NFP (Nod Factor Perception) — Medicago truncatula — research notes

UniProt: Q0GXS4 (NFP_MEDTR). Gene: MTR_5g019040. 595 aa precursor.
Also called Nod-factor receptor 5 (NFR5 orthologue of Lotus japonicus).

Summary of gene function

NFP is a plasma-membrane LysM-domain receptor-like kinase (LysM-RLK) of the model
legume Medicago truncatula. It is the Nod factor receptor that perceives
rhizobial lipo-chitooligosaccharide (LCO) signals ("Nod factors") secreted by
Sinorhizobium meliloti, and triggers the earliest steps of the nitrogen-fixing
root nodule symbiosis. NFP is essential and non-redundant for Nod factor
perception: nfp mutants are completely Nod-negative.

Architecture: signal peptide (1-27), extracellular region (28-246) with three
LysM domains (LysM1 ~51-98, LysM2 ~113-160, plus a third predicted LysM), a single
transmembrane helix (247-267), and an intracellular protein-kinase-like domain
(284-573). The LysM ectodomain is heavily N-glycosylated (9 sites).

Nod factor perception by the LysM ectodomain

The extracellular LysM domains bind chitooligosaccharide / Nod factor ligands.
PMID:16723404 and PMID:16723404.

LysM domain residues are functionally required for Nod factor recognition:
the L154P substitution (in LysM2) impairs nodulation [PMID:22087221 / UniProt
SITE 154 "Required for nodulation"].

NFP is the most upstream component of the Nod factor signalling pathway. The
nfp mutant fails every assayed Nod-factor response PMID:12753588 and PMID:12753588.

NFP is a pseudokinase (catalytically dead intracellular domain)

The intracellular "kinase" domain of NFP is a pseudokinase — it lacks
catalytic activity. PMID:16844829 and
PMID:16844829.

NFP therefore depends on an active co-receptor kinase to transduce the signal.
The InterPro/PROSITE-derived "Tyr protein kinase family" classification (UniProt
SIMILARITY line, PROSITE PS00109 PROTEIN_KINASE_TYR) is a sequence-motif
artefact: NFP is annotated by UniProt itself as a serine/threonine RLK, and
plant RLKs are Ser/Thr kinases — there is no evidence for tyrosine kinase
activity. The web literature confirms NFP/NFR5 "has no detectable
autophosphorylation activity and is considered a pseudokinase" and that "the
inactive kinase domain of MtNFP can be weakly transphosphorylated by the active
kinase of MtLYK3."

Implication for GO: "protein tyrosine kinase activity" (GO:0004713) is doubly
wrong (pseudokinase + Ser/Thr family, not Tyr). "protein kinase activity"
(GO:0004672, current InterPro IEA) is also unsupported — the domain is
catalytically dead.

The NFP/LYK3 receptor complex

NFP and the active LysM-RLK LYK3 form heteromeric receptor complexes at the cell
periphery. PMID:25351493. NFP and LYK3
co-localize "in a narrow zone of about two cell layers at the nodule apex"
PMID:25351493. LYK3 (UniProt Q6UD73) is the active-kinase co-receptor; NFP
contributes ligand-binding/scaffolding but not phosphotransfer.

NFP also interacts with the small GTPase ROP10: PMID:25794934 and
PMID:25794934.
ROP10 (UniProt B2MVQ1) is a type II Rho-of-plants small GTPase.

Nodulation: organogenesis and infection

NFP acts in both the epidermis and the cortex during nodulation.
PMID:22874912. NFP is required throughout the
infection process: PMID:16844829. NFP is needed for intracellular infection / rhizobial
release: in nfp mutants "Infection threads enter the cells, but the release
of the bacteria is hampered" (UniProt DISRUPTION PHENOTYPE, ECO from
PMID:25351493).

Disruption phenotype: complete Nod- phenotype, no calcium flux/spiking, no early
nodulin expression, no root hair deformation/curling, no infection threads
[PMID:12753588; PMID:16844829].

NFP in pathogen resistance (defense)

Beyond symbiosis, NFP contributes to M. truncatula immunity against
filamentous pathogens. PMID:23432463 and PMID:23432463. This
supports specific curated terms — positive regulation of defense response to
oomycetes (GO:1902290) and regulation of defense response to fungus
(GO:1900150) — both IMP from PMID:23432463. A broad keyword-derived "defense
response" (GO:0006952) adds nothing beyond these.

Subcellular localization

Plasma membrane (cell periphery); also vacuolar lumen in cells where receptors
are being broken down. PMID:25351493 — NFP-GFP localizes at the cell
periphery, and "Vacuolar localization is observed in cells undergoing breakdown
of the receptors" (UniProt SUBCELLULAR LOCATION). Single-pass type I membrane
protein.

Glycosylation

NFP is highly N-glycosylated PMID:16723404. UniProt lists 9 N-glyc
sites. The IDA "glycoprotein biosynthetic process" (GO:0009101) GO annotation
captures NFP being a glycoprotein substrate — NFP is not an enzyme of the
glycosylation machinery, so this is a marginal/over-annotation as a process the
gene is "involved in."

Core function synthesis

  1. Molecular function: Nod factor (lipo-chitooligosaccharide) receptor —
    transmembrane signalling receptor whose LysM ectodomain binds the rhizobial
    LCO ligand. Carbohydrate (chitin-type/LCO) binding via LysM domains.
    NOT a catalytically active kinase (pseudokinase).
  2. Biological process: nodulation / root nodule symbiosis — perception of Nod
    factors and initiation of nodule organogenesis and rhizobial infection.
  3. Secondary process: contribution to immunity against oomycete/fungal
    pathogens.
  4. Cellular component: plasma membrane (forms heteromeric complex with LYK3).

GO term ID verification (OLS)