1 (via its C-terminal ERCC4 domain) directly binds and cleaves branched DNA substrates in vitro, with four conserved residues required for activity (Du et al. 2025, PMID:40333587). OsEME1 is a single-copy nuclear gene; the OsEME1-GFP fusion localizes to the nucleus. Its dominant biological role in rice is somatic DNA-damage repair: oseme1 loss-of-function mutants are hypersensitive to the DNA-damaging agents MMS and Zeocin, accumulate gamma-H2AX foci, show S/G2 cell-cycle arrest, and have a striped-albino-leaf / defective-chloroplast phenotype that is strongly enhanced by high light. The chloroplast defect is a downstream consequence of nuclear genome-maintenance failure (OsEME1 cleaves damaged DNA in nuclear chloroplast-development genes such as OsGLK1/OsGLK2). Consistent with the rice MUS81 meiosis study (Mu et al. 2022, PMID:36495065), the MUS81-EME1 complex in rice has only a minor meiotic role - resolution of atypical meiotic recombination intermediates - and is NOT required for crossover designation; the "Essential meiotic endonuclease" name is historical (from S. pombe eme1) and is misleading for the plant protein, which acts predominantly in mitotic/somatic HR repair and replication-fork rescue.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0051321 meiotic cell cycle | IEA GO_REF:0000043 | MARK AS OVER ANNOTATED | Summary: SPKW (GO_REF:0000043) annotation derived from the UniProt keyword "Meiosis"; snapshot-only, removed in the current GOA release. EME1/MUS81 is a structure-specific endonuclease acting on branched DNA in BOTH mitotic/somatic DNA repair and meiotic recombination - it is not meiosis-restricted. Reason: GOA's removal of this annotation was JUSTIFIED. The keyword "Meiosis" reflects the historical "Essential meiotic endonuclease" name (inherited from S. pombe eme1) but mapping it to "meiotic cell cycle" is over-specific for the rice protein. The dominant, experimentally demonstrated role of OsEME1 in rice is somatic DNA-damage repair: oseme1 mutants are hypersensitive to MMS/Zeocin, accumulate gamma-H2AX foci and show cell-cycle arrest in vegetative tissue, with a striped-leaf/chloroplast phenotype [PMID:40333587]. The rice MUS81-EME1 complex contributes only minimally to meiosis - mus81 mutants have normal chiasma numbers and normal crossover designation and the complex acts only on atypical meiotic intermediates [PMID:36495065]. A keyword-based blanket "meiotic cell cycle" term is therefore an over-annotation; the genuine meiotic contribution is more precisely captured by the IBA term "resolution of meiotic recombination intermediates" (GO:0000712), which is retained in current GOA. Supporting Evidence: PMID:36495065 the total chiasma numbers in mus81 mutants were indistinguishable from wild-type. The numbers of HEI10 foci ... in mus81 were also similar to that of wild-type. PMID:40333587 treatment with 75 ΞΌg/mL of MMS or 50 ΞΌg/mL of Zeocin strongly inhibited root and shoot growth, especially in the mutants PMID:40333587 OsEME1 regulates chloroplast development and division by maintaining the transcription of chloroplast-related genes and nuclear genome integrity |
| GO:0051301 cell division | IEA GO_REF:0000043 | MARK AS OVER ANNOTATED | Summary: SPKW (GO_REF:0000043) annotation derived from the UniProt keywords "Cell division" / "Mitosis"; snapshot-only, removed in current GOA. EME1 acts in cell-cycle-coupled DNA repair, but "cell division" per se is not its molecular role. Reason: GOA's removal of this annotation was JUSTIFIED. The keyword mapping produces an overly generic process term. OsEME1 is a DNA-repair endonuclease whose activity is cell-cycle regulated (MUS81-EME1 is activated at G2/M and during the DNA-damage response in other species [PMID:23584455]), and oseme1 mutants show cell-cycle arrest as a CONSEQUENCE of unrepaired DNA damage [PMID:40333587]. The protein does not have a direct role in the cell-division process itself (e.g. cytokinesis, chromosome segregation machinery). "Cell division" is an indirect downstream/contextual term and is better replaced by specific DNA-repair process terms (DNA repair, double-strand break repair) that are retained in current GOA. Supporting Evidence: PMID:40333587 The DNA contents at the S and G2 stages following Zeocin treatment increased in ... cells compared to KY131 PMID:40333587 mutations in OsEME1 led to cell cycle arrest and a DNA damage response |
| GO:0006310 DNA recombination | IEA GO_REF:0000043 | MARK AS OVER ANNOTATED | Summary: SPKW (GO_REF:0000043) annotation derived from the UniProt keyword "DNA recombination"; snapshot-only, removed in current GOA. EME1/MUS81 resolves homologous-recombination intermediates, so the essence of the term is biologically correct, but the keyword mapping produces a non-specific parent term. Reason: GOA's removal of this annotation was reasonable and did NOT lose correct biology. OsEME1 genuinely participates in homologous recombination - it binds and cleaves branched HR intermediates (Y12, pre-X12, X12 substrates) in vitro [PMID:40333587] - so "DNA recombination" is not wrong. However, it is a broad parent term, and the specific HR-repair function is better and still represented in current GOA by the IBA terms "double-strand break repair" (GO:0006302) and "resolution of meiotic recombination intermediates" (GO:0000712) and the IEA term "DNA repair" (GO:0006281). A NEW more precise term, "double-strand break repair via homologous recombination" (GO:0000724), is proposed below. Removal of the generic keyword-derived term is therefore acceptable. Supporting Evidence: PMID:40333587 OsEME1 directly binds to and cleaves Y12, pre-X12 and X12, which are typical substrates after HR repair of DNA damage file:ORYSJ/EME1/EME1-deep-research-falcon.md rice OsEME1 likely participates in the canonical SSE pathway for processing recombination/replication structures |
| GO:0004519 endonuclease activity | IEA GO_REF:0000043 | MODIFY | Summary: SPKW (GO_REF:0000043) annotation derived from the UniProt keywords "Endonuclease"/"Nuclease"; snapshot-only, removed in current GOA. EME1 IS a structure-specific endonuclease (EC 3.1.22.-), and recombinant OsEME1 directly binds and cleaves branched DNA substrates in vitro via its C-terminal ERCC4 domain. Reason: GOA's removal of this annotation was NOT justified - a correct, core molecular-function annotation was lost. EME1 is genuinely an endonuclease: the UniProt RecName is "Crossover junction endonuclease EME1" with EC 3.1.22.-, and Du et al. (2025) showed directly that recombinant MBP-OsEME1 and its C-terminal fragment bind and cleave the branched Y12/pre-X12/X12 substrates, with four conserved residues required for activity [PMID:40333587]. Critically, the current (2026) GOA release contains NO catalytic molecular-function term for OsEME1 at all - only "DNA binding" (GO:0003677). Removing "endonuclease activity" without replacement leaves the gene with no MF describing its core enzymatic activity. The annotation should be retained, but MODIFIED to the more specific and informative term "crossover junction DNA endonuclease activity" (GO:0008821), which precisely captures the EME1/MUS81 structure-specific branched-DNA cleavage activity (see also the NEW entry below). Proposed replacements: crossover junction DNA endonuclease activity Supporting Evidence: PMID:40333587 The major cleavage products were obtained in OsEME1 and OsEME1-C, and their levels gradually increased over time PMID:40333587 OsEME1 directly binds to and cleaves Y12, pre-X12 and X12, which are typical substrates after HR repair of DNA damage file:ORYSJ/EME1/EME1-deep-research-falcon.md Purified OsEME1 directly binds and cleaves branched DNA substrates typical of HR intermediates, including Y12, pre-X12, and X12 ... Supports annotation as a crossover-junction/branched-DNA endonuclease involved in HR-mediated DSB repair. |
| GO:0016787 hydrolase activity | IEA GO_REF:0000043 | MARK AS OVER ANNOTATED | Summary: SPKW (GO_REF:0000043) annotation derived from the UniProt keyword "Hydrolase"; snapshot-only, removed in current GOA. "Hydrolase activity" is the high-level parent of the gene's true endonuclease (phosphodiester-bond hydrolase) activity. Reason: GOA's removal of this annotation was JUSTIFIED. "Hydrolase activity" is a very broad grouping term; an endonuclease is a hydrolase, so the term is not wrong, but it is uninformative. The correct, specific catalytic function (endonuclease / crossover junction DNA endonuclease activity) is demonstrated experimentally [PMID:40333587] and should be annotated directly (see the MODIFY on GO:0004519 and the NEW GO:0008821 entry). Retaining a top-level "hydrolase activity" term provides no additional information once the specific endonuclease MF is present. Removal of the vague parent is appropriate. Supporting Evidence: PMID:40333587 we measured the endonuclease activity of OsEME1 by performing a nuclease assay, followed by gel electrophoresis file:ORYSJ/EME1/EME1-deep-research-falcon.md the most direct biochemical description is that **OsEME1 binds and cleaves branched DNA substrates** representing recombination/repair intermediates ... This is an **endonucleolytic cleavage** of DNA phosphodiester bonds (EC class **3.1.22.-**) on structured substrates. |
| GO:0046872 metal ion binding | IEA GO_REF:0000043 | MARK AS OVER ANNOTATED | Summary: SPKW (GO_REF:0000043) annotation derived from the UniProt keywords "Metal-binding"/"Magnesium"/"Calcium"; snapshot-only, removed in current GOA. The MUS81-EME1 nuclease reaction is metal-dependent (Mg2+/Ca2+ cofactors). Reason: GOA's removal of this generic keyword-derived term was acceptable. The UniProt entry lists Mg(2+) and Ca(2+) as cofactors (by similarity), and structure-specific nuclease chemistry is divalent-metal-dependent, so the gene does bind metal ions. However, "metal ion binding" is a broad term inferred from a keyword rather than from gene-specific experimental evidence, and no metal-coordinating residues are annotated on the rice protein. If a metal-binding MF were retained it should be the specific "magnesium ion binding" (GO:0000287); but as a free-standing keyword-derived annotation the broad term adds little, so its removal is reasonable. The metal dependence is implicit in the endonuclease MF. Supporting Evidence: PMID:40333587 Eme1 [methyl methanesulfonate 4 (Mms4) in ...] forms a heterodimeric endonuclease with Mus81 ..., cleaving branched DNA substrates such as HJs, 3β²-DNA flaps and replication forks file:ORYSJ/EME1/EME1-deep-research-falcon.md activity is influenced by divalent cations (Mg2+/Ca2+ support activity; Mn2+ can increase activity and product diversity). |
| GO:0031297 replication fork processing | IBA GO_REF:0000033 | ACCEPT | Summary: IBA annotation propagated across the EME1/MUS81 phylogenetic group. The MUS81-EME1 complex processes stalled/collapsed replication-fork intermediates - a conserved mitotic function of the complex. Reason: Well supported by conserved biology and consistent with the UniProt FUNCTION statement ("May be required in mitosis for the processing of stalled or collapsed replication fork intermediates"). In Arabidopsis, MUS81 and RECQ4A process recombination-induced aberrant intermediates during replication, and recq4A mus81 double mutants are lethal [PMID:20971895]. Branched fork structures (3'-flaps, replication forks) are canonical MUS81-EME1 substrates and OsEME1 cleaves replication-fork-type Y/X branched substrates in vitro [PMID:40333587]. The IBA annotation is at an appropriate level of specificity. Supporting Evidence: PMID:20971895 RECQ4A and MUS81 are required for processing recombination-induced aberrant intermediates during replication PMID:24008669 RuvC is also known to cut branched DNA intermediates that originate directly from blocked replication forks, targeting them for origin-independent replication restart |
| GO:0048476 Holliday junction resolvase complex | IBA GO_REF:0000033 | ACCEPT | Summary: IBA annotation: EME1 is a subunit of the MUS81-EME1 structure-specific endonuclease, which acts as a Holliday-junction-resolving complex. Confirmed in rice by direct OsEME1-OsMUS81 interaction. Reason: Strongly supported. EME1/MUS81 heterodimers (heterotetramers) are conserved Holliday- junction resolvases across yeast, mammals and plants. In rice, OsEME1 directly interacts with OsMUS81 - shown by yeast two-hybrid, luciferase complementation and BiFC, with the OsEME1 ERCC4 domain and the OsMUS81 HhH motif mediating the interaction [PMID:40333587]. This is a core cellular-component annotation for EME1. Supporting Evidence: PMID:40333587 OsEME1 interacts with OsMUS81 and ... the ERCC4 domain of OsEME1 is required for this interaction PMID:40333587 Homologues of EME1 and MUS81 interact to form heterotetramers in mammals, yeasts and Arabidopsis file:ORYSJ/EME1/EME1-deep-research-falcon.md OsEME1 physically interacts with OsMUS81; interaction depends on the OsEME1 ERCC4 domain and OsMUS81 HhH motif, and interaction signal localizes to nuclei ... Strong evidence that rice OsEME1 functions as the MUS81 partner in a nuclear structure-specific nuclease complex. |
| GO:0000712 resolution of meiotic recombination intermediates | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: IBA annotation: the MUS81-EME1 complex resolves meiotic recombination intermediates, contributing to a subset of (interference-insensitive) crossovers. In rice this role is minor and limited to atypical meiotic intermediates. Reason: The annotation is correct but reflects a minor, non-core function for the rice protein. Rice MUS81 is required for resolution of ATYPICAL meiotic recombination intermediates (mus81 zep1 and mus81 fancm double mutants show chromosome fragments and bridges) and the FANCM-dependent interference-insensitive extra crossovers require MUS81 for resolution [PMID:36495065, PMID:37632767]. However, rice mus81 single mutants have wild-type chiasma numbers and normal crossover designation, so meiotic crossover resolution is not the dominant function [PMID:36495065]. Given that the demonstrated dominant role of OsEME1 in rice is somatic DSB/replication repair [PMID:40333587], this meiotic-intermediate-resolution term should be retained but classified as non-core. Supporting Evidence: PMID:36495065 MUS81 ... plays a crucial role in the resolution of atypical meiotic intermediates by working together with other anti-crossover factors PMID:37632767 the meiotic extra COs are not marked with HEI10 and require MUS81 resolvase for resolution |
| GO:0006302 double-strand break repair | IBA GO_REF:0000033 | ACCEPT | Summary: IBA annotation: EME1/MUS81 functions in double-strand break repair. This is the core biological process of OsEME1, supported directly by rice mutant phenotypes. Reason: This is a core function and is well supported by direct experimental evidence in rice. oseme1 loss-of-function mutants are hypersensitive to the DNA-damaging agents MMS and Zeocin, accumulate gamma-H2AX foci (a DSB marker) and show S/G2 cell-cycle arrest, and OsEME1 binds and cleaves branched HR-repair intermediates in vitro [PMID:40333587]. In Arabidopsis, MUS81 is required for efficient synthesis-dependent strand annealing (an HR-mediated DSB repair pathway) [PMID:20971895]. The IBA term is at the right level of specificity; a more precise term (GO:0000724, double-strand break repair via homologous recombination) is proposed below. Supporting Evidence: PMID:40333587 The ... and ... mutants exhibited significantly more Ξ³2HAX foci than KY131 with or without Zeocin treatment ... OsEME1 regulates DSB repair and the cell cycle PMID:20971895 MUS81 and RECQ4A are required for efficient synthesis-dependent strand annealing (SDSA) file:ORYSJ/EME1/EME1-deep-research-falcon.md Loss of OsEME1 caused **hypersensitivity to DNA-damaging agents** ... consistent with a function in HR-mediated repair and/or recovery from replication-associated lesions ... Supports a role in HR-mediated DSB repair and replication-associated genome stability. |
| GO:0031573 mitotic intra-S DNA damage checkpoint signaling | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: IBA annotation propagated from fission yeast, where Mus81-Eme1 activity is integrated with the intra-S/DNA-damage checkpoint via ATR(Rad3)/CDK phosphorylation of Eme1. Reason: The annotation captures a genuine, conserved regulatory connection but is not a core function and is supported only indirectly for rice. In S. pombe, DNA-damage-induced activation of Mus81-Eme1 requires Cdc2(CDK1)- and Rad3(ATR)-dependent phosphorylation of Eme1 [PMID:23584455]. In rice, oseme1 mutants show DNA-damage-induced cell-cycle arrest and a DNA-damage response [PMID:40333587], consistent with checkpoint coupling, but there is no direct evidence that OsEME1 itself transduces checkpoint signaling - it is a downstream effector (an endonuclease) whose activity is checkpoint- regulated rather than a checkpoint signaling component. Retain as non-core; OsEME1's relationship to the checkpoint is being regulated BY it, not enacting it. Supporting Evidence: PMID:23584455 DNA damage-induced activation of Mus81-Eme1 ... requires both Cdc2(CDK1)- and Rad3(ATR)-dependent phosphorylation of Eme1 PMID:40333587 mutations in ... led to cell cycle arrest and a DNA damage response |
| GO:0003677 DNA binding | IEA GO_REF:0000002 | ACCEPT | Summary: IEA annotation from InterPro (IPR006166, ERCC4 domain). OsEME1 binds DNA directly - confirmed biochemically. Reason: Correct. The ERCC4 domain has nucleic-acid-binding activity, and recombinant OsEME1 and OsEME1-C show major binding shifts on branched Y12 substrates in EMSA, with a measured substrate Kd of ~16 microM by microscale thermophoresis [PMID:40333587]. "DNA binding" is a generic term; the more informative activity is the structure- specific endonuclease MF (see the NEW GO:0008821 entry), but the DNA-binding IEA is not incorrect and can be accepted. Supporting Evidence: PMID:40333587 Major binding shifts were detected in the OsEME1 and OsEME1-C lines but not in the MBP control |
| GO:0005634 nucleus | IEA GO_REF:0000120 | ACCEPT | Summary: IEA annotation for nuclear localization. Directly confirmed in rice by GFP imaging. Reason: Strongly supported by direct experimental evidence: the OsEME1-GFP fusion protein localizes to the nucleus and overlaps with the nuclear marker H2B-mCherry in a transient expression assay [PMID:40333587]. Nuclear localization is consistent with its role as a nuclear DNA-repair endonuclease and with the UniProt subcellular location. Supporting Evidence: PMID:40333587 the OsEME1-GFP fusion protein localized to the nucleus and overlapped closely with the nuclear protein H2B-mCherry file:ORYSJ/EME1/EME1-deep-research-falcon.md Direct evidence from interaction imaging assays indicates that the **OsEME1βOsMUS81 interaction occurs in the nucleus**, supporting a primary nuclear role in processing DNA repair/recombination intermediates. |
| GO:0006281 DNA repair | IEA GO_REF:0000002 | ACCEPT | Summary: IEA annotation from InterPro (IPR033310, Mms4/EME1/EME2). DNA repair is a core biological process of OsEME1. Reason: Core function, strongly supported by direct rice evidence. oseme1 mutants are hypersensitive to DNA-damaging agents (MMS, Zeocin), accumulate gamma-H2AX foci and show DNA-damage-induced cell-cycle arrest [PMID:40333587]. OsEME1 cleaves branched HR-repair intermediates in vitro. The term is appropriate, though the more specific "double-strand break repair" (GO:0006302, IBA, retained) and the proposed GO:0000724 better capture the HR-specific mechanism. Supporting Evidence: PMID:40333587 we discovered a biochemical role for OsEME1 in HR repair and a biological role for this protein in chloroplast development |
| GO:0048476 Holliday junction resolvase complex | IEA GO_REF:0000002 | ACCEPT | Summary: IEA annotation from InterPro (IPR033310) for the Holliday junction resolvase complex; duplicates the IBA annotation to the same term. Reason: Correct and consistent with the IBA annotation to the same term and with direct evidence that OsEME1 interacts with OsMUS81 to form a structure-specific endonuclease complex [PMID:40333587]. Duplicate annotations with different evidence codes are acceptable; the IEA provides additional computational support for a well-established complex membership. Supporting Evidence: PMID:40333587 OsEME1 interacts with OsMUS81 and ... the ERCC4 domain of OsEME1 is required for this interaction |
| GO:0009411 response to UV | IEP PMID:12869764 Collection, mapping, and annotation of over 28,000 cDNA clon... | REMOVE | Summary: IEP annotation citing PMID:12869764, which is the rice full-length cDNA consortium paper ("Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice"). That paper contains no gene-specific UV-response expression experiment. Reason: This annotation is not supported by its cited reference. PMID:12869764 is a large-scale cDNA collection/sequencing/annotation paper; it reports only clone collection, genome mapping and InterPro-based function assignment, with no expression-response assay for this gene. The IEP (Inferred from Expression Pattern) almost certainly derives from the stress-treated source of a cDNA library (library-of-origin metadata), which is not a valid measurement of UV-induced expression and does not demonstrate biological "involvement in" a UV response. Expression presence is not function. While OsEME1 IS a DNA-damage-repair gene (and could plausibly act in UV-DSB repair), the only experimental DNA-damage data [PMID:40333587] used MMS and Zeocin, not UV. This keyword/library-derived IEP should be removed. Supporting Evidence: PMID:12869764 We collected and completely sequenced 28,469 full-length complementary DNA clones from Oryza sativa L. ssp. japonica cv. Nipponbare. |
| GO:0009644 response to high light intensity | IEP PMID:12869764 Collection, mapping, and annotation of over 28,000 cDNA clon... | REMOVE | Summary: IEP annotation citing PMID:12869764 (rice full-length cDNA collection paper), which contains no gene-specific high-light-response expression experiment for this gene. Reason: The cited reference does not support this annotation. PMID:12869764 is a cDNA collection/annotation paper with no expression-response assay for OsEME1; the IEP is a library-of-origin / keyword artefact, and expression is not function. Notably, OsEME1 high-light sensitivity IS genuine - but it was demonstrated in a different, later paper (Du et al. 2025, PMID:40333587), where oseme1 mutants show severe leaf striping and cell death after high-light treatment. Even there, high-light sensitivity is a downstream consequence of a nuclear genome-maintenance defect (failure to repair oxidative/replication DNA damage), not a primary "response to high light intensity" function of the protein. This particular IEP annotation, as attributed to PMID:12869764, is unsupported and should be removed. Supporting Evidence: PMID:12869764 Through homology searches of publicly available sequence data, we assigned tentative protein functions to 21,596 clones (75.86%). |
| GO:0010332 response to gamma radiation | IEP PMID:12869764 Collection, mapping, and annotation of over 28,000 cDNA clon... | REMOVE | Summary: IEP annotation citing PMID:12869764 (rice full-length cDNA collection paper), which contains no gene-specific gamma-radiation-response expression experiment. Reason: Not supported by the cited reference. PMID:12869764 reports cDNA clone collection, mapping and annotation, with no gamma-irradiation expression experiment for OsEME1. The IEP reflects library-of-origin metadata rather than a measured expression response, and expression presence is not evidence of biological involvement. The gene's DNA-repair role is real and captured by the DNA-repair / DSB-repair process terms, but this specific "response to gamma radiation" IEP is an over-annotation attributed to a paper that does not test it, and should be removed. Supporting Evidence: PMID:12869764 Mapping of the cDNA clones to genomic DNA revealed that there are 19,000 to 20,500 transcription units in the rice genome. |
| GO:0008821 crossover junction DNA endonuclease activity | IDA PMID:40333587 ESSENTIAL MEIOTIC ENDONUCLEASE 1 is required for chloroplast... | NEW | Summary: OsEME1 is a structure-specific endonuclease that binds and cleaves branched Holliday-junction-type DNA substrates. This catalytic molecular function is not represented in current GOA and should be added. Reason: The current GOA release has NO catalytic MF term for OsEME1 (only "DNA binding"), and the retired SPKW "endonuclease activity" was the only catalytic annotation lost. Du et al. (2025) demonstrated directly that recombinant OsEME1 / OsEME1-C bind and cleave the branched Y12, pre-X12 and X12 substrates (typical Holliday-junction / crossover-junction structures generated during HR), and that four conserved ERCC4-domain residues are required for activity [PMID:40333587]. The EME1/MUS81 complex is the canonical crossover-junction (Holliday junction) resolvase. "Crossover junction DNA endonuclease activity" (GO:0008821) is the accurate, specific MF and corresponds to the UniProt RecName "Crossover junction endonuclease EME1" and EC 3.1.22.-. IDA is justified by the in vitro nuclease/EMSA assays. Supporting Evidence: PMID:40333587 OsEME1 directly binds to and cleaves Y12, pre-X12 and X12, which are typical substrates after HR repair of DNA damage PMID:40333587 these four conserved amino acids are essential for the endonuclease activity of OsEME1 file:ORYSJ/EME1/EME1-deep-research-falcon.md Conserved residues L439, P487, E490, and K494 are important for activity; L439V, E490A, and K494E markedly reduce binding/cleavage ... Identifies functionally critical conserved residues for annotation of catalytic mechanism/structure-function relationships. |
| GO:0000724 double-strand break repair via homologous recombination | IMP PMID:40333587 ESSENTIAL MEIOTIC ENDONUCLEASE 1 is required for chloroplast... | NEW | Summary: OsEME1 acts in homologous-recombination-mediated repair of DNA double-strand breaks, resolving the branched HR intermediates (Holliday junctions) that arise during repair. Reason: Current GOA captures "double-strand break repair" (GO:0006302, IBA) and "DNA repair" (GO:0006281, IEA) but not the specific HR mechanism. Du et al. (2025) show that oseme1 mutants are hypersensitive to DNA-damaging agents, accumulate gamma-H2AX foci and show DNA-damage-induced cell-cycle arrest, and that OsEME1 binds/cleaves the branched substrates produced after HR repair; the authors explicitly conclude a "biochemical role for OsEME1 in HR repair" [PMID:40333587]. In Arabidopsis, MUS81 is required for synthesis-dependent strand annealing, an HR sub-pathway [PMID:20971895]. GO:0000724 is the precise process term. IMP is justified by the oseme1 loss-of-function DNA-damage-sensitivity phenotypes. Supporting Evidence: PMID:40333587 This study highlights the role of OsEME1 in regulating chloroplast development by modulating homologous recombination repair in response to damage to double-stranded DNA PMID:40333587 The MUS81βEME complex directly binds to and cleaves typical DNA substrates produced after HR repair, a process conserved in yeasts, mammals, dicots and monocots file:ORYSJ/EME1/EME1-deep-research-falcon.md OsEME1 is best annotated as a **nuclear, structure-specific endonuclease** that cleaves **branched/junction DNA substrates** consistent with HR/replication intermediates ... rice OsEME1 likely participates in the canonical SSE pathway for processing recombination/replication structures |
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Download this section (compressed HTML)Q: Does rice OsEME1 have intrinsic catalytic activity, or is its in vitro cleavage activity dependent on co-purified or contaminating MUS81 - given that yeast and human EME1 are non-catalytic regulatory subunits?
Suggested experts: Guijie Du
Q: What is the relative contribution of OsEME1/OsMUS81 versus OsGEN1 to somatic versus meiotic Holliday junction resolution in rice?
Suggested experts: Zhukuan Cheng
Q: Is the striped-leaf/chloroplast phenotype of oseme1 entirely explained by nuclear genome-maintenance failure, or does OsEME1 also act on the chloroplast genome?
Suggested experts: Guijie Du
Experiment: Reconstitute the OsEME1-OsMUS81 heterodimer from separately expressed, highly purified subunits and compare nuclease activity on Holliday-junction, 3'-flap and replication-fork substrates with each subunit alone, to determine whether OsEME1 is catalytic or regulatory.
Hypothesis: OsEME1 is the regulatory subunit and MUS81 the catalytic subunit, as in yeast and humans; apparent OsEME1-alone activity reflects the heterodimer being the functional unit.
Type: in vitro reconstituted endonuclease assay
Experiment: Generate oseme1 osgen1 double mutants and quantify meiotic chiasmata, chromosome fragmentation, pollen viability and somatic DNA-damage sensitivity.
Hypothesis: OsEME1/OsMUS81 and OsGEN1 act in partially redundant Holliday-junction resolution pathways, so the double mutant shows synthetic genome-instability defects.
Type: genetic epistasis analysis
Experiment: Test oseme1 mutant sensitivity directly to UV-B/UV-C, gamma irradiation and interstrand-crosslinking agents (e.g. mitomycin C) and measure HR-repair efficiency with a chromosomal recombination reporter.
Hypothesis: OsEME1 is required for repair of replication-blocking and double-strand lesions induced by UV, gamma radiation and crosslinkers, consistent with its branched- DNA substrate preference.
Type: genotoxin-sensitivity and recombination-reporter assay
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