Cf-9 (Hcr9-9C) is a cell-surface receptor-like protein (RLP) of currant tomato that confers race-specific resistance to the leaf mould fungus Fulvia fulva (Cladosporium fulvum) strains carrying the avirulence gene Avr9. The 863-residue type I transmembrane glycoprotein has a signal peptide, an N-terminal cysteine-rich flanking domain, 27 extracellular leucine-rich repeats (LRRs), a single transmembrane segment and a short cytoplasmic tail with no kinase domain. It is heavily N-glycosylated and resides in the plasma membrane, with its ectodomain facing the apoplast where the fungus grows and secretes the AVR9 cystine-knot peptide. Recognition specificity for AVR9 maps to the central LRRs (10-18), and membrane-proximal cytosolic residues are needed for signalling. AVR9 perception triggers a hypersensitive response (localized cell death) and other defence outputs that restrict fungal growth. Lacking its own kinase, Cf-9 signals in a complex with receptor-like kinases: after AVR9 elicitation the co-receptor BAK1/SERK3 associates with Cf-9, as described for the paralogous Cf-4/SOBIR1 system. Whether Cf-9 binds AVR9 directly is unresolved, because a high-affinity AVR9 binding site is present on plasma membranes of tomato lines with or without Cf-9. Cf-9 lies in a cluster of five Hcr9 paralogues (Cf-9A to Cf-9E) at the short arm of chromosome 1; it arose by intragenic recombination, and a second natural AVR9-recognizing allele (9DC) occurs in wild populations.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0002238 response to molecule of fungal origin | IEP PMID:26768363 Transcriptional and posttranscriptional regulation of the to... | KEEP AS NON CORE | Summary: Based on Cf-9 transcript induction by the fungal elicitor AVR9 (10.8-54.7 fold in Cf-9/Avr9 seedlings) and its temperature sensitivity [PMID:26768363]. Reason: The IEP evidence (transcriptional induction of Cf-9 by AVR9) does support a change in state in response to a fungal molecule, and functionally Cf-9 is the receptor through which tomato responds to AVR9, so the term is not wrong. It is, however, a broad response term grounded on an expression readout rather than on what the protein does; the mechanistic role (perception of AVR9 and initiation of cell-surface immune receptor signalling) is captured in core_functions. Kept as non-core. Supporting Evidence: PMID:26768363 Expression of the Cf-9 gene was 10.8-54.7 folds higher in the Cf-9/Avr9 tomato lines than in the Cf-9 lines depending on the seedling age, indicating that the Cf-9 gene expression was strongly induced by Avr9. |
| GO:0005515 protein binding | IPI PMID:26315781 A mutational analysis of the cytosolic domain of the tomato ... | REMOVE | Summary: Yeast two-hybrid interaction between the Cf-9 cytosolic domain (domain G) and the tomato thioredoxin CITRX (Q9LKW0) [PMID:26315781]. Reason: Generic protein binding is uninformative and does not describe a Cf-9 molecular function. In addition, the biological relevance of this particular interaction is doubtful: the original paper proposing CITRX as a Cf-9 regulator (PMID:15131698) was retracted in 2019 because CITRX turned out to be chloroplast-localized, "rendering a role in Cf-9 signalling unlikely" [PMID:31310343]; UniProt now names Q9LKW0 "Thioredoxin-like protein CITRX, chloroplastic". The interaction itself was only shown in yeast. Removal does not assert that the yeast interaction is false; there is no evidence-backed specific MF to replace it with. Supporting Evidence: PMID:26315781 Interaction between CITRX and domain G of Cf-9 was confirmed by the growth of co-transformants carrying CITRX:AD and domain G:BD fusions in the absence of histidine PMID:31310343 it has become clear that the thioredoxin that interacts in yeast 2-hybrid with the Cf-9 C-terminus is in fact localized in the chloroplast, rendering a role in Cf-9 signalling unlikely |
| 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: functional c-myc-tagged Cf-9 was enriched in two-phase-partitioned plasma membrane fractions and detected on the protoplast surface by immunogold labelling [PMID:10758503], consistent with perception of the apoplastic AVR9 peptide. Supporting Evidence: PMID:10758503 Plasma membranes were isolated using two-phase partitioning, and c-myc : Cf-9 was enriched in these fractions, indicating that Cf-9 is a plasma membrane protein. |
| GO:0050832 defense response to fungus | IDA PMID:11517316 Intragenic recombination generated two distinct Cf genes tha... | ACCEPT | Summary: Survey of natural L. pimpinellifolium populations showing that AVR9 recognition (HR on AVR9 injection) is conferred by Cf-9 or the related allele 9DC, with agroinfiltration assays of Cf-9/9DC activity [PMID:11517316]. Reason: Cf-9 is the receptor that recognizes F. fulva AVR9 and initiates the defence response that restricts the fungus; the gene product does part of the work (perception and signal initiation), so this is participation, not mere necessity. The paper shows Cf-9 (and 9DC) presence correlates exactly with AVR9 responsiveness and that Cf-9 mediates AVR9-dependent HR in transient assays. Supporting Evidence: PMID:11517316 All AVR9-responsive plants contained either Cf-9 or 9DC, indicating that these are the only two genes that confer AVR9 recognition in the Lp population. PMID:11517316 Recognition by resistant plants results in the activation of multiple defense responses that limit further fungal growth. |
| GO:0050832 defense response to fungus | IDA PMID:7973631 Isolation of the tomato Cf-9 gene for resistance to Cladospo... | ACCEPT | Summary: Cloning of Cf-9 by transposon tagging; the gene confers resistance to C. fulvum races carrying Avr9 [PMID:7973631]. Reason: Foundational paper (abstract only in cache) establishing Cf-9 as the resistance gene against Avr9-carrying C. fulvum. Defence against the fungus is the core biological role of the receptor. Supporting Evidence: PMID:7973631 The tomato Cf-9 gene confers resistance to infection by races of the fungus Cladosporium fulvum that carry the avirulence gene Avr9. |
| GO:0050832 defense response to fungus | IDA PMID:9413991 Novel disease resistance specificities result from sequence ... | ACCEPT | Summary: Analysis of the Cf-4/9 locus, its tandem Hcr9 genes and the origin of new resistance specificities by sequence exchange [PMID:9413991]. Reason: Only the abstract is cached; it addresses Cf genes and Cf-9 homologues conferring C. fulvum resistance. UniProt cites this paper for Cf-9 function, and the function is clearly correct for Cf-9, so the curator's annotation is accepted. Supporting Evidence: PMID:9413991 Tomato Cf genes confer resistance to C. fulvum, reside in complex loci carrying multiple genes, and encode predicted membrane-bound proteins with extracytoplasmic leucine-rich repeats. |
| GO:0050832 defense response to fungus | IEA GO_REF:0000117 | ACCEPT | Summary: ARBA machine-learning rule assigning defense response to fungus. Reason: Consistent with the extensive experimental evidence that Cf-9 mediates resistance to F. fulva [PMID:7973631]. Redundant with the experimental rows but correct. Supporting Evidence: PMID:7973631 The tomato Cf-9 gene confers resistance to infection by races of the fungus Cladosporium fulvum that carry the avirulence gene Avr9. |
| GO:0050832 defense response to fungus | IMP PMID:15166169 Genetic variation at the tomato Cf-4/Cf-9 locus induced by E... | ACCEPT | Summary: EMS-induced cf-9 mutant alleles and recombinant haplotypes selected by loss of Avr9-dependent seedling death [PMID:15166169]. Reason: Loss-of-function cf-9 alleles abolish Avr9-dependent defence (seedling death), supporting the role of Cf-9 in the AVR9-triggered defence response. Abstract-only in cache; the annotation is consistent with the stated design. Supporting Evidence: PMID:15166169 This selection is based on the ability of Avr4 and Avr9 to induce Cf-4- or Cf-9-dependent seedling death. PMID:15166169 As part of a structure-function analysis of Cf-9 and Cf-4, nine EMS-induced mutant alleles have been characterized. |
| GO:0050832 defense response to fungus | IMP PMID:15722474 Structure-function analysis of cf-9, a receptor-like protein... | ACCEPT | Summary: Structure-function analysis of 66 site-directed Cf-9 mutants for Avr9 recognition (HR) and protein stability [PMID:15722474]. Reason: Mutations in the LRR domain, N-flanking cysteine pairs and glycosylation sites alter Avr9-triggered responses, directly linking Cf-9 ectodomain structure to initiation of the defence response. Supporting Evidence: PMID:15722474 A total of 66 site-directed mutants of Cf-9 were analyzed for activity in Avr9 recognition and for protein stability and the results interpreted with the help of a homology model of the Cf-9 structure. |
| GO:0050832 defense response to fungus | IMP PMID:26315781 A mutational analysis of the cytosolic domain of the tomato ... | ACCEPT | Summary: Mutational scan of the Cf-9 cytosolic domain showing membrane-proximal residues (T835, Q836, Y837, P838) are needed for Avr9-dependent necrosis [PMID:26315781]. Reason: Defines cytosolic residues required for Cf-9 to signal the AVR9-triggered hypersensitive cell death that underlies resistance; consistent with the core role of Cf-9 in defence against F. fulva. Supporting Evidence: PMID:26315781 Our results indicate that the membrane-proximal region of the cytosolic domain of Cf-9 plays an important role in Cf-9-mediated necrosis, and two amino acids within this region, a threonine (T835) and a proline (P838), are particularly important for Cf-9 function. |
| GO:0140376 innate immune receptor activity | IMP PMID:11226184 Domain swapping and gene shuffling identify sequences requir... | NEW | Summary: Proposed MF: Cf-9 receives the AVR9 signal at the cell surface and transmits it to initiate an innate immune response, with recognition specificity residing in its own LRR domain. Reason: The GOA set has no informative molecular function for Cf-9. GO:0140376 ("receiving a signal and transmitting it in a cell to initiate an innate immune response") does not require direct ligand binding, which is appropriate because direct Cf-9-AVR9 binding is unproven [PMID:12239406]. Gene-specific evidence: domain swaps map AVR9 specificity to Cf-9 LRRs 10-18 [PMID:11226184]; site-directed mutants in the ectodomain and cytosolic tail abolish AVR9 recognition/signalling [PMID:15722474, PMID:26315781]; and AVR9 promotes association of the co-receptor BAK1/SERK3 with Cf-9 [PMID:26765243]. Comparator check: the paralogous RLP Cf-4 (O50025), in the same role towards Avr4, already carries GO:0140376 (EXP) in GOA, so this is not a term GO reserves for other kinds of gene product. Supporting Evidence: PMID:11226184 Therefore, important sequence determinants of Cf-9 function are located in LRRs 10 to 18. 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. file:SOLPI/CF-9/CF-9-deep-research-falcon.md Direct physical Cf-9–Avr9 binding has not been demonstrated. |
| GO:0002768 immune response-regulating cell surface receptor signaling pathway | IMP PMID:26315781 A mutational analysis of the cytosolic domain of the tomato ... | NEW | Summary: Proposed BP: Cf-9 is the cell-surface receptor that initiates the AVR9-triggered signalling pathway leading to hypersensitive cell death and resistance. Reason: Participation test: Cf-9 is the receptor that starts this pathway, not a substrate or downstream output; its cytosolic membrane-proximal residues are required for signalling [PMID:26315781] and the ligand-dependent recruitment of BAK1/SERK3 to Cf-9 is the first step of the signalling complex [PMID:26765243]. Comparator check: Cf-4 (O50025) carries GO:0002768 (EXP, PMID:23716655) in GOA. This term is more mechanistic than defense response to fungus and is the process Cf-9 directly performs. Supporting Evidence: PMID:26315781 Although the N-terminal half of the extracellular leucine-rich repeat (eLRR) domain of the Cf-9 protein determines its specificity for Avr9, the C-terminal half, including its small cytosolic domain, is postulated to be involved in signalling. PMID:26765243 These observations indicate that RLP-mediated resistance and endocytosis require ligand-induced recruitment of BAK1/SERK3 |
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Download this section (compressed HTML)Q: Does Cf-9 bind AVR9 directly, or is AVR9 perceived by the Cf-9-independent high-affinity plasma-membrane binding site, with Cf-9 acting as a guard or co-receptor? This determines whether a binding MF (e.g. a pathogen effector binding term) is warranted.
Q: Given the 2019 retraction of the CITRX study, should GOA retain the IPI protein binding row between Cf-9 and the chloroplastic thioredoxin CITRX (Q9LKW0)?
Q: Does Cf-9, like Cf-4, constitutively associate with SOBIR1 and undergo ligand-induced endocytosis, or are these steps only inferred from Cf-4?
Experiment: Test direct AVR9 binding by purified Cf-9 ectodomain (with and without SOBIR1/BAK1 ectodomains) using ITC or photo-affinity cross-linking with labelled AVR9, and compare with Cf-0 membranes to identify the Cf-9-independent binding protein.
Experiment: Co-immunoprecipitation and live imaging of Cf-9-GFP with SOBIR1 in tomato and N. benthamiana, with and without AVR9, to establish whether the Cf-4 signalling and endocytosis model applies directly to Cf-9.
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