CEBiP (chitin elicitor-binding protein, also Os-LYP1) is a plasma membrane-associated LysM receptor-like protein of rice that lacks an intracellular kinase domain. The mature 328-residue, heavily N-glycosylated ectodomain carries three tandem LysM modules (two canonical LysMs plus an N-terminal LysM0 seen in the crystal structure) followed by a cysteine-rich domain, and is anchored at the C terminus by a short hydrophobic segment. CEBiP is the major high-affinity binding site for fungal chitin oligosaccharides in rice cells; it preferentially binds long, fully N-acetylated oligomers (heptamer-octamer) through its central LysM, and two CEBiP ectodomains sandwich a single chitin octamer, driving receptor dimerization. Chitin binding promotes formation of a hetero-oligomeric receptor complex with the LysM receptor kinase OsCERK1, which transduces the signal (via OsRacGEF1-OsRac1 and RLCK185-MAPK cascades) to the oxidative burst, defence-gene expression and phytoalexin synthesis. Loss of CEBiP strongly reduces chitin-triggered responses but not responses to peptidoglycan or lipopolysaccharide, and makes rice more permissive to the rice blast fungus Magnaporthe oryzae, whose secreted LysM effector Slp1 competes with CEBiP for chitin oligomers to evade this recognition.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0005515 protein binding | IPI PMID:21070404 Two LysM receptor molecules, CEBiP and OsCERK1, cooperativel... | MODIFY | Summary: Shimizu et al. 2010 showed by yeast two-hybrid (ectodomains), co-immunoprecipitation from chitin-treated rice cell membranes, BN-PAGE and cross-linking that CEBiP interacts with the LysM receptor kinase OsCERK1 (D7UPN3) and forms homo-oligomers. The interaction is real and functionally central, but "protein binding" conveys nothing about CEBiP's role, which is to act as the ligand-binding pattern-recognition subunit of a chitin receptor complex in which OsCERK1 is the signal-transducing kinase. Reason: The experiment is sound (curator-read full text is cached and confirms the CEBiP-OsCERK1 complex), but the uninformative protein binding term should be replaced by the activity this complex formation serves. The paper itself assigns the roles: CEBiP binds the chitin elicitor and OsCERK1 transduces. GO:0038187 pattern recognition receptor activity ("combining with a PAMP ... to initiate an innate immune response") captures the CEBiP side of the complex; it is the same term carried by OsCERK1 (EXP) and used for the analogous non-catalytic chitin-binding receptor LYK5 in Arabidopsis. Proposed replacements: pattern recognition receptor activity Supporting Evidence: PMID:21070404 Immunoprecipitation using a membrane preparation from rice cells treated with chitin oligosaccharides suggested the ligand-induced formation of a receptor complex containing both CEBiP and OsCERK1. PMID:21070404 However, it does appear that CEBiP plays a major role in chitin elicitor binding and that OsCERK1 functions as a signal transducer through its Ser/Thr kinase activity in rice. PMID:24395781 Based on these observations, we proposed a hypothetical model for the ligand-induced activation of a receptor complex, involving both CEBiP and Oryza sativa chitin-elicitor receptor kinase-1. |
| GO:0005886 plasma membrane | IEA GO_REF:0000120 | ACCEPT | Summary: CEBiP was originally purified by chitin-oligosaccharide affinity from rice plasma membrane preparations, and subsequent work consistently places it in the plasma membrane together with OsCERK1. The electronic annotation agrees with this direct evidence. Reason: Experimentally well supported (biochemical purification from plasma membranes; affinity labelling of membrane binding sites lost in the knockout). The plasma membrane is where CEBiP meets extracellular chitin fragments and OsCERK1. Whether the C-terminal hydrophobic segment remains a transmembrane helix or is replaced by a GPI anchor is not resolved, but either way the protein is at the plasma membrane. Supporting Evidence: PMID:16829581 a high-affinity binding protein for this elicitor was isolated from the plasma membrane of suspension-cultured rice cells PMID:24173912 CEBiP, a plasma membrane-localized glycoprotein of rice, directly binds with chitin elicitors (CE) PMID:23601108 OsCEBiP, a chitin-binding protein, and OsCERK1, a receptor-like kinase, are plasma membrane (PM) proteins that form a receptor complex essential for fungal chitin-driven immune responses in rice. |
| GO:0008061 chitin binding | IBA GO_REF:0000033 | ACCEPT | Summary: Chitin binding is the defining biochemical activity of CEBiP and is supported by extensive direct evidence on the rice protein itself: affinity purification on (GlcNAc)8, affinity labelling, NMR epitope mapping and mutagenesis (central LysM, Ile122), and crystal structures of the ectodomain bound to chitin. The IBA (node seeded by the Arabidopsis orthologue LYM2/AtCEBiP, AT2G17120, which also binds chitin with high affinity) is consistent with this. Reason: Correct and core. Direct experimental support exists for the rice protein (PMID:16829581, PMID:24395781, PMID:27238968, PMID:24173912), and the PAINT node placement is consistent with conserved chitin binding in the CEBiP/LYM2 subfamily. Supporting Evidence: PMID:24395781 Deletion and domain-swapping experiments showed that the central lysine motif in the ectodomain of CEBiP is essential for the binding of chitin oligosaccharides. PMID:24395781 Epitope mapping by NMR spectroscopy indicated the preferential binding of longer-chain chitin oligosaccharides, such as heptamer-octamer, to CEBiP, and also the importance of N-acetyl groups for the binding. PMID:27238968 Here we report the crystal structures of the ectodomain of OsCEBiP (OsCEBiP-ECD) in free and chitin-bound forms. PMID:24173912 Affinity-labeling analysis using biotinylated N-acetylchitooctaose demonstrated that CEBiP is the major CE-binding protein in rice cultured cells and leaves PMID:22891159 Only one of three CEBiP homologs, AtCEBiP (LYM2), showed a high-affinity binding for chitin oligosaccharides similar to rice CEBiP. |
| GO:0032491 detection of molecule of fungal origin | IMP PMID:16829581 Plant cells recognize chitin fragments for defense signaling... | NEW | Summary: CEBiP is the receptor that perceives fungal chitin oligosaccharides at the rice cell surface: it is the major chitin-binding site in rice membranes, and its knockdown or knockout greatly diminishes chitin-induced oxidative burst and gene responses while leaving peptidoglycan and LPS responses intact. Reason: Participation: the detection step itself (binding of the fungal molecule by the receptor) is performed by CEBiP; OsCERK1 knockdown does not reduce membrane chitin binding, so CEBiP is the entity doing the recognition, not merely a requirement for it. Comparator: Arabidopsis CERK1 and LYK5 (the analogous high-affinity chitin-binding subunit) carry this term. Not an ancestor or descendant of any other term proposed or held. Note the contrast with the Arabidopsis orthologue LYM2/AtCEBiP, which binds chitin but is dispensable for chitin signalling; this term should not be transferred to LYM2 by orthology. Supporting Evidence: PMID:16829581 Knockdown of CEBiP gene by RNA interference resulted in the suppression of the elicitor-induced oxidative burst as well as the gene responses, showing that CEBiP plays a key role in the perception and transduction of chitin oligosaccharide elicitor in the rice cells. PMID:24173912 The response to peptidoglycan and lipopolysaccharides in cebip cells was not affected, strongly suggesting that CEBiP is a CE-specific receptor. PMID:22891159 indicating that AtCEBiP is biochemically functional as a chitin-binding protein but does not contribute to signaling |
| GO:0002752 cell surface pattern recognition receptor signaling pathway | IMP PMID:16829581 Plant cells recognize chitin fragments for defense signaling... | NEW | Summary: Chitin binding by CEBiP initiates the cell-surface PRR signalling pathway: it induces CEBiP sandwich-type dimerization and ligand-dependent complex formation with OsCERK1, whose kinase then activates OsRacGEF1-OsRac1 and downstream immune outputs. Blocking CEBiP dimerization with a half-deacetylated oligomer blocks chitin-induced ROS. Reason: Participation: the pathway is defined as initiated by ligand binding to a cell-surface PRR, and CEBiP performs that initiating ligand-binding step and the ligand-induced receptor assembly (dimerization, recruitment of OsCERK1); the downstream phosphorylation steps belong to OsCERK1 and are not asserted here. Comparator: OsCERK1 carries this term (IBA) and Arabidopsis CERK1 carries it too. Not an ancestor or descendant of GO:0032491. Supporting Evidence: PMID:24395781 The model was further supported by the observations that the addition of (GlcNAc)8 induced dimerization of the ectodomain of CEBiP in vitro, and the dimerization and (GlcNAc)8-induced reactive oxygen generation were also inhibited by a unique oligosaccharide PMID:21070404 Once the system is activated by chitin oligosaccharides, a receptor complex including both CEBiP and OsCERK1 is transiently formed, resulting in activation of downstream signaling for defense responses. PMID:23601108 Collectively, our results suggest that OsCEBiP, OsCERK1, OsRacGEF1, and OsRac1 function as key components of a "defensome" critically engaged early during chitin-induced immunity. |
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Download this section (compressed HTML)Q: CEBiP is a non-catalytic ligand-binding subunit that recruits the kinase OsCERK1. Is GO:0038187 pattern recognition receptor activity the right MF for such subunits, or would a dedicated ligand-binding co-receptor term better separate it from the signalling kinase?
Q: Is the C-terminal hydrophobic segment of CEBiP retained as a transmembrane helix (as UniProt annotates) or replaced by a GPI anchor, as proposed for CEBiP/LYM-type proteins in other species?
Q: The PAINT chitin binding node is seeded by Arabidopsis LYM2, which binds chitin but does not contribute to chitin signalling. How should orthology-based transfer of receptor/process terms between rice CEBiP and Arabidopsis LYM2 be constrained, given their functional divergence in signalling?
Q: Does CEBiP influence arbuscular mycorrhizal colonization only indirectly, by competing with OsMYR1 for OsCERK1, or does it have a direct role in symbiotic signalling?
Experiment: Structural determination (cryo-EM) of the full CEBiP-OsCERK1 ectodomain complex bound to chitin octamer, to define stoichiometry and test the sandwich/sliding dimerization models in the context of the kinase partner.
Experiment: Phospholipase C (PI-PLC) sensitivity and anchor analysis of native CEBiP in rice plasma membranes to determine whether it is GPI-anchored or transmembrane.
Experiment: Complement cebip knockout rice with chitin-binding-defective variants (e.g. Ile122 and structure-guided LysM mutants) and measure chitin responses and blast resistance in the presence and absence of the fungal Slp1 effector.
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