EFR (EF-TU RECEPTOR; At5g20480) is a plasma membrane-localized leucine-rich repeat receptor-like serine/threonine protein kinase (LRR-RLK) that serves as the pattern-recognition receptor (PRR) for the bacterial pathogen-associated molecular pattern (PAMP) elongation factor Tu (EF-Tu), specifically perceiving its conserved N-terminal epitope elf18. The protein is a single-pass type I membrane protein with an extracellular leucine-rich repeat ectodomain (the last two LRRs are required for elf18 binding), a single transmembrane helix, and an intracellular serine/threonine kinase domain. Upon binding elf18, EFR forms a ligand-induced complex with the co-receptor BAK1/SERK3 (and related SERK family kinases SERK4/BKK1, SERK1, SERK2), autophosphorylates, and is activated by tyrosine phosphorylation (notably Tyr-836). Activated EFR directly phosphorylates the receptor-like cytoplasmic kinase BIK1 and triggers PAMP-triggered immunity (PTI), including a calcium-associated plasma membrane anion channel/depolarization response, a reactive oxygen species burst, MAPK activation, defense gene induction, callose deposition, and modulation of defense hormones (jasmonic acid and salicylic acid) via a PRR-BIK1-WRKY axis. Proper biogenesis and folding of EFR require endoplasmic reticulum quality-control machinery, including the STT3a-containing oligosaccharyltransferase complex, calreticulin-3 (CRT3), UDP-glucose:glycoprotein glycosyltransferase (UGGT), and ER-resident chaperones. EFR-mediated immunity restricts bacterial pathogens and reduces Agrobacterium-mediated transformation, and it is a frequent target of bacterial effectors (e.g. AvrPto, AvrPtoB, HopAO1).
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0004672 protein kinase activity | IEA GO_REF:0000120 | KEEP AS NON CORE | Summary: EFR is a protein kinase, so this term is correct, but it is a generic parent of the more specific (and experimentally supported) serine/threonine and serine kinase terms. Reason: Correct but uninformative parent; the specific Ser/Thr kinase activity (GO:0106310/GO:0004674) is the core molecular function. Supporting Evidence: file:ARATH/EFR/EFR-notes.md EC 2.7.11.1; serine/threonine protein kinase. |
| GO:0004674 protein serine/threonine kinase activity | IEA GO_REF:0000003 | ACCEPT | Summary: EFR is a serine/threonine protein kinase (EC 2.7.11.1) that autophosphorylates and phosphorylates BIK1. This EC-based mapping is correct and consistent with experimental kinase activity. Reason: Accurate description of EFR catalytic activity, supported by experimental autophosphorylation and BIK1 phosphorylation. Supporting Evidence: PMID:29649442 EFR regulates the phytohormone jasmonic acid (JA) through direct phosphorylation of a receptor-like cytoplasmic kinase, BIK1 |
| GO:0005524 ATP binding | IEA GO_REF:0000002 | ACCEPT | Summary: As a protein kinase EFR binds ATP; the cytoplasmic kinase domain has a defined ATP-binding region. Supportive molecular function consistent with its catalytic activity. Reason: ATP binding is required for the kinase activity; consistent with the protein kinase ATP-binding site annotated in UniProt. Supporting Evidence: file:ARATH/EFR/EFR-notes.md kinase requires ATP (BINDING 718-726, 741) |
| GO:0005886 plasma membrane | IEA GO_REF:0000044 | ACCEPT | Summary: EFR is a single-pass type I plasma membrane protein and acts as a cell-surface PRR at the plasma membrane. This is a core localization. Reason: Well-established plasma membrane localization of this cell-surface pattern-recognition receptor. Supporting Evidence: PMID:27317676 Plasma membrane-localized pattern recognition receptors (PRRs) such as FLAGELLIN SENSING2 (FLS2), EF-TU RECEPTOR (EFR) file:ARATH/EFR/EFR-deep-research-falcon.md EFR is a surface-exposed transmembrane LRR-RK and the active signaling receptor functions at the plasma membrane. |
| GO:0009617 response to bacterium | IEA GO_REF:0000117 | KEEP AS NON CORE | Summary: EFR participates in the response to bacteria by perceiving bacterial EF-Tu, but this is a broad parent of the more specific experimentally supported terms (detection of bacterium, response to molecule of bacterial origin). Reason: Correct but generic; more specific terms better capture EFR function. Supporting Evidence: PMID:16713565 Arabidopsis plants detect a variety of PAMPs including conserved domains of bacterial flagellin and of bacterial EF-Tu |
| GO:0012505 endomembrane system | IEA GO_REF:0000044 | KEEP AS NON CORE | Summary: EFR transits the secretory/endomembrane system during biogenesis (it is also annotated as single-pass type I endomembrane protein), but plasma membrane is the functionally relevant and more informative location. Reason: True but broad; reflects ER transit/biogenesis rather than the site of receptor action. Supporting Evidence: PMID:19763087 act in concert with STT3A-containing oligosaccharyltransferase complex in an N-glycosylation pathway in the endoplasmic reticulum |
| GO:0031349 positive regulation of defense response | IEA GO_REF:0000117 | ACCEPT | Summary: EFR positively regulates plant defense; perception of EF-Tu/elf18 activates PTI defense responses and increases resistance, and loss of EFR enhances pathogen susceptibility. Reason: EFR is a positive regulator of defense responses; consistent with experimental loss- and gain-of-function evidence. Supporting Evidence: PMID:16713565 plant defense responses induced by PAMPs such as EF-Tu reduce transformation by Agrobacterium file:ARATH/EFR/EFR-deep-research-falcon.md EFR contributes to antibacterial immunity and induced resistance, including restriction of Pseudomonas syringae pv. tomato DC3000 growth after elf18 pretreatment. |
| GO:0106310 protein serine kinase activity | IEA GO_REF:0000116 | ACCEPT | Summary: EFR is a protein serine kinase (Rhea/EC mapping). Same activity is also experimentally supported (EXP annotations below). Core molecular function. Reason: Accurate; the same activity is corroborated by experimental EXP annotations. Supporting Evidence: PMID:18158241 AvrPto binds receptor kinases, including Arabidopsis FLS2 and EFR |
| GO:0005515 protein binding | IPI PMID:23395902 Pseudomonas HopU1 modulates plant immune receptor levels by ... | MARK AS OVER ANNOTATED | Summary: GRP7/RBG7 associates with EFR at the plasma membrane and binds EFR mRNA; this is a real interaction but the bare protein binding term is uninformative about EFR's function. The biologically meaningful relationship is regulatory (RNA-binding-protein co-association). Reason: Bare protein binding is not informative as a core molecular function; per curation guidance more specific terms should capture the relationship. Supporting Evidence: PMID:23395902 GRP7 directly interacts in vivo with the PRRs FLS2 and EFR in a specific manner |
| GO:0005515 protein binding | IPI PMID:24625928 A bacterial tyrosine phosphatase inhibits plant pattern reco... | MARK AS OVER ANNOTATED | Summary: This IPI captures EFR interactions with BAK1 and with the bacterial effector HopAO1/hopD2 (effector that dephosphorylates EFR). Real interactions but the bare protein binding term is uninformative. Reason: Generic protein binding; the meaningful co-receptor and effector-targeting relationships are better captured by specific terms. Supporting Evidence: PMID:24625928 A tyrosine phosphatase, HopAO1, secreted by P. syringae, reduces EFR phosphorylation |
| GO:0005515 protein binding | IPI PMID:29320478 An extracellular network of Arabidopsis leucine-rich repeat ... | MARK AS OVER ANNOTATED | Summary: From a large-scale extracellular LRR-RK binary interaction network; multiple EFR ectodomain interactions (SERK5, BAK1, NIK1, etc.). Real high-throughput interactions but the bare protein binding term is uninformative. Reason: Generic protein binding from a high-throughput screen; uninformative as a core function. Supporting Evidence: PMID:29320478 An extracellular network of Arabidopsis leucine-rich repeat receptor kinases |
| GO:0106310 protein serine kinase activity | EXP PMID:18158241 Pseudomonas syringae effector AvrPto blocks innate immunity ... | ACCEPT | Summary: Experimental evidence for EFR protein serine kinase activity (autophosphorylation and catalytic activity; UniProt cites this PMID for EC 2.7.11.1). Core molecular function. Reason: Experimentally supported core kinase activity of EFR. Supporting Evidence: file:ARATH/EFR/EFR-notes.md EC 2.7.11.1; serine/threonine protein kinase. CATALYTIC ACTIVITY records cite PubMed:18158241 and PubMed:29649442. |
| GO:0106310 protein serine kinase activity | EXP PMID:29649442 The Receptor-like Cytoplasmic Kinase BIK1 Localizes to the N... | ACCEPT | Summary: Experimental evidence that EFR directly phosphorylates BIK1, demonstrating its protein serine kinase activity. Core molecular function. Reason: Experimentally supported; EFR directly phosphorylates the substrate BIK1. Note from the Falcon deep-research synthesis - a more recent allosteric-activation model (Muhlenbeck/Bender/Zipfel 2024) proposes that EFR catalytic activity can be partly dispensable in vivo and that BIK1 trans-phosphorylation is driven largely by EFR-activated BAK1; the direct EFR->BIK1 kinase-substrate annotation is retained but this mechanistic nuance should be considered when interpreting EFR's catalytic role. Supporting Evidence: PMID:29649442 EFR regulates the phytohormone jasmonic acid (JA) through direct phosphorylation of a receptor-like cytoplasmic kinase, BIK1 |
| GO:0140426 pathogen-associated molecular pattern receptor signaling pathway | IMP PMID:20113440 Early signaling through the Arabidopsis pattern recognition ... | ACCEPT | Summary: EFR initiates PAMP-triggered immune signaling upon elf18 perception, including BAK1-dependent calcium-associated early signaling. This is the defining biological process for EFR. Reason: Core biological process; EFR is the PRR that initiates the PAMP receptor signaling pathway. Supporting Evidence: PMID:20113440 activation of FLS2 and EFR lead to BAK1-dependent, calcium-associated plasma membrane anion channel opening as an initial step in the pathogen defense pathway file:ARATH/EFR/EFR-deep-research-falcon.md elf18 perception by EFR triggers canonical PTI outputs including ROS burst, MAPK activation, Ca2+-linked signaling, defense gene induction, callose deposition, and seedling growth inhibition. |
| GO:0002237 response to molecule of bacterial origin | IMP PMID:29649442 The Receptor-like Cytoplasmic Kinase BIK1 Localizes to the N... | ACCEPT | Summary: EFR responds to the bacterial molecule EF-Tu (elf18) to activate immune signaling. Core function consistent with its identity as the EF-Tu receptor. Reason: EFR perceives bacterial EF-Tu/elf18; well-supported core process. Supporting Evidence: PMID:29649442 EFR is a PRR that recognizes bacterial EF-Tu and activates immune signaling |
| GO:0005515 protein binding | IPI PMID:29649442 The Receptor-like Cytoplasmic Kinase BIK1 Localizes to the N... | MARK AS OVER ANNOTATED | Summary: EFR binds the cytoplasmic kinase BIK1 (associates in absence of ligand, dissociates upon PAMP perception, and phosphorylates it). A real and functionally important interaction, but the bare protein binding term is uninformative; the kinase-substrate relationship is captured by the Ser/Thr kinase activity terms. Reason: Bare protein binding; the meaningful EFR-BIK1 kinase-substrate relationship is better represented by the kinase activity annotations. Supporting Evidence: PMID:29649442 direct phosphorylation of a receptor-like cytoplasmic kinase, BIK1 |
| GO:0005886 plasma membrane | ISM GO_REF:0000122 | ACCEPT | Summary: Predicted (AtSubP) plasma membrane localization, consistent with the experimentally and structurally supported plasma membrane location of this cell-surface PRR. Core localization. Reason: Consistent with established plasma membrane localization of EFR. Supporting Evidence: PMID:27317676 Plasma membrane-localized pattern recognition receptors (PRRs) such as FLAGELLIN SENSING2 (FLS2), EF-TU RECEPTOR (EFR) |
| GO:0005515 protein binding | IPI PMID:27317676 The Arabidopsis Malectin-Like/LRR-RLK IOS1 Is Critical for B... | MARK AS OVER ANNOTATED | Summary: EFR forms a complex with the malectin-like LRR-RLK IOS1, which primes PTI. Real interaction, but the bare protein binding term is uninformative about EFR function. Reason: Generic protein binding with a regulatory partner; uninformative as a core molecular function. Supporting Evidence: PMID:27317676 complexes between the membrane-localized IOS1 and BRASSINOSTEROID INSENSITIVE1-ASSOCIATED KINASE1 (BAK1)-dependent PRRs FLS2 and EFR |
| GO:0005515 protein binding | IPI PMID:18158241 Pseudomonas syringae effector AvrPto blocks innate immunity ... | MARK AS OVER ANNOTATED | Summary: EFR binds the Pseudomonas effector AvrPto, which inhibits receptor kinase activity. Real interaction, but the bare protein binding term is uninformative; the relevant biology (effector targeting) is not captured by this generic term. Reason: Generic protein binding (effector interaction); uninformative as core function. Supporting Evidence: PMID:18158241 AvrPto binds receptor kinases, including Arabidopsis FLS2 and EFR |
| GO:0002764 immune response-regulating signaling pathway | IMP PMID:19763087 Receptor quality control in the endoplasmic reticulum for pl... | ACCEPT | Summary: EFR signaling regulates plant immune responses; this paper studies EFR function and its ER quality-control dependence (EFR accumulation and signalling impaired in psl/stt3a mutants). Consistent with EFR's role in immune signaling. Reason: EFR initiates and regulates immune response signaling; supported by EFR functional/quality-control studies. Supporting Evidence: PMID:19763087 EFR accumulation and signalling, but not of FLS2, are impaired in psl1, psl2, and stt3a plants |
| GO:0009626 plant-type hypersensitive response | IMP PMID:19763087 Receptor quality control in the endoplasmic reticulum for pl... | MARK AS OVER ANNOTATED | Summary: This paper concerns ER quality control of EFR and elf18-triggered (PTI) responses (anthocyanin de-repression, SA-dependent defense), not a classical EFR-dependent hypersensitive response (programmed cell death). Surface PRRs like EFR drive PTI and generally do not by themselves trigger HR, which is the hallmark of NLR-mediated effector-triggered immunity. The abstract does not mention hypersensitive response. Reason: HR/programmed cell death is not a core EFR (surface PRR) output; this IMP annotation likely over-propagates a general defense role to the specific HR term. Retained (not removed) as an experimental TAIR annotation whose full reasoning cannot be fully verified from the cached text. Supporting Evidence: file:ARATH/EFR/EFR-notes.md PTI by surface PRRs like EFR generally does NOT trigger HR/cell death (that is the hallmark of ETI/intracellular NLRs) |
| GO:0019199 transmembrane receptor protein kinase activity | TAS PMID:19763087 Receptor quality control in the endoplasmic reticulum for pl... | ACCEPT | Summary: EFR is a single-pass transmembrane receptor that combines elf18 ligand perception (ectodomain) with intracellular serine/threonine kinase signaling. This is the most informative molecular function term for EFR, capturing both the receptor and catalytic activities. Reason: Most informative MF term; matches the GO definition (combining with a signal and transmitting it across the membrane to initiate change via protein phosphorylation). Core function. Supporting Evidence: PMID:16713565 a receptor kinase essential for EF-Tu perception, which we called EFR |
| GO:0016045 detection of bacterium | IDA PMID:16713565 Perception of the bacterial PAMP EF-Tu by the receptor EFR r... | ACCEPT | Summary: EFR detects the bacterial PAMP EF-Tu; transient expression in N. benthamiana confers EF-Tu binding and responsiveness, and efr mutants are altered in bacterial interaction. Core biological process. Reason: Direct experimental evidence that EFR detects bacterial EF-Tu; core to its function as the EF-Tu receptor. Supporting Evidence: PMID:16713565 Nicotiana benthamiana, a plant unable to perceive EF-Tu, acquires EF-Tu binding sites and responsiveness upon transient expression of EFR |
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Download this section (compressed HTML)Q: Does EFR-mediated PTI ever contribute to localized cell death/hypersensitive-response-like outputs, or is the GO:0009626 annotation an over-extension of a general defense role?
Suggested experts: Plant immunity researchers
Q: What is the complete set of direct EFR kinase substrates beyond BIK1, and how does tyrosine phosphorylation (e.g. Y836) shape substrate selection?
Suggested experts: Plant receptor kinase signaling researchers
Experiment: Compare elf18-triggered responses (ROS, MAPK, callose, defense gene induction) versus cell-death markers in wild-type and efr mutants, and test whether HR-associated readouts are EFR-independent.
Hypothesis: EFR-dependent PTI does not require a hypersensitive-response/programmed cell death module
Experiment: Use EFR Y836F and kinase-dead (D849N) variants to measure BIK1 phosphorylation, JA/SA accumulation, and resistance to P. syringae, dissecting the contribution of tyrosine versus serine/threonine phosphorylation.
Hypothesis: Tyrosine phosphorylation of EFR (Y836) gates substrate phosphorylation of BIK1 and downstream hormone outputs
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