LYM2 (LysM domain-containing GPI-anchored protein 2; also called AtCEBiP) is the Arabidopsis thaliana homologue of the rice chitin elicitor-binding protein CEBiP. It is a secreted, N-glycosylated receptor-like protein with an extracellular region containing LysM domains and a C-terminal glycosylphosphatidylinositol (GPI) anchor, and it has no transmembrane or intracellular signalling domain. LYM2 binds chitin oligosaccharides with high affinity and is the major chitin-binding protein of Arabidopsis membranes, whereas its paralogues LYM1 and LYM3 bind peptidoglycan instead. Unlike rice CEBiP, LYM2 is dispensable for the canonical CERK1-dependent chitin responses (ROS burst, MAPK activation and defense-gene induction), which in Arabidopsis are initiated by the LysM receptor kinase LYK5 together with CERK1. Instead, LYM2 resides in the plasma membrane and is enriched in the plasmodesmal plasma membrane, where chitin increases its accumulation and clustering. There it mediates a CERK1-independent, chitin-specific response that closes plasmodesmata: chitin perception through LYM2, together with the LysM receptor kinases LYK4 and LYK5, the calcium-dependent kinases CPK6 and CPK11 and the NADPH oxidase RBOHD, leads to plasmodesmal callose deposition and reduced cell-to-cell molecular flux. LYM2 contributes to resistance against the fungal pathogens Botrytis cinerea and Alternaria brassicicola but not against the bacterium Pseudomonas syringae.
Definition: Any process that stops, prevents or reduces the frequency, rate or extent of the movement of substances between cells via plasmodesmata, for example by callose deposition that narrows the plasmodesmal aperture.
Justification: GO has GO:0010497 plasmodesmata-mediated intercellular transport but no regulation children. LYM2 (and FLS2, LYK4, LYK5, CPK6, CPK11, RBOHD, PDLP1/5) mediate pathogen-pattern-triggered plasmodesmal closure, a well-characterized response that currently cannot be captured precisely; LYM2 does not itself transport anything, so the parent transport term would be inappropriate.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0005739 mitochondrion | HDA PMID:28887381 Global Analysis of Membrane-associated Protein Oligomerizati... | MARK AS OVER ANNOTATED | Summary: High-throughput assignment from a protein correlation profiling study of membrane-associated protein oligomerization. LYM2 has an N-terminal signal peptide, multiple N-glycosylation sites and a C-terminal GPI-anchor signal, and fluorescent fusions localize it to the plasma membrane and plasmodesmata. Reason: The co-fractionation profiling method does not resolve organelle membranes cleanly, and a secretory-pathway GPI-anchored LysM protein is not expected to reach mitochondria. Direct imaging places LYM2 at the plasma membrane with enrichment at plasmodesmata (PMID:23674687). The detection is a real high-throughput observation, so the row is marked as over-annotated rather than removed: no targeted experiment excludes the organelle (ARATH organelle audit rule 3, projects/ARATH/organelle-audit.md). Supporting Evidence: PMID:28887381 the apparent masses of >1350 membrane-associated proteins PMID:23674687 In accordance with a role in the regulation of intercellular flux, LYM2 is resident at the plasma membrane and is enriched at plasmodesmata. |
| GO:0005886 plasma membrane | HDA PMID:17644812 A high content in lipid-modified peripheral proteins and int... | ACCEPT | Summary: LYM2 was identified in a purified Arabidopsis plasma membrane proteome that is rich in lipid-modified (including GPI-anchored) peripheral proteins. Reason: Consistent with the GPI anchor and with direct imaging of LYM2-mCitrine at the plasma membrane (PMID:23674687). Plasma membrane is where LYM2 perceives chitin. Supporting Evidence: PMID:17644812 16% of the identified proteins are predicted to be lipid-modified, specifically involving double lipid linkage through N-terminal myristoylation, S-palmitoylation, C-terminal prenylation, or glycosylphosphatidylinositol anchors PMID:23674687 LYM2 Is a Plasma Membrane-Located Protein with PD Association. |
| GO:0005886 plasma membrane | HDA PMID:22923678 Putative glycosyltransferases and other plant Golgi apparatu... | ACCEPT | Summary: LOPIT organelle proteomics assigned LYM2 to the plasma membrane cluster. Reason: Independent high-throughput support for plasma membrane location, consistent with imaging data (PMID:23674687). Supporting Evidence: PMID:22923678 These include 197 Golgi apparatus proteins, 79 of which have not been localized previously by a high-confidence method, as well as the localization of 304 endoplasmic reticulum and 208 plasma membrane proteins. |
| GO:0005886 plasma membrane | IDA PMID:12805588 Identification of glycosylphosphatidylinositol-anchored prot... | ACCEPT | Summary: Borner et al. identified LYM2 among phospholipase C-sensitive GPI-anchored proteins (one of the four receptor-like proteins) in Arabidopsis callus cells. Reason: PI-PLC release demonstrates GPI anchoring at the cell surface; consistent with imaging of LYM2 at the plasma membrane (PMID:23674687). Supporting Evidence: PMID:12805588 Using liquid chromatography-tandem mass spectrometry, 30 GAPs were identified, including six beta-1,3 glucanases, five phytocyanins, four fasciclin-like arabinogalactan proteins, four receptor-like proteins PMID:23674687 In accordance with a role in the regulation of intercellular flux, LYM2 is resident at the plasma membrane and is enriched at plasmodesmata. |
| GO:0005886 plasma membrane | IEA GO_REF:0000120 | ACCEPT | Summary: Electronic plasma membrane annotation from ARBA/UniProt subcellular location (cell membrane, GPI-anchor). Reason: Correct and consistent with experimental data (PMID:23674687, PMID:12805588). Supporting Evidence: PMID:23674687 LYM2 Is a Plasma Membrane-Located Protein with PD Association. |
| GO:0008061 chitin binding | IBA GO_REF:0000033 | ACCEPT | Summary: Phylogenetic inference of chitin binding for the CEBiP/LYM2 clade of LysM receptor-like proteins; LYM2 itself is among the experimental sources. Reason: LYM2 and rice CEBiP both bind chitin oligosaccharides with high affinity. LYM2 appearing in its own WITH/FROM reflects its own experimental grounding (PMID:22891159, PMID:22744984) and is expected, not circular. The node placement excludes LYM1/LYM3, which do not bind chitin. Supporting Evidence: PMID:22891159 Only one of three CEBiP homologs, AtCEBiP (LYM2), showed a high-affinity binding for chitin oligosaccharides similar to rice CEBiP. |
| GO:0008061 chitin binding | IDA PMID:22744984 LYK4, a lysin motif receptor-like kinase, is important for c... | ACCEPT | Summary: Wan et al. recovered CEBiP-like1 (= LYM2, At2g17120) from Arabidopsis extracts on chitin magnetic beads, eluted with chitooctaose, repeating Petutschnig et al. 2010. Reason: Chitin-bead affinity capture with specific oligomer elution supports chitin binding, and Shinya et al. 2012 independently showed high-affinity, specific binding of chitin oligosaccharides by LYM2 (PMID:22891159). Chitin binding is the core molecular activity of LYM2. 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:20610395 we identified the CEBiP homolog LYM2 as a potential chitin-binding protein in our affinity chromatography experiments PMID:22891159 AtCEBiP also represented the major chitin-binding protein in the Arabidopsis membrane. |
| GO:0009506 plasmodesma | HDA PMID:21533090 Arabidopsis plasmodesmal proteome. | ACCEPT | Summary: LYM2 was identified in the purified Arabidopsis plasmodesmal proteome. Reason: Confirmed by imaging: LYM2-mCitrine is enriched at plasmodesmata and chitin increases its plasmodesmal accumulation (PMID:23674687, PMID:32284410). The plasmodesmal plasma membrane is where LYM2 executes its known function. Supporting Evidence: PMID:21533090 the total number of proteins identified from these samples was 1341 PMID:23674687 LYM2 is one member of a three-member protein family and was identified in protein extracts from purified PD PMID:32284410 The mean PD index of Citrine-LYM2 was significantly higher following 30 min of chitin treatment than it was following 30 min of water treatment. |
| GO:0016020 membrane | TAS PMID:12068095 Prediction of glycosylphosphatidylinositol-anchored proteins... | KEEP AS NON CORE | Summary: Bioinformatic prediction of LYM2 as a GPI-anchored protein (membrane). Reason: Correct but uninformative; fully subsumed by the experimentally supported plasma membrane and plasmodesma annotations. Supporting Evidence: PMID:12068095 Glycosylphosphatidylinositol (GPI) anchoring of proteins provides a potential mechanism for targeting to the plant plasma membrane and cell wall. |
| GO:0016020 membrane | TAS PMID:12805588 Identification of glycosylphosphatidylinositol-anchored prot... | KEEP AS NON CORE | Summary: Membrane location from the proteomic identification of GPI-anchored proteins. Reason: Correct but uninformative; redundant with the IDA plasma membrane annotation from the same paper. Supporting Evidence: PMID:12805588 Triton X-114 phase partitioning and sensitivity to phosphatidylinositol-specific phospholipase C were used to prepare GAP-rich fractions from Arabidopsis callus cells. |
| GO:0071323 cellular response to chitin | IMP PMID:23674687 LYM2-dependent chitin perception limits molecular flux via p... | NEW | Summary: lym2 mutants fail to reduce plasmodesmal molecular flux in response to chitin (but respond normally to flg22), and fail to deposit plasmodesmal callose after chitin. Reason: LYM2 binds chitin and is the chitin-perceiving receptor component for the plasmodesmal branch of the chitin response, so it performs the ligand-recognition step rather than being a passive requirement. Comparator check: the other chitin-binding LysM receptors in Arabidopsis, LYK5 (IBA, IEP) and CERK1, carry chitin-response terms; the absence for LYM2 reflects the lack of any BP curation of Faulkner et al. 2013 and Cheval et al. 2020, not a convention. The term is chosen over defense-response terms because the evidence is a specific chitin-triggered cellular output. Supporting Evidence: PMID:23674687 For this response, lym2-1 mutants are insensitive to the presence of chitin, but not to the flagellin derivative flg22. PMID:23674687 Here we have identified LYM2 as a chitin PRR that mediates a decrease in molecular flux between cells in the presence of chitin. PMID:32284410 Our data have identified that while chitin is perceived and signals via a CERK1-dependent cascade in the PM, chitin signaling in the plasmodesmal PM occurs via a LYM2/LYK4/LYK5-dependent cascade to produce a specific, localized response. |
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Download this section (compressed HTML)Q: Should LYM2 be annotated to a defense response to fungus term? lym2 mutants are more susceptible to Botrytis cinerea and Alternaria brassicicola, but this is necessity evidence; is the plasmodesmal-closure mechanism sufficient to treat LYM2 as a participant in the defense response?
Q: Is LYM2 itself a pattern recognition receptor (GO:0038187) given that it binds chitin but has no intracellular domain and requires LYK4/LYK5 to signal, or should it be annotated only as a ligand-binding component of a receptor complex?
Q: Does LYM2 have any function in the non-plasmodesmal plasma membrane, given that it is the major chitin-binding protein of Arabidopsis membranes yet dispensable for CERK1-dependent responses?
Experiment: Measure affinity and stoichiometry of purified LYM2 ectodomain for (GlcNAc)n by ITC, and test LysM point mutants for loss of chitin binding and loss of complementation of chitin-induced plasmodesmal closure in lym2-1.
Hypothesis: LYM2 binds chitin oligomers through a CEBiP-like sandwich-type dimerization mode that promotes clustering in the plasmodesmal membrane.
Type: in vitro binding and structural analysis
Experiment: TurboID-LYM2 proximity labelling with and without chitin in leaf tissue, and genetic tests of identified callose synthases (CalS/GSL) for chitin-induced plasmodesmal callose deposition.
Hypothesis: Chitin-bound LYM2 recruits LYK4 and a defined set of signalling partners (CPKs, RBOHD, callose synthases) into a plasmodesmal signalling platform.
Type: proximity proteomics at plasmodesmata
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