LYK4 (LysM-containing receptor-like kinase 4, At2g23770) is a single-pass type I plasma membrane protein of the Arabidopsis LysM receptor-like kinase family. It has a signal peptide, an extracellular region with three LysM motifs, a transmembrane helix and an intracellular kinase-like domain. The kinase domain lacks key catalytic residues and recombinant LYK4 shows no detectable kinase activity, so LYK4 is best regarded as a pseudokinase. LYK4 is the closest paralog of LYK5 and acts with it as a chitin-binding co-receptor of the active kinase CERK1 in fungal chitin perception. LYK4 is recovered with chitin beads, although soluble chitin oligomers compete its binding only weakly. Its ectodomain homodimerizes and binds the LYK5 ectodomain, and LYK4 associates with CERK1 independently of chitin, consistent with a LYK5-associated co-receptor or scaffold role in a CERK1-LYK5-LYK4 receptor complex. lyk4 mutants show reduced chitin-induced gene expression, calcium elevation and ROS, and are more susceptible to Alternaria brassicicola and Pseudomonas syringae; lyk4 lyk5 double mutants lose all tested chitin responses, like cerk1. LYK4 is also present in the plasmodesmal plasma membrane, where it associates with the GPI-anchored chitin-binding protein LYM2, and both LYK4 and LYK5 are required for chitin-triggered, CERK1-independent callose deposition and closure of plasmodesmata.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0004672 protein kinase activity | IEA GO_REF:0000002 | REMOVE | Summary: InterPro2GO mapping from the Ser/Thr/Tyr kinase catalytic domain signature (IPR001245). The LYK4 intracellular domain has the kinase fold but lacks key catalytic residues, and recombinant LYK4 failed to phosphorylate myelin basic protein; LYK4 is treated as a pseudokinase whose signalling partner CERK1 supplies the kinase activity. Reason: Domain-based mapping that ignores loss of catalytic residues. Wan et al. 2012 report missing key residues (domain VII, needed to align ATP for phosphotransfer) and no activity in an in vitro kinase assay, and Cao et al. 2014 model LYK4 and LYK5 as kinase-inactive receptors with CERK1 as the signalling kinase. A catalytic activity term is therefore not supported for LYK4. Supporting Evidence: PMID:22744984 LYK4 also appears to be an inactive kinase, since the comparison of the LYK4 kinase domain with other typical kinases revealed that certain key residues are missing PMID:22744984 kinase assays using recombinant LYK4 protein isolated after expression in Escherichia coli failed to show phosphorylation of the common kinase substrate Myelin Basic Protein 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). file:ARATH/LYK4/LYK4-deep-research-falcon.md LYK4 has no detectable intrinsic kinase-domain autophosphorylation in the cited biochemical assays. |
| GO:0004674 protein serine/threonine kinase activity | IEA GO_REF:0000003 | REMOVE | Summary: EC-mapping annotation from the UniProt EC 2.7.11.1 assignment, which is family-based and not supported by any LYK4 activity measurement. Recombinant LYK4 is kinase-inactive. Reason: The EC number is inherited from the protein kinase superfamily classification. LYK4 lacks key catalytic residues and showed no phosphotransfer activity in vitro, so the EC-derived Ser/Thr kinase activity is demonstrably wrong for this pseudokinase. Supporting Evidence: PMID:22744984 kinase assays using recombinant LYK4 protein isolated after expression in Escherichia coli failed to show phosphorylation of the common kinase substrate Myelin Basic Protein PMID:22744984 LYK4 also appears to be an inactive kinase, since the comparison of the LYK4 kinase domain with other typical kinases revealed that certain key residues are missing |
| GO:0005524 ATP binding | IEA GO_REF:0000002 | MARK AS OVER ANNOTATED | Summary: InterPro2GO mapping from the protein kinase domain signature (IPR000719). LYK4 lacks residues that align ATP for phosphotransfer; nucleotide binding by the LYK4 pseudokinase has not been tested. Reason: Some pseudokinases still bind ATP, so the term is not demonstrably wrong, but it is inferred only from the kinase fold, and the residues missing in LYK4 are those involved in aligning ATP. Without a nucleotide-binding measurement the term over-states what is known. Treated the same way as in the LYK5 review. Supporting Evidence: PMID:22744984 especially those residues involved in aligning ATP for Ξ³-phosphate group transfer in domain VII |
| GO:0005886 plasma membrane | IBA GO_REF:0000033 | ACCEPT | Summary: Phylogenetic inference of plasma membrane localization across the LysM-RLK family, consistent with the experimental localization of LYK4 (the target appears among the donors, as expected for a gene with its own experimental annotation). Reason: LYK4 is a single-pass receptor with an extracellular LysM region, and fluorescent fusions localize to the plasma membrane, where it functions in chitin perception with CERK1 and LYK5. Supporting Evidence: PMID:22744984 Similar to LYK1/CERK1, the LYK4 protein was also localized to the plasma membrane. PMID:25340959 These results indicate that together with AtCERK1 and AtLYK4, AtLYK5 is a membrane-localized protein. |
| GO:0005886 plasma membrane | IDA PMID:22744984 LYK4, a lysin motif receptor-like kinase, is important for c... | ACCEPT | Summary: Direct localization of a LYK4 fusion protein to the plasma membrane. Reason: Direct experimental evidence; matches the predicted type I membrane topology and the receptor role of LYK4. Independently confirmed in Cheval et al. 2020. Supporting Evidence: PMID:22744984 Similar to LYK1/CERK1, the LYK4 protein was also localized to the plasma membrane. PMID:32284410 they localized to the PM in the absence and presence of chitin and showed no enrichment at plasmodesmata |
| GO:0005886 plasma membrane | IEA GO_REF:0000120 | ACCEPT | Summary: Electronic annotation from UniProt subcellular location (cell membrane), itself based on the Wan et al. 2012 experiment. Reason: Correct and consistent with experimental data. Supporting Evidence: PMID:22744984 LYK4 was further shown to be induced by chitin and located at the PM |
| GO:0008061 chitin binding | IBA GO_REF:0000033 | ACCEPT | Summary: Phylogenetic inference of chitin binding for the LYK4/LYK5 clade node (PTN001988303). LYK4 itself is among the donors, reflecting its own experimental chitin-binding annotation. Reason: Chitin binding is shared by the LYK4/LYK5 clade; LYK5 binds chitooctaose with high affinity, and LYK4 is recovered by chitin beads in two independent studies. The target appearing in its own WITH/FROM is expected and indicates experimental grounding on LYK4. Supporting Evidence: PMID:25340959 As shown in Figure 3βfigure supplement 1, besides AtCERK1, only AtLYK4 and AtLYK5 were also pulled down by chitin beads. 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 |
| GO:0008061 chitin binding | IDA PMID:22744984 LYK4, a lysin motif receptor-like kinase, is important for c... | ACCEPT | Summary: LYK4 was pulled down by chitin magnetic beads from plant membranes and eluted by chitooctaose (Wan et al. 2012, repeating Petutschnig et al. 2010); Cao et al. 2014 likewise recovered LYK4 with chitin beads, although competition by soluble chitin oligomers was weak compared with LYK5. Reason: Chitin-bead pull-down with specific elution by chitooctaose supports chitin binding. No affinity constant has been measured for LYK4, and pull-down from membranes cannot exclude binding via a complex partner, but LYK4 has the conserved LysM ectodomain of the LYK4/LYK5 clade and the evidence is consistent across studies. 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 with AtLYK5 was strongly inhibited by chitoheptaose and chitooctaose, whereas the binding with AtCERK1 or AtLYK4 was only slightly reduced by the same competitors |
| GO:0009507 chloroplast | ISM GO_REF:0000122 | REMOVE | Summary: AtSubP sequence-based prediction of chloroplast localization. LYK4 has an N-terminal secretory signal peptide, an extracellular LysM region and a transmembrane helix, and is experimentally at the plasma membrane and plasmodesmata. Reason: The N-terminal signal peptide is misread as a transit peptide by the predictor. Experimental localization is plasma membrane (and plasmodesmal plasma membrane); there is no evidence for a plastid pool. Supporting Evidence: PMID:22744984 Similar to LYK1/CERK1, the LYK4 protein was also localized to the plasma membrane. |
| GO:0045087 innate immune response | IBA GO_REF:0000033 | ACCEPT | Summary: Phylogenetic inference of innate immune response for the LysM-RLK node; consistent with LYK4's role as a chitin co-receptor in pattern-triggered immunity. Reason: LYK4 is part of the chitin receptor complex that triggers pattern-triggered immunity, and lyk4 and lyk4 lyk5 mutants are compromised in chitin responses and in resistance to fungal and bacterial pathogens. Supporting Evidence: PMID:25340959 The functions of AtLYK4 and AtLYK5 are partially redundant in that single mutants retain residual responses to chitin, while Atlyk4/Atlyk5-2 double mutant plants show a complete lack of response to chitin, similar to the Atcerk1 mutants. PMID:31270545 our data suggest that LYK4 functions as a LYK5-associated co-receptor or scaffold protein that enhances chitin-induced signaling in Arabidopsis |
| GO:0045087 innate immune response | IEA GO_REF:0000117 | ACCEPT | Summary: ARBA machine-learning annotation to innate immune response; correct for LYK4. Reason: Redundant with the IBA and experimental annotations, but correct. Supporting Evidence: PMID:22744984 Therefore, LYK4 may play a role in the chitin recognition receptor complex to assist chitin signal transduction and plant innate immunity. |
| GO:0045087 innate immune response | IGI PMID:25340959 The kinase LYK5 is a major chitin receptor in Arabidopsis an... | ACCEPT | Summary: Genetic interaction with LYK5; lyk4 lyk5-2 double mutants lose all tested chitin responses (ROS, MAPK phosphorylation) and chitin-induced resistance to Alternaria brassicicola. Reason: The double-mutant data show LYK4 and LYK5 act redundantly in chitin-triggered immunity. Combined with the biochemical evidence that LYK4 is a component of the receptor complex, LYK4 participates in (rather than being merely necessary for) the immune signalling. Supporting Evidence: PMID:25340959 The functions of AtLYK4 and AtLYK5 are partially redundant in that single mutants retain residual responses to chitin, while Atlyk4/Atlyk5-2 double mutant plants show a complete lack of response to chitin, similar to the Atcerk1 mutants. |
| GO:0045087 innate immune response | IMP PMID:22744984 LYK4, a lysin motif receptor-like kinase, is important for c... | ACCEPT | Summary: lyk4 mutants show reduced chitin-responsive gene induction and calcium elevation and enhanced susceptibility to Pseudomonas syringae pv. tomato DC3000 and Alternaria brassicicola. Reason: Direct mutant evidence for LYK4 in innate immunity, consistent with its co-receptor role. Supporting Evidence: PMID:22744984 The lyk4 mutants showed reduced induction of chitin-responsive genes and diminished chitin-induced cytosolic calcium elevation as well as enhanced susceptibility to both the bacterial pathogen Pseudomonas syringae pv tomato DC3000 and the fungal pathogen Alternaria |
| GO:0071219 cellular response to molecule of bacterial origin | IBA GO_REF:0000033 | MARK AS OVER ANNOTATED | Summary: Phylogenetic inference from the LYK4/LYK5 clade node; the only donor is LYK4 itself, whose grounding is the IEP annotation below (LYK4 transcript induced by flg22). Reason: No bacterial molecule perceived by LYK4 has been identified. lyk4 mutants are more susceptible to Pst DC3000, but mutation of LYK4 has negligible impact on flg22 or elf26 signalling, and recognition of peptidoglycan or another bacterial elicitor is only speculated. The term over-states a susceptibility phenotype that may reflect reduced chitin-like or general immune signalling. Not removed because the node placement is a PAINT judgment and a bacterial ligand remains possible. Propagation Review Root cause: PROPAGATION BAD Failure modes: FUNCTIONAL DIVERGENCE Sources checked: PANTHER:PTN001988303 Β· LYK4/LYK5 clade node UNRESOLVED The node's only listed donor is LYK4 itself, whose experimental basis is an expression (IEP) observation after flg22 treatment rather than a demonstrated response to a bacterial molecule. AGI_LocusCode:AT2G23770 Β· LYK4 UNRESOLVED LYK4 transcript is induced by flg22, but lyk4 mutants have negligible defects in flg22 and elf26 signalling. Supporting Evidence: PMID:22744984 the mutations in LYK1 and LYK4 have a negligible impact on fls22 or elf26 signaling, based on the gene expression analysis PMID:22744984 they may be able to recognize and bind another unidentified elicitor from bacterial pathogens |
| GO:0071219 cellular response to molecule of bacterial origin | IEP PMID:22744984 LYK4, a lysin motif receptor-like kinase, is important for c... | MARK AS OVER ANNOTATED | Summary: Based on moderate induction of LYK4 transcripts by flg22. Expression induction does not show that LYK4 participates in the cellular response, and the same paper found that lyk4 mutation has negligible impact on flg22 and elf26 signalling. Reason: An IEP transcript-induction result is weak evidence for involvement, and here the same study tested and did not find a role in the flagellin/EF-Tu responses. A bacterial ligand for LYK4 (e.g. peptidoglycan) is hypothesized only. Kept as over-annotation rather than removed in deference to the curator and because the bacterial susceptibility phenotype is real. Supporting Evidence: PMID:22744984 the mutations in LYK1 and LYK4 have a negligible impact on fls22 or elf26 signaling, based on the gene expression analysis |
| GO:0071323 cellular response to chitin | IBA GO_REF:0000033 | ACCEPT | Summary: Phylogenetic inference of cellular response to chitin, grounded on LYK4 and LYK5 experimental data. Reason: LYK4 is a chitin-binding co-receptor in the CERK1-LYK5 receptor complex; lyk4 single and lyk4 lyk5 double mutants are defective in chitin responses. Supporting Evidence: PMID:25340959 The functions of AtLYK4 and AtLYK5 are partially redundant in that single mutants retain residual responses to chitin, while Atlyk4/Atlyk5-2 double mutant plants show a complete lack of response to chitin, similar to the Atcerk1 mutants. PMID:31270545 by analysing mutants we confirmed a role of LYK4 in chitin perception |
| GO:0071323 cellular response to chitin | IEP PMID:22744984 LYK4, a lysin motif receptor-like kinase, is important for c... | ACCEPT | Summary: Based on chitin induction of LYK4 transcripts; the same paper also provides mutant evidence that LYK4 is required for chitin-induced gene expression and calcium elevation. Reason: The term is correct for LYK4 as a chitin co-receptor; the expression evidence code is weak, but the process is strongly supported by mutant and biochemical data in the same and later studies. Supporting Evidence: PMID:22744984 The lyk4 mutants showed reduced induction of chitin-responsive genes and diminished chitin-induced cytosolic calcium elevation PMID:22744984 LYK4 was further shown to be induced by chitin and located at the PM |
| GO:0106310 protein serine kinase activity | IEA GO_REF:0000116 | REMOVE | Summary: Rhea-mapping annotation from the family-based catalytic activity in the UniProt entry. LYK4 is a pseudokinase with no detectable kinase activity. Reason: Same basis as the EC-derived Ser/Thr kinase annotation; contradicted by the missing catalytic residues and the negative in vitro kinase assay. Supporting Evidence: PMID:22744984 kinase assays using recombinant LYK4 protein isolated after expression in Escherichia coli failed to show phosphorylation of the common kinase substrate Myelin Basic Protein |
| GO:1901701 cellular response to oxygen-containing compound | IEA GO_REF:0000117 | MARK AS OVER ANNOTATED | Summary: ARBA annotation to a very general grouping term; chitin is formally an oxygen-containing compound, so this is a distant ancestor of cellular response to chitin. Reason: Uninformative grouping term that is fully covered by the more specific cellular response to chitin; treated the same way as in the LYK5 review. Supporting Evidence: PMID:25340959 The functions of AtLYK4 and AtLYK5 are partially redundant in that single mutants retain residual responses to chitin, while Atlyk4/Atlyk5-2 double mutant plants show a complete lack of response to chitin, similar to the Atcerk1 mutants. |
| GO:0015026 coreceptor activity | IPI PMID:31270545 LYK4 is a component of a tripartite chitin receptor complex ... | NEW | Summary: LYK4 ectodomains homodimerize and bind LYK5 ectodomains, LYK4 co-immunoprecipitates with LYK5 and CERK1 after chitin treatment, and LYK4 associates with CERK1 independently of chitin. LYK4 binds chitin but lacks kinase activity and is partially redundant with LYK5, which is the main chitin receptor. Reason: LYK4 does part of the work of chitin perception (it is a chitin-binding receptor subunit of the CERK1-LYK5 complex) rather than being a downstream requirement, so a receptor-type MF is warranted to capture its role beyond chitin binding. Coreceptor activity (combining with a messenger in cooperation with a nearby primary receptor) matches the authors' conclusion that LYK4 is a LYK5-associated co-receptor or scaffold, better than pattern recognition receptor activity, which is used for LYK5 as the main high-affinity chitin receptor. Comparator check - LYK5 (GO:0038187, NEW in its review) and CERK1 carry receptor-type MFs; no LYK4 MF beyond chitin binding is in GOA because the relevant interaction papers have not been curated. Supporting Evidence: PMID:31270545 our data suggest that LYK4 functions as a LYK5-associated co-receptor or scaffold protein that enhances chitin-induced signaling in Arabidopsis PMID:31270545 found that the ectodomain of LYK4 homodimerizes and also interacts with the ectodomain of LYK5 in vitro PMID:25340959 AtLYK4 interacts with AtCERK1 independently of the presence of chitin, while AtLYK5-AtCERK1 interaction is chitin dependent. |
| GO:0009506 plasmodesma | IDA PMID:32284410 Chitin perception in plasmodesmata characterizes submembrane... | NEW | Summary: LYK4-HA, but not LYK5-HA, was detected in purified plasmodesmal membrane fractions (expressed in Nicotiana benthamiana), and LYK4 associates with the plasmodesmal chitin-binding protein LYM2. Reason: Direct biochemical localization to plasmodesmata, supporting a LYM2-LYK4 complex that mediates CERK1-independent chitin-triggered plasmodesmal closure. Location annotation; the LYM2 review carries the same term. Caveat - fractionation was done with a heterologously expressed tagged protein, and LYK4 is not enriched at plasmodesmata by imaging, so this is a sub-pool of the plasma membrane protein. Supporting Evidence: PMID:32284410 We detected PDLP5-HA and LYK4-HA in purified plasmodesmata extracts, but not LYK5-HA or H+-ATPase PMID:32284410 LYM2 can associate with both LYK4 and LYK5, but we detected only LYK4 in plasmodesmata, suggesting that chitin-triggered plasmodesmal signaling is mediated directly by a LYM2-LYK4 complex. |
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Download this section (compressed HTML)Q: Should LYK4 carry coreceptor activity (GO:0015026) or pattern recognition receptor activity (GO:0038187) like LYK5? LYK4 binds chitin weakly, interacts with CERK1 independently of chitin, and is described as a LYK5-associated co-receptor or scaffold.
Q: Does LYK4 bind chitin directly with measurable affinity, or is its recovery on chitin beads mediated by LYK5 or CERK1 in the same membrane complex?
Q: Is there a bacterial ligand (for example peptidoglycan) for LYK4 that explains the enhanced susceptibility of lyk4 to Pseudomonas syringae, given that flg22 and elf26 responses are unaffected?
Q: Once GO has a term for regulation of plasmodesmata-mediated intercellular transport (proposed in the LYM2 review), should LYK4 be annotated to it given its plasmodesmal localization and association with LYM2?
Experiment: Measure chitooctaose binding by the purified LYK4 ectodomain (ITC or microscale thermophoresis) alongside LYK5 and CERK1 to establish whether LYK4 binds chitin directly and with what affinity.
Experiment: Complement lyk4 lyk5 double mutants with LYK4 variants carrying LysM mutations or lacking the ectodomain-ectodomain interaction with LYK5 to test which LYK4 property restores chitin signalling.
Experiment: Test nucleotide binding by the purified LYK4 pseudokinase domain (thermal shift or MANT-ATP) to resolve whether the ATP binding annotation has any basis.
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