COI1 is the F-box/LRR substrate-recognition subunit of the Arabidopsis SCF(COI1) ubiquitin ligase and a hormone-binding component of the COI1-JAZ jasmonate co-receptor. Bioactive jasmonate conjugates such as JA-Ile, and the bacterial mimic coronatine, promote association with JAZ repressors. COI1 recruits these repressors for SCF-dependent ubiquitylation and proteasomal degradation, releasing transcription factors to activate jasmonate responses. Inositol phosphate supports high-affinity co-receptor assembly. This mechanism controls defense, wound responses, root growth and reproductive development and integrates jasmonate signaling with light responses. In roots, COI1 also represses immunity-related gene expression independently of JA-Ile and promotes susceptibility to Verticillium longisporum. Complementation with a COI1 variant impaired in JAZ interaction supports separation of this repression from canonical JAZ perception. The molecular partners and requirement for SCF assembly in this root function remain unresolved.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0019005 SCF ubiquitin ligase complex | IDA PMID:12172031 The SCF(COI1) ubiquitin-ligase complexes are required for ja... | ACCEPT | Summary: COI1 is a component of SCF(COI1) E3 ubiquitin ligase complexes. Reason: The SCF complex context is central to COI1 function as an F-box substrate receptor. Supporting Evidence: PMID:12172031 In this study, we demonstrate that COI1 associates physically with AtCUL1, AtRbx1, and either of the Arabidopsis Skp1-like proteins ASK1 or ASK2 to assemble ubiquitin-ligase complexes, which we have designated SCF(COI1). |
| GO:1990756 ubiquitin-like ligase-substrate adaptor activity | IDA PMID:20927106 Jasmonate perception by inositol-phosphate-potentiated COI1-... | NEW | Summary: COI1 is the F-box substrate-recognition/adaptor subunit of SCF(COI1), recruiting JAZ repressors in the jasmonate co-receptor complex. Reason: The seeded GO annotations capture SCF complex membership and degradation, but not the specific substrate-adaptor molecular function of COI1. Supporting Evidence: PMID:20927106 The F-box protein CORONATINE INSENSITIVE 1 (COI1) mediates jasmonate signalling by promoting hormone-dependent ubiquitylation and degradation of transcriptional repressor JAZ proteins. PMID:12172031 In this study, we demonstrate that COI1 associates physically with AtCUL1, AtRbx1, and either of the Arabidopsis Skp1-like proteins ASK1 or ASK2 to assemble ubiquitin-ligase complexes, which we have designated SCF(COI1). PMID:20927106 High-affinity hormone binding requires a bipartite JAZ degron sequence consisting of a conserved Ξ±-helix for COI1 docking and a loop region to trap the hormone in its binding pocket. |
| GO:0009901 anther dehiscence | IMP PMID:23573263 New clothes for the jasmonic acid receptor COI1: delayed abs... | KEEP AS NON CORE | Summary: COI1 affects anther dehiscence through jasmonate-dependent reproductive development. Reason: This is a downstream reproductive output of COI1 jasmonate signaling. Supporting Evidence: PMID:23573263 plants were functionally male sterile due to a lack of dehiscence |
| GO:0006952 defense response | TAS PMID:9582125 COI1: an Arabidopsis gene required for jasmonate-regulated d... | KEEP AS NON CORE | Summary: COI1 is required for jasmonate-regulated defense responses. Reason: Defense response is a major output, but the core role is SCF(COI1)-JAZ regulation of JA signaling. Supporting Evidence: PMID:9582125 The coi1 mutation defines an Arabidopsis gene required for response to jasmonates, which regulate defense against insects and pathogens, wound healing, and pollen fertility. |
| GO:0042742 defense response to bacterium | IMP PMID:16959575 Plant stomata function in innate immunity against bacterial ... | UNDECIDED | Summary: The accessible abstract establishes pathogen-triggered stomatal closure and virulence-factor-induced reopening, but does not identify the COI1-specific assay. Reason: PMID:16959575 is abstract-only in the cache, and the original COI1 experiment could not be retrieved. COI1-mediated coronatine perception is established by PMID:20927106, but receptor binding alone does not independently verify this source-specific stomatal or bacterial-defense phenotype. Do not infer a direct defensive direction from pathogen exploitation of the jasmonate pathway. |
| GO:0050832 defense response to fungus | IMP PMID:17513501 ABA is an essential signal for plant resistance to pathogens... | MODIFY | Summary: The cited paper concerns the oomycete Pythium irregulare, not a fungus. Reason: The supported pathogen class is oomycete; the fungus term is taxonomically wrong for PMID:17513501. Proposed replacements: defense response to oomycetes Supporting Evidence: PMID:17513501 Analyses of Arabidopsis thaliana defense response to the damping-off oomycete pathogen Pythium irregulare show that resistance to P. irregulare requires a multicomponent defense strategy. |
| GO:0106167 extracellular ATP signaling | IMP PMID:30630869 Extracellular ATP Shapes a Defense-Related Transcriptome Bot... | KEEP AS NON CORE | Summary: COI1 is implicated in extracellular ATP-associated defense transcriptome responses. Reason: This is a pathway interaction/output, not the core COI1 molecular role. Supporting Evidence: PMID:30630869 In conclusion, we present a model ( Fig. 10 ) in which ATP binding to P2K1 results in defense gene activation, where more than half of ATP-responsive genes required signaling by one or more of the pathways through EIN2, NPR1, and COI1, but with a more substantial reliance on COI1. |
| GO:0009861 jasmonic acid and ethylene-dependent systemic resistance | TAS PMID:11418339 Genes controlling expression of defense responses in Arabido... | UNDECIDED | Summary: The accessible source supports jasmonate/defense signaling but does not resolve the particular systemic-resistance assay supporting COI1. Reason: The cached abstract does not establish the distal, induced-resistance phenotype required by this specific JA/ethylene-dependent systemic-resistance annotation. The source-specific TAS evidence remains unresolved; a general role in jasmonate defense is not sufficient to independently verify systemic resistance. |
| GO:0009861 jasmonic acid and ethylene-dependent systemic resistance | TAS PMID:9582125 COI1: an Arabidopsis gene required for jasmonate-regulated d... | UNDECIDED | Summary: The accessible source supports jasmonate/defense signaling but does not resolve the particular systemic-resistance assay supporting COI1. Reason: The cached abstract does not establish the distal, induced-resistance phenotype required by this specific JA/ethylene-dependent systemic-resistance annotation. The source-specific TAS evidence remains unresolved; a general role in jasmonate defense is not sufficient to independently verify systemic resistance. |
| GO:0009867 jasmonic acid mediated signaling pathway | IMP PMID:17637677 JAZ repressor proteins are targets of the SCF(COI1) complex ... | ACCEPT | Summary: JA-Ile promotes COI1-JAZ1 interaction and SCF(COI1)-dependent JAZ1 degradation, initiating jasmonate signaling. Reason: This captures the central biological process controlled by COI1. Supporting Evidence: PMID:17637677 Jasmonate treatment causes JAZ1 degradation and this degradation is dependent on activities of the SCF(COI1) ubiquitin ligase and the 26S proteasome. |
| GO:0031348 negative regulation of defense response | IMP PMID:16732289 Conserved requirement for a plant host cell protein in powde... | KEEP AS NON CORE | Summary: Independent root experiments support COI1-mediated negative regulation of defense; the original mlo-paper experiment remains unverified. Reason: Retain the biological assertion using independent primary evidence from PMID:39945499 and PMID:34145662: coi1 roots derepress immunity-related genes, and interfering with that expression partially suppresses coi1-mediated Verticillium tolerance. This supports negative regulation of defense response in a root/pathogen context. It does not verify the different mlo experiment in the unchanged original_reference_id PMID:16732289, whose full text remains unavailable. The latter citation limitation is recorded separately in its reference review. The newer evidence supports the more informative defense-regulatory term already present here; a separate NEW assertion for the same term is not novel under the repository GOA validation model, and a generic parent is unnecessary. JA-Ile independence and JAZ-interaction-impaired complementation do not establish SCF independence or direct transcriptional repression. Supporting Evidence: PMID:39945499 The biggest difference between the transcriptomes was due to 316 immunity-related genes that were constitutively higher expressed in coi1 as compared to the susceptible genotypes. PMID:39945499 Interfering with the expression of a sub-group of these genes partially suppressed the coi1-mediated tolerance phenotype. PMID:34145662 On the other hand, genes affected by COI1 but not by JA-Ile were still strongly repressed by COI1AA . |
| GO:0009909 regulation of flower development | IMP PMID:20435902 Jasmonate and phytochrome A signaling in Arabidopsis wound a... | KEEP AS NON CORE | Summary: COI1 affects flower development through jasmonate signaling. Reason: Flower development is a downstream developmental output. Supporting Evidence: PMID:20435902 We previously noticed that coi1- 16 mutants flower early, and in some growth conditions display elongated, hyponastic petioles, and elongated hypocotyls, phenotypes that are classic indicators of deficient responses to light quality |
| GO:0010218 response to far red light | IMP PMID:20435902 Jasmonate and phytochrome A signaling in Arabidopsis wound a... | KEEP AS NON CORE | Summary: COI1/JAZ stability connects jasmonate signaling with far-red/shade responses. Reason: This is signaling cross-talk downstream of the core COI1-JAZ module. Supporting Evidence: PMID:20435902 Additionally, we demonstrate that the FR light-induced expression of transcription factor genes is dependent on CORONATINE INSENSITIVE1 (COI1), a central component of JA signaling, and is suppressed by JA. |
| GO:0009625 response to insect | IMP PMID:15923339 Major signaling pathways modulate Arabidopsis glucosinolate ... | KEEP AS NON CORE | Summary: COI1 affects constitutive glucosinolate levels and insect performance, although insect-induced glucosinolate accumulation in this study does not require COI1. Reason: Read the original full PMC1150428 article through the NCBI report endpoint: its Results report the best insect growth on coi1 and distinguish consumption from growth. The negative result for one induced-metabolite endpoint does not negate the broader response-to-insect annotation. The prior REMOVE conflated these endpoints. Retain insect interaction as a non-core physiological output. Supporting Evidence: PMID:15923339 Blocked JA signaling in coronatine-insensitive (coi1) and enhanced expression of SA-signaled disease resistance in hypersensitive response-like (hrl1) mutants reduced constitutive GS concentrations, |
| GO:0009753 response to jasmonic acid | IMP PMID:16021335 Expression profiling reveals COI1 to be a key regulator of g... | ACCEPT | Summary: COI1 is required for jasmonate-responsive gene expression. Reason: Jasmonate responsiveness is central to COI1 hormone perception and signaling. A broad response term still represents core biology; its breadth does not make the role peripheral. The cited primary study directly establishes COI1-dependent jasmonate responses. Supporting Evidence: PMID:16021335 We show that COI1 is required for expression of approximately 84% of 212 genes induced by JA, and for expression of approximately 44% of 153 genes induced by wounding. |
| GO:0009753 response to jasmonic acid | IMP PMID:17637677 JAZ repressor proteins are targets of the SCF(COI1) complex ... | ACCEPT | Summary: COI1 is required for jasmonate-responsive JAZ degradation and signaling. Reason: Jasmonate responsiveness is central to COI1 hormone perception and signaling. A broad response term still represents core biology; its breadth does not make the role peripheral. The cited primary study directly establishes COI1-dependent jasmonate responses. Supporting Evidence: PMID:17637677 Furthermore, the jasmonoyl-isoleucine (JA-Ile) conjugate, but not other jasmonate-derivatives such as jasmonate, 12-oxo-phytodienoic acid, or methyl-jasmonate, promotes physical interaction between COI1 and JAZ1 proteins in the absence of other plant proteins. |
| GO:0009611 response to wounding | IMP PMID:16021335 Expression profiling reveals COI1 to be a key regulator of g... | KEEP AS NON CORE | Summary: COI1 participates in wound-induced jasmonate responses. Reason: Wound response is a downstream JA output. Supporting Evidence: PMID:16021335 We show that COI1 is required for expression of approximately 84% of 212 genes induced by JA, and for expression of approximately 44% of 153 genes induced by wounding. |
| GO:0048364 root development | IMP PMID:27756820 Endogenous Bioactive Jasmonate Is Composed of a Set of (+)-7... | KEEP AS NON CORE | Summary: COI1 is required for root growth inhibition by bioactive jasmonate analogues. Reason: Full PMC5129707 Results and Fig.5 compare coi1-1 and wild-type root length: loss of COI1 prevents the analogue-dependent root inhibition. This is a verified developmental response downstream of receptor action. The partial cached text lacks that Results section; the companion primary SCF study also places COI1 in jasmonate-regulated root growth. Supporting Evidence: PMID:12172031 required for response to jasmonates (JAs), which regulate root growth, pollen fertility, wound healing, and defense against insects and pathogens. |
| GO:0031146 SCF-dependent proteasomal ubiquitin-dependent protein catabolic process | IMP PMID:17637675 The JAZ family of repressors is the missing link in jasmonat... | ACCEPT | Summary: COI1 directs JAZ repressors into SCF-dependent proteasomal degradation. Reason: This is a core mechanistic process for COI1 function. Supporting Evidence: PMID:17637675 Our results demonstrate that JAI3 and other JAZs are direct targets of the SCF(COI1) E3 ubiquitin ligase and jasmonate treatment induces their proteasome degradation. |
| GO:0009641 shade avoidance | IMP PMID:20435902 Jasmonate and phytochrome A signaling in Arabidopsis wound a... | KEEP AS NON CORE | Summary: COI1/JAZ stability links jasmonate signaling to shade avoidance. Reason: This is a downstream pathway-output/cross-talk annotation. Supporting Evidence: PMID:20435902 These mutants display exaggerated shade responses to low, but not high, R/FR ratio light, suggesting a role for JA in phytochrome A (phyA) signaling. |
| GO:0048443 stamen development | IMP PMID:27756820 Endogenous Bioactive Jasmonate Is Composed of a Set of (+)-7... | KEEP AS NON CORE | Summary: COI1-dependent jasmonate signaling affects reproductive phenotypes including male fertility and anther dehiscence. Reason: Full PMC5129707 Results and Fig.1 show restoration of fertility in opr3 but not coi1-1 after ligand treatment; this supports the source-specific COI1 reproductive requirement. PMID:23573263 independently documents failure of anther dehiscence. Retain stamen development as a downstream physiological role, without conflating ligand rescue of biosynthesis mutants with rescue of coi1. Supporting Evidence: PMID:23573263 plants were functionally male sterile due to a lack of dehiscence |
| GO:0010118 stomatal movement | IMP PMID:16959575 Plant stomata function in innate immunity against bacterial ... | UNDECIDED | Summary: The accessible abstract establishes pathogen-triggered stomatal closure and virulence-factor-induced reopening, but does not identify the COI1-specific assay. Reason: PMID:16959575 is abstract-only in the cache, and the original COI1 experiment could not be retrieved. COI1-mediated coronatine perception is established by PMID:20927106, but receptor binding alone does not independently verify this source-specific stomatal or bacterial-defense phenotype. Do not infer a direct defensive direction from pathogen exploitation of the jasmonate pathway. |
| GO:0006511 ubiquitin-dependent protein catabolic process | TAS PMID:11019805 Protein degradation in signaling. | MODIFY | Summary: COI1 functions in ubiquitin-dependent degradation, but the SCF-dependent term is more precise. Reason: The original PMID:11019805 review abstract gives broad proteolysis context. The specific replacement is independently demonstrated by PMID:17637677, where JAZ1 degradation requires SCF(COI1) and the 26S proteasome; PMID:12172031 demonstrates SCF assembly. Thus this specialization uses explicit primary evidence rather than assuming the review abstract itself contains the mechanism. Proposed replacements: SCF-dependent proteasomal ubiquitin-dependent protein catabolic process Supporting Evidence: PMID:17637677 Jasmonate treatment causes JAZ1 degradation and this degradation is dependent on activities of the SCF(COI1) ubiquitin ligase and the 26S proteasome. |
| GO:0042562 hormone binding | IDA PMID:20927106 Jasmonate perception by inositol-phosphate-potentiated COI1-... | NEW | Summary: COI1 directly contacts JA-Ile within the COI1-JAZ co-receptor. Reason: Structural and pharmacological measurements establish a ligand pocket in COI1 and JA-Ile binding by the co-receptor. Hormone binding captures this experimentally supported MF separately from ubiquitin-ligase substrate adaptation. High-affinity perception requires JAZ, so this is not a claim that isolated COI1 is a complete high-affinity receptor. A specific JA-Ile-binding GO term was not found in the ontology search. Supporting Evidence: PMID:20927106 Here we present structural and pharmacological data to show that the true Arabidopsis jasmonate receptor is a complex of both COI1 and JAZ. COI1 contains an open pocket that recognizes the bioactive hormone (3R,7S)-jasmonoyl-l-isoleucine (JA-Ile) with high specificity. |
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Download this section (compressed HTML)Q: How do different JAZ degrons and inositol-phosphate cofactors alter the ligand selectivity of the COI1-JAZ co-receptor?
Q: Which COI1 developmental/defense outputs should be modeled as downstream targets rather than direct gene annotations?
Q: Which molecular partners mediate JA-Ile-independent root defense-gene repression by COI1, does it require SCF assembly, and can a residual contribution from JAZ proteins be excluded?
Experiment: Map COI1-dependent JAZ degradation and transcriptional release across developmental and defense contexts using matched proteomics and RNA-seq.
Hypothesis: JAZ degradation and transcriptional release differ in timing across developmental and defense contexts.
Experiment: Test whether eATP, far-red, and shade annotations require canonical JA-Ile/COI1/JAZ signaling or separate COI1 functions.
Hypothesis: COI1-dependent ATP and light responses require canonical ligand-dependent JAZ turnover.
Experiment: Compare root complementation of coi1 with wild-type COI1, the JAZ-interaction-impaired COI1 variant, and an SCF-assembly-defective COI1 variant while matching protein abundance and localization; assay root defense-gene expression and Verticillium tolerance, and verify SCF and JAZ interactions directly.
Hypothesis: JA-Ile-independent root repression is separable from canonical JAZ perception; testing SCF assembly distinguishes a noncanonical ubiquitin-ligase pathway from an SCF-independent function.
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