OsEIL2 (Q8W3L9; ETHYLENE-INSENSITIVE3-LIKE 2, also OsEIL2/EIL2, Os07g0685700) is a plant-specific, nuclear EIN3/EIL-family transcription factor that acts as a central transducer of ethylene signaling in rice. EIN3/EIL proteins are the master transcriptional outputs of the canonical ethylene cascade: ethylene perceived by ER-localized receptors is relayed through CTR-type kinases to EIN2, after which EIN2-dependent events promote accumulation of EIN3/EIL transcription factors that directly bind target-gene promoters and reprogram transcription (deep-research synthesis, file:ORYSJ/EIL2/EIL2-deep-research-falcon.md). Canonical rice ethylene signaling places OsEIL2 downstream of the receptors/OsCTR2 and OsEIN2, and OsEIL2 together with its paralog OsEIL1 (MHZ6) is described as one of "two master regulators of rice ethylene signaling" (Qiao et al. 2024). OsEIL2 binds DNA in a sequence-specific manner - recombinant protein binds the DNA element recognized by a wound-inducible tobacco EIL (Hiraga et al. 2009, PMID:19798512), and UniProt records sequence-specific binding to the 5'-ATGTACCT-3' motif found in some wound-inducible gene promoters - and possesses transactivation activity in protoplasts (UniProt FUNCTION; Yang et al. 2015, PMID:25995326). The OsEIL2 protein localizes to the nucleus, and OsEIL2-GFP/YFP nuclear fluorescence increases after ACC (ethylene precursor) and after the proteasome inhibitor MG132, consistent with ethylene-regulated, EBF-mediated turnover of EIN3/EIL proteins (file:ORYSJ/EIL2/EIL2-deep-research-falcon.md). Functionally OsEIL2 is required for ethylene-promoted coleoptile elongation (silencing causes coleoptile ethylene insensitivity), and it directs distinct context-dependent output programs: in coleoptiles it cooperates with OsEIL1 to activate ROS-scavenging genes (OsVTC1-3, peroxidases) to reduce ROS and enable seedling emergence (Qiao et al. 2024); in abiotic-stress contexts it directly activates the cell-wall/BURP gene OsBURP16 (promoting polygalacturonase activity and pectin remodeling) and the Na+ transporter OsHKT2;1, acting as a negative regulator of salt tolerance (Yang et al. 2015, PMID:25995326; Jin et al. 2020); and it participates in wound signaling as a wound- and jasmonate-inducible EIL that regulates wound-responsive genes (Hiraga et al. 2009). Because EIN3/EIL transcription factors are genuine, defining components of the ethylene-activated signaling pathway (the master nuclear effectors of the cascade, distinct from purely downstream ERF response factors), "ethylene-activated signaling pathway" (GO:0009873) is a CORRECT and core annotation for OsEIL2; the retired SPKW keyword mapping in this case captured a true biological role, comparable to legitimate cases such as DELLA/NSP1.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0009873 ethylene-activated signaling pathway | IEA GO_REF:0000043 | ACCEPT | Summary: SPKW (GO_REF:0000043) annotation derived from the UniProt keyword "Ethylene signaling pathway"; snapshot-only, removed in the current GOA release. OsEIL2 is an EIN3/EIL-family transcription factor that functions as a central nuclear transducer of ethylene signaling, so this term is biologically CORRECT and core for the gene. Reason: GOA's removal of this annotation was NOT justified - this is collateral damage from retiring the keyword2GO pipeline, not a correction of an over-annotation. EIN3/EIL proteins are the master transcriptional effectors of the ethylene-activated signaling pathway, acting downstream of the ER receptors/CTR1->EIN2 module to directly drive ethylene-responsive transcription; unlike purely downstream ERF response factors, the EIN3/EIL transcription factors are canonically considered defining COMPONENTS of the pathway. OsEIL2 is explicitly described, with its paralog OsEIL1, as one of "two master regulators of rice ethylene signaling", and canonical rice ethylene signaling places OsEIL2 downstream of the receptors/OsCTR2 and OsEIN2 [file:ORYSJ/EIL2/EIL2-deep-research-falcon.md]. The UniProt FUNCTION statement calls it a "Transcription factor acting as a positive regulator in the ethylene response pathway" [PMID:19798512, PMID:25995326] and it is required for ethylene-promoted coleoptile elongation [PMID:25995326]. This is a Tier A keyword (the keyword names the exact pathway the protein operates in) and the verdict is LEGITIMATE: the term should be retained as a core biological process for OsEIL2. (The current GOA release retains the more specific "regulation of ethylene-activated signaling pathway" GO:0010104, but the parent pathway-membership term GO:0009873 is also appropriate and informative.) Supporting Evidence: file:ORYSJ/EIL2/EIL2-deep-research-falcon.md Canonical rice ethylene signaling places OsEIL2 downstream of receptors/OsCTR2 and OsEIN2 file:ORYSJ/EIL2/EIL2-deep-research-falcon.md two master regulators of rice ethylene signaling PMID:25995326 MHZ6 encodes ETHYLENE INSENSITIVE3-LIKE1 (OsEIL1), a rice homolog of ETHYLENE INSENSITIVE3 (EIN3), which is the master transcriptional regulator of ethylene signaling in Arabidopsis |
| GO:0003700 DNA-binding transcription factor activity | IEA GO_REF:0000120 | ACCEPT | Summary: IEA annotation from combined automated methods (ARBA / InterPro EIN3 DNA-binding domain signatures). OsEIL2 is a bona fide DNA-binding transcription factor; this is a core molecular function. Reason: Correct and core. The protein carries the EIN3 DNA-binding domain (Pfam PF04873; InterPro IPR006957/IPR023278/IPR047091) and was shown experimentally to be a transcription factor: recombinant OsEIL2 binds specific DNA sequences (PMID:19798512) and the protein has transactivation activity in protoplasts (UniProt FUNCTION; PMID:25995326). The IEA term is at an appropriate level; the duplicate IDA annotation (PMID:25995326) provides direct experimental support. A more specific transcription-activator term is proposed below (GO:0001228). Supporting Evidence: file:ORYSJ/EIL2/EIL2-deep-research-falcon.md OsEIL2 functions as a transcriptional activator PMID:19798512 recombinant OsEIL1 and 2 proteins bound to specific DNA sequences that are recognized by a wound-inducible tobacco EIL |
| GO:0005634 nucleus | IEA GO_REF:0000120 | ACCEPT | Summary: IEA annotation for nuclear localization from combined automated methods. Directly confirmed in rice by fluorescent-fusion imaging. Reason: Correct and consistent with the duplicate IDA annotation (PMID:25995326) and the UniProt SUBCELLULAR LOCATION (Nucleus; ECO:0000269|PubMed:25995326). OsEIL2-GFP/YFP fusions accumulate in nuclei, and nuclear fluorescence increases after ACC (ethylene precursor) and after the proteasome inhibitor MG132, consistent with ethylene-regulated stabilization of an EIN3/EIL transcription factor [file:ORYSJ/EIL2/EIL2-deep-research-falcon.md]. Nuclear localization is the expected and required site for its transcription-factor function. Supporting Evidence: file:ORYSJ/EIL2/EIL2-deep-research-falcon.md OsEIL2 fused to GFP/YFP accumulated in nuclei file:ORYSJ/EIL2/EIL2-deep-research-falcon.md nuclear fluorescence was detectable/enhanced after treatment with the ethylene precursor |
| GO:0010104 regulation of ethylene-activated signaling pathway | IEA GO_REF:0000117 | ACCEPT | Summary: IEA annotation (ARBA) for regulation of the ethylene-activated signaling pathway. OsEIL2 is a core component/effector of ethylene signaling; this term is accepted (it duplicates the IDA and IMP annotations to the same term). Reason: Correct and core. OsEIL2 acts as a positive regulator/effector in the ethylene response pathway downstream of OsEIN2, and its activity tunes the output of the cascade [PMID:25995326, file:ORYSJ/EIL2/EIL2-deep-research-falcon.md]. This IEA duplicates the experimentally supported IDA (PMID:19798512) and IMP (PMID:25995326) annotations to the same term and is at an appropriate level of specificity. Supporting Evidence: file:ORYSJ/EIL2/EIL2-deep-research-falcon.md Canonical rice ethylene signaling places OsEIL2 downstream of receptors/OsCTR2 and OsEIN2 PMID:25995326 silencing of the closely related OsEIL2 led to ethylene insensitivity mainly in coleoptiles of etiolated seedlings |
| GO:0043565 sequence-specific DNA binding | IEA GO_REF:0000117 | ACCEPT | Summary: IEA annotation (ARBA) for sequence-specific DNA binding. Directly demonstrated for OsEIL2 by EMSA; duplicates the IDA annotation (PMID:19798512). Reason: Correct and core. OsEIL2 binds DNA sequence-specifically: electrophoretic mobility shift assays showed recombinant OsEIL2 bound the specific element recognized by a wound-inducible tobacco EIL [PMID:19798512], and the UniProt FUNCTION statement records sequence-specific binding to the 5'-ATGTACCT-3' motif in the promoters of some wound-inducible genes. This is consistent with the EIN3-family DNA-binding domain (Pfam PF04873) and supports the transcription-factor function. Supporting Evidence: PMID:19798512 recombinant OsEIL1 and 2 proteins bound to specific DNA sequences that are recognized by a wound-inducible tobacco EIL PMID:19798512 the corresponding DNA-binding activity in nuclear extracts of rice leaves was increased at 1 h after wounding |
| GO:0045893 positive regulation of DNA-templated transcription | IEA GO_REF:0000117 | ACCEPT | Summary: IEA annotation (ARBA) for positive regulation of transcription. OsEIL2 is a transcriptional activator; duplicates the IDA annotation (PMID:25995326). Reason: Correct. OsEIL2 possesses transactivation activity in protoplasts (UniProt FUNCTION, ECO:0000269|PubMed:25995326) and acts as a transcriptional activator that directly activates target genes such as OsHKT2;1 and ROS-scavenging genes [PMID:25995326, file:ORYSJ/EIL2/EIL2-deep-research-falcon.md]. The term is accurate though generic; a more specific RNA-polymerase-II activator process term (GO:0045944) is proposed below. Supporting Evidence: file:ORYSJ/EIL2/EIL2-deep-research-falcon.md acts as a transcriptional activator of downstream genes involved in stress/senescence and coleoptile development PMID:25995326 the direct regulation of HIGH-AFFINITY K(+) TRANSPORTER2;1 expression and Na(+) uptake in roots |
| GO:0003700 DNA-binding transcription factor activity | IDA PMID:25995326 MAOHUZI6/ETHYLENE INSENSITIVE3-LIKE1 and ETHYLENE INSENSITIV... | ACCEPT | Summary: IDA annotation: OsEIL2 has transactivation activity in protoplasts, confirming DNA-binding transcription factor activity. Core molecular function. Reason: Strongly supported by direct experimental evidence. Yang et al. (2015) showed OsEIL2 possesses transactivation activity in protoplasts (UniProt FUNCTION, ECO:0000269|PubMed:25995326) and directly regulates target-gene expression (e.g. OsHKT2;1) [PMID:25995326]. Together with the sequence-specific DNA-binding data this firmly establishes OsEIL2 as a DNA-binding transcription factor. A more specific transcription-activator term (GO:0001228) is proposed below. Supporting Evidence: file:ORYSJ/EIL2/EIL2-deep-research-falcon.md OsEIL2 functions as a transcriptional activator PMID:25995326 the direct regulation of HIGH-AFFINITY K(+) TRANSPORTER2;1 expression and Na(+) uptake in roots |
| GO:0005634 nucleus | IDA PMID:25995326 MAOHUZI6/ETHYLENE INSENSITIVE3-LIKE1 and ETHYLENE INSENSITIV... | ACCEPT | Summary: IDA annotation: OsEIL2 localizes to the nucleus (Yang et al. 2015). Core cellular component, the site of its transcription-factor function. Reason: Strongly supported by direct evidence; UniProt records SUBCELLULAR LOCATION: Nucleus with ECO:0000269|PubMed:25995326. OsEIL2-GFP/YFP fusions accumulate in nuclei and nuclear fluorescence is ethylene(ACC)/proteasome(MG132)-sensitive [file:ORYSJ/EIL2/EIL2-deep-research-falcon.md]. Nuclear localization is required for and consistent with the gene's role as a transcription factor. Supporting Evidence: file:ORYSJ/EIL2/EIL2-deep-research-falcon.md OsEIL2 fused to GFP/YFP accumulated in nuclei file:ORYSJ/EIL2/EIL2-deep-research-falcon.md nuclear fluorescence was detectable/enhanced after treatment with the ethylene precursor |
| GO:0010104 regulation of ethylene-activated signaling pathway | IDA PMID:19798512 Involvement of two rice ETHYLENE INSENSITIVE3-LIKE genes in ... | ACCEPT | Summary: IDA annotation citing the wound-signaling study (Hiraga et al. 2009). OsEIL2 is a wound- and JA-inducible EIL that binds DNA and regulates wound-responsive genes, operating within the ethylene/EIL signaling module. Reason: Supported. Hiraga et al. (2009) showed OsEIL2 is a wound-inducible EIN3-LIKE transcription factor whose recombinant protein binds the EIL DNA recognition element and whose suppression down-regulates wound-inducible candidate target genes [PMID:19798512]. As an EIN3/EIL transcription factor, OsEIL2 is a core effector of the ethylene-activated signaling pathway, so "regulation of ethylene-activated signaling pathway" is appropriate. Accepted as core. Supporting Evidence: PMID:19798512 ETHYLENE INSENSITIVE3 (EIN3), which is an essential transcription factor for ethylene signaling PMID:19798512 only OsEIL1 and 2 were found to be wound-inducible EIL |
| GO:0010104 regulation of ethylene-activated signaling pathway | IMP PMID:25995326 MAOHUZI6/ETHYLENE INSENSITIVE3-LIKE1 and ETHYLENE INSENSITIV... | ACCEPT | Summary: IMP annotation: silencing OsEIL2 causes ethylene insensitivity in coleoptiles, demonstrating its role in (regulation of) the ethylene-activated signaling pathway. Core function. Reason: Strongly supported by loss-of-function genetics. Silencing OsEIL2 led to ethylene insensitivity mainly in coleoptiles of etiolated seedlings, and plants silencing EIL2 exhibit insensitivity in ethylene-promoted coleoptile elongation [PMID:25995326]. This is direct mutant-phenotype evidence that OsEIL2 is required for ethylene signaling output, supporting the term at an appropriate level. Supporting Evidence: PMID:25995326 silencing of the closely related OsEIL2 led to ethylene insensitivity mainly in coleoptiles of etiolated seedlings PMID:25995326 Disruption of MHZ6/OsEIL1 caused ethylene |
| GO:0043565 sequence-specific DNA binding | IDA PMID:19798512 Involvement of two rice ETHYLENE INSENSITIVE3-LIKE genes in ... | ACCEPT | Summary: IDA annotation: EMSA shows recombinant OsEIL2 binds a specific DNA element (Hiraga et al. 2009). Core molecular function underpinning its transcription-factor activity. Reason: Strongly supported by direct in vitro binding data. Electrophoretic mobility shift assays showed recombinant OsEIL2 bound the specific DNA sequence recognized by a wound-inducible tobacco EIL, and wound-induced DNA-binding activity increased in rice nuclear extracts [PMID:19798512]; UniProt records binding to the 5'-ATGTACCT-3' motif. Core MF. Supporting Evidence: PMID:19798512 recombinant OsEIL1 and 2 proteins bound to specific DNA sequences that are recognized by a wound-inducible tobacco EIL PMID:19798512 the corresponding DNA-binding activity in nuclear extracts of rice leaves was increased at 1 h after wounding |
| GO:0045893 positive regulation of DNA-templated transcription | IDA PMID:25995326 MAOHUZI6/ETHYLENE INSENSITIVE3-LIKE1 and ETHYLENE INSENSITIV... | ACCEPT | Summary: IDA annotation: OsEIL2 directly activates target-gene transcription (e.g. OsHKT2;1) and has transactivation activity (Yang et al. 2015). Accepted. Reason: Supported. OsEIL2 has transactivation activity in protoplasts (UniProt FUNCTION, ECO:0000269|PubMed:25995326) and directly activates target genes including the Na+ transporter OsHKT2;1 [PMID:25995326]. The term is correct; a more precise RNA-polymerase-II-specific activator process term (GO:0045944) is proposed below as a complementary NEW annotation. Supporting Evidence: PMID:25995326 the direct regulation of HIGH-AFFINITY K(+) TRANSPORTER2;1 expression and Na(+) uptake in roots file:ORYSJ/EIL2/EIL2-deep-research-falcon.md acts as a transcriptional activator of downstream genes involved in stress/senescence and coleoptile development |
| GO:1901001 negative regulation of response to salt stress | IMP PMID:25995326 MAOHUZI6/ETHYLENE INSENSITIVE3-LIKE1 and ETHYLENE INSENSITIV... | KEEP AS NON CORE | Summary: IMP annotation: OsEIL2 negatively regulates salt tolerance in rice (loss of function improves tolerance; overexpression causes hypersensitivity). A genuine but non-core, context-dependent process for this transcription factor. Reason: Supported by loss- and gain-of-function genetics: lack of OsEIL2 improves salt tolerance whereas overexpression confers salt hypersensitivity, and OsEIL2 (with OsEIL1) negatively regulates salt tolerance in part by directly activating OsHKT2;1 and Na+ uptake in roots [PMID:25995326]. This is a real, demonstrated role, but it is a downstream, tissue/stress-context-specific output of OsEIL2's transcription-factor activity rather than its defining core molecular function (which is ethylene-signaling transcription-factor activity). Retain as non-core. Supporting Evidence: PMID:25995326 lack of MHZ6/OsEIL1 or OsEIL2 functions improves salt tolerance, whereas the overexpressing lines exhibit salt hypersensitivity at the seedling stage PMID:25995326 MHZ6/OsEIL1 and OsEIL2 negatively regulate salt tolerance in rice PMID:25995326 this negative regulation by MHZ6/OsEIL1 and OsEIL2 in salt tolerance is likely attributable in part to the direct regulation of HIGH-AFFINITY K(+) TRANSPORTER2;1 expression and Na(+) uptake in roots |
| GO:1903034 regulation of response to wounding | IDA PMID:19798512 Involvement of two rice ETHYLENE INSENSITIVE3-LIKE genes in ... | KEEP AS NON CORE | Summary: IDA annotation: OsEIL2 is a wound- and JA-inducible EIL transcription factor that regulates wound-responsive genes (Hiraga et al. 2009). A genuine but non-core, context-specific process. Reason: Supported. OsEIL2 transcript is wound-inducible (and JA-inducible), its DNA-binding activity rises after wounding, and suppression of OsEIL1/2 down-regulated several wound-inducible candidate target genes, indicating involvement in wound signaling [PMID:19798512]. This is a real role, but it is one context-specific output program of an EIN3/EIL transcription factor whose core identity is ethylene-signaling transcription-factor activity; retain as non-core. Supporting Evidence: PMID:19798512 only OsEIL1 and 2 were found to be wound-inducible EIL. OsEIL2 was also induced by JA PMID:19798512 These results indicate the importance of inducible OsEILs in wound signaling in rice |
| GO:0001228 DNA-binding transcription activator activity, RNA polymerase II-specific | IDA PMID:25995326 MAOHUZI6/ETHYLENE INSENSITIVE3-LIKE1 and ETHYLENE INSENSITIV... | NEW | Summary: OsEIL2 is a sequence-specific DNA-binding transcriptional ACTIVATOR (it has transactivation activity and directly upregulates protein-coding target genes). The more specific activator MF term better captures its function than the generic "DNA-binding transcription factor activity". Reason: Current GOA has the generic "DNA-binding transcription factor activity" (GO:0003700) but not the more informative activator term. OsEIL2 possesses transactivation activity in protoplasts (UniProt FUNCTION, ECO:0000269|PubMed:25995326), acts as a transcriptional activator, and directly activates expression of protein-coding targets including OsHKT2;1 [PMID:25995326] and ROS-scavenging genes (OsVTC1-3, peroxidases) [file:ORYSJ/EIL2/EIL2-deep-research-falcon.md]. As a nuclear, sequence-specific activator of protein-coding genes, "DNA-binding transcription activator activity, RNA polymerase II-specific" (GO:0001228) is the precise molecular function. IDA is justified by the protoplast transactivation assay reported in UniProt/PMID:25995326. Supporting Evidence: file:ORYSJ/EIL2/EIL2-deep-research-falcon.md OsEIL2 functions as a transcriptional activator file:ORYSJ/EIL2/EIL2-deep-research-falcon.md acts as a transcriptional activator of downstream genes involved in stress/senescence and coleoptile development PMID:25995326 the direct regulation of HIGH-AFFINITY K(+) TRANSPORTER2;1 expression and Na(+) uptake in roots |
| GO:0045944 positive regulation of transcription by RNA polymerase II | IDA PMID:25995326 MAOHUZI6/ETHYLENE INSENSITIVE3-LIKE1 and ETHYLENE INSENSITIV... | NEW | Summary: OsEIL2 directly activates transcription of protein-coding ethylene/stress target genes. The RNA-polymerase-II-specific positive-regulation term is more precise than the generic "positive regulation of DNA-templated transcription" already present. Reason: OsEIL2 directly binds promoters and activates expression of protein-coding target genes - OsHKT2;1 [PMID:25995326] and ROS-scavenging genes (OsVTC1-3, peroxidases) [file:ORYSJ/EIL2/EIL2-deep-research-falcon.md]. These are RNA-polymerase-II-transcribed genes, so "positive regulation of transcription by RNA polymerase II" (GO:0045944) is the specific process term complementing the generic GO:0045893 already annotated. IDA is justified by direct target-activation (ChIP/EMSA/dual-LUC) and transactivation evidence. Supporting Evidence: file:ORYSJ/EIL2/EIL2-deep-research-falcon.md OsEIL2 directly binds promoters and activates transcription of file:ORYSJ/EIL2/EIL2-deep-research-falcon.md OsEIL1/OsEIL2 directly activate ROS-scavenging genes including PMID:25995326 the direct regulation of HIGH-AFFINITY K(+) TRANSPORTER2;1 expression and Na(+) uptake in roots |
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Download this section (compressed HTML)Q: How functionally redundant are OsEIL1 and OsEIL2 in rice ethylene signaling, and what determines their organ-specific divergence (OsEIL1 mainly in roots, OsEIL2 mainly in coleoptiles)?
Suggested experts: Jin-Song Zhang
Q: Does OsEIL2 directly bind a defined ethylene-response cis-element genome-wide (e.g. by ChIP-seq), and how does its in vivo target set differ from OsEIL1's?
Suggested experts: Hua Qin
Q: Is OsEIL2 protein turnover controlled by rice OsEBF1/2 F-box proteins and the MHZ9 translational-control module in the same way demonstrated for OsEIL1?
Suggested experts: Cui-Cui Yin
Experiment: Perform ChIP-seq with an epitope-tagged OsEIL2 under ethylene (ACC) treatment to define its direct genome-wide binding sites and consensus cis-element, and integrate with RNA-seq of oseil2 loss-of-function and overexpression lines to define the direct ethylene-responsive regulon.
Hypothesis: OsEIL2 directly binds an EIN3/EIL-type cis-element in the promoters of ethylene- and stress-responsive genes and activates their transcription as a primary effector of the ethylene-activated signaling pathway.
Type: ChIP-seq + RNA-seq regulon mapping
Experiment: Test OsEIL2 protein stability in response to ACC and MG132, and in oseil2 backgrounds expressing OsEBF1/2 variants, to determine whether OsEIL2 is stabilized by ethylene via repression of EBF-mediated proteasomal degradation, as for EIN3/OsEIL1.
Hypothesis: OsEIL2, like other EIN3/EIL proteins, is degraded by EBF1/2-directed proteolysis in the absence of ethylene and stabilized upon ethylene perception.
Type: protein-stability / proteasome-dependence assay
Experiment: Generate clean oseil1 oseil2 single and double CRISPR mutants and quantify ethylene-response phenotypes (coleoptile/root elongation, triple response, seedling emergence from soil) and salt/wound responses, to dissect their individual and combined contributions to the pathway.
Hypothesis: OsEIL1 and OsEIL2 act partially redundantly as master ethylene-signaling transcription factors, with the double mutant showing strongly attenuated ethylene responses and ROS-dependent emergence defects.
Type: genetic loss-of-function / epistasis analysis
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