Gene Ontology annotation through association of InterPro records with GO terms
Gene Ontology annotation based on UniProtKB/Swiss-Prot keyword mapping
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SwissProt keyword-derived (SPKW) annotations present in the Sept 2025 goa_uniprot_gcrp snapshot but removed from the current GOA release after GOA retired the keyword2GO pipeline for cellular organisms.
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For EME1, the keyword "Endonuclease" mapped to a genuinely correct catalytic MF; its removal without replacement left the gene with no catalytic function term.
Annotation inferences using phylogenetic trees
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EME1/MUS81 functions (Holliday junction resolvase complex, replication fork processing, double-strand break repair, meiotic recombination intermediate resolution) are conserved across the PTHR21077 phylogenetic group.
Combined Automated Annotation using Multiple IEA Methods
Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice.
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A large-scale rice full-length cDNA collection, sequencing, genome-mapping and InterPro-based annotation paper.
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Contains no gene-specific expression-response experiment for EME1; cannot support IEP annotations for response to UV, high light or gamma radiation.
ESSENTIAL MEIOTIC ENDONUCLEASE 1 is required for chloroplast development and DNA repair in rice.
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OsEME1 (LOC_Os04g55500) is a single-copy nuclear gene; the OsEME1-GFP fusion localizes to the nucleus.
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Recombinant OsEME1 and its C-terminal ERCC4-domain fragment directly bind and cleave branched DNA substrates (Y12, pre-X12, X12) in vitro; four conserved residues are required for activity.
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OsEME1 interacts with OsMUS81 (Y2H, luciferase complementation, BiFC); the OsEME1 ERCC4 domain and the OsMUS81 HhH motif mediate the interaction.
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oseme1 loss-of-function mutants are hypersensitive to MMS and Zeocin, accumulate gamma-H2AX foci and show S/G2 cell-cycle arrest.
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oseme1 mutants have a striped-albino-leaf / defective-chloroplast phenotype enhanced by high light; the chloroplast defect is downstream of nuclear genome-maintenance failure.
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OsEME1 functions in homologous-recombination repair of DNA damage.
MUS81 is required for atypical recombination intermediate resolution but not crossover designation in rice.
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rice mus81 mutants have wild-type chiasma numbers and normal HEI10 foci; MUS81 does not function in crossover designation in rice.
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MUS81 resolves atypical meiotic recombination intermediates - mus81 zep1 and mus81 fancm double mutants show chromosome fragments and bridges.
FANCM interacts with the MHF1-MHF2 complex to limit crossover frequency during rice meiosis.
Regulation of Mus81-Eme1 Holliday junction resolvase in response to DNA damage.
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In fission yeast, DNA-damage-induced activation of Mus81-Eme1 requires both Cdc2(CDK1)- and Rad3(ATR)-dependent phosphorylation of Eme1.
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Mus81-Eme1 activation links the DNA-damage response to checkpoint/cell-cycle progression.
RAD5A, RECQ4A, and MUS81 have specific functions in homologous recombination and define different pathways of DNA repair in Arabidopsis thaliana.
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Arabidopsis MUS81 and RECQ4A process recombination-induced aberrant intermediates during replication; recq4A mus81 double mutants are lethal.
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MUS81 is required for efficient synthesis-dependent strand annealing (SDSA), an HR-mediated DSB repair pathway.
Resolving branched DNA intermediates with structure-specific nucleases during replication in eukaryotes.
Resolvase OsGEN1 Mediates DNA Repair by Homologous Recombination.
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Yen1/GEN1 resolvases work together with MUS81-EME1 and SLX1-SLX4 in HR-mediated DNA repair to maintain genome stability.
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rice osgen1 mutants show reduced chiasma frequency and persistent DSBs in microspores, indicating overlapping resolvase activities in plants.
Deep-research report (falcon / Edison Scientific Literature) - functional annotation of rice EME1 (Q0J9J6).
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Synthesizes the rice-specific Du et al. 2025 study (Plant Biotechnology Journal, DOI 10.1111/pbi.70101, = PMID:40333587) with Arabidopsis and yeast/human MUS81 literature, concluding OsEME1 is best annotated as a nuclear, structure-specific endonuclease that cleaves branched/junction DNA substrates (Y12, pre-X12, X12) consistent with HR/replication intermediates and interacts with OsMUS81 in the nucleus.
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Quantifies the rice biochemistry - purified OsEME1 binds the Y12 junction substrate with Kd = 16.3 +/- 2.2 microM (microscale thermophoresis); the C-terminal ERCC4 fragment carries most nuclease activity; conserved residues L439, P487, E490 and K494 are required (L439V/E490A/K494E abolish binding/cleavage).
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Independently corroborates the rice mutant phenotypes - oseme1/k48 is hypersensitive to MMS (75 microg/mL) and Zeocin (50 microg/mL), shows S-phase accumulation and gamma-H2AX-like foci, and has a striped/albino chloroplast phenotype (Fv/Fm 0.53 vs 0.72 WT) enhanced by high light, with 970 (normal-light) and 3548 (high-light) DEGs.
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Notes the chloroplast defect is most parsimoniously explained by nuclear genome maintenance and/or regulation of nuclear chloroplast-biogenesis genes (OsEME1 cleaves GLK1/GLK2-derived structured DNA in vitro); no evidence of stable chloroplast localization of the OsEME1 protein.
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Flags as a caution that in the rice study OsMUS81 bound but did not cleave X-structure substrates while OsEME1 produced cleavage products - deviating from the canonical cross-species view that MUS81 supplies the catalytic site; to be interpreted cautiously and treated as conserved-pathway inference where direct rice data are absent.