LYK5 (At2g33580, O22808) curation notes

Sources

• Deep research: LYK5-deep-research-falcon.md (present).
• Cached papers: PMID:25340959 (Cao 2014, full text), PMID:22744984 (Wan 2012, partial full text: abstract plus discussion), PMID:34558681 (Giovannoni 2021, full text), PMID:28513921 (Erwig 2017, abstract only), PMID:28195333 (Liao 2017, abstract only), PMID:32595659 (Huang 2020, CPK5).

Key findings

• LYK5 is the primary high-affinity chitin receptor PMID:25340959.
• It forms a chitin-dependent complex with CERK1 PMID:25340959.
• It is redundant with LYK4 PMID:25340959.
• The kinase domain is a pseudokinase but is required for function PMID:25340959. The K395E variant still complements, while ΔKD fails and cannot co-IP with CERK1.
• Ligand-independent homodimer PMID:25340959.
• No basal bacterial phenotype PMID:25340959. Giovannoni 2021 says the opposite in passing, citing the same paper; we rely on the primary paper.
• Localization and trafficking PMID:28513921 After chitin, CERK1 phosphorylates LYK5, which is internalized.
• PUB13 controls basal LYK5 abundance PMID:28195333.
• CPK5/CPK6 phosphorylate LYK5 at S323 and S542 PMID:32595659.
• Weak interaction with LYK2 PMID:34558681.

Decisions

• protein binding (CERK1, LYK2): REMOVE as uninformative, consistent with the CERK1 review.
• extracellular region (ISM): REMOVE. This is a signal-peptide default; LYK5 is a type I plasma membrane protein.
• ATP binding (IEA): MARK_AS_OVER_ANNOTATED. Pseudokinase; the K395E variant rescues; ATP binding never tested.
• response to molecule of bacterial origin (IBA): MARK_AS_OVER_ANNOTATED, with a propagation_review.
• cellular response to oxygen-containing compound (ARBA): over-annotated ancestor of cellular response to chitin.
• NEW GO:0038187 pattern recognition receptor activity. Comparators carrying the term: RLP23, RLP42 (a non-catalytic ligand-binding PRR), SOBIR1.
• NEW GO:0032491 detection of molecule of fungal origin. Comparators carrying the term: CERK1 (IMP), RLP23, RLP30.
• Considered but not added: GO:0002752 (cell surface PRR signaling pathway). PAINT gives the IBA to CERK1 and LYK3 but not LYK5, so this looks like a deliberate node placement.
• No LYK5 node in gocams/index.tsv.

Project relevance (PLANT_FUNGAL_INTERACTIONS Q2, Q4)

• No leakage of effector or symbiont terms. The receptor-side annotations are chitin binding and chitin-response terms only.
• LYK5 has no symbiosis annotations, so no defense/symbiosis conflation arises (Arabidopsis is non-mycorrhizal).