Research journal for the GO annotation review. Provenance is inline as
[PMID:xxxx "verbatim quote"] or from the UniProt record (C0LGT6).
EFR is a plasma-membrane-localized leucine-rich repeat receptor-like
serine/threonine kinase (LRR-RLK) that is the pattern-recognition receptor (PRR)
for the bacterial pathogen-associated molecular pattern (PAMP) elongation factor
Tu (EF-Tu), specifically perceiving its N-terminal epitope elf18. Ligand
perception triggers PAMP-triggered immunity (PTI). EFR is a single-pass type I
membrane protein: extracellular LRR ectodomain (residues 25–653, 21 LRRs),
transmembrane helix (654–674), cytoplasmic kinase domain (712–1001)
(UniProt C0LGT6 FT lines).
Molecular function:
- GO:0019199 transmembrane receptor protein kinase activity (TAS, PMID:19763087): ACCEPT, CORE. Most informative MF term — captures both receptor (ligand→transmembrane signal) and Ser/Thr kinase nature. Definition matches EFR exactly.
- GO:0106310 protein serine kinase activity (EXP PMID:18158241, EXP PMID:29649442): ACCEPT, CORE. Backed by experimental autophosphorylation + BIK1 phosphorylation; EC 2.7.11.1.
- GO:0004674 protein serine/threonine kinase activity (IEA EC): ACCEPT (core kinase activity; consistent with EC mapping).
- GO:0004672 protein kinase activity (IEA): KEEP_AS_NON_CORE — correct but a generic parent of the more specific Ser/Thr term; redundant.
- GO:0005524 ATP binding (IEA InterPro): ACCEPT — kinase requires ATP (BINDING 718-726, 741); supportive MF.
- GO:0005515 protein binding (IPI, ×8 across 6 papers): all real interactions, but uninformative bare term. MARK_AS_OVER_ANNOTATED per curation guidance (avoid endorsing bare protein binding as core); the biologically meaningful relationship (co-receptor binding, substrate, effector targeting) belongs in more specific MF/process terms.
Cellular component:
- GO:0005886 plasma membrane (IEA UniProtKB-SubCell; and ISM:TAIR): ACCEPT, CORE — EFR is a PM PRR.
- GO:0012505 endomembrane system (IEA UniProtKB-SubCell): KEEP_AS_NON_CORE — reflects ER transit/biogenesis and broad CC; true but less informative than plasma membrane.
Biological process:
- GO:0140426 PAMP receptor signaling pathway (IMP PMID:20113440): ACCEPT, CORE — the defining process.
- GO:0002237 response to molecule of bacterial origin (IMP PMID:29649442): ACCEPT (core; elf18/EF-Tu response).
- GO:0016045 detection of bacterium (IDA PMID:16713565): ACCEPT, CORE — EFR detects bacterial EF-Tu; gain-of-function and loss-of-function support.
- GO:0009617 response to bacterium (IEA ARBA): KEEP_AS_NON_CORE — correct but a broad parent of the IMP/IDA terms.
- GO:0031349 positive regulation of defense response (IEA ARBA): ACCEPT — EFR positively regulates defense (PTI activation; positive regulator).
- GO:0002764 immune response-regulating signaling pathway (IMP PMID:19763087): ACCEPT — EFR signaling regulates immune responses; supported by EFR functional studies.
- GO:0009626 plant-type hypersensitive response (IMP PMID:19763087): UNDECIDED → leaning MARK_AS_OVER_ANNOTATED. PMID:19763087 is about ER quality control of EFR and elf18-triggered (PTI) responses/anthocyanin de-repression, not a classic EFR-dependent HR (programmed cell death). PTI by surface PRRs like EFR generally does NOT trigger HR/cell death (that is the hallmark of ETI/intracellular NLRs). The abstract does not mention hypersensitive response. Cached full text is available but the abstract foregrounds N-glycosylation QC, anthocyanin, and SA-dependent (EFR-independent) defense. Mark as over-annotated: HR is not a core EFR output; the IMP TAIR annotation likely over-propagates "defense" to HR. Not REMOVE because it is an experimental TAIR annotation whose full reasoning I cannot fully verify (use MARK_AS_OVER_ANNOTATED rather than REMOVE).
IBA terms present in UniProt DR block but NOT in GOA stub (not part of existing_annotations to review): GO:0038023 signaling receptor activity (IBA), GO:0009755 hormone-mediated signaling pathway (IBA). Noted for completeness; GO:0009755 (hormone-mediated signaling) is a questionable IBA propagation for a PRR — EFR regulates hormone levels downstream (via BIK1) but is not itself a hormone-signaling receptor.
Incorporated the Falcon/Edison deep-research report
(file:ARATH/EFR/EFR-deep-research-falcon.md) as supporting context. It corroborates
the core verdicts (PRR for EF-Tu elf18/elf26; plasma-membrane signaling; PTI outputs
ROS/MAPK/Ca2+/callose; antibacterial immunity restricting Pto DC3000), which were
added as supported_by entries on the PRR, PTI-signaling, plasma-membrane,
PAMP-receptor-signaling-pathway, and positive-regulation-of-defense annotations/core
functions.
Refinement (not a verdict flip): the report emphasizes a recent allosteric-activation
model (Muhlenbeck/Bender/Zipfel 2024, eLife; Bender et al. 2021 PNAS) in which EFR's
own catalytic activity can be partly dispensable in vivo for antibacterial immunity,
and BIK1 trans-phosphorylation is driven largely by EFR-activated BAK1 rather than by
EFR acting as the sole/primary BIK1 kinase [file:ARATH/EFR/EFR-deep-research-falcon.md
"kinase-dead EFR still retains some capacity to enhance BAK1->BIK1 phosphorylation,
supporting the non-catalytic EFR model"]. The direct EFR->BIK1 kinase-substrate
annotation (PMID:29649442, EXP) is retained but a mechanistic caveat was appended to
its reason field. This is conservative; the curator-asserted experimental annotation
is not overruled.
The report also reinforces the existing MARK_AS_OVER_ANNOTATED verdict on
GO:0009626 (plant-type hypersensitive response): "Retrieved EFR-focused studies do
not directly support EFR as an executor of apoptosis, PCD, HR, pyroptosis."