UniProt: Q0J9J6 | Gene: EME1 / OsEME1 | Locus: Os04g0648700, LOC_Os04g55500
"Crossover junction endonuclease EME1" / "Essential meiotic endonuclease 1"; EC 3.1.22.-
Family: EME1/MMS4 family; PANTHER PTHR21077:SF5 (CROSSOVER JUNCTION ENDONUCLEASE MMS4)
EME1 (Eme1 in fission yeast; Mms4 in budding yeast; EME1/EME2 in humans) is the
non-catalytic regulatory subunit of a heterodimeric, structure-specific DNA
endonuclease whose catalytic subunit is MUS81. EME1 itself lacks endonuclease
activity in yeast and human; the interaction with MUS81 stimulates and regulates
MUS81's endonucleolytic activity.
MUS81-EME1 is one of three structure-selective endonuclease systems
(MUS81-EME1/MMS4, SLX1-SLX4, GEN1/Yen1) that resolve branched DNA
intermediates ("Holliday junction resolvases" in the broad sense). MUS81-EME1
has substrate preference for nicked Holliday junctions, 3'-flaps, D-loops and
replication-fork structures — i.e. branched substrates with a 5'-end at the
branch — and resolves intact HJs only with reduced efficiency.
UniProt FUNCTION (Q0J9J6, by similarity): "Interacts with MUS81 to form a DNA
structure-specific endonuclease with substrate preference for branched DNA
structures with a 5'-end at the branch nick. Typical substrates include 3'-flap
structures, D-loops, replication forks, nicked Holliday junctions and also
intact Holliday junctions with a reduced efficiency. May be required in mitosis
for the processing of stalled or collapsed replication fork intermediates.
Plays a role in DNA repair and in genotoxic stress-induced homologous
recombination (HR) in somatic cells. Mediates a subset of meiotic recombination
events that are insensitive to crossover interference."
This dual mitotic/meiotic role is key: MUS81-EME1 functions in BOTH (a) somatic
(mitotic) replication-fork rescue and DSB repair AND (b) meiotic crossover
formation (the interference-insensitive / "class II" CO pathway). It is NOT a
meiosis-restricted enzyme.
MUS81-EME1 activity is cell-cycle and DNA-damage regulated. In fission yeast,
DNA-damage-induced activation of Mus81-Eme1 requires Cdc2(CDK1)- and
Rad3(ATR)-dependent phosphorylation of Eme1; the complex is activated at G2/M.
PMID:23584455
PMID:40333587
In meiosis, MUS81-EME1 (with Yen1/GEN1 and SLX1-SLX4) must be kept inactive
during prophase I to allow proper CO patterning; precocious activation disrupts
crossover distribution.
PMID:29920281
PMID:40333587 / DOI:10.1111/pbi.70101 — "ESSENTIAL MEIOTIC ENDONUCLEASE 1 is
required for chloroplast development and DNA repair in rice." This is the
definitive functional characterization of OsEME1 (Q0J9J6).
Key findings:
OsEME1 is a single-copy gene in rice. Unlike Arabidopsis (which has EME1A
and EME1B), rice has only one EME1.
PMID:40333587
OsEME1 is an endonuclease with intrinsic DNA cleavage activity in vitro.
Recombinant MBP-OsEME1 and the C-terminal fragment (OsEME1-C, containing the
ERCC4 domain) both bind and cleave the Y12 branched substrate. This is notable:
in yeast/human, EME1 is the non-catalytic subunit. In the rice in vitro assay,
OsEME1 alone produced cleavage products.
PMID:40333587
PMID:40333587
PMID:40333587
Four conserved residues required for activity. Point mutants of four
conserved residues (modelled on mammalian EME1 catalytic residues) reduced
binding/cleavage, confirming the ERCC4 domain is the catalytic region.
PMID:40333587
OsEME1 binds Mg2+/branched DNA substrates — substrate Kd ~16 µM for Y12.
UniProt cofactor: Mg(2+), Ca(2+).
OsEME1 interacts with OsMUS81. Y2H, luciferase complementation (LCI) and
BiFC all confirm interaction; the ERCC4 domain of OsEME1 and the HhH motif of
OsMUS81 mediate the interaction.
PMID:40333587
PMID:40333587
OsMUS81 binds X-structure substrates but did not itself add cleavage in
the in vitro assay — in the rice system OsEME1-C was the cleaver.
PMID:40333587
Nuclear localization. OsEME1-GFP localizes to the nucleus and overlaps with
the nuclear marker H2B-mCherry.
PMID:40333587
DNA-damage phenotypes. EMS mutant (pale1) and CRISPR oseme1 mutants are
hypersensitive to the DNA-damaging agents MMS and Zeocin (reduced shoot/root
growth). Mutants show increased S/G2 DNA content (cell-cycle arrest), more
S-phase (EdU+) cells, and increased γH2AX foci (a DSB / DNA-damage marker)
with or without Zeocin.
PMID:40333587
PMID:40333587
OsEME1 is involved in HR repair. The proposed model: under high light or
genotoxic stress, DSBs form, the DNA-damage response is activated, repair
proceeds via HR, double Holliday junctions accumulate, and OsEME1 is recruited
to bind and cleave the HJ substrates, maintaining genome stability.
PMID:40333587
Chloroplast / striped-leaf phenotype. oseme1 mutants have a striped-albino
leaf phenotype, defective chloroplast development, reduced chlorophyll/
carotenoids, low PSII efficiency; the phenotype is strongly enhanced by
high-light stress. OsEME1 globally regulates expression of photosynthesis and
DNA-repair genes. Mechanistic model: OsEME1 maintains genome/transcription
integrity of nuclear chloroplast-development genes (e.g. OsGLK1/OsGLK2), which
in turn drive chloroplast development. The chloroplast phenotype is a
downstream consequence of genome-maintenance failure, not a direct chloroplast
function (OsEME1 is nuclear).
PMID:40333587
PMID:40333587
High-light sensitivity is real and experimentally demonstrated in this
paper (oseme1 mutants are hypersensitive to high light, with severe leaf
striping and cell death after HL treatment). This is genuine functional
evidence — but note this paper is PMID:40333587, NOT the IEP reference
PMID:12869764.
PMID:36495065 / DOI:10.1111/nph.18668 — "MUS81 is required for atypical
recombination intermediate resolution but not crossover designation in rice."
So the rice MUS81-EME1 complex has a meiotic role — but it is a minor/atypical-
intermediate-resolution role, NOT a meiosis-restricted "essential meiotic
endonuclease" role. The "Essential meiotic endonuclease" name is historical
(from S. pombe Eme1) and is somewhat misleading for the plant ortholog.
PMID:12869764 (Kikuchi et al. 2003, Science) is "Collection, mapping, and
annotation of over 28,000 cDNA clones from japonica rice." It is a large-scale
full-length cDNA sequencing/annotation consortium paper. Its abstract describes
ONLY cDNA collection, sequencing, mapping to genomic DNA, and InterPro-based
function assignment. There is NO gene-specific expression-profiling experiment
for EME1 and NO experiment testing response to UV, gamma radiation or high
light.
The three IEP annotations (response to UV GO:0009411, response to high light
intensity GO:0009644, response to gamma radiation GO:0010332) all cite
PMID:12869764 as the IEP (Inferred from Expression Pattern) reference. This is
almost certainly a curation artefact: the rice FL-cDNA consortium built cDNA
libraries from many tissues and stress conditions, and a clone for this gene may
have come from a stress-treated library (UV-/gamma-/high-light-treated tissue).
The presence of a cDNA clone in a stress library is library-of-origin
information, NOT an expression-response measurement, and certainly not evidence
of biological "involvement in" a stress response. IEP from this kind of source
is not appropriate functional evidence. Expression ≠ function.
Note: high-light sensitivity of OsEME1 IS genuinely demonstrated — but in
PMID:40333587 (oseme1 mutants hypersensitive to high light), as a downstream
consequence of a genome-maintenance defect, not a primary "response to high
light" function. The IEP annotations remain unsupported by their cited
reference.
The six retired SPKW (GO_REF:0000043) annotations were keyword-to-GO mappings:
- meiotic cell cycle (GO:0051321) <- KW "Meiosis" — OVER-SPECIFIC. EME1/MUS81 is
not meiosis-restricted; its dominant role in rice is somatic DSB/replication
repair. Removal justified.
- cell division (GO:0051301) <- KW "Cell division" — weakly supported, generic;
EME1 acts in cell-cycle-coupled repair but "cell division" per se is not its
function. Removal justified (over-annotation).
- DNA recombination (GO:0006310) <- KW "DNA recombination" — correct in essence
(EME1 resolves HR intermediates) but generic; better captured by HR-repair /
resolution terms. Removal acceptable; correct biology retained by current
IBA/IEA terms.
- endonuclease activity (GO:0004519) <- KW "Endonuclease/Nuclease" — GENUINELY
CORRECT. EME1 IS an endonuclease (EC 3.1.22.-), demonstrated biochemically in
rice (PMID:40333587). Current GOA has NO catalytic MF term — only "DNA
binding". Removing endonuclease activity LOST a correct, core annotation. This
removal was NOT justified; a NEW catalytic MF term should be added.
- hydrolase activity (GO:0016787) <- KW "Hydrolase" — correct but vague parent
of endonuclease activity. Removal of the vague term is acceptable IF a
specific endonuclease MF is present (it is not — see above).
- metal ion binding (GO:0046872) <- KW "Metal-binding" — correct (Mg2+/Ca2+
cofactor) but the keyword mapping is generic. MUS81-EME1 nuclease chemistry is
Mg2+-dependent. Removal of the generic term is acceptable; magnesium ion
binding (GO:0000287) would be the accurate specific term if retained.