CTR1 is an Arabidopsis Raf-like protein serine/threonine kinase that acts as a central negative regulator of ethylene signaling. In the absence of ethylene, CTR1 is associated with the ER-localized ethylene receptor complex and phosphorylates EIN2, preventing downstream EIN2/EIN3 signaling. Ethylene perception relieves CTR1 inhibition, allowing EIN2 signaling to activate nuclear ethylene responses. Root, stem cell, floral transition, sugar, gibberellin, and hypoxia phenotypes are retained as downstream or cross-talk outputs, but the core function is ER-associated protein kinase control of the ethylene pathway.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0005789 endoplasmic reticulum membrane | IDA PMID:12821658 Localization of the Raf-like kinase CTR1 to the endoplasmic ... | ACCEPT | Summary: CTR1 localizes to the ER receptor signaling complex. Reason: ER membrane association is the correct cellular context for CTR1's role upstream of EIN2. |
| GO:0004674 protein serine/threonine kinase activity | IDA PMID:12535337 Biochemical and functional analysis of CTR1, a protein kinas... | ACCEPT | Summary: CTR1 is an active Raf-like protein serine/threonine kinase. Reason: Protein serine/threonine kinase activity is the core molecular function of CTR1. Supporting Evidence: file:ARATH/CTR1/CTR1-deep-research-falcon.md |
| GO:0004712 protein serine/threonine/tyrosine kinase activity | ISS PMID:16429265 Genome-wide analysis and experimentation of plant serine/ th... | MODIFY | Summary: The broader serine/threonine/tyrosine kinase annotation is less precise than the established Ser/Thr kinase activity. Reason: CTR1 is a Raf-like Ser/Thr kinase, and the direct experimental annotation should be preferred. Proposed replacements: protein serine/threonine kinase activity |
| GO:0009686 gibberellin biosynthetic process | IMP PMID:17389366 The plant stress hormone ethylene controls floral transition... | MARK AS OVER ANNOTATED | Summary: ctr1 alleles alter bioactive gibberellin levels through ethylene pathway cross-talk, but CTR1 is not a gibberellin biosynthetic enzyme. Reason: The paper supports CTR1/EIN3-dependent ethylene effects on GA-DELLA signaling, not a direct CTR1 role in gibberellin biosynthesis. |
| GO:0010105 negative regulation of ethylene-activated signaling pathway | TAS PMID:12535337 Biochemical and functional analysis of CTR1, a protein kinas... | ACCEPT | Summary: CTR1 negatively regulates ethylene signaling. Reason: This directly captures CTR1's central biological role upstream of EIN2. |
| GO:0010105 negative regulation of ethylene-activated signaling pathway | TAS PMID:12821658 Localization of the Raf-like kinase CTR1 to the endoplasmic ... | ACCEPT | Summary: CTR1 negatively regulates ethylene signaling from the ER receptor complex. Reason: This directly captures CTR1's central biological role upstream of EIN2. |
| GO:0010105 negative regulation of ethylene-activated signaling pathway | TAS PMID:8431946 CTR1, a negative regulator of the ethylene response pathway ... | ACCEPT | Summary: The original ctr1 genetic study established CTR1 as a negative regulator of ethylene responses. Reason: This directly captures CTR1's central biological role upstream of EIN2. |
| GO:0010105 negative regulation of ethylene-activated signaling pathway | TAS PMID:9560288 Association of the Arabidopsis CTR1 Raf-like kinase with the... | ACCEPT | Summary: CTR1 association with ethylene receptors supports its negative regulatory position in the pathway. Reason: This directly captures CTR1's central biological role upstream of EIN2. Supporting Evidence: PMID:9560288 The pathway also contains a negative regulator of ethylene responses, CTR1 |
| GO:2000069 regulation of post-embryonic root development | IMP PMID:17656722 Ethylene modulates stem cell division in the Arabidopsis tha... | UNDECIDED | Summary: Ethylene modulates post-embryonic root stem-cell behavior, but the cached abstract does not verify the CTR1-specific IMP annotation. Reason: The accessible PMID:17656722 abstract supports ethylene effects on root development but does not mention CTR1/ctr1 specifically. |
| GO:2000035 regulation of stem cell division | IMP PMID:17656722 Ethylene modulates stem cell division in the Arabidopsis tha... | UNDECIDED | Summary: Ethylene modulates root stem-cell division, but the cached abstract does not verify the CTR1-specific IMP annotation. Reason: The accessible PMID:17656722 abstract supports ethylene effects on quiescent-center division but does not mention CTR1/ctr1 specifically. |
| GO:0048510 regulation of timing of transition from vegetative to reproductive phase | IMP PMID:17389366 The plant stress hormone ethylene controls floral transition... | KEEP AS NON CORE | Summary: CTR1 affects floral transition timing through ethylene and DELLA-related pathway cross-talk. Reason: This is a pathway output rather than CTR1's direct kinase or signaling-regulator role. |
| GO:0009723 response to ethylene | IMP PMID:8431946 CTR1, a negative regulator of the ethylene response pathway ... | KEEP AS NON CORE | Summary: ctr1 mutants show constitutive ethylene-response phenotypes. Reason: The response phenotype is correct, but the more informative core term is negative regulation of ethylene signaling. |
| GO:0009750 response to fructose | IMP PMID:21253566 Signaling role of fructose mediated by FINS1/FBP in Arabidop... | KEEP AS NON CORE | Summary: CTR1/sis1 alleles affect fructose signaling through hormone cross-talk. Reason: Fructose response is a downstream/cross-talk phenotype, not the core molecular function. |
| GO:0001666 response to hypoxia | IMP PMID:25284079 Arabidopsis acyl-CoA-binding protein ACBP3 participates in p... | KEEP AS NON CORE | Summary: CTR1 participates in hypoxia-related ethylene signaling modulation. Reason: Hypoxia response is a context-specific output of ethylene pathway regulation. |
| GO:0009744 response to sucrose | IMP PMID:11162499 The sugar-insensitive1 (sis1) mutant of Arabidopsis is allel... | KEEP AS NON CORE | Summary: CTR1/sis1 alleles affect sucrose response through hormone signaling cross-talk. Reason: Sucrose response is a downstream phenotype rather than the core CTR1 kinase function. |
| GO:0010182 sugar mediated signaling pathway | TAS PMID:12663220 Sugar and hormone connections. | UNDECIDED | Summary: Sugar-hormone signaling reviews describe sugar/ethylene cross-talk, but the cached PMID:12663220 abstract does not verify a CTR1-specific pathway annotation. Reason: CTR1/sis1 sucrose-response evidence exists from PMID:11162499, but the cached PMID:12663220 entry is abstract-only and lacks accessible CTR1-specific support for this broader sugar-mediated signaling annotation. |
| GO:0007165 signal transduction | IBA GO_REF:0000033 | MODIFY | Summary: Generic signal transduction under-describes the CTR1-specific ethylene pathway role. Reason: The specific, supported process is negative regulation of ethylene-activated signaling. Propagation Review Root cause: TERM SCOPING PROBLEM Failure modes: GRANULARITY MISMATCH Sources checked: GO_REF:0000033 · PAINT IBA (no WITH/FROM recorded in GOA row) UNRESOLVED The GOA row carries no WITH/FROM, so the exact IBD node cannot be pinned; both GO:0007165 IBD nodes in the PTHR44329 slice (PTN001148170, PTN001908418) carry only this generic term, consistent with a granularity refinement rather than a propagation failure. Proposed replacements: negative regulation of ethylene-activated signaling pathway |
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Download this section (compressed HTML)Q: Should GOA add an explicit phosphorylation-of-EIN2 annotation using an extension to represent CTR1's direct substrate?
Q: Which sugar and hypoxia annotations should remain on CTR1 versus being represented only as ethylene pathway outputs?
Experiment: Quantitatively map CTR1-dependent EIN2 phosphorylation in ethylene receptor complex mutants and hypoxia/ceramide perturbations.
Experiment: Test whether sugar-response phenotypes in ctr1 alleles are fully EIN2/EIN3-dependent.
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