LYK5 (LysM-containing receptor-like kinase 5, At2g33580) is a single-pass type I plasma membrane receptor of the LysM receptor-like kinase family. It has an N-glycosylated extracellular region with three LysM motifs and an intracellular pseudokinase domain that lacks the P-loop, RD and DFG catalytic residues and shows no detectable kinase activity. LYK5 is the main high-affinity receptor for fungal chitin in Arabidopsis: its ectodomain binds long-chain chitin oligomers (chitooctaose, Kd about 1.7 uM), much more tightly than CERK1. Chitin binding drives formation of a LYK5-CERK1 complex, which leads to CERK1 homodimerization and phosphorylation. CERK1 supplies the active kinase that triggers downstream responses: ROS burst, calcium influx, MPK3/MPK6 activation, defense gene expression and resistance to fungi such as Alternaria brassicicola. The pseudokinase domain is needed for association with CERK1 but not for catalysis. LYK5 forms ligand-independent homodimers. It overlaps in function with its paralog LYK4: lyk4 lyk5 double mutants lose all chitin responses. After chitin perception, CERK1 phosphorylates LYK5, which is then internalized into late endosomes. CPK5 also phosphorylates LYK5. Its basal abundance is limited by the U-box E3 ligase PUB13.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0002237 response to molecule of bacterial origin | IBA GO_REF:0000033 | MARK AS OVER ANNOTATED | Summary: IBA from the PANTHER LysM-RLK node (PTN001232170) to response to molecule of bacterial origin. LYK5 is a chitin (fungal MAMP) receptor; there is no evidence that LYK5 perceives a bacterial molecule. Untreated lyk5-2 plants had wild-type resistance to Pst DC3000; the only bacterial phenotype is loss of chitin-induced priming against Pst. Bacterial peptidoglycan perception in Arabidopsis is attributed to LYM1/LYM3 with CERK1, not LYK5. Reason: The family node includes CERK1 (peptidoglycan co-receptor) and LYK4 (bacterial susceptibility phenotype), so the term may be valid for some members, but LYK5-specific evidence argues against direct involvement: lyk5-2 shows wild-type basal resistance to Pst DC3000, and its ligand is fungal chitin. Not removed outright because the IBA reflects a PAINT node judgment and LYK5 contributes indirectly through chitin-primed resistance. Propagation Review Root cause: PROPAGATION BAD Failure modes: FUNCTIONAL DIVERGENCE Sources checked: PANTHER:PTN001232170 · LysM receptor-like kinase family node SUPPORTS SOURCE BUT NOT TARGET The node spans CERK1, LYK4 and LYK5. The bacterial-molecule response fits members that are peptidoglycan co-receptors or have bacterial phenotypes. LYK5 is a chitin-specific receptor with wild-type basal resistance to Pst. AGI_LocusCode:AT2G23770 · LYK4 SUPPORTS SOURCE BUT NOT TARGET lyk4 mutants are more susceptible to Pst DC3000 (Wan et al. 2012). There is no equivalent basal phenotype for lyk5-2. UniProtKB:Q0GXS4 UNRESOLVED Donor not traced in this review. Supporting Evidence: PMID:25340959 Untreated Atcerk1 and Atlyk5-2 mutant plants showed wild-type levels of resistance to the bacterial pathogen Pseudomonas syringae pv. tomato DC3000. PMID:25340959 In this model, AtLYK5 (or AtLYK4) serves as a chitin perception, while AtCERK1 is responsible for chitin signaling transduction due to lack of kinase activity of AtLYK5 (or AtLYK4). |
| GO:0005515 protein binding | IPI PMID:25340959 The kinase LYK5 is a major chitin receptor in Arabidopsis an... | REMOVE | Summary: IPI with CERK1 (AT3G21630) from Cao et al. 2014: LYK5 forms a chitin-induced complex with CERK1, and the LYK5 pseudokinase domain is required for this association. Reason: Generic protein binding is uninformative. The interaction is real and functionally central (chitin-induced LYK5-CERK1 receptor complex), but it is captured better by the receptor activity and chitin perception terms (see core_functions and NEW GO:0038187). Removal does not dispute the interaction. Consistent with the treatment of the reciprocal row in the CERK1 review. Supporting Evidence: PMID:25340959 AtLYK5 interacts with AtCERK1 in a chitin-dependent manner. Chitin binding to AtLYK5 is indispensable for chitin-induced AtCERK1 phosphorylation. |
| GO:0005515 protein binding | IPI PMID:34558681 The Arabidopsis thaliana LysM-containing Receptor-Like Kinas... | REMOVE | Summary: IPI with LYK2 (AT3G01840) from Giovannoni et al. 2021: co-IP in N. benthamiana and BiFC in N. tabacum show that LYK2 and LYK5 interact constitutively when overexpressed. Reason: Generic protein binding is uninformative. The LYK2-LYK5 association is based on heterologous overexpression, and its functional meaning is unclear (LYK2 is largely dispensable for chitin perception). No more specific MF term is supported. Removal does not mean the interaction is false. Supporting Evidence: PMID:34558681 could also co‐purify LYK5‐myc when both proteins were co‐expressed in N. benthamiana (Figure 9a), suggesting that LYK2 and LYK5 can physically interact |
| GO:0005524 ATP binding | IEA GO_REF:0000002 | MARK AS OVER ANNOTATED | Summary: InterPro kinase-domain (IPR000719) IEA for ATP binding. The LYK5 intracellular domain is a pseudokinase: it lacks the P-loop, RD and DFG residues, shows no kinase activity in vitro, and the K395E variant (predicted to disrupt ATP binding) fully complements lyk5-2. Reason: Nucleotide binding by LYK5 has not been tested and is not needed for function: the ATP-binding-site mutant K395E rescues all chitin responses. Some pseudokinases still bind ATP, so the annotation is not shown to be wrong. But it is a domain-signature transfer to a pseudoenzyme with no supporting evidence. Supporting Evidence: PMID:25340959 several residues generally considered essential for kinase activity are missing from the AtLYK5 sequence (Figure 6—figure supplement 1), including those in the P-loop sub-domain I, RD domain in sub-domain VIa, and DFG domain in sub-domain VII PMID:25340959 The data show that expression of AtLYK5 or AtLYK5K395E could complement the Atlyk5-2 mutant phenotype, as measured by chitin-triggered ROS production, MAPK phosphorylation, and AtCERK1 phosphorylation file:ARATH/LYK5/LYK5-deep-research-falcon.md No reaction catalyzed by LYK5 or enzymatic substrate has been established. |
| GO:0005576 extracellular region | ISM GO_REF:0000122 | REMOVE | Summary: ISM (AtSubP) prediction of extracellular region, presumably driven by the N-terminal signal peptide (residues 1-26). LYK5 is a single-pass type I plasma membrane protein whose LysM ectodomain faces the apoplast; the mature protein is not secreted. Reason: Experimental localization (GFP fusions; native-promoter LYK5-mCitrine) places LYK5 at the plasma membrane and in endosomes after chitin, never free in the extracellular space. A transmembrane receptor whose ectodomain faces the apoplast should be annotated to plasma membrane, not extracellular region. This is a signal-peptide localization default. Supporting Evidence: PMID:25340959 Confocal microscopy showed that AtLYK5-GFP co-localized with the plasma membrane dye, FM4-64 PMID:28513921 Both CERK1 and LYK5 localized to the plasma membrane and showed constitutive endomembrane trafficking. |
| GO:0005886 plasma membrane | IBA GO_REF:0000033 | ACCEPT | Summary: IBA plasma membrane for the LysM-RLK family; consistent with direct localization of LYK5. Reason: LYK5 is a single-pass plasma membrane receptor; confirmed by GFP fusion and native-promoter imaging. Supporting Evidence: PMID:25340959 Confocal microscopy showed that AtLYK5-GFP co-localized with the plasma membrane dye, FM4-64 PMID:28513921 Both CERK1 and LYK5 localized to the plasma membrane and showed constitutive endomembrane trafficking. |
| GO:0005886 plasma membrane | IDA PMID:34558681 The Arabidopsis thaliana LysM-containing Receptor-Like Kinas... | ACCEPT | Summary: IDA plasma membrane from Giovannoni et al. 2021, based on BiFC signal from LYK2-NYFP/LYK5-CYFP "likely at the PM" in N. tabacum. Reason: The evidence in this paper is indirect (a heterologous BiFC complex), but plasma membrane localization of LYK5 is independently established by Cao et al. 2014 and Erwig et al. 2017, so the annotation is correct. Supporting Evidence: PMID:34558681 co‐transformation with 35S:LYK2‐NYFP and 35S:LYK5‐CYFP resulted in a YFP fluorescence signal, likely at the PM PMID:28513921 Both CERK1 and LYK5 localized to the plasma membrane and showed constitutive endomembrane trafficking. |
| GO:0005886 plasma membrane | IEA GO_REF:0000120 | ACCEPT | Summary: IEA plasma membrane (ARBA/SubCell mapping); correct. Reason: Consistent with experimental localization. Supporting Evidence: PMID:25340959 Confocal microscopy showed that AtLYK5-GFP co-localized with the plasma membrane dye, FM4-64 |
| GO:0008061 chitin binding | IDA PMID:22744984 LYK4, a lysin motif receptor-like kinase, is important for c... | ACCEPT | Summary: IDA chitin binding from Wan et al. 2012 (LYK4 paper): in a chitin-bead pull-down, LYK5 was recovered together with LYK1/CERK1, LYK4 and CEBiP-like1 and eluted with chitooctaose. Reason: This pull-down from plant extract does not on its own show direct binding. Direct, high-affinity binding by the LYK5 ectodomain was later shown by ITC (Cao et al. 2014). Chitin binding is the core molecular activity of LYK5. Supporting Evidence: PMID:22744984 We repeated this experiment and also found that LYK1, LYK4, LYK5, and CEBiP-like1 were pulled down by chitin magnetic beads and eluted by chitooctaose PMID:25340959 the binding affinity of AtLYK5 for chitooctaose was measured (Kd = 1.72 µM), which is roughly 200-fold higher than measured for AtCERK1 under the same conditions (Kd = 455 µM) |
| GO:0008061 chitin binding | IDA PMID:25340959 The kinase LYK5 is a major chitin receptor in Arabidopsis an... | ACCEPT | Summary: IDA chitin binding from Cao et al. 2014: LYK5 is pulled down by chitin beads, and its purified ectodomain binds chitooctaose with Kd 1.72 µM by ITC, about 200-fold tighter than CERK1. Y128 and S206 mutations impair binding and fail to complement. Reason: Direct quantitative binding evidence. This is the defining molecular activity of LYK5 as the primary chitin receptor. Supporting Evidence: PMID:25340959 the binding affinity of AtLYK5 for chitooctaose was measured (Kd = 1.72 µM), which is roughly 200-fold higher than measured for AtCERK1 under the same conditions (Kd = 455 µM) PMID:25340959 As shown in Figure 3—figure supplement 1, besides AtCERK1, only AtLYK4 and AtLYK5 were also pulled down by chitin beads. |
| GO:0042803 protein homodimerization activity | IPI PMID:25340959 The kinase LYK5 is a major chitin receptor in Arabidopsis an... | KEEP AS NON CORE | Summary: IPI homodimerization (LYK5 with itself) from Cao et al. 2014: LYK5 homodimers detected by co-IP before and after chitin, independent of CERK1; DTT converts dimer to monomer. Reason: The observation is direct, but the functional role of the constitutive (likely disulfide-linked) LYK5 homodimer is only modelled (a possible pre-formed dimer that recruits CERK1 into a tetramer). It is not part of the established core receptor function. Supporting Evidence: PMID:25340959 AtLYK5 homodimers were detected even in the absence of chitin and this association was independent of the presence of AtCERK1 |
| GO:0045087 innate immune response | IBA GO_REF:0000033 | ACCEPT | Summary: IBA innate immune response for the LysM-RLK family node; LYK5 contributes to chitin-triggered immunity. Reason: LYK5 is a pattern-recognition receptor whose chitin binding starts PAMP-triggered immunity: ROS, Ca2+ influx, MAPK activation, defense gene induction, and resistance to Alternaria brassicicola. Supporting Evidence: PMID:25340959 Mutations in AtLYK5 resulted in a significant reduction in chitin response. However, AtLYK5 shares overlapping function with AtLYK4 and, therefore, Atlyk4/Atlyk5-2 double mutants show a complete loss of chitin response. PMID:25340959 Both Atcerk1 and Atlyk5-2 mutant plants showed increased susceptibility to the fungal pathogen Alternaria brassicicola compared with Col-0 wild-type plants. |
| GO:0045087 innate immune response | IEA GO_REF:0000117 | ACCEPT | Summary: ARBA IEA innate immune response; correct, same as the IBA. Reason: Supported by mutant and receptor-complex data. Supporting Evidence: PMID:25340959 AtLYK5 interacts with AtCERK1 in a chitin-dependent manner. Chitin binding to AtLYK5 is indispensable for chitin-induced AtCERK1 phosphorylation. |
| GO:0045087 innate immune response | IMP PMID:25340959 The kinase LYK5 is a major chitin receptor in Arabidopsis an... | ACCEPT | Summary: IMP innate immune response from Cao et al. 2014: lyk5-2 shows reduced chitin-triggered ROS, Ca2+ influx, MAPK phosphorylation and WRKY induction, and is more susceptible to A. brassicicola. lyk4 lyk5-2 loses all chitin responses. Reason: Direct genetic evidence with complementation. LYK5 is the ligand-binding receptor at the start of this pathway, so it participates rather than only being required. Supporting Evidence: PMID:25340959 Mutations in AtLYK5 resulted in a significant reduction in chitin response. However, AtLYK5 shares overlapping function with AtLYK4 and, therefore, Atlyk4/Atlyk5-2 double mutants show a complete loss of chitin response. PMID:25340959 Both Atcerk1 and Atlyk5-2 mutant plants showed increased susceptibility to the fungal pathogen Alternaria brassicicola compared with Col-0 wild-type plants. |
| GO:0071323 cellular response to chitin | IBA GO_REF:0000033 | ACCEPT | Summary: IBA cellular response to chitin (PTN008701127, the CERK1/LYK4/LYK5 clade). Reason: LYK5 is the primary chitin receptor; matches the experimental data on the target itself. Supporting Evidence: PMID:25340959 AtLYK5 interacts with AtCERK1 in a chitin-dependent manner. Chitin binding to AtLYK5 is indispensable for chitin-induced AtCERK1 phosphorylation. PMID:25340959 Mutations in AtLYK5 resulted in a significant reduction in chitin response. However, AtLYK5 shares overlapping function with AtLYK4 and, therefore, Atlyk4/Atlyk5-2 double mutants show a complete loss of chitin response. |
| GO:0071323 cellular response to chitin | IEP PMID:22744984 LYK4, a lysin motif receptor-like kinase, is important for c... | ACCEPT | Summary: IEP cellular response to chitin from Wan et al. 2012, based on moderate induction of LYK5 transcript by chitohexaose/chitooctaose (the UniProt INDUCTION line). Reason: Expression induction alone would not justify a process annotation, but the term is correct for LYK5 on independent genetic and biochemical evidence (Cao et al. 2014). Accepted on the strength of that evidence, not on the IEP data. Supporting Evidence: PMID:25340959 Mutations in AtLYK5 resulted in a significant reduction in chitin response. However, AtLYK5 shares overlapping function with AtLYK4 and, therefore, Atlyk4/Atlyk5-2 double mutants show a complete loss of chitin response. |
| GO:1901701 cellular response to oxygen-containing compound | IEA GO_REF:0000117 | MARK AS OVER ANNOTATED | Summary: ARBA IEA cellular response to oxygen-containing compound, a high-level grouping class that is an ancestor of cellular response to chitin. Reason: Technically true (chitin is an oxygen-containing compound) but uninformative and redundant with the more specific cellular response to chitin (GO:0071323), of which it is an ancestor. Supporting Evidence: PMID:25340959 AtLYK5 interacts with AtCERK1 in a chitin-dependent manner. Chitin binding to AtLYK5 is indispensable for chitin-induced AtCERK1 phosphorylation. |
| GO:0038187 pattern recognition receptor activity | IDA PMID:25340959 The kinase LYK5 is a major chitin receptor in Arabidopsis an... | NEW | Summary: LYK5 binds the fungal PAMP chitin (chitooctaose) through its LysM ectodomain with high affinity, and this binding is needed for chitin-induced recruitment and phosphorylation of CERK1 and for downstream immunity. Reason: Fits the term definition exactly ("combining with a PAMP ... to initiate an innate immune response"). Participation: LYK5 itself does the ligand-recognition step. Comparator: in Arabidopsis this term is carried by RLP23, RLP42 and SOBIR1, including RLP42, a non-catalytic ligand-binding PRR like LYK5. CERK1 does not carry it, but CERK1 has low chitin affinity and acts as the signalling kinase. Chitin binding alone (GO:0008061) does not capture the receptor role. Supporting Evidence: PMID:25340959 the binding affinity of AtLYK5 for chitooctaose was measured (Kd = 1.72 µM), which is roughly 200-fold higher than measured for AtCERK1 under the same conditions (Kd = 455 µM) PMID:25340959 AtLYK5 interacts with AtCERK1 in a chitin-dependent manner. Chitin binding to AtLYK5 is indispensable for chitin-induced AtCERK1 phosphorylation. |
| GO:0032491 detection of molecule of fungal origin | IMP PMID:25340959 The kinase LYK5 is a major chitin receptor in Arabidopsis an... | NEW | Summary: LYK5 is the high-affinity receptor that detects fungal chitin oligomers and converts binding into CERK1 activation. Reason: Participation: the detection step (ligand binding by the receptor) is performed by LYK5; binding-defective Y128/S206 mutants fail to complement. Comparator: CERK1 (IMP), RLP23 and RLP30 carry this term for their roles in perceiving fungal/oomycete molecules. Not an ancestor or descendant of cellular response to chitin. Supporting Evidence: PMID:25340959 AtLYK5 interacts with AtCERK1 in a chitin-dependent manner. Chitin binding to AtLYK5 is indispensable for chitin-induced AtCERK1 phosphorylation. PMID:25340959 In this model, AtLYK5 (or AtLYK4) serves as a chitin perception, while AtCERK1 is responsible for chitin signaling transduction due to lack of kinase activity of AtLYK5 (or AtLYK4). |
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Download this section (compressed HTML)Q: LYK5 is a non-catalytic, ligand-binding receptor subunit that recruits an active kinase (CERK1). Is GO:0038187 pattern recognition receptor activity the right MF for such subunits, or should a co-receptor / ligand-binding receptor-subunit term be used, with CERK1 carrying the signalling kinase activity?
Q: The PAINT node PTN001232170 propagates response to molecule of bacterial origin to LYK5, but lyk5-2 has wild-type basal resistance to Pst DC3000. Should this IBA be restricted to the CERK1 lineage (the peptidoglycan co-receptor)?
Q: Is the ligand-independent, DTT-sensitive LYK5 homodimer functionally required for chitin perception, or is it an artefact of overexpression?
Q: Does chitin-induced, CERK1-dependent endocytosis of LYK5 attenuate signalling (receptor removal), or is it needed for signalling from endosomes?
Experiment: Structural determination (cryo-EM or crystallography) of the LYK5 ectodomain bound to chitooctaose, alone and in complex with the CERK1 ectodomain, to define binding residues and complex stoichiometry.
Experiment: Test nucleotide binding by the purified LYK5 pseudokinase domain (e.g. thermal shift or MANT-ATP assays) to resolve whether the ATP binding annotation has any basis.
Experiment: Complement lyk4 lyk5 double mutants with LYK5 variants defective in homodimerization (cysteine mutants) to test whether the pre-formed homodimer is required for chitin signalling.
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