Plant chitin perception by LysM receptor complexes

Flowering plants detect chitin oligosaccharides released from fungal cell walls at the plasma membrane with lysin-motif (LysM) pattern recognition receptors. Perception needs two activities that different plant lineages divide differently between receptor proteins: high-affinity binding of long-chain chitin oligomers, and an active intracellular serine/threonine kinase. In rice, the kinase-less LysM receptor-like protein CEBiP is the chitin-binding subunit; two CEBiP ectodomains sandwich one chitin octamer, and ligand-induced association with the LysM receptor kinase OsCERK1 supplies the kinase, while OsCERK1 itself is not the chitin binder. In Arabidopsis, the LysM receptor kinase LYK5, whose intracellular domain is a catalytically inactive pseudokinase, is the high-affinity chitin binder, and it recruits CERK1, which both binds chitin with low affinity and is the active kinase. The LYK5 paralog LYK4, also a pseudokinase, binds chitin only weakly and acts as a LYK5-associated co-receptor or scaffold that enhances signalling; lyk4 lyk5 double mutants lose chitin responses. In both configurations the activated CERK1 kinase phosphorylates receptor-like cytoplasmic kinases (RLCKs) of the PBL27/OsRLCK185 type, which phosphorylate MAP kinase kinase kinases (MAPKKK5 in Arabidopsis; OsMAPKKKepsilon and OsMAPKKK18 in rice) that activate the MKK4/MKK5 to MPK3/MPK6 relay, driving defence gene expression and callose deposition. In Arabidopsis, RLCK VII-4 kinases such as PBL19 also phosphorylate MAPKKK5 and may carry most of this step, so the genetic weight of PBL27 is disputed. A parallel branch through BIK1 activates the plasma membrane NADPH oxidase RBOHD, which produces the apoplastic burst of reactive oxygen species. The two branches separate genetically: loss of MAPKKK5 or PBL27 does not reduce the ROS burst.

Boundary. The module covers chitin perception at the plasma membrane and its two immediate CERK1-dependent signalling branches, ending at activated MPK3/MPK6 and at RBOHD superoxide production. Transcriptional outputs (WRKY33 and other MPK3/MPK6 substrates), camalexin and callose synthesis, and receptor turnover (PUB13, CPK5 phosphorylation of LYK5, LYK5 endocytosis) are outside it. Peptidoglycan perception (CERK1 with LYM1/LYM3 or OsLYP4/OsLYP6) and the OsMYR1-OsCERK1 mycorrhizal receptor, which share CERK1, are separate modules; the OsCERK1 gene review records the mycorrhizal role as a separate core function. Receptor variant set. The two configurations are modelled as variants on the axis "which protein binds chitin". They are not exclusive across plants (Arabidopsis has a CEBiP homologue, LYM2, and rice has LYK-type proteins), so the selection is ONE_OR_MORE, but each variant names the configuration the gene reviews support as primary in its species. Consistent with the gene reviews, chitin binding is asserted on CEBiP, LYK5, LYK4 (weak) and Arabidopsis CERK1, and not on OsCERK1 (the OsCERK1 review removed it); CEBiP has no kinase domain; LYK5 and LYK4 are pseudokinases, so no kinase activity is asserted for them (the LYK5 review marks ATP binding as over-annotated). Pattern recognition receptor activity is asserted on LYK5 only; LYK4 carries coreceptor activity (GO:0015026), following the LYK4 review, which describes it as a LYK5-associated co-receptor or scaffold that binds chitin weakly and associates with CERK1 independently of chitin. MAPK relay. The MAPKKK5 -> MKK4/MKK5 -> MPK3/MPK6 steps are an inner bundle that conforms_to MODULE:mapk_relay, so the tier chemistry and phosphotransfer topology are taken from that motif rather than re-modelled; only the plant kinase families and representative members are added here. LYM2 is out of scope. LYM2 (O23006) binds chitin in the plasmodesmal plasma membrane and, with LYK4, LYK5, CPK6/CPK11 and RBOHD, closes plasmodesmata. CERK1 is not required for this response, and its relay (calcium-dependent kinases) and output (plasmodesmal callose and reduced cell-to-cell flux) differ from the CERK1-dependent pathway modelled here. It is not a variant, because a variant is an alternative way to do the same job, and the LYM2 pathway runs in the same cells alongside the CERK1 pathway with a different output. It is recorded as a knowledge gap and candidate separate module. Fungal LysM effectors are antagonists, not parts. Secreted LysM effectors of fungal pathogens, such as Slp1 of Magnaporthe oryzae (G4N906, gene review genes/PYRO7/slp1) and Ecp6 of Cladosporium fulvum (B3VBK9, gene review genes/FULFL/ECP6), bind chitin oligosaccharides in the apoplast and compete with the plant receptors for them. Slp1 competes with CEBiP for binding of chitin oligosaccharides (PMID:22267486) and Ecp6 sequesters chitin oligosaccharides released from the cell walls of invading hyphae (PMID:20724636), with a composite LysM1-LysM3 site of ultra-high affinity (PMID:23840930). They are proteins of another organism that remove the ligand, so they do no step of the signalling; their gene reviews annotate them to chitin binding (GO:0008061) and effector-mediated suppression of host pattern-triggered immunity signaling (GO:0140423). They are not modelled as parts or as a connection, because a module connection must join two elements of this document and the effector is not one; ligand sequestration upstream of the receptor is recorded here instead. Falcon deep research (modules/chitin_perception-deep-research-falcon.md) was used as retrieval support and agrees with this structure (ligand capture versus kinase transmission; separable MAPK and ROS branches; CERK1-independent plasmodesmal response). Points it raised that are not modelled: partial redundancy of MAPKKK3 with MAPKKK5 and feedback phosphorylation of MAPKKK5 by MPK6 (Bi et al. 2018; both now recorded in the MAPKKK5 gene review, but MAPKKK3 has no review and is not added as a member); a guard-cell output in which PBL27 phosphorylates the anion channel SLAH3 for chitin-induced stomatal closure (Liu et al. 2019), which is a third, cell-type-specific output outside this boundary; a functional LYK5-type receptor in grapevine (VvLYK5-1 with VvLYK1-1), consistent with the LYK5 variant extending beyond Arabidopsis. Rice downstream steps. The rice RLCK OsRLCK185 is grounded as a representative member of the PBL27-type step. Following the OsRLCK185 gene review, its MAP3K substrates are OsMAPKKKepsilon (OsMAPKKK24), whose C-terminal regulatory domain it phosphorylates (PMID:28111288), and OsMAPKKK18 (PMID:28371870), both upstream of OsMKK4 and OsMPK3/OsMPK6; OsRLCK185 does not act on Arabidopsis MAPKKK5. These rice MAP3Ks, OsMKK4 and OsMPK3/OsMPK6 are named in prose only, because they have no gene reviews and no UniProt accessions verified here, so the MAP3K, MAP2K and MAPK tiers are grounded only in Arabidopsis. The rice ROS route (OsRLCK176, OsRacGEF1-OsRac1, rice RBOH) is not grounded; see knowledge gaps. ROS-branch RLCK. BIK1 is the grounded RBOHD kinase. PBL1, its closest paralog, is not modelled as a member of the chitin ROS step: its gene review finds no evidence that PBL1 alone phosphorylates RBOHD (RBOHD phosphosite loss was measured only in bik1 pbl1 double mutants), pbl1 (cce5) mutants have a normal chitin-induced Ca2+ response (PMID:25522736), and its core functions are framed through LRR-type receptors (FLS2, EFR, PEPR1, MIK2). It may act redundantly with BIK1; see knowledge gaps. Gene reviews. Completed reviews ground CEBIP, CERK1 and RLCK185 (ORYSJ), and CERK1, LYK5, LYK4, PBL27, BIK1, MAPKKK5, MKK4, MKK5, MPK3, MPK6 and RBOHD (ARATH), plus PBL1, LYM2, slp1 and ECP6 cited in notes. The MKK4 review (MAP kinase kinase activity, redundant with MKK5) agrees with the MKK4/MKK5 annoton. None of representative accessions LYK4 (O64825), PBL27 (Q1PDV6), OsRLCK185 (Q6I5Q6), MAPKKK5 (Q9C5H5), MKK4 (O80397) and MKK5 (Q8RXG3) is in the local PANTHER member index, so no PANTHER family ids are asserted. No production GO-CAM in gocams/index.tsv contains these proteins. Curation follow-ups (not knowledge gaps). The rice MAP3K, MAP2K and MAPK tiers downstream of OsRLCK185 and the rice ROS route (OsRLCK176, OsRacGEF1-OsRac1 and the rice RBOH) are not yet grounded as members: review OsMAPKKKepsilon/OsMAPKKK24, OsMAPKKK18, OsMKK4, OsMPK3/OsMPK6, OsRLCK176 and OsRacGEF1/OsRac1, verify their UniProt accessions and add them as rice representative members. The CERK1-independent plasmodesmal chitin pathway (LYM2 with LYK4/LYK5, CPK6/CPK11 and RBOHD; PMID:23674687, PMID:32284410) is outside this module and is a candidate for its own module once CPK6 and CPK11 are reviewed; the LYM2 review proposes a GO term for negative regulation of plasmodesmata-mediated intercellular transport.