FRK1 (FLG22-INDUCED RECEPTOR-LIKE KINASE 1; also SIRK, SENESCENCE-INDUCED RECEPTOR-LIKE KINASE; At2g19190) is a single-pass type I transmembrane receptor-like kinase of Arabidopsis thaliana belonging to the malectin-like/LRR receptor-like kinase group (LRR-RLK subfamily I, IOS1-like). It has an N-terminal signal peptide, an extracellular ectodomain composed of a malectin-like domain followed by three leucine-rich repeats, a transmembrane helix, and a cytoplasmic Ser/Thr protein kinase domain that retains the canonical ATP-binding and catalytic residues. FRK1 is best known as a transcriptional marker: its expression is rapidly induced by the bacterial MAMP flg22 downstream of the FLS2 receptor, the MEKK1-MKK4/5-MPK3/6 MAP kinase cascade and WRKY22/WRKY29, and it is induced by bacteria, leaf-microbiota colonization and fungal infection (strongest in cells in direct contact with Colletotrichum hyphae). It is also strongly induced during leaf senescence as a direct target of WRKY6. Its own biochemical activity, ligand, substrates and physiological role remain essentially uncharacterized; no loss-of-function phenotype in immunity or senescence has been reported.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0004672 protein kinase activity | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro-based protein kinase activity; FRK1 has a complete cytoplasmic protein kinase domain with conserved ATP-binding and catalytic residues. Reason: Correct but general; the more specific Ser/Thr kinase activity is supplied by the IBA. Catalytic activity of FRK1 has not been demonstrated biochemically, but the kinase domain retains the catalytic Asp (proton acceptor) and ATP-binding Lys, so the domain-based inference is sound. Supporting Evidence: file:ARATH/FRK1/FRK1-bioinformatics/RESULTS.md all canonical catalytic motifs of a eukaryotic protein kinase are intact |
| GO:0004674 protein serine/threonine kinase activity | IBA GO_REF:0000033 | ACCEPT | Summary: Phylogenetically inferred Ser/Thr protein kinase activity for this LRR receptor-like kinase. Reason: FRK1 sits within the PANTHER PTHR45631 malectin-like/LRR-RLK family and retains a canonical Ser/Thr kinase domain (STKc_IRAK-like) with all catalytic motifs intact (GKGGFG loop, VAVK Lys601, alphaC Glu617, HRD catalytic loop with Asp697, DFG), i.e. an RD-type kinase predicted to be catalytically competent rather than a pseudokinase. There is no evidence of loss of catalytic residues that would argue against the PAINT node placement. This is the best-supported molecular function for FRK1, although no in vitro kinase assay or substrate has been published. Supporting Evidence: file:ARATH/FRK1/FRK1-bioinformatics/RESULTS.md all canonical catalytic motifs of a eukaryotic protein kinase are intact file:ARATH/FRK1/FRK1-notes.md MF: protein Ser/Thr kinase activity (IBA + domain/catalytic residues) is the only defensible activity file:ARATH/FRK1/FRK1-deep-research-falcon.md It would therefore be unjustified to assign cellotriose, flg22, or IDA as its substrate or ligand. |
| GO:0005515 protein binding | IPI PMID:29320478 An extracellular network of Arabidopsis leucine-rich repeat ... | REMOVE | Summary: High-throughput in vitro ectodomain-ectodomain binding from the CSILRR LRR-RK extracellular interaction screen. Reason: Generic protein binding is uninformative. The interaction was detected between recombinant ectodomains expressed in insect S2 cells in a large-scale screen, with no functional follow-up for FRK1; it does not support a more specific molecular function (e.g. coreceptor or ligand binding). Removal does not imply the interaction is false. Supporting Evidence: PMID:29320478 The ECDs cloned into the pECIA2 (for expression as bait) and pECIA14 (for expression as a prey) vectors were expressed using transient transfection of Drosophila Schneider 2 (S2) cells cultured at 27°C. |
| GO:0005515 protein binding | IPI PMID:29320478 An extracellular network of Arabidopsis leucine-rich repeat ... | REMOVE | Summary: High-throughput in vitro ectodomain-ectodomain binding from the CSILRR LRR-RK extracellular interaction screen. Reason: Generic protein binding is uninformative. The interaction was detected between recombinant ectodomains expressed in insect S2 cells in a large-scale screen, with no functional follow-up for FRK1; it does not support a more specific molecular function (e.g. coreceptor or ligand binding). Removal does not imply the interaction is false. Supporting Evidence: PMID:29320478 The ECDs cloned into the pECIA2 (for expression as bait) and pECIA14 (for expression as a prey) vectors were expressed using transient transfection of Drosophila Schneider 2 (S2) cells cultured at 27°C. |
| GO:0005515 protein binding | IPI PMID:29320478 An extracellular network of Arabidopsis leucine-rich repeat ... | REMOVE | Summary: High-throughput in vitro ectodomain-ectodomain binding from the CSILRR LRR-RK extracellular interaction screen. Reason: Generic protein binding is uninformative. The interaction was detected between recombinant ectodomains expressed in insect S2 cells in a large-scale screen, with no functional follow-up for FRK1; it does not support a more specific molecular function (e.g. coreceptor or ligand binding). Removal does not imply the interaction is false. Supporting Evidence: PMID:29320478 The ECDs cloned into the pECIA2 (for expression as bait) and pECIA14 (for expression as a prey) vectors were expressed using transient transfection of Drosophila Schneider 2 (S2) cells cultured at 27°C. |
| GO:0005515 protein binding | IPI PMID:29320478 An extracellular network of Arabidopsis leucine-rich repeat ... | REMOVE | Summary: High-throughput in vitro ectodomain-ectodomain binding from the CSILRR LRR-RK extracellular interaction screen. Reason: Generic protein binding is uninformative. The interaction was detected between recombinant ectodomains expressed in insect S2 cells in a large-scale screen, with no functional follow-up for FRK1; it does not support a more specific molecular function (e.g. coreceptor or ligand binding). Removal does not imply the interaction is false. Supporting Evidence: PMID:29320478 The ECDs cloned into the pECIA2 (for expression as bait) and pECIA14 (for expression as a prey) vectors were expressed using transient transfection of Drosophila Schneider 2 (S2) cells cultured at 27°C. |
| GO:0005524 ATP binding | IEA GO_REF:0000002 | ACCEPT | Summary: ATP binding inferred from the protein kinase ATP-binding signature. Reason: The kinase domain contains the canonical glycine-rich ATP-binding loop and Lys601; ATP binding is a standard supporting molecular function of a predicted active kinase. Supporting Evidence: file:ARATH/FRK1/FRK1-bioinformatics/RESULTS.md all canonical catalytic motifs of a eukaryotic protein kinase are intact |
| GO:0005576 extracellular region | ISM GO_REF:0000122 | REMOVE | Summary: AtSubP prediction of extracellular localization, presumably driven by the N-terminal signal peptide. Reason: FRK1 is a single-pass type I transmembrane receptor-like kinase: the signal peptide targets it to the secretory pathway, but a transmembrane helix (518-538) anchors it in the membrane with the ectodomain facing the apoplast and the kinase domain in the cytoplasm. The protein is not released to the extracellular region; plasma membrane (IBA) is the appropriate location. Supporting Evidence: file:ARATH/FRK1/FRK1-notes.md signal peptide 1-24; extracellular domain 25-517; TM helix 518-538; cytoplasmic 539-876 |
| GO:0005886 plasma membrane | IBA GO_REF:0000033 | ACCEPT | Summary: Plasma membrane localization inferred phylogenetically for malectin-like/LRR receptor-like kinases. Reason: Consistent with the type I single-pass topology (signal peptide, ectodomain, TM, cytoplasmic kinase) typical of plasma-membrane receptor kinases. No direct imaging of FRK1 protein is published, but the IBA is well grounded. Supporting Evidence: file:ARATH/FRK1/FRK1-notes.md single-pass type I membrane protein file:ARATH/FRK1/FRK1-deep-research-falcon.md Plasma-membrane residence is a strong topology-based inference, but the examined literature did not directly localize FRK1 using a fluorescent fusion, fractionation or immunolocalization. |
| GO:0009617 response to bacterium | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: Phylogenetically propagated response to bacterium; FRK1 itself is among the experimental sources (its TAIR IEP annotation). Reason: FRK1 transcription is strongly induced by bacteria and bacterial MAMPs, so a 'response to' annotation is appropriate under GO conventions for expression evidence. It describes regulation of FRK1, not an activity FRK1 performs, so it is kept as non-core. FRK1 appearing in its own WITH/FROM reflects experimental grounding on the target and is not circular; another donor, the paralog IOS1 (At1g51800), has genuine loss-of-function evidence in antibacterial PTI, but that participation should not be transferred to FRK1, for which no such evidence exists. Supporting Evidence: PMID:16678099 nonhost/nonpathogenic Pseudomonas syringae sustains but pathogenic P. syringae suppresses early MAMP (microbe-associated molecular pattern) marker-gene activation PMID:27317676 ios1 mutants showed defective PTI responses, notably delayed upregulation of the PTI marker gene FLG22-INDUCED RECEPTOR-LIKE KINASE1 |
| GO:0009617 response to bacterium | IEP PMID:38895612 Chloride salt enhances plant resistance to biotic stresses. | MODIFY | Summary: Expression-based annotation from a study in which FRK1 transcript was measured after flg22 infiltration of chloride-salt-treated plants. Reason: In this paper FRK1 expression was measured only in response to the flagellin peptide flg22, a bacterial MAMP, not to bacterial infection; the more accurate expression-based term is response to molecule of bacterial origin. (Response to bacterium remains supported independently by the IBA and other literature.) Proposed replacements: response to molecule of bacterial origin Supporting Evidence: PMID:38895612 Relative transcript level of FRK1 (At2g19190) upon Flg22 induction. RNA samples were collected 3 h post infiltration with 100 nM Flg22. |
| GO:0016020 membrane | IEA GO_REF:0000044 | ACCEPT | Summary: Membrane location from UniProt subcellular location (single-pass type I membrane protein). Reason: Correct; less specific than plasma membrane (IBA) but not wrong. Supporting Evidence: file:ARATH/FRK1/FRK1-notes.md single-pass type I membrane protein |
| GO:0042742 defense response to bacterium | IDA PMID:16678099 Specific bacterial suppressors of MAMP signaling upstream of... | UNDECIDED | Summary: TAIR annotation from He et al. 2006, a study that used early MAMP marker genes (FRK1 among them) as transcriptional readouts to identify bacterial effectors suppressing MAMP signalling. Reason: The abstract describes FRK1-type genes as MAMP marker genes whose activation is sustained by nonpathogenic and suppressed by pathogenic P. syringae, which suggests the observation is induction of FRK1 expression by bacteria. No evidence found elsewhere shows that FRK1 itself executes a step of the defence response, and no frk1 loss-of-function immunity phenotype has been reported, so the likely correct term is response to bacterium (GO:0009617). However, this is an experimental (IDA) TAIR annotation with the weak acts_upstream_of_or_within qualifier, and the full text of He et al. 2006 is not available; the curator may have relied on an FRK1-specific experiment not described in the abstract. Per project guidance the annotation is left UNDECIDED rather than modified until the full text can be checked. Access was attempted again for the 2026 ARATH follow-up curation; the paper is not in PMC, Europe PMC lists the full text as subscription-only, the Cell Press page returned HTTP 403, and the BGPT full-text evidence service was over quota, so the evidence remains inaccessible. Supporting Evidence: PMID:16678099 nonhost/nonpathogenic Pseudomonas syringae sustains but pathogenic P. syringae suppresses early MAMP (microbe-associated molecular pattern) marker-gene activation file:ARATH/FRK1/FRK1-notes.md FRK1 appears in the literature almost exclusively as a transcriptional marker file:ARATH/FRK1/FRK1-deep-research-falcon.md No cognate extracellular ligand has been established for FRK1. |
| GO:0042742 defense response to bacterium | IEP PMID:39627368 Plant microbiota feedbacks through dose-responsive expressio... | MODIFY | Summary: Expression-based (IEP) annotation of defense response to bacterium from a leaf-microbiota study of general non-self response gene expression. Reason: IEP evidence (transcript induction) can support only a 'response to' term; 'defense response to bacterium' asserts that the gene product participates in defence, which requires functional evidence that does not exist for FRK1. The study measured transcriptional responses to colonization by commensal leaf bacteria and their MAMPs; FRK1 is not named in the main text and its mutant was not among those tested for microbiota phenotypes. The supportable claim is response to bacterium. Proposed replacements: response to bacterium Supporting Evidence: PMID:39627368 We link the GNSR to pattern-triggered immunity, as diverse microbe- or danger-associated molecular patterns cause dynamic GNSR gene expression. PMID:39627368 The tested GNSR mutants harboured deficiencies in genes affecting the synthesis of secondary metabolites (IGMT3, CYP71A12, CYP71A13 and GSTF6) |
| GO:0009620 response to fungus | IEP PMID:37741284 Cell-type-specific responses to fungal infection in plants r... | NEW | Summary: FRK1 expression is induced in Arabidopsis leaf cells during Colletotrichum higginsianum infection, most strongly in cells directly contacting fungal hyphae (single-cell transcriptomics and pFRK1::3xVenus-NLS reporter imaging). Reason: Expression-based 'response to' annotation, acceptable under GO conventions for IEP. The FRK1-specific data (pseudotime-associated induction, Figure 4B; reporter fluorescence strongest in colonized cells and decreasing in neighbours, Figure 4C) are in the full text, which is not in the publication cache (abstract only); FRK1 is used there purely as a marker of early immune activation, so no participation term (e.g. defense response to fungus) is proposed. Supporting Evidence: file:ARATH/FRK1/FRK1-notes.md pFRK1::3xVenus-NLS reporter showed "The strongest yellow fluorescence signals were observed in cells directly colonized by the fungus PMID:37741284 Trajectory inference identifies cells that had different interactions with the invading fungus. |
Loading supporting content…
Download this section (compressed HTML)Q: Is FRK1 a catalytically active kinase, and if so what are its substrates and does its activity change after flg22 perception?
Suggested experts: Plant receptor kinase biochemists
Q: Does FRK1 contribute functionally to pattern-triggered immunity or senescence, or is it solely a transcriptional output? Are single frk1 mutants phenotypically silent because of redundancy with paralogous malectin-like LRR-RLKs (e.g. At1g51800, At1g51850, At1g51890 in the same PANTHER clade)?
Suggested experts: Plant immunity geneticists
Q: Does the FRK1 malectin-like/LRR ectodomain bind a ligand (e.g. a cell-wall-derived or microbial glycan) and are the CSILRR ectodomain interactions (At1g12460, At3g28040, PXC2) relevant in planta?
Suggested experts: Structural biologists, Plant cell-surface receptor researchers
Experiment: Generate CRISPR higher-order mutants of FRK1 and its closest malectin-like LRR-RLK paralogues; assay flg22-induced ROS, MAPK activation, callose deposition, and growth of Pseudomonas syringae and Colletotrichum higginsianum.
Hypothesis: FRK1 contributes to PTI redundantly with its closest paralogues.
Experiment: Express the cytoplasmic domain (WT and D697N/K601E mutants) and test autophosphorylation and transphosphorylation of generic and candidate substrates in vitro; map in vivo phosphosites after flg22 treatment.
Hypothesis: FRK1 is an active Ser/Thr kinase.
Loading supporting content…
Download this section (compressed HTML)Loading supporting content…
Download this section (compressed HTML)Loading supporting content…
Download this section (compressed HTML)Loading supporting content…
Download this section (compressed HTML)Loading supporting content…
Download this section (compressed HTML)