EIN3 is a nuclear sequence-specific DNA-binding transcription factor that transduces Arabidopsis ethylene signaling into gene expression. It binds ethylene-response cis-regulatory elements and activates early targets including ERF1 and the feedback regulator EBF2. EIN3 acts with EIL1 and cooperates with EIN2-dependent chromatin acetylation through transcriptional positive feedback. It also directly represses targets such as SID2 and ABI4, connecting ethylene signaling to salicylic-acid immunity and ascorbate/ROS regulation. Its abundance and activity are controlled by proteolysis and kinase-dependent regulation. EIN3/EIL1 has also been implicated in ethylene-mediated preadaptation to low oxygen through the PGB1/NO/ERFVII pathway.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0005634 nucleus | IDA PMID:9215635 Activation of the ethylene gas response pathway in Arabidops... | ACCEPT | Summary: EIN3 is a nuclear protein. Reason: Nuclear localization is the correct compartment for EIN3 transcriptional regulation. Supporting Evidence: PMID:9215635 The EIN3 gene encodes a novel nuclear-localized protein that shares sequence similarity, structural features, and genetic function with three EIN3-LIKE (EIL) proteins. |
| GO:0003682 chromatin binding | IDA PMID:28874528 EIN2 mediates direct regulation of histone acetylation in th... | ACCEPT | Summary: EIN3 preferentially binds accessible ENAP1-associated chromatin at ethylene-responsive genes. Reason: PMID:28874528 directly examines EIN3 ChIP-seq enrichment at these loci. Chromatin occupancy is part of its central transcriptional mechanism, not a peripheral function simply because DNA-binding transcription factor activity is more descriptive. Supporting Evidence: PMID:28874528 Specifically, in the presence of ethylene, ENAP1-binding regions are more accessible upon the interaction with EIN2, and more EIN3 proteins bind to the loci where ENAP1 is enriched for a quick response. |
| GO:0003677 DNA binding | IDA PMID:26352699 Biochemical and Structural Insights into the Mechanism of DN... | MODIFY | Summary: EIN3 binds DNA, but a cis-regulatory-region binding term is more informative. Reason: The evidence supports sequence/cis-regulatory DNA binding by a transcription factor rather than generic DNA binding. Proposed replacements: transcription cis-regulatory region binding Supporting Evidence: PMID:26352699 Results from systematic biochemical analyses reveal that both the number of EIN3-binding sites (EBSs) and the spacing length between two EBSs affect the binding affinity of EIN3; |
| GO:0003700 DNA-binding transcription factor activity | IDA PMID:18466304 Ethylene signaling in Arabidopsis involves feedback regulati... | ACCEPT | Summary: EIN3 functions as a DNA-binding transcription factor in ethylene signaling. Reason: This is the core molecular function of EIN3. Supporting Evidence: PMID:18466304 Furthermore, the results of protoplast transient assays in vivo and electrophoretic mobility shift assays in vitro have revealed that EIN3 can bind and activate the EBF2 promoter, indicating that EIN3 modulates EBF2 gene expression in planta. |
| GO:0003700 DNA-binding transcription factor activity | IDA PMID:23795294 Temporal transcriptional response to ethylene gas drives gro... | ACCEPT | Summary: Ethylene transcriptional response studies support EIN3 transcription factor activity. Reason: This is the core molecular function of EIN3. Supporting Evidence: PMID:23795294 We characterized the dynamic ethylene transcriptional response by identifying targets of the master regulator of the ethylene signaling pathway, ETHYLENE INSENSITIVE3 (EIN3), using chromatin immunoprecipitation sequencing and transcript sequencing during a timecourse of ethylene treatment. |
| GO:0003700 DNA-binding transcription factor activity | IDA PMID:9851977 Nuclear events in ethylene signaling: a transcriptional casc... | ACCEPT | Summary: EIN3 directly regulates ethylene-response transcription. Reason: This is the core molecular function of EIN3. Supporting Evidence: PMID:9851977 In this study, we show that EIN3 and EILs comprise a family of novel sequence-specific DNA-binding proteins that regulate gene expression by binding directly to a primary ethylene response element (PERE) related to the tomato E4-element. |
| GO:0042393 histone binding | IDA PMID:28874528 EIN2 mediates direct regulation of histone acetylation in th... | REMOVE | Summary: The cited experiments support the separately retained chromatin-binding annotation, without establishing a distinct EIN3 histone-binding activity. Reason: Remove this unsupported distinct histone-binding assertion: PMID:28874528 demonstrates EIN3 chromatin occupancy, already retained as GO:0003682 with the same IDA evidence and paper. PMID:27694846 distinguishes EIN3-ENAP1 interaction from ENAP1-histone binding. Redirecting this row would duplicate the existing chromatin annotation. This removes an unsupported curation claim, not evidence that EIN3 can never contact histones; neither absence of a histone-reader domain nor unexamined supplements establishes such a negative. EIN3-dependent acetylation feedback from PMID:33793786 remains supported independently. Supporting Evidence: PMID:28874528 Specifically, in the presence of ethylene, ENAP1-binding regions are more accessible upon the interaction with EIN2, and more EIN3 proteins bind to the loci where ENAP1 is enriched for a quick response. PMID:28874528 The average EIN3-binding signals were significantly higher in cobound genes than in the genes bound only by EIN3 |
| GO:0019900 kinase binding | IPI PMID:28600557 Regulatory Functions of Cellular Energy Sensor SNF1-Related ... | KEEP AS NON CORE | Summary: EIN3 binds the energy-sensor kinase KIN10, which regulates EIN3 stability. Reason: Kinase binding is a regulatory input to EIN3 rather than EIN3's core transcriptional activity. Supporting Evidence: PMID:28600557 Our plant cell-based functional and biochemical assays have demonstrated that SNF1-RELATED KINASE1 (SnRK1) directly interacts, phosphorylates, and destabilizes the key transcription factor ETHYLENE INSENSITIVE3 (EIN3) in senescence-promoting hormone ethylene signaling. |
| GO:0000976 transcription cis-regulatory region binding | IDA PMID:26134166 Ethylene Regulates the Arabidopsis Microtubule-Associated Pr... | ACCEPT | Summary: EIN3 binds cis-regulatory DNA at EIN3-regulated promoters such as WDL5. Reason: This is a specific molecular description of EIN3's transcription factor role. Supporting Evidence: PMID:26134166 ETHYLENE-INSENSITIVE3, a key transcription factor in the ethylene signaling pathway, directly targets and up-regulates WDL5. |
| GO:0042742 defense response to bacterium | IGI PMID:19717619 ETHYLENE INSENSITIVE3 and ETHYLENE INSENSITIVE3-LIKE1 repres... | KEEP AS NON CORE | Summary: EIN3/EIL1 modulate salicylic-acid-dependent bacterial defense outputs. Reason: Defense response is a downstream signaling context, not the primary EIN3 molecular function. Supporting Evidence: PMID:19717619 Plants lacking EIN3 and EIL1 display enhanced PAMP defenses and heightened resistance to Pseudomonas syringae bacteria. |
| GO:0040029 epigenetic regulation of gene expression | IMP PMID:28874528 EIN2 mediates direct regulation of histone acetylation in th... | ACCEPT | Summary: EIN3-dependent transcription and positive feedback cooperate with EIN2-mediated histone acetylation in ethylene responses. Reason: The original PMID:28874528 establishes EIN3 recruitment to the EIN2/ENAP1 chromatin response. The later primary study PMID:33793786 directly shows EIN3 is required for ethylene-induced H3K14Ac/H3K23Ac in the presence of EIN2. This makes epigenetic regulation part of the core mechanism, without assigning EIN3 intrinsic acetyltransferase activity. Supporting Evidence: PMID:33793786 Additionally, although EIN3 does not direct affect histone acetylation levels in the absence of EIN2, it is required for the ethylene-induced elevation of H3K14Ac and H3K23Ac in the presence of EIN2. |
| GO:0009873 ethylene-activated signaling pathway | IMP PMID:28874528 EIN2 mediates direct regulation of histone acetylation in th... | ACCEPT | Summary: EIN3 is a central positive regulator of ethylene signaling. Reason: Ethylene-activated signaling is the core biological pathway in which EIN3 functions. Supporting Evidence: PMID:28874528 in the presence of ethylene, EIN2 interacts with ENAP1, elevating the levels of H3K14Ac and H3K23Ac, promoting more EIN3 binding to the targets shared with ENAP1 and resulting in a rapid transcriptional regulation. |
| GO:0006355 regulation of DNA-templated transcription | TAS PMID:9851977 Nuclear events in ethylene signaling: a transcriptional casc... | ACCEPT | Summary: EIN3 regulates transcription of ethylene-responsive genes. Reason: This is an appropriate biological-process level annotation for the transcription factor role. Supporting Evidence: PMID:9851977 EIN3 is necessary and sufficient for ERF1 expression |
| GO:2000082 regulation of L-ascorbic acid biosynthetic process | IEP PMID:30723177 Ascorbic Acid Integrates the Antagonistic Modulation of Ethy... | KEEP AS NON CORE | Summary: EIN3 represses ABI4 transcription, connecting ethylene signaling to regulation of VTC2-dependent ascorbate biosynthesis and ROS levels. Reason: PMID:30723177 resolves an EIN3-ABI4-VTC2 regulatory cascade, not merely a loose ROS correlation. Retain this physiological branch as non-core relative to the general ethylene transcriptional mechanism. Supporting Evidence: PMID:30723177 We found that ethylene and ABA antagonistically regulate AsA biosynthesis via ETHYLENE-INSENSITIVE3 (EIN3) and ABA INSENSITIVE4 (ABI4), which are key factors in the ethylene and ABA signaling pathways, respectively. In addition, ABI4 is transcriptionally repressed by EIN3 in ethylene-regulated AsA biosynthesis. |
| GO:0009723 response to ethylene | IMP PMID:19717619 ETHYLENE INSENSITIVE3 and ETHYLENE INSENSITIVE3-LIKE1 repres... | ACCEPT | Summary: EIN3 is a central transcriptional component of the ethylene response. Reason: A broad response-to-ethylene term still describes the core hormone response; breadth alone does not make it non-core. PMID:19717619 studies EIN3/EIL1 ethylene signaling and immune crosstalk, while the original molecular characterization PMID:9215635 directly demonstrates ethylene-response defects. Supporting Evidence: PMID:9215635 Mutations in the Arabidopsis ETHYLENE-INSENSITIVE3 (EIN3) gene severely limit a plant's response to the gaseous hormone ethylene. ein3 mutants show a loss of ethylene-mediated effects including gene expression, the triple response, cell growth inhibition, and accelerated senescence. |
| GO:0001666 response to hypoxia | IMP PMID:25284079 Arabidopsis acyl-CoA-binding protein ACBP3 participates in p... | UNDECIDED | Summary: The original ein3-1 submergence experiment is inconclusive; later ethylene-preconditioning evidence suggests an EIN3/EIL1 pathway role but leaves the exact hypoxia-response assignment unresolved. Reason: PMID:25284079 reports no significant ein3-1 phenotype under dark or light submergence and no modification of ACBP3-overexpression sensitivity. This does not refute a redundant function. PMID:31488841 provides an EIN3/EIL1 preadaptation model and names the double mutant in Methods, but the genotype-specific survival panel in Supplementary Fig.1 remains inaccessible. Its positive quotation describes a model, not a verified EIN3-specific phenotype. Ethylene-triggered preconditioning occurs before lowered oxygen; its downstream survival benefit does not by itself establish a response elicited by hypoxia in this gene. Retain the newer source as a mechanistic lead while withholding a conclusive GO:0001666 decision pending genotype-specific data and stimulus interpretation. Supporting Evidence: PMID:25284079 However, the ein3-1 mutant was not significantly different to wild type under either DS or LS (Figure 6b), possibly due to the functional redundancy of the EIL1 gene in Arabidopsis. |
| GO:0010182 sugar mediated signaling pathway | TAS PMID:12663220 Sugar and hormone connections. | UNDECIDED | Summary: Sugar-hormone cross-talk is relevant to ethylene signaling, but the cached PMID:12663220 abstract does not verify an EIN3-specific annotation. Reason: The cached PMID:12663220 entry is abstract-only and discusses sugar, ABA, and ethylene signaling generally without naming EIN3, so UNDECIDED is more appropriate than REMOVE until full-text evidence is available. |
Loading supporting content…
Download this section (compressed HTML)Q: Which EIN3 chromatin-binding annotations should be represented directly versus as part of EIN2/ENAP1-mediated histone acetylation?
Q: Should kinase-binding annotations for KIN10/MPK inputs remain on EIN3 or be captured only in pathway models?
Experiment: Combine native EIN3 ChIP-seq with rapid ethylene treatment and ein2/enap1 perturbation to distinguish direct DNA-binding targets from chromatin-state effects.
Hypothesis: EIN2/ENAP1-dependent chromatin changes alter EIN3 occupancy at only a subset of ethylene-responsive loci.
Experiment: Quantitatively test KIN10, MPK3, and MPK6 effects on EIN3 target occupancy and transcriptional activation.
Hypothesis: Kinase perturbations change EIN3 promoter occupancy or activation beyond their effects on EIN3 abundance.
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)