Cf-4 (Hcr9-4D) is a cell-surface receptor-like protein (RLP) from the wild tomato Solanum habrochaites (Lycopersicon hirsutum), introgressed into cultivated tomato, that confers race-specific resistance to the leaf mould fungus Fulvia fulva (Cladosporium fulvum) strains secreting the effector AVR4. The 806-residue type I transmembrane glycoprotein has a signal peptide, N-terminal flanking domains, 25 extracellular leucine-rich repeats (LRRs), a single transmembrane segment and a short cytoplasmic tail with no kinase domain. It shares more than 91% identity with its paralogue Cf-9 (27 LRRs, recognises AVR9); recognition specificity maps to the N-terminal domains, the central LRRs (notably LRRs 11-12) and LRR copy number. Cf-4 resides in the plasma membrane with its ectodomain facing the apoplast, where the fungus grows. It forms a constitutive complex with the receptor-like kinase SOBIR1, which is needed for Cf-4 stability and signalling; AVR4 perception recruits the co-receptor BAK1/SERK3, triggers endocytosis of Cf-4 to late endosomes, and initiates reactive oxygen species production, MAP kinase activation and a hypersensitive cell-death response that restricts fungal growth. Direct binding of AVR4 by Cf-4 has not been demonstrated. Cf-4 lies in a cluster of five Hcr9 paralogues on chromosome 1; functional AVR4-recognising homologues occur throughout wild tomato species.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0002768 immune response-regulating cell surface receptor signaling pathway | EXP PMID:23716655 Receptor-like kinase SOBIR1/EVR interacts with receptor-like... | ACCEPT | Summary: Liebrand et al. showed that the RLK SOBIR1/EVR interacts with Cf-4 in planta, is required for Cf-4 stability, and is required for the Cf-4-mediated hypersensitive response and immunity [PMID:23716655]. Reason: Cf-4 is the cell-surface receptor that starts this pathway: it lacks a kinase domain and signals through a constitutive complex with SOBIR1, with the co-receptor BAK1/SERK3 recruited after AVR4 elicitation [PMID:26765243]. This is participation (receptor initiating the signal), not mere necessity, and is more mechanistic than defense response to fungus. A slightly more specific term (GO:0002429 immune response-activating cell surface receptor signaling pathway) would also fit, but the current term is correct and matches the paralogous CF-9 review. Supporting Evidence: PMID:23716655 Here we show that the tomato ortholog of the Arabidopsis thaliana RLK Suppressor Of BIR1-1/Evershed (SOBIR1/EVR) and its close homolog S. lycopersicum (Sl)SOBIR1-like interact in planta with both Cf-4 and Ve1 and are required for the Cf-4- and Ve1-mediated hypersensitive response and immunity. PMID:26765243 after elicitation with matching effector ligands Avr4 and Avr9, BRI1-ASSOCIATED KINASE 1/SOMATIC EMBRYOGENESIS RECEPTOR KINASE 3 (BAK1/SERK3) associates with Cf-4 and Cf-9. |
| GO:0005886 plasma membrane | IEA GO_REF:0000044 | ACCEPT | Summary: UniProt subcellular-location mapping (cell membrane; single-pass type I membrane protein). Reason: Correct and experimentally supported: live-cell imaging showed that Cf-4 interacts with SOBIR1 at the plasma membrane before AVR4-triggered recruitment to late endosomes [PMID:26765243]. Plasma-membrane location fits perception of the apoplastic AVR4 effector. Endosomes are a post-activation trafficking compartment, not the site of recognition. Supporting Evidence: PMID:26765243 Cf-4 interacts with SOBIR1 at the plasma membrane and is recruited to late endosomes upon Avr4 trigger, also depending on BAK1/SERK3. |
| GO:0038187 pattern recognition receptor activity | EXP PMID:23716655 Receptor-like kinase SOBIR1/EVR interacts with receptor-like... | MODIFY | Summary: Same paper as above: SOBIR1/EVR forms a complex with Cf-4 and is required for Cf-4-mediated immunity [PMID:23716655]. Reason: Cf-4 is an immune receptor, but GO:0038187 is defined as combining with a pathogen-associated molecular pattern, "a structure conserved among microbial species". AVR4 is a race-specific effector of F. fulva (strains evade Cf-4 by AVR4 mutation), not a broadly conserved PAMP, and direct Cf-4-AVR4 binding has not been shown. The paper itself demonstrates complex formation with SOBIR1 and requirement for signalling, not ligand binding. GO:0140376 innate immune receptor activity ("receiving a signal and transmitting it in a cell to initiate an innate immune response") describes the demonstrated activity without asserting PAMP binding; it is already annotated to Cf-4 by EXP and is the term used for the paralogue Cf-9. Proposed replacements: innate immune receptor activity Supporting Evidence: PMID:23716655 The RLPs Cf-4 and Ve1 of tomato (Solanum lycopersicum) mediate resistance to the fungal pathogens Cladosporium fulvum and Verticillium dahliae, respectively. file:SOLHA/Cf-4/Cf-4-deep-research-falcon.md the evidence examined here does not establish a purified-protein binding constant or a resolved direct Cf-4–Avr4 structure |
| GO:0050832 defense response to fungus | IEA GO_REF:0000117 | ACCEPT | Summary: ARBA machine-learning rule assigning defense response to fungus. Reason: Correct for Cf-4, which recognises AVR4 and initiates the defence response that restricts F. fulva; transgenic and chimera studies show Cf-4 sequences are required for AVR4-dependent HR and resistance to the fungus [PMID:11226184]. The receptor performs part of the process (perception and signal initiation), so this is participation. Consistent with the CF-9 review. Supporting Evidence: PMID:11226184 The tomato Cf-4 and Cf-9 genes confer resistance to infection by the biotrophic leaf mold pathogen Cladosporium. Their protein products induce a hypersensitive response (HR) upon recognition of the fungus-encoded Avr4 and Avr9 peptides. |
| GO:0140376 innate immune receptor activity | EXP PMID:15469522 Cladosporium fulvum circumvents the second functional resist... | ACCEPT | Summary: Westerink et al. isolated Avr4E, the ligand recognised by Hcr9-4E, a second functional Hcr9 at the Cf-4 locus; the abstract identifies Hcr9-4D as the functional Cf-4 gene matching Avr4 [PMID:15469522]. Reason: The cached abstract centres on Hcr9-4E/Avr4E rather than on Cf-4 (Hcr9-4D, this entry), and only the abstract is available, so what the curator (PHI-base) used from the full text (e.g. Cf-4/Avr4 controls in MM-Cf4 plants) cannot be checked. The function asserted is nonetheless clearly correct for Cf-4, which receives the AVR4 signal and initiates innate immunity [PMID:23716655, PMID:26765243], so the annotation is accepted, deferring to the curator. Whether this row was intended for the Hcr9-4E entry is raised as a suggested question. Supporting Evidence: PMID:15469522 While Hcr9-4D represents the functional Cf-4 resistance gene matching Avr4, Hcr9-4E confers resistance towards C. fulvum by mediating recognition of the novel avirulence determinant Avr4E. PMID:26765243 These observations indicate that RLP-mediated resistance and endocytosis require ligand-induced recruitment of BAK1/SERK3 |
| GO:0140376 innate immune receptor activity | EXP PMID:9437864 Characterization of the tomato Cf-4 gene for resistance to C... | ACCEPT | Summary: Cloning and characterisation of Cf-4, a membrane-anchored extracellular LRR glycoprotein whose N-terminal differences from Cf-9 delimit the region that determines recognitional specificity [PMID:9437864]. Reason: Core molecular function. Cf-4 receives the AVR4 signal at the cell surface and transmits it, via SOBIR1 and BAK1/SERK3, to initiate an innate immune response. GO:0140376 does not require direct ligand binding, which is appropriate since direct Cf-4-AVR4 binding is not established. Specificity determinants lie in Cf-4 itself (N-terminal domains and LRRs 11-12) [PMID:11226184]. Supporting Evidence: PMID:9437864 Amino acid differences distinguishing Cf-4 and Cf-9 are confined to their N termini, delimiting a region that determines the recognitional specificity of ligand binding. PMID:11226184 Additional sequences required for Cf-4 function are located in LRRs 11 and 12, a region that contains only eight of the 67 amino acids that distinguish it from Cf-9. |
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Download this section (compressed HTML)Q: Does Cf-4 bind AVR4 directly, or does it act with an additional AVR4-binding component? A specific binding MF would be warranted only if direct binding is shown.
Q: The PHI-base EXP row for innate immune receptor activity citing PMID:15469522 concerns a paper about Hcr9-4E/Avr4E. Was it intended for the Hcr9-4E (Cf-4E) UniProt entry rather than Cf-4 (Hcr9-4D, O50025)?
Q: GO:0038187 pattern recognition receptor activity is defined by PAMP binding; is there a GO convention for annotating cell-surface receptors of race-specific apoplastic effectors (such as Cf-4, Cf-9, Ve1), which currently fall between PRR and innate immune receptor terms?
Experiment: Test direct AVR4 binding by purified Cf-4 ectodomain (alone and with SOBIR1 and BAK1 ectodomains) using ITC or cross-linking with labelled AVR4, and solve a receptor-effector complex structure to define the recognition interface.
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