EIL2

Existing Annotations Review

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

Core Functions

OsEIL2 is a nuclear, sequence-specific DNA-binding transcriptional activator of the EIN3/EIL family that acts as a central transducer/effector of the ethylene-activated signaling pathway, driving ethylene-responsive transcription downstream of OsEIN2.

Molecular Function:

DNA-binding transcription activator activity, RNA polymerase II-specific

Directly Involved In:

ethylene-activated signaling pathway positive regulation of transcription by RNA polymerase II

Cellular Locations:

nucleus

Supporting Evidence:

file:ORYSJ/EIL2/EIL2-deep-research-falcon.md
Canonical rice ethylene signaling places OsEIL2 downstream of receptors/OsCTR2 and OsEIN2
PMID:25995326
ETHYLENE INSENSITIVE3 (EIN3), which is the master transcriptional regulator of ethylene signaling in Arabidopsis
file:ORYSJ/EIL2/EIL2-deep-research-falcon.md
OsEIL2 functions as a transcriptional activator

OsEIL2 binds DNA sequence-specifically (via its EIN3 DNA-binding domain) at ethylene/wound-responsive promoter elements and regulates downstream gene programs - including ROS-scavenging genes, the cell-wall/BURP gene OsBURP16, and the Na+ transporter OsHKT2;1 - thereby contributing to ethylene-promoted coleoptile elongation, seedling emergence, and (negatively) salt-stress responses.

Molecular Function:

sequence-specific DNA binding

Directly Involved In:

regulation of ethylene-activated signaling pathway

Cellular Locations:

nucleus

Supporting Evidence:

PMID:19798512
recombinant OsEIL1 and 2 proteins bound to specific DNA sequences that are recognized by a wound-inducible tobacco EIL
PMID:25995326
silencing of the closely related OsEIL2 led to ethylene insensitivity mainly in coleoptiles of etiolated seedlings
file:ORYSJ/EIL2/EIL2-deep-research-falcon.md
OsEIL2 directly binds promoters and activates transcription of

References

GO_REF:0000043

Gene Ontology annotation based on UniProtKB/Swiss-Prot keyword mapping

SwissProt keyword-derived (SPKW) annotations present in the Sept 2025 goa_uniprot_gcrp snapshot but removed from the current GOA release after GOA retired the keyword2GO pipeline for cellular organisms.
For OsEIL2, the keyword "Ethylene signaling pathway" mapped to a genuinely correct, core process term (GO:0009873 ethylene-activated signaling pathway); its removal is collateral damage, not a correction, because EIN3/EIL transcription factors are defining components of the ethylene-activated signaling pathway.

GO_REF:0000117

Electronic Gene Ontology annotations created by ARBA machine learning models

ARBA models assign sequence-specific DNA binding, positive regulation of DNA-templated transcription and regulation of the ethylene-activated signaling pathway to OsEIL2, all consistent with experimental data for this EIN3/EIL transcription factor.

GO_REF:0000120

Combined Automated Annotation using Multiple IEA Methods

Combined IEA methods assign DNA-binding transcription factor activity and nuclear localization to OsEIL2; both are confirmed experimentally (PMID:25995326).

PMID:19798512

Involvement of two rice ETHYLENE INSENSITIVE3-LIKE genes in wound signaling.

OsEIL2 is one of only two rice EIL genes (with OsEIL1) found to be wound-inducible; OsEIL2 is also induced by jasmonic acid.
Recombinant OsEIL2 binds specific DNA sequences recognized by a wound-inducible tobacco EIL (EMSA), and wound-induced DNA-binding activity increased in rice nuclear extracts; suppression of OsEIL1/2 down-regulated several wound-inducible candidate target genes, indicating involvement in wound signaling.
EIN3 is described as an essential transcription factor for ethylene signaling; OsEIL proteins are its rice EIN3-LIKE homologs.

PMID:25995326

MAOHUZI6/ETHYLENE INSENSITIVE3-LIKE1 and ETHYLENE INSENSITIVE3-LIKE2 Regulate Ethylene Response of Roots and Coleoptiles and Negatively Affect Salt Tolerance in Rice.

OsEIL1 (MHZ6) is a rice homolog of Arabidopsis EIN3, the master transcriptional regulator of ethylene signaling; OsEIL2 is its close relative.
Silencing OsEIL2 causes ethylene insensitivity mainly in coleoptiles of etiolated seedlings; OsEIL2 is required for ethylene-promoted coleoptile elongation.
OsEIL2 has transactivation activity in protoplasts and localizes to the nucleus.
OsEIL1/OsEIL2 negatively regulate salt tolerance, in part by directly activating OsHKT2;1 expression and Na+ uptake in roots; loss of function improves salt tolerance, overexpression causes salt hypersensitivity.

file:ORYSJ/EIL2/EIL2-deep-research-falcon.md

Deep-research report (falcon / Edison Scientific Literature) - functional annotation of rice EIL2 (Q8W3L9).

Canonical rice ethylene signaling places OsEIL2 downstream of the receptors/OsCTR2 and OsEIN2; OsEIL1 and OsEIL2 are described as the closest functional equivalents to Arabidopsis EIN3 and as "two master regulators of rice ethylene signaling".
OsEIL2 functions as a transcriptional activator with transactivation activity (the report maps the OsEIL2 transactivation domain to the C-terminal region, aa 344-583); it acts as a transcriptional activator of downstream genes involved in stress/senescence and coleoptile development.
OsEIL2 fused to GFP/YFP accumulated in nuclei; nuclear fluorescence increased after ACC (ethylene precursor) and after MG132 (proteasome inhibitor), consistent with ethylene/proteasome-regulated stability.
OsEIL2 directly binds promoters and activates transcription of target genes including OsBURP14/OsBURP16; with OsEIL1 it directly activates ROS-scavenging genes (OsVTC1-3, peroxidases) linked to coleoptile elongation and seedling emergence, and it acts as a negative regulator of salt/drought tolerance.

Suggested Experiments

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

Deep Research

Falcon

(EIL2-deep-research-falcon.md)

this with annotations you find in gene/protein databases, but these can be outdated or inaccurate. Falcon Edison Scientific Literature 30 citations 2 artifacts 2026-05-30T09:25:10.801746

Edison artifact artifact-00 (text/markdown)

## Context ID: pqac-00000007 The regulation of ROS scavenging genes and their role in rice coleoptile elongation by OsEIL1/OsEIL2 is summarized across several f (image/png)

The research report should be a detailed narrative explaining the function, biological processes, and localization of the gene product. Citations should be given for all claims.

You should prioritize authoritative reviews and primary scientific literature when conducting research. You can supplement
this with annotations you find in gene/protein databases, but these can be outdated or inaccurate.

We are specifically interested in the primary function of the gene - for enzymes, what reaction is catalyzed, and what is the substrate specificity? For transporters, what is the substrate? For structural proteins or adapters, what is the broader structural role? For signaling molecules, what is the role in the pathway.

We are interested in where in or outside the cell the gene product carries out its function.

We are also interested in the signaling or biochemical pathways in which the gene functions. We are less interested in broad pleiotropic effects, except where these elucidate the precise role.

Include evidence where possible. We are interested in both experimental evidence as well as inference from structure, evolution, or bioinformatic analysis. Precise studies should be prioritized over high-throughput, where available.

Research report: Functional annotation of rice EIL2 / OsEIL2 (UniProt Q8W3L9; locus LOC_Os07g48630 / Os07g0685700) in Oryza sativa ssp. japonica

0) Target verification (mandatory disambiguation)

The literature synthesized here pertains specifically to rice OsEIL2 (EIN3-like transcription factor) encoded by LOC_Os07g48630, matching the UniProt accession Q8W3L9 and the description “ETHYLENE-INSENSITIVE 3-like 2 / OsEIL2”. This is supported by direct functional characterization of OsEIL2 in rice (ZH11 background) (jin2020ethyleneinsensitive3like2(oseil2) pages 1-4, jin2020ethyleneinsensitive3like2(oseil2) pages 4-7) and by a recent rice ethylene-signaling study explicitly treating OsEIL1/OsEIL2 as “master regulators” (qiao2024oseil1andoseil2 pages 1-2).

1) Key concepts and definitions (current understanding)

1.1 EIN3/EIL transcription factors

EIN3/EIL (ETHYLENE INSENSITIVE 3 / EIN3-LIKE) proteins are nuclear transcription factors that act as major integrators of ethylene signaling, converting upstream receptor/EIN2 signals into large transcriptional reprogramming. In canonical ethylene signaling, ethylene perception leads to relief of CTR-mediated inhibition, enabling EIN2 signaling and culminating in stabilized/active EIN3/EIL TFs that activate downstream transcriptional cascades (yang2015ethylenesignalingin pages 6-7, zhao2021ethylenesignalingin pages 1-4).

Rice contains a small EIN3/EIL family; reviews emphasize that OsEIL1 and OsEIL2 are the closest functional equivalents to Arabidopsis EIN3 and are core regulators of rice ethylene responses (yang2015ethylenesignalingin pages 6-7, yang2015ethylenesignalingin pages 7-8).

1.2 Canonical ethylene signaling to EIN3/EILs (rice context)

A conserved model places ethylene receptors (ER-localized) upstream of CTR-like kinases (e.g., OsCTR2) which negatively regulate OsEIN2; ethylene suppresses CTR activity, enabling EIN2-dependent signaling to the nucleus and stabilization of EIN3/EIL TFs (yang2015ethylenesignalingin pages 6-7, zhao2021ethylenesignalingin pages 11-14). Reviews also describe rice-specific regulatory features, including a proposed parallel phosphorelay route and additional modulators of OsEIN2 stability and OsCTR2 regulation (zhao2021ethylenesignalingin pages 65-68, zhao2021ethylenesignalingin pages 20-23).

2) Molecular function of OsEIL2 (what it does)

2.1 Molecular function: DNA-binding transcriptional regulator

OsEIL2 functions as a DNA-binding, nuclear transcriptional regulator in ethylene signaling. It exhibits transactivation activity and acts as a transcriptional activator of downstream genes involved in stress/senescence and coleoptile development (jin2020ethyleneinsensitive3like2(oseil2) pages 10-13, jin2020ethyleneinsensitive3like2(oseil2) pages 4-7).

2.2 DNA-binding and promoter recognition

A recent rice study mapped functional promoter recognition for OsEIL1/OsEIL2 via EBS motifs defined as ATGTA/TACAT in the OsVTC1-3 promoter. OsEIL2 occupancy and activation were supported by ChIP-PCR/ChIP-qPCR, dual-luciferase (dual-LUC) activation assays, and EMSA with N-terminal EIL protein fragments and mutated motif controls (qiao2024oseil1andoseil2 pages 6-7).

3) Subcellular localization (where it acts)

OsEIL2 is nuclear-localized. In a functional characterization study, OsEIL2 fused to GFP/YFP accumulated in nuclei; nuclear fluorescence was detectable/enhanced after treatment with the ethylene precursor ACC and after MG132 (proteasome inhibitor), consistent with ethylene-responsive accumulation and proteasome-linked turnover (jin2020ethyleneinsensitive3like2(oseil2) pages 10-13, jin2020ethyleneinsensitive3like2(oseil2) pages 4-7).

4) Upstream regulation (how OsEIL2 is controlled)

4.1 EBF/proteasome axis and ethylene-dependent stabilization (conceptual)

Canonical pathway models describe EIN3/EIL protein abundance as controlled by EBF1/EBF2 F-box proteins that target EIN3/EILs for proteasomal degradation in the absence of ethylene; ethylene signaling (via EIN2) stabilizes EIN3/EILs by suppressing this degradation framework (yang2015ethylenesignalingin pages 6-7, jin2020ethyleneinsensitive3like2(oseil2) pages 19-21).

In rice OsEIL2 experiments, the observation that MG132 increases nuclear OsEIL2-YFP/GFP signal supports the idea that OsEIL2 is subject to proteasome-sensitive regulation (jin2020ethyleneinsensitive3like2(oseil2) pages 10-13, jin2020ethyleneinsensitive3like2(oseil2) pages 4-7).

4.2 2023–2024 mechanistic advance: translational regulation upstream of EILs (MHZ9)

A major recent advance in rice is the discovery of MHZ9 (GYF-domain protein) as a translational regulator that binds OsEIN2 and directly binds OsEBF1/2 mRNAs to inhibit their translation in RNA processing bodies (P-bodies), thereby enabling OsEIL1 protein accumulation and ethylene responses (huang2023atranslationalregulator pages 1-2, huang2023atranslationalregulator pages 10-11). Ribo-seq analysis indicated MHZ9 is required for the regulation of ~90% of ethylene-responsive translational efficiency changes, emphasizing widespread post-transcriptional control in the ethylene response network (huang2023atranslationalregulator pages 1-2, huang2023atranslationalregulator pages 9-10). While this study provides direct evidence for EIL1 accumulation, it supports an updated mechanistic framework in which translational control of EBFs can broadly modulate downstream EIN3/EIL outputs in rice (huang2023atranslationalregulator pages 10-11, huang2023atranslationalregulator pages 9-10).

4.3 Rice-specific regulators upstream of the EIL layer (review evidence)

Reviews describe additional rice-specific modulators of early ethylene signaling, including mechanisms influencing OsCTR2 phosphorylation and OsEIN2 stability (e.g., MHZ11 sterol-dependent modulation of receptor–OsCTR2 interaction; MHZ3 protection of OsEIN2 from ubiquitination), reinforcing that OsEIL1/OsEIL2 outputs can be tuned by rice-unique regulators (zhao2021ethylenesignalingin pages 11-14, zhao2021ethylenesignalingin pages 20-23).

5) Downstream targets, pathways, and biological roles of OsEIL2

Two OsEIL2-centered, experimentally supported modules currently provide the clearest functional annotation.

5.1 Abiotic stress sensitivity and senescence via BURP genes and cell-wall remodeling

A rice functional characterization study concluded that OsEIL2 negatively regulates salt and drought tolerance and promotes senescence-related phenotypes. Key points:

Induction: OsEIL2 transcript is induced by abiotic and hormonal cues (e.g., NaCl, PEG/drought mimic, darkness, ABA), supporting a role in stress and senescence responses (jin2020ethyleneinsensitive3like2(oseil2) pages 1-4, jin2020ethyleneinsensitive3like2(oseil2) pages 13-16).
Direct transcriptional targets: OsEIL2 directly binds promoters and activates transcription of OsBURP14 and OsBURP16 (a PG1β-like BURP gene), supported by promoter-binding assays (ChIP/EMSA) and transcriptional activation evidence (jin2020ethyleneinsensitive3like2(oseil2) pages 1-4, jin2020ethyleneinsensitive3like2(oseil2) pages 10-13, jin2020ethyleneinsensitive3like2(oseil2) pages 16-19).
Biochemical mechanism: OsEIL2 overexpression increases polygalacturonase (PG) activity and reduces pectin content, consistent with cell-wall remodeling that can reduce cell adhesion and predispose seedlings to abiotic stress sensitivity (jin2020ethyleneinsensitive3like2(oseil2) pages 1-4, jin2020ethyleneinsensitive3like2(oseil2) pages 10-13). The methods specify PG activity reporting units (mmol reducing end groups per 100 mg cell wall material) and uronic-acid-based pectin quantification, though numerical values were not available in the retrieved text segments (jin2020ethyleneinsensitive3like2(oseil2) pages 16-19).

Interpretation: In rice, OsEIL2 acts as a transcriptional activator that links ethylene signaling to cell-wall pectin remodeling through a BURP/PG axis, with consequences for stress sensitivity and senescence progression (jin2020ethyleneinsensitive3like2(oseil2) pages 1-4, jin2020ethyleneinsensitive3like2(oseil2) pages 10-13).

5.2 Coleoptile elongation and direct-seeding emergence via ROS scavenging genes (2024)

A 2024 study positions OsEIL1 and OsEIL2 as “two master regulators of rice ethylene signaling” that promote coleoptile elongation and seedling emergence (direct seeding context) via ROS management:

Direct targets: OsEIL1/OsEIL2 directly activate ROS-scavenging genes including OsVTC1-3 (GDP-mannose pyrophosphorylase in ascorbate biosynthesis) and peroxidase genes OsPRX37, OsPRX81, OsPRX82, OsPRX88, supported by promoter motif mapping (EBS), ChIP-PCR/qPCR, EMSA, and dual-LUC assays (qiao2024oseil1andoseil2 pages 6-7).
Pathway effect: This activation attenuates ROS accumulation in the upper coleoptile region and supports growth responses (qiao2024oseil1andoseil2 pages 1-2, qiao2024oseil1andoseil2 pages 7-8).
Genetic evidence: Overexpression of OsVTC1-3 in an eil1 background rescues the short-coleoptile phenotype, supporting a downstream role for this ROS-scavenging pathway in ethylene/EIL-regulated coleoptile growth (qiao2024oseil1andoseil2 pages 6-7).
Quantitative phenotype statistics: Under ethylene, RbohH overexpression (increasing ROS production) reduced the magnitude of ethylene-driven coleoptile cell-length increase (~10%) and apex-thickness decrease (~6%), whereas VTC1-3 overexpression increased these responses (~23% cell-length increase and ~18% apex-thickness decrease); significance testing used t-tests and ANOVA/Tukey, with typical n ≥ 20 seedlings or 20–30 cells for cellular measures (qiao2024oseil1andoseil2 pages 6-7).
Real-world framing: The authors explicitly link these findings to direct-seeding rice, noting the work provides guidance for breeders to develop varieties suitable for direct seeding by improving uniform seedling emergence (qiao2024oseil1andoseil2 pages 7-8).

Visual evidence: Key figure panels illustrating downregulation of OsVTC1-3/PRX genes in ethylene-signaling mutants and genetic rescue by VTC1-3 overexpression are available (qiao2024oseil1andoseil2 media 8927e337, qiao2024oseil1andoseil2 media 6ddcba1c).

6) Phenotypes of OsEIL2 perturbation (gain/loss of function)

6.1 OsEIL2 overexpression vs knockdown (stress/senescence module)

In rice transgenics, OsEIL2 overexpression was associated with growth retardation (shorter roots/shoots), enhanced ethylene sensitivity, accelerated dark-induced senescence, and reduced salt and drought tolerance, whereas OsEIL2-RNAi lines displayed opposite trends including improved stress tolerance and delayed senescence (jin2020ethyleneinsensitive3like2(oseil2) pages 1-4, jin2020ethyleneinsensitive3like2(oseil2) pages 10-13, jin2020ethyleneinsensitive3like2(oseil2) pages 4-7). The stress assays described include 200 mM NaCl irrigation and drought-withholding designs with survival scoring after recovery (methods provided, numeric outcomes not present in retrieved segments) (jin2020ethyleneinsensitive3like2(oseil2) pages 13-16).

6.2 EIL1/EIL2 mutant context (coleoptile emergence module)

In the 2024 coleoptile study, ein2 and eil1 eil2 mutants showed reduced expression of ROS scavenging genes and impaired ethylene-regulated coleoptile growth/emergence traits (qiao2024oseil1andoseil2 pages 1-2, qiao2024oseil1andoseil2 media 8927e337, qiao2024oseil1andoseil2 media 6ddcba1c).

7) Expert opinions and analysis (authoritative synthesis)

Two authoritative reviews frame OsEIL2’s interpretation:

Conserved core, divergent outputs: Rice ethylene signaling shares the receptor→CTR→EIN2→EIL logic with Arabidopsis, but rice has multiple unique regulators and organ-specific outcomes (e.g., coleoptile elongation) that are agronomically important (yang2015ethylenesignalingin pages 6-7, zhao2021ethylenesignalingin pages 65-68).
OsEIL1/OsEIL2 as central nodes: Reviews highlight that, among rice OsEILs, OsEIL1 and OsEIL2 are especially central to ethylene output, supporting the interpretation that OsEIL2 functional perturbation will have system-level consequences across growth and stress modules (yang2015ethylenesignalingin pages 6-7, yang2015ethylenesignalingin pages 7-8).

8) Current applications and real-world implementations

8.1 Direct-seeded rice: improving emergence via OsEIL2-linked ROS scavenging

Direct seeding demands uniform seedling emergence. The 2024 Plant Communications study explicitly positions the OsEIL1/OsEIL2→(OsVTC1-3, PRXs) module as a mechanistic route by which ethylene promotes coleoptile elongation and seedling emergence from soil and states that the work provides guidance for breeders targeting direct-seeding suitability (qiao2024oseil1andoseil2 pages 7-8, qiao2024oseil1andoseil2 pages 6-7).

8.2 Stress resilience tradeoffs: OsEIL2 as a negative regulator of salt/drought tolerance

OsEIL2 overexpression reduces salt/drought tolerance through BURP/pectin/PG-mediated cell-wall remodeling, whereas knockdown enhances tolerance, suggesting that OsEIL2 is a candidate target for engineering or breeding for abiotic resilience—potentially at the cost of other ethylene-dependent traits (jin2020ethyleneinsensitive3like2(oseil2) pages 1-4, jin2020ethyleneinsensitive3like2(oseil2) pages 10-13).

8.3 Regulatory intervention points beyond OsEIL2: translational control (MHZ9)

The discovery of MHZ9 introduces an upstream lever (translation of OsEBF1/2) that can modulate downstream EIL responses, potentially enabling tuning of ethylene outputs without directly manipulating EIL coding sequence (huang2023atranslationalregulator pages 1-2, huang2023atranslationalregulator pages 10-11).

9) Statistics and data highlights (from recent studies)

Coleoptile cellular morphology response under ethylene: VTC1-3-OX lines show ~23% increase in coleoptile cell length and ~18% decrease in apex thickness; RbohH-OX shows ~10% cell-length increase and ~6% apex-thickness decrease; experiments report statistical testing (t-test; ANOVA/Tukey) and typically n ≥ 20 seedlings or 20–30 cells (qiao2024oseil1andoseil2 pages 6-7).
Scale of translational regulation in ethylene response (MHZ9): MHZ9 is required for ~90% of ethylene-responsive translational efficiency changes in rice, underscoring that post-transcriptional control is a major layer in ethylene signaling (huang2023atranslationalregulator pages 1-2, huang2023atranslationalregulator pages 9-10).

10) Evidence summary table

Category	Evidence summary	Experimental basis	Quantitative/statistical notes	Key sources with year/URL
Identity / domains	OsEIL2 is the rice (Oryza sativa subsp. japonica) EIN3-like transcription factor encoded by LOC_Os07g48630, corresponding to UniProt Q8W3L9; reviews place it in the small rice EIN3/EIL family and identify OsEIL1/OsEIL2 as the closest functional equivalents of Arabidopsis EIN3. OsEIL proteins are nuclear DNA-binding TFs with a conserved EIN3/EIL DNA-binding region and less-conserved C termini that likely confer regulatory specificity. (jin2020ethyleneinsensitive3like2(oseil2) pages 1-4, yang2015ethylenesignalingin pages 6-7, yang2015ethylenesignalingin pages 7-8, chowdhory2025genomewidecharacterizationand pages 1-2)	Primary functional characterization plus pathway reviews/family summaries	Rice family size reported as six OsEILs in reviews; OsEIL1/OsEIL2 highlighted as core ethylene regulators rather than all family members equally. (yang2015ethylenesignalingin pages 6-7, yang2015ethylenesignalingin pages 7-8)	Jin 2020 Plant Science, https://doi.org/10.1016/j.plantsci.2019.110353; Yang 2015 Molecular Plant, https://doi.org/10.1016/j.molp.2015.01.003; Zhao 2021 JIPB, https://doi.org/10.1111/jipb.13028
Localization	OsEIL2 is nuclear-localized. OsEIL2-GFP/OsEIL2-YFP colocalized with a nuclear marker, and nuclear fluorescence increased after ACC or MG132 treatment, consistent with ethylene-responsive accumulation and proteasome-sensitive turnover. (jin2020ethyleneinsensitive3like2(oseil2) pages 10-13, jin2020ethyleneinsensitive3like2(oseil2) pages 4-7, jin2020ethyleneinsensitive3like2(oseil2) pages 13-16)	Transient/stable GFP or YFP localization; ACC and MG132 treatments in rice/N. benthamiana systems	ACC and MG132 treatments were applied for fluorescence detection; exact effect sizes are figure-based and not numerically reported in the retrieved text. (jin2020ethyleneinsensitive3like2(oseil2) pages 10-13, jin2020ethyleneinsensitive3like2(oseil2) pages 13-16)	Jin 2020 Plant Science, https://doi.org/10.1016/j.plantsci.2019.110353
Upstream regulation in ethylene signaling	Canonical rice ethylene signaling places OsEIL2 downstream of receptors/OsCTR2 and OsEIN2. In conserved models, ethylene suppresses CTR activity, enabling EIN2 signaling and reducing EBF-mediated turnover of EIN3/EIL proteins. Rice-specific regulators include MHZ3 (stabilizes OsEIN2), MHZ11 (sterol/lipid-dependent modulation of receptor–OsCTR2), and MHZ9, which binds OsEIN2 and represses translation of OsEBF1/2 mRNAs, permitting OsEIL1 accumulation; MHZ9 likely affects broader EIL outputs indirectly, potentially including OsEIL2. (zhao2021ethylenesignalingin pages 65-68, yang2015ethylenesignalingin pages 6-7, zhao2021ethylenesignalingin pages 20-23, huang2023atranslationalregulator pages 1-2, huang2023atranslationalregulator pages 10-11, huang2023atranslationalregulator pages 9-10)	Genetic mutants/reviews for OsCTR2/OsEIN2/MHZ regulators; MHZ9 study used BiFC, RIP/CLIP-seq, Ribo-seq, polysome profiling, western blot	MHZ9 required for ~90% of ethylene-responsive translational changes; translation efficiency of OsEBF1/2 was strongly reduced in WT but disrupted in mhz9. Direct OsEIL2-specific MHZ9 quantitation was not provided. (huang2023atranslationalregulator pages 1-2, huang2023atranslationalregulator pages 10-11, huang2023atranslationalregulator pages 9-10)	Zhao 2021 JIPB, https://doi.org/10.1111/jipb.13028; Yang 2015 Molecular Plant, https://doi.org/10.1016/j.molp.2015.01.003; Huang 2023 Nature Communications, https://doi.org/10.1038/s41467-023-40429-0
DNA-binding motif / transcriptional mechanism	OsEIL2 functions as a transcriptional activator. For VTC1-3, OsEIL1/OsEIL2 bind EBS motifs defined in the paper as ATGTA/TACAT. EMSA used N-terminal EIL proteins for binding, while ChIP-qPCR and dual-LUC supported promoter occupancy/activation in vivo. OsEIL2 also directly binds BURP promoters (OsBURP14/16), although the exact motif sequence was not given in the retrieved Jin text. (jin2020ethyleneinsensitive3like2(oseil2) pages 10-13, qiao2024oseil1andoseil2 pages 1-2, qiao2024oseil1andoseil2 pages 6-7, jin2020ethyleneinsensitive3like2(oseil2) pages 16-19)	Yeast transactivation, ChIP-PCR/qPCR, EMSA, dual-LUC	OsEIL2 transactivation domain was mapped to the C-terminal region aa 344–583 in one retrieved summary; EMSA for VTC1-3 used mutated EBS controls for specificity. (jin2020ethyleneinsensitive3like2(oseil2) pages 1-4, qiao2024oseil1andoseil2 pages 6-7)	Jin 2020 Plant Science, https://doi.org/10.1016/j.plantsci.2019.110353; Qiao 2024 Plant Communications, https://doi.org/10.1016/j.xplc.2023.100771
Direct target genes	Best-supported direct OsEIL2 targets are OsBURP16 and OsBURP14 (cell-wall/PG-related BURP genes), plus ROS-scavenging genes OsVTC1-3, OsPRX37, OsPRX81, OsPRX82, and OsPRX88. Reviews also note OsEIL2 can directly repress GY1, linking ethylene to jasmonate/lipid-related growth pathways. OsACO2 expression changes in OsEIL2 transgenics, but direct binding evidence was not shown in the retrieved excerpts. (jin2020ethyleneinsensitive3like2(oseil2) pages 1-4, jin2020ethyleneinsensitive3like2(oseil2) pages 10-13, jin2020ethyleneinsensitive3like2(oseil2) pages 4-7, qiao2024oseil1andoseil2 pages 1-2, zhao2021ethylenesignalingin pages 65-68, qiao2024oseil1andoseil2 pages 6-7)	ChIP-qPCR, EMSA, dual-LUC, expression analysis in OX/RNAi/mutant backgrounds	VTC1-3 and multiple PRX genes were significantly downregulated in ein2 and eil1 eil2 mutants; OsACO2 up in OX and down in RNAi was reported without direct-target confirmation. (jin2020ethyleneinsensitive3like2(oseil2) pages 4-7, qiao2024oseil1andoseil2 media 8927e337, qiao2024oseil1andoseil2 media 6ddcba1c)	Jin 2020 Plant Science, https://doi.org/10.1016/j.plantsci.2019.110353; Qiao 2024 Plant Communications, https://doi.org/10.1016/j.xplc.2023.100771; Zhao 2021 JIPB, https://doi.org/10.1111/jipb.13028
Downstream processes / pathway outputs	OsEIL2 links ethylene signaling to cell-wall remodeling, ROS homeostasis, abiotic stress responses, senescence, and seedling emergence. In the BURP16 module, OsEIL2 increases PG activity and lowers pectin content, reducing cell adhesion and increasing salt/drought sensitivity. In coleoptiles, OsEIL1/OsEIL2 activate ROS-scavenging genes, elevating ascorbate/peroxidase activity and reducing ROS in the coleoptile apex, thereby promoting elongation and emergence from soil. Reviews further connect OsEIL2 to JA crosstalk via repression of GY1. (jin2020ethyleneinsensitive3like2(oseil2) pages 1-4, jin2020ethyleneinsensitive3like2(oseil2) pages 10-13, qiao2024oseil1andoseil2 pages 1-2, zhao2021ethylenesignalingin pages 65-68, qiao2024oseil1andoseil2 pages 7-8, qiao2024oseil1andoseil2 pages 6-7)	PG and pectin assays; ROS/H2O2, ascorbate, peroxidase assays; emergence and coleoptile measurements; pathway review synthesis	Qiao 2024 reports ROS-scavenging genes down in ein2 and eil1 eil2 and rescue of eil1 short-coleoptile phenotype by VTC1-3 overexpression; Jin 2020 reports PG/pectin directionality but retrieved text lacked numerical values. (qiao2024oseil1andoseil2 media 8927e337, qiao2024oseil1andoseil2 media 6ddcba1c, qiao2024oseil1andoseil2 pages 6-7)	Jin 2020 Plant Science, https://doi.org/10.1016/j.plantsci.2019.110353; Qiao 2024 Plant Communications, https://doi.org/10.1016/j.xplc.2023.100771; Zhao 2021 JIPB, https://doi.org/10.1111/jipb.13028
Phenotypes from gain/loss of function	OsEIL2 overexpression causes shorter roots, slightly dwarfed shoots, increased ACC sensitivity, delayed flowering/leaf development, accelerated dark-induced senescence, and reduced salt/drought tolerance; RNAi/knockdown lines show taller shoots, reduced ethylene sensitivity, delayed senescence, and improved salt/drought tolerance. Recent work on eil1 eil2 double mutants shows impaired coleoptile elongation/ethylene response and reduced expression of ROS-scavenging genes, impairing seedling emergence from soil. (jin2020ethyleneinsensitive3like2(oseil2) pages 1-4, jin2020ethyleneinsensitive3like2(oseil2) pages 10-13, jin2020ethyleneinsensitive3like2(oseil2) pages 4-7, qiao2024oseil1andoseil2 pages 1-2, qiao2024oseil1andoseil2 pages 6-7, jin2020ethyleneinsensitive3like2(oseil2) pages 13-16)	Overexpression and RNAi transgenics; ACC dose-response; dark senescence assays; salt/drought survival assays; mutant phenotyping under ethylene/soil cover	Stress assays in Jin 2020 used 200 mM NaCl, 20% PEG, 10 µM ACC, 100 µM ABA, and dark treatment; exact survival percentages and growth values are figure-based in retrieved text. Qiao 2024 reports measurable changes in cell length/apex thickness and emergence rate, with significance by ANOVA/t-tests. (qiao2024oseil1andoseil2 pages 6-7, jin2020ethyleneinsensitive3like2(oseil2) pages 13-16)	Jin 2020 Plant Science, https://doi.org/10.1016/j.plantsci.2019.110353; Qiao 2024 Plant Communications, https://doi.org/10.1016/j.xplc.2023.100771
Quantitative / statistical notes	Available snippets preserve some quantitative details from Qiao 2024: VTC1-3-OX seedlings showed larger ethylene-induced increases in coleoptile cell length (~23%) and decreases in coleoptile apex thickness (~18%) versus WT (~22%/14% in Nip; ~20%/5% in ZH17 depending on comparison shown). RbohH-OX showed smaller changes (~10% increase in cell length and ~6% decrease in apex thickness). Statistical testing included Student’s t-test and one-way ANOVA with Tukey’s test; many assays used three biological replicates, whereas length/cell measurements used ≥20 seedlings or 20–30 cells. (qiao2024oseil1andoseil2 pages 7-8, qiao2024oseil1andoseil2 pages 6-7, jin2020ethyleneinsensitive3like2(oseil2) pages 13-16, jin2020ethyleneinsensitive3like2(oseil2) pages 16-19)	Figure-linked quantitative phenotyping and biochemical assays	Jin 2020 methods state qPCR datasets had three replicates and experiments were repeated twice; ChIP used ~2 g seedlings; PG activity expressed as mmol reducing end groups per 100 mg CWM. (jin2020ethyleneinsensitive3like2(oseil2) pages 13-16, jin2020ethyleneinsensitive3like2(oseil2) pages 16-19)	Qiao 2024 Plant Communications, https://doi.org/10.1016/j.xplc.2023.100771; Jin 2020 Plant Science, https://doi.org/10.1016/j.plantsci.2019.110353
Related immunity context / caution	Strong direct immunity evidence in the retrieved set is for OsEIL1 rather than OsEIL2: OsEIL1 activates OsrbohA/B and OsOPR4 to enhance blast resistance through ROS/JA/phytoalexin pathways. For OsEIL2, retrieved direct evidence supports abiotic stress, senescence, and coleoptile ROS-scavenging functions; reviews note hormone crosstalk and mention GY1 repression and possible defense connections, but OsEIL2-specific immunity claims should be stated cautiously unless the dedicated 2024 immunity paper is consulted directly. (yang2017activationofethylene pages 1-4, zhao2021ethylenesignalingin pages 65-68, chowdhory2025genomewidecharacterizationand pages 15-17)	Primary immunity study plus reviews	Avoid over-attributing OsEIL1 immunity data to OsEIL2 without direct paper access. (yang2017activationofethylene pages 1-4, chowdhory2025genomewidecharacterizationand pages 15-17)	Yang 2017 The Plant Journal, https://doi.org/10.1111/tpj.13388; Zhao 2021 JIPB, https://doi.org/10.1111/jipb.13028

Table: This table condenses the strongest available evidence for the identity, regulation, targets, localization, and phenotypes of rice OsEIL2 (Q8W3L9/LOC_Os07g48630). It is designed to support functional annotation by separating direct experimental findings from broader pathway inferences.

11) Key limitations of this synthesis

Several OsEIL2 results (e.g., exact PG activity/pectin percentage changes; survival percentages under salt/drought) are referenced in figures of the primary study but were not numerically available in the retrieved text segments, limiting quantitative reporting for those assays (jin2020ethyleneinsensitive3like2(oseil2) pages 10-13, jin2020ethyleneinsensitive3like2(oseil2) pages 13-16).
Strong OsEIL2-specific biotic immunity claims were not supported by a directly retrieved OsEIL2 immunity primary paper in the current evidence set; one high-quality immunity paper in the retrieved set primarily supports OsEIL1 roles in defense (yang2017activationofethylene pages 1-4). Therefore, OsEIL2 immunity statements should be treated as provisional unless the dedicated OsEIL2 immunity literature is consulted.

References (URLs and publication dates)

Qiao et al. “OsEIL1 and OsEIL2… facilitate coleoptile elongation and seedling emergence from soil.” Plant Communications (published online 2024-03-11). https://doi.org/10.1016/j.xplc.2023.100771 (qiao2024oseil1andoseil2 pages 1-2, qiao2024oseil1andoseil2 pages 7-8, qiao2024oseil1andoseil2 pages 6-7)
Huang et al. “A translational regulator MHZ9 modulates ethylene signaling in rice.” Nature Communications (2023-08). https://doi.org/10.1038/s41467-023-40429-0 (huang2023atranslationalregulator pages 1-2, huang2023atranslationalregulator pages 10-11, huang2023atranslationalregulator pages 9-10)
Jin et al. “Ethylene insensitive3-like2 (OsEIL2) confers stress sensitivity…” Plant Science (2020-03). https://doi.org/10.1016/j.plantsci.2019.110353 (jin2020ethyleneinsensitive3like2(oseil2) pages 1-4, jin2020ethyleneinsensitive3like2(oseil2) pages 10-13, jin2020ethyleneinsensitive3like2(oseil2) pages 4-7)
Zhao et al. “Ethylene signaling in rice and Arabidopsis: New regulators and mechanisms.” Journal of Integrative Plant Biology (2021-01). https://doi.org/10.1111/jipb.13028 (zhao2021ethylenesignalingin pages 65-68, zhao2021ethylenesignalingin pages 20-23, zhao2021ethylenesignalingin pages 11-14)
Yang et al. “Ethylene signaling in rice and Arabidopsis: conserved and diverged aspects.” Molecular Plant (2015-04). https://doi.org/10.1016/j.molp.2015.01.003 (yang2015ethylenesignalingin pages 6-7, yang2015ethylenesignalingin pages 7-8)
Yang et al. “Activation of ethylene signaling pathways enhances disease resistance…” The Plant Journal (2017-01). https://doi.org/10.1111/tpj.13388 (yang2017activationofethylene pages 1-4)

References

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(jin2020ethyleneinsensitive3like2(oseil2) pages 4-7): Jing Jin, Jianli Duan, Chi Shan, Zhiling Mei, Haiying Chen, Huafeng Feng, Jian Zhu, and Weiming Cai. Ethylene insensitive3-like2 (oseil2) confers stress sensitivity by regulating osburp16, the β subunit of polygalacturonase (pg1β-like) subfamily gene in rice. Plant science : an international journal of experimental plant biology, 292:110353, Mar 2020. URL: https://doi.org/10.1016/j.plantsci.2019.110353, doi:10.1016/j.plantsci.2019.110353. This article has 43 citations.
(qiao2024oseil1andoseil2 pages 1-2): Jinzhu Qiao, Ruidang Quan, Juan Wang, Yuxiang Li, Dinglin Xiao, Zihan Zhao, Rongfeng Huang, and Hua Qin. Oseil1 and oseil2, two master regulators of rice ethylene signaling, promote the expression of ros scavenging genes to facilitate coleoptile elongation and seedling emergence from soil. Plant Communications, 5(3):100771, Mar 2024. URL: https://doi.org/10.1016/j.xplc.2023.100771, doi:10.1016/j.xplc.2023.100771. This article has 34 citations and is from a peer-reviewed journal.
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(zhao2021ethylenesignalingin pages 11-14): He Zhao, Cui‐Cui Yin, Biao Ma, Shou‐Yi Chen, and Jin‐Song Zhang. Ethylene signaling in rice and arabidopsis: new regulators and mechanisms. Journal of Integrative Plant Biology, 63:102-125, Jan 2021. URL: https://doi.org/10.1111/jipb.13028, doi:10.1111/jipb.13028. This article has 238 citations and is from a peer-reviewed journal.
(zhao2021ethylenesignalingin pages 65-68): He Zhao, Cui‐Cui Yin, Biao Ma, Shou‐Yi Chen, and Jin‐Song Zhang. Ethylene signaling in rice and arabidopsis: new regulators and mechanisms. Journal of Integrative Plant Biology, 63:102-125, Jan 2021. URL: https://doi.org/10.1111/jipb.13028, doi:10.1111/jipb.13028. This article has 238 citations and is from a peer-reviewed journal.
(zhao2021ethylenesignalingin pages 20-23): He Zhao, Cui‐Cui Yin, Biao Ma, Shou‐Yi Chen, and Jin‐Song Zhang. Ethylene signaling in rice and arabidopsis: new regulators and mechanisms. Journal of Integrative Plant Biology, 63:102-125, Jan 2021. URL: https://doi.org/10.1111/jipb.13028, doi:10.1111/jipb.13028. This article has 238 citations and is from a peer-reviewed journal.
(jin2020ethyleneinsensitive3like2(oseil2) pages 10-13): Jing Jin, Jianli Duan, Chi Shan, Zhiling Mei, Haiying Chen, Huafeng Feng, Jian Zhu, and Weiming Cai. Ethylene insensitive3-like2 (oseil2) confers stress sensitivity by regulating osburp16, the β subunit of polygalacturonase (pg1β-like) subfamily gene in rice. Plant science : an international journal of experimental plant biology, 292:110353, Mar 2020. URL: https://doi.org/10.1016/j.plantsci.2019.110353, doi:10.1016/j.plantsci.2019.110353. This article has 43 citations.
(qiao2024oseil1andoseil2 pages 6-7): Jinzhu Qiao, Ruidang Quan, Juan Wang, Yuxiang Li, Dinglin Xiao, Zihan Zhao, Rongfeng Huang, and Hua Qin. Oseil1 and oseil2, two master regulators of rice ethylene signaling, promote the expression of ros scavenging genes to facilitate coleoptile elongation and seedling emergence from soil. Plant Communications, 5(3):100771, Mar 2024. URL: https://doi.org/10.1016/j.xplc.2023.100771, doi:10.1016/j.xplc.2023.100771. This article has 34 citations and is from a peer-reviewed journal.
(jin2020ethyleneinsensitive3like2(oseil2) pages 19-21): Jing Jin, Jianli Duan, Chi Shan, Zhiling Mei, Haiying Chen, Huafeng Feng, Jian Zhu, and Weiming Cai. Ethylene insensitive3-like2 (oseil2) confers stress sensitivity by regulating osburp16, the β subunit of polygalacturonase (pg1β-like) subfamily gene in rice. Plant science : an international journal of experimental plant biology, 292:110353, Mar 2020. URL: https://doi.org/10.1016/j.plantsci.2019.110353, doi:10.1016/j.plantsci.2019.110353. This article has 43 citations.
(huang2023atranslationalregulator pages 1-2): Yi-Hua Huang, Jia-Qi Han, Biao Ma, Wu-Qiang Cao, Xin-Kai Li, Qing Xiong, He Zhao, Rui Zhao, Xun Zhang, Yang Zhou, Wei Wei, Jian-Jun Tao, Wan-Ke Zhang, Wenfeng Qian, Shou-Yi Chen, Chao Yang, Cui-Cui Yin, and Jin-Song Zhang. A translational regulator mhz9 modulates ethylene signaling in rice. Nature Communications, Aug 2023. URL: https://doi.org/10.1038/s41467-023-40429-0, doi:10.1038/s41467-023-40429-0. This article has 21 citations and is from a highest quality peer-reviewed journal.
(huang2023atranslationalregulator pages 10-11): Yi-Hua Huang, Jia-Qi Han, Biao Ma, Wu-Qiang Cao, Xin-Kai Li, Qing Xiong, He Zhao, Rui Zhao, Xun Zhang, Yang Zhou, Wei Wei, Jian-Jun Tao, Wan-Ke Zhang, Wenfeng Qian, Shou-Yi Chen, Chao Yang, Cui-Cui Yin, and Jin-Song Zhang. A translational regulator mhz9 modulates ethylene signaling in rice. Nature Communications, Aug 2023. URL: https://doi.org/10.1038/s41467-023-40429-0, doi:10.1038/s41467-023-40429-0. This article has 21 citations and is from a highest quality peer-reviewed journal.
(huang2023atranslationalregulator pages 9-10): Yi-Hua Huang, Jia-Qi Han, Biao Ma, Wu-Qiang Cao, Xin-Kai Li, Qing Xiong, He Zhao, Rui Zhao, Xun Zhang, Yang Zhou, Wei Wei, Jian-Jun Tao, Wan-Ke Zhang, Wenfeng Qian, Shou-Yi Chen, Chao Yang, Cui-Cui Yin, and Jin-Song Zhang. A translational regulator mhz9 modulates ethylene signaling in rice. Nature Communications, Aug 2023. URL: https://doi.org/10.1038/s41467-023-40429-0, doi:10.1038/s41467-023-40429-0. This article has 21 citations and is from a highest quality peer-reviewed journal.
(jin2020ethyleneinsensitive3like2(oseil2) pages 13-16): Jing Jin, Jianli Duan, Chi Shan, Zhiling Mei, Haiying Chen, Huafeng Feng, Jian Zhu, and Weiming Cai. Ethylene insensitive3-like2 (oseil2) confers stress sensitivity by regulating osburp16, the β subunit of polygalacturonase (pg1β-like) subfamily gene in rice. Plant science : an international journal of experimental plant biology, 292:110353, Mar 2020. URL: https://doi.org/10.1016/j.plantsci.2019.110353, doi:10.1016/j.plantsci.2019.110353. This article has 43 citations.
(jin2020ethyleneinsensitive3like2(oseil2) pages 16-19): Jing Jin, Jianli Duan, Chi Shan, Zhiling Mei, Haiying Chen, Huafeng Feng, Jian Zhu, and Weiming Cai. Ethylene insensitive3-like2 (oseil2) confers stress sensitivity by regulating osburp16, the β subunit of polygalacturonase (pg1β-like) subfamily gene in rice. Plant science : an international journal of experimental plant biology, 292:110353, Mar 2020. URL: https://doi.org/10.1016/j.plantsci.2019.110353, doi:10.1016/j.plantsci.2019.110353. This article has 43 citations.
(qiao2024oseil1andoseil2 pages 7-8): Jinzhu Qiao, Ruidang Quan, Juan Wang, Yuxiang Li, Dinglin Xiao, Zihan Zhao, Rongfeng Huang, and Hua Qin. Oseil1 and oseil2, two master regulators of rice ethylene signaling, promote the expression of ros scavenging genes to facilitate coleoptile elongation and seedling emergence from soil. Plant Communications, 5(3):100771, Mar 2024. URL: https://doi.org/10.1016/j.xplc.2023.100771, doi:10.1016/j.xplc.2023.100771. This article has 34 citations and is from a peer-reviewed journal.
(qiao2024oseil1andoseil2 media 8927e337): Jinzhu Qiao, Ruidang Quan, Juan Wang, Yuxiang Li, Dinglin Xiao, Zihan Zhao, Rongfeng Huang, and Hua Qin. Oseil1 and oseil2, two master regulators of rice ethylene signaling, promote the expression of ros scavenging genes to facilitate coleoptile elongation and seedling emergence from soil. Plant Communications, 5(3):100771, Mar 2024. URL: https://doi.org/10.1016/j.xplc.2023.100771, doi:10.1016/j.xplc.2023.100771. This article has 34 citations and is from a peer-reviewed journal.
(qiao2024oseil1andoseil2 media 6ddcba1c): Jinzhu Qiao, Ruidang Quan, Juan Wang, Yuxiang Li, Dinglin Xiao, Zihan Zhao, Rongfeng Huang, and Hua Qin. Oseil1 and oseil2, two master regulators of rice ethylene signaling, promote the expression of ros scavenging genes to facilitate coleoptile elongation and seedling emergence from soil. Plant Communications, 5(3):100771, Mar 2024. URL: https://doi.org/10.1016/j.xplc.2023.100771, doi:10.1016/j.xplc.2023.100771. This article has 34 citations and is from a peer-reviewed journal.
(chowdhory2025genomewidecharacterizationand pages 1-2): Maria Chowdhory, Sanjana Tabassum Tuba, Jaber Bin Azim, and Arif Hasan Khan Robin. Genome-wide characterization and expression profiling of ein3/eil family genes in oryza sativa var. japonica. Discover Plants, Dec 2025. URL: https://doi.org/10.1007/s44372-025-00422-x, doi:10.1007/s44372-025-00422-x. This article has 0 citations.
(yang2017activationofethylene pages 1-4): Chao Yang, Wen Li, Jidong Cao, Fanwei Meng, Yongqi Yu, Junkai Huang, Lan Jiang, Muxing Liu, Zhengguang Zhang, Xuewei Chen, Koji Miyamoto, Hisakazu Yamane, Jinsong Zhang, Shouyi Chen, and Jun Liu. Activation of ethylene signaling pathways enhances disease resistance by regulating ros and phytoalexin production in rice. The Plant Journal, 89:338–353, Jan 2017. URL: https://doi.org/10.1111/tpj.13388, doi:10.1111/tpj.13388. This article has 251 citations.
(chowdhory2025genomewidecharacterizationand pages 15-17): Maria Chowdhory, Sanjana Tabassum Tuba, Jaber Bin Azim, and Arif Hasan Khan Robin. Genome-wide characterization and expression profiling of ein3/eil family genes in oryza sativa var. japonica. Discover Plants, Dec 2025. URL: https://doi.org/10.1007/s44372-025-00422-x, doi:10.1007/s44372-025-00422-x. This article has 0 citations.

Artifacts

Edison artifact artifact-00

Citations

yang2017activationofethylene pages 1-4
yang2015ethylenesignalingin pages 6-7
zhao2021ethylenesignalingin pages 1-4
yang2015ethylenesignalingin pages 7-8
zhao2021ethylenesignalingin pages 11-14
zhao2021ethylenesignalingin pages 65-68
zhao2021ethylenesignalingin pages 20-23
huang2023atranslationalregulator pages 1-2
huang2023atranslationalregulator pages 10-11
huang2023atranslationalregulator pages 9-10
chowdhory2025genomewidecharacterizationand pages 1-2
chowdhory2025genomewidecharacterizationand pages 15-17
https://doi.org/10.1016/j.plantsci.2019.110353;
https://doi.org/10.1016/j.molp.2015.01.003;
https://doi.org/10.1111/jipb.13028
https://doi.org/10.1016/j.plantsci.2019.110353
https://doi.org/10.1111/jipb.13028;
https://doi.org/10.1038/s41467-023-40429-0
https://doi.org/10.1016/j.xplc.2023.100771
https://doi.org/10.1016/j.xplc.2023.100771;
https://doi.org/10.1111/tpj.13388;
https://doi.org/10.1016/j.molp.2015.01.003
https://doi.org/10.1111/tpj.13388
https://doi.org/10.1016/j.plantsci.2019.110353,
https://doi.org/10.1016/j.xplc.2023.100771,
https://doi.org/10.1016/j.molp.2015.01.003,
https://doi.org/10.1111/jipb.13028,
https://doi.org/10.1038/s41467-023-40429-0,
https://doi.org/10.1007/s44372-025-00422-x,
https://doi.org/10.1111/tpj.13388,

📄 View Raw YAML

id: Q8W3L9
gene_symbol: EIL2
product_type: PROTEIN
status: COMPLETE
taxon:
  id: NCBITaxon:39947
  label: Oryza sativa subsp. japonica
description: >
  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.
existing_annotations:
# --- SPKW keyword-mapping annotation (GO_REF:0000043) ---
# Present in the Sept 2025 goa_uniprot_gcrp snapshot (go-db plant.ddb); REMOVED from the
# current (2026) GOA release when GOA retired the keyword2GO pipeline for cellular
# organisms. Reviewed retrospectively to assess whether removal was justified. For OsEIL2
# this keyword captured a GENUINE, core function (ethylene signaling), so its removal is
# a case of collateral damage rather than correction.
- term:
    id: GO:0009873
    label: ethylene-activated signaling pathway
  evidence_type: IEA
  original_reference_id: GO_REF:0000043
  retired: true
  review:
    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.
    action: ACCEPT
    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.)
    supported_by:
    - reference_id: file:ORYSJ/EIL2/EIL2-deep-research-falcon.md
      supporting_text: "Canonical rice ethylene signaling places OsEIL2 downstream of
        receptors/OsCTR2 and OsEIN2"
    - reference_id: file:ORYSJ/EIL2/EIL2-deep-research-falcon.md
      supporting_text: "two master regulators of rice ethylene signaling"
    - reference_id: PMID:25995326
      supporting_text: "MHZ6 encodes ETHYLENE INSENSITIVE3-LIKE1 (OsEIL1), a rice homolog of
        ETHYLENE INSENSITIVE3 (EIN3), which is the master transcriptional regulator of ethylene
        signaling in Arabidopsis"
# --- Current GOA annotations (2026 release) ---
- term:
    id: GO:0003700
    label: DNA-binding transcription factor activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  qualifier: enables
  review:
    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.
    action: ACCEPT
    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).
    supported_by:
    - reference_id: file:ORYSJ/EIL2/EIL2-deep-research-falcon.md
      supporting_text: "OsEIL2 functions as a transcriptional activator"
    - reference_id: PMID:19798512
      supporting_text: "recombinant OsEIL1 and 2 proteins bound to specific DNA sequences that
        are recognized by a wound-inducible tobacco EIL"
- term:
    id: GO:0005634
    label: nucleus
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  qualifier: located_in
  review:
    summary: >
      IEA annotation for nuclear localization from combined automated methods. Directly
      confirmed in rice by fluorescent-fusion imaging.
    action: ACCEPT
    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.
    supported_by:
    - reference_id: file:ORYSJ/EIL2/EIL2-deep-research-falcon.md
      supporting_text: "OsEIL2 fused to GFP/YFP accumulated in nuclei"
    - reference_id: file:ORYSJ/EIL2/EIL2-deep-research-falcon.md
      supporting_text: "nuclear fluorescence was detectable/enhanced after treatment with the
        ethylene precursor"
- term:
    id: GO:0010104
    label: regulation of ethylene-activated signaling pathway
  evidence_type: IEA
  original_reference_id: GO_REF:0000117
  qualifier: involved_in
  review:
    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).
    action: ACCEPT
    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.
    supported_by:
    - reference_id: file:ORYSJ/EIL2/EIL2-deep-research-falcon.md
      supporting_text: "Canonical rice ethylene signaling places OsEIL2 downstream of
        receptors/OsCTR2 and OsEIN2"
    - reference_id: PMID:25995326
      supporting_text: "silencing of the closely related OsEIL2 led to ethylene insensitivity
        mainly in coleoptiles of etiolated seedlings"
- term:
    id: GO:0043565
    label: sequence-specific DNA binding
  evidence_type: IEA
  original_reference_id: GO_REF:0000117
  qualifier: enables
  review:
    summary: >
      IEA annotation (ARBA) for sequence-specific DNA binding. Directly demonstrated for
      OsEIL2 by EMSA; duplicates the IDA annotation (PMID:19798512).
    action: ACCEPT
    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.
    supported_by:
    - reference_id: PMID:19798512
      supporting_text: "recombinant OsEIL1 and 2 proteins bound to specific DNA sequences that
        are recognized by a wound-inducible tobacco EIL"
    - reference_id: PMID:19798512
      supporting_text: "the corresponding DNA-binding activity in nuclear extracts of rice
        leaves was increased at 1 h after wounding"
- term:
    id: GO:0045893
    label: positive regulation of DNA-templated transcription
  evidence_type: IEA
  original_reference_id: GO_REF:0000117
  qualifier: involved_in
  review:
    summary: >
      IEA annotation (ARBA) for positive regulation of transcription. OsEIL2 is a
      transcriptional activator; duplicates the IDA annotation (PMID:25995326).
    action: ACCEPT
    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.
    supported_by:
    - reference_id: file:ORYSJ/EIL2/EIL2-deep-research-falcon.md
      supporting_text: "acts as a transcriptional activator of downstream genes involved in
        stress/senescence and coleoptile development"
    - reference_id: PMID:25995326
      supporting_text: "the direct regulation of HIGH-AFFINITY K(+) TRANSPORTER2;1 expression
        and Na(+) uptake in roots"
- term:
    id: GO:0003700
    label: DNA-binding transcription factor activity
  evidence_type: IDA
  original_reference_id: PMID:25995326
  qualifier: enables
  review:
    summary: >
      IDA annotation: OsEIL2 has transactivation activity in protoplasts, confirming
      DNA-binding transcription factor activity. Core molecular function.
    action: ACCEPT
    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.
    supported_by:
    - reference_id: file:ORYSJ/EIL2/EIL2-deep-research-falcon.md
      supporting_text: "OsEIL2 functions as a transcriptional activator"
    - reference_id: PMID:25995326
      supporting_text: "the direct regulation of HIGH-AFFINITY K(+) TRANSPORTER2;1 expression
        and Na(+) uptake in roots"
- term:
    id: GO:0005634
    label: nucleus
  evidence_type: IDA
  original_reference_id: PMID:25995326
  qualifier: located_in
  review:
    summary: >
      IDA annotation: OsEIL2 localizes to the nucleus (Yang et al. 2015). Core cellular
      component, the site of its transcription-factor function.
    action: ACCEPT
    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.
    supported_by:
    - reference_id: file:ORYSJ/EIL2/EIL2-deep-research-falcon.md
      supporting_text: "OsEIL2 fused to GFP/YFP accumulated in nuclei"
    - reference_id: file:ORYSJ/EIL2/EIL2-deep-research-falcon.md
      supporting_text: "nuclear fluorescence was detectable/enhanced after treatment with the
        ethylene precursor"
- term:
    id: GO:0010104
    label: regulation of ethylene-activated signaling pathway
  evidence_type: IDA
  original_reference_id: PMID:19798512
  qualifier: involved_in
  review:
    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.
    action: ACCEPT
    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.
    supported_by:
    - reference_id: PMID:19798512
      supporting_text: "ETHYLENE INSENSITIVE3 (EIN3), which is an essential transcription factor
        for ethylene signaling"
    - reference_id: PMID:19798512
      supporting_text: "only OsEIL1 and 2 were found to be wound-inducible EIL"
- term:
    id: GO:0010104
    label: regulation of ethylene-activated signaling pathway
  evidence_type: IMP
  original_reference_id: PMID:25995326
  qualifier: involved_in
  review:
    summary: >
      IMP annotation: silencing OsEIL2 causes ethylene insensitivity in coleoptiles,
      demonstrating its role in (regulation of) the ethylene-activated signaling pathway.
      Core function.
    action: ACCEPT
    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.
    supported_by:
    - reference_id: PMID:25995326
      supporting_text: "silencing of the closely related OsEIL2 led to ethylene insensitivity
        mainly in coleoptiles of etiolated seedlings"
    - reference_id: PMID:25995326
      supporting_text: "Disruption of MHZ6/OsEIL1 caused ethylene"
- term:
    id: GO:0043565
    label: sequence-specific DNA binding
  evidence_type: IDA
  original_reference_id: PMID:19798512
  qualifier: enables
  review:
    summary: >
      IDA annotation: EMSA shows recombinant OsEIL2 binds a specific DNA element (Hiraga et al.
      2009). Core molecular function underpinning its transcription-factor activity.
    action: ACCEPT
    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.
    supported_by:
    - reference_id: PMID:19798512
      supporting_text: "recombinant OsEIL1 and 2 proteins bound to specific DNA sequences that
        are recognized by a wound-inducible tobacco EIL"
    - reference_id: PMID:19798512
      supporting_text: "the corresponding DNA-binding activity in nuclear extracts of rice
        leaves was increased at 1 h after wounding"
- term:
    id: GO:0045893
    label: positive regulation of DNA-templated transcription
  evidence_type: IDA
  original_reference_id: PMID:25995326
  qualifier: involved_in
  review:
    summary: >
      IDA annotation: OsEIL2 directly activates target-gene transcription (e.g. OsHKT2;1) and
      has transactivation activity (Yang et al. 2015). Accepted.
    action: ACCEPT
    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.
    supported_by:
    - reference_id: PMID:25995326
      supporting_text: "the direct regulation of HIGH-AFFINITY K(+) TRANSPORTER2;1 expression
        and Na(+) uptake in roots"
    - reference_id: file:ORYSJ/EIL2/EIL2-deep-research-falcon.md
      supporting_text: "acts as a transcriptional activator of downstream genes involved in
        stress/senescence and coleoptile development"
- term:
    id: GO:1901001
    label: negative regulation of response to salt stress
  evidence_type: IMP
  original_reference_id: PMID:25995326
  qualifier: involved_in
  review:
    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.
    action: KEEP_AS_NON_CORE
    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.
    supported_by:
    - reference_id: PMID:25995326
      supporting_text: "lack of MHZ6/OsEIL1 or OsEIL2 functions improves salt tolerance, whereas
        the overexpressing lines exhibit salt hypersensitivity at the seedling stage"
    - reference_id: PMID:25995326
      supporting_text: "MHZ6/OsEIL1 and OsEIL2 negatively regulate salt tolerance in rice"
    - reference_id: PMID:25995326
      supporting_text: "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"
- term:
    id: GO:1903034
    label: regulation of response to wounding
  evidence_type: IDA
  original_reference_id: PMID:19798512
  qualifier: involved_in
  review:
    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.
    action: KEEP_AS_NON_CORE
    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.
    supported_by:
    - reference_id: PMID:19798512
      supporting_text: "only OsEIL1 and 2 were found to be wound-inducible EIL. OsEIL2 was also
        induced by JA"
    - reference_id: PMID:19798512
      supporting_text: "These results indicate the importance of inducible OsEILs in wound
        signaling in rice"
# --- NEW annotations proposed from the literature ---
- term:
    id: GO:0001228
    label: DNA-binding transcription activator activity, RNA polymerase II-specific
  evidence_type: IDA
  original_reference_id: PMID:25995326
  qualifier: enables
  review:
    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".
    action: NEW
    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.
    supported_by:
    - reference_id: file:ORYSJ/EIL2/EIL2-deep-research-falcon.md
      supporting_text: "OsEIL2 functions as a transcriptional activator"
    - reference_id: file:ORYSJ/EIL2/EIL2-deep-research-falcon.md
      supporting_text: "acts as a transcriptional activator of downstream genes involved in
        stress/senescence and coleoptile development"
    - reference_id: PMID:25995326
      supporting_text: "the direct regulation of HIGH-AFFINITY K(+) TRANSPORTER2;1 expression
        and Na(+) uptake in roots"
- term:
    id: GO:0045944
    label: positive regulation of transcription by RNA polymerase II
  evidence_type: IDA
  original_reference_id: PMID:25995326
  qualifier: involved_in
  review:
    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.
    action: NEW
    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.
    supported_by:
    - reference_id: file:ORYSJ/EIL2/EIL2-deep-research-falcon.md
      supporting_text: "OsEIL2 directly binds promoters and activates transcription of"
    - reference_id: file:ORYSJ/EIL2/EIL2-deep-research-falcon.md
      supporting_text: "OsEIL1/OsEIL2 directly activate ROS-scavenging genes including"
    - reference_id: PMID:25995326
      supporting_text: "the direct regulation of HIGH-AFFINITY K(+) TRANSPORTER2;1 expression
        and Na(+) uptake in roots"
core_functions:
- description: >
    OsEIL2 is a nuclear, sequence-specific DNA-binding transcriptional activator of the
    EIN3/EIL family that acts as a central transducer/effector of the ethylene-activated
    signaling pathway, driving ethylene-responsive transcription downstream of OsEIN2.
  molecular_function:
    id: GO:0001228
    label: DNA-binding transcription activator activity, RNA polymerase II-specific
  directly_involved_in:
  - id: GO:0009873
    label: ethylene-activated signaling pathway
  - id: GO:0045944
    label: positive regulation of transcription by RNA polymerase II
  locations:
  - id: GO:0005634
    label: nucleus
  supported_by:
  - reference_id: file:ORYSJ/EIL2/EIL2-deep-research-falcon.md
    supporting_text: "Canonical rice ethylene signaling places OsEIL2 downstream of
      receptors/OsCTR2 and OsEIN2"
  - reference_id: PMID:25995326
    supporting_text: "ETHYLENE INSENSITIVE3 (EIN3), which is the master transcriptional
      regulator of ethylene signaling in Arabidopsis"
  - reference_id: file:ORYSJ/EIL2/EIL2-deep-research-falcon.md
    supporting_text: "OsEIL2 functions as a transcriptional activator"
- description: >
    OsEIL2 binds DNA sequence-specifically (via its EIN3 DNA-binding domain) at
    ethylene/wound-responsive promoter elements and regulates downstream gene programs -
    including ROS-scavenging genes, the cell-wall/BURP gene OsBURP16, and the Na+ transporter
    OsHKT2;1 - thereby contributing to ethylene-promoted coleoptile elongation, seedling
    emergence, and (negatively) salt-stress responses.
  molecular_function:
    id: GO:0043565
    label: sequence-specific DNA binding
  directly_involved_in:
  - id: GO:0010104
    label: regulation of ethylene-activated signaling pathway
  locations:
  - id: GO:0005634
    label: nucleus
  supported_by:
  - reference_id: PMID:19798512
    supporting_text: "recombinant OsEIL1 and 2 proteins bound to specific DNA sequences that
      are recognized by a wound-inducible tobacco EIL"
  - reference_id: PMID:25995326
    supporting_text: "silencing of the closely related OsEIL2 led to ethylene insensitivity
      mainly in coleoptiles of etiolated seedlings"
  - reference_id: file:ORYSJ/EIL2/EIL2-deep-research-falcon.md
    supporting_text: "OsEIL2 directly binds promoters and activates transcription of"
proposed_new_terms: []
suggested_questions:
- question: 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)?
  experts:
  - Jin-Song Zhang
- question: 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?
  experts:
  - Hua Qin
- question: 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?
  experts:
  - Cui-Cui Yin
suggested_experiments:
- description: 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.
  experiment_type: ChIP-seq + RNA-seq regulon mapping
- description: 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.
  experiment_type: protein-stability / proteasome-dependence assay
- description: 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.
  experiment_type: genetic loss-of-function / epistasis analysis
references:
- id: GO_REF:0000043
  title: Gene Ontology annotation based on UniProtKB/Swiss-Prot keyword mapping
  findings:
  - statement: SwissProt keyword-derived (SPKW) annotations present in the Sept 2025
      goa_uniprot_gcrp snapshot but removed from the current GOA release after GOA retired the
      keyword2GO pipeline for cellular organisms.
  - statement: For OsEIL2, the keyword "Ethylene signaling pathway" mapped to a genuinely
      correct, core process term (GO:0009873 ethylene-activated signaling pathway); its removal
      is collateral damage, not a correction, because EIN3/EIL transcription factors are
      defining components of the ethylene-activated signaling pathway.
- id: GO_REF:0000117
  title: Electronic Gene Ontology annotations created by ARBA machine learning models
  findings:
  - statement: ARBA models assign sequence-specific DNA binding, positive regulation of
      DNA-templated transcription and regulation of the ethylene-activated signaling pathway to
      OsEIL2, all consistent with experimental data for this EIN3/EIL transcription factor.
- id: GO_REF:0000120
  title: Combined Automated Annotation using Multiple IEA Methods
  findings:
  - statement: Combined IEA methods assign DNA-binding transcription factor activity and
      nuclear localization to OsEIL2; both are confirmed experimentally (PMID:25995326).
- id: PMID:19798512
  title: Involvement of two rice ETHYLENE INSENSITIVE3-LIKE genes in wound signaling.
  findings:
  - statement: OsEIL2 is one of only two rice EIL genes (with OsEIL1) found to be
      wound-inducible; OsEIL2 is also induced by jasmonic acid.
  - statement: Recombinant OsEIL2 binds specific DNA sequences recognized by a wound-inducible
      tobacco EIL (EMSA), and wound-induced DNA-binding activity increased in rice nuclear
      extracts; suppression of OsEIL1/2 down-regulated several wound-inducible candidate target
      genes, indicating involvement in wound signaling.
  - statement: EIN3 is described as an essential transcription factor for ethylene signaling;
      OsEIL proteins are its rice EIN3-LIKE homologs.
- id: PMID:25995326
  title: MAOHUZI6/ETHYLENE INSENSITIVE3-LIKE1 and ETHYLENE INSENSITIVE3-LIKE2 Regulate
    Ethylene Response of Roots and Coleoptiles and Negatively Affect Salt Tolerance in Rice.
  findings:
  - statement: OsEIL1 (MHZ6) is a rice homolog of Arabidopsis EIN3, the master transcriptional
      regulator of ethylene signaling; OsEIL2 is its close relative.
  - statement: Silencing OsEIL2 causes ethylene insensitivity mainly in coleoptiles of
      etiolated seedlings; OsEIL2 is required for ethylene-promoted coleoptile elongation.
  - statement: OsEIL2 has transactivation activity in protoplasts and localizes to the nucleus.
  - statement: OsEIL1/OsEIL2 negatively regulate salt tolerance, in part by directly activating
      OsHKT2;1 expression and Na+ uptake in roots; loss of function improves salt tolerance,
      overexpression causes salt hypersensitivity.
- id: file:ORYSJ/EIL2/EIL2-deep-research-falcon.md
  title: Deep-research report (falcon / Edison Scientific Literature) - functional annotation
    of rice EIL2 (Q8W3L9).
  findings:
  - statement: Canonical rice ethylene signaling places OsEIL2 downstream of the
      receptors/OsCTR2 and OsEIN2; OsEIL1 and OsEIL2 are described as the closest functional
      equivalents to Arabidopsis EIN3 and as "two master regulators of rice ethylene signaling".
  - statement: OsEIL2 functions as a transcriptional activator with transactivation activity
      (the report maps the OsEIL2 transactivation domain to the C-terminal region, aa 344-583);
      it acts as a transcriptional activator of downstream genes involved in stress/senescence
      and coleoptile development.
  - statement: OsEIL2 fused to GFP/YFP accumulated in nuclei; nuclear fluorescence increased
      after ACC (ethylene precursor) and after MG132 (proteasome inhibitor), consistent with
      ethylene/proteasome-regulated stability.
  - statement: OsEIL2 directly binds promoters and activates transcription of target genes
      including OsBURP14/OsBURP16; with OsEIL1 it directly activates ROS-scavenging genes
      (OsVTC1-3, peroxidases) linked to coleoptile elongation and seedling emergence, and it
      acts as a negative regulator of salt/drought tolerance.

Gene Description

Existing Annotations Review

Core Functions

OsEIL2 is a nuclear, sequence-specific DNA-binding transcriptional activator of the EIN3/EIL family that acts as a central transducer/effector of the ethylene-activated signaling pathway, driving ethylene-responsive transcription downstream of OsEIN2.

References

Suggested Questions for Experts

Suggested Experiments

Deep Research

Falcon

Research report: Functional annotation of rice EIL2 / OsEIL2 (UniProt Q8W3L9; locus LOC_Os07g48630 / Os07g0685700) in Oryza sativa ssp. japonica

0) Target verification (mandatory disambiguation)

1) Key concepts and definitions (current understanding)

1.1 EIN3/EIL transcription factors

1.2 Canonical ethylene signaling to EIN3/EILs (rice context)

2) Molecular function of OsEIL2 (what it does)

2.1 Molecular function: DNA-binding transcriptional regulator

2.2 DNA-binding and promoter recognition

3) Subcellular localization (where it acts)

4) Upstream regulation (how OsEIL2 is controlled)

4.1 EBF/proteasome axis and ethylene-dependent stabilization (conceptual)

4.2 2023–2024 mechanistic advance: translational regulation upstream of EILs (MHZ9)

4.3 Rice-specific regulators upstream of the EIL layer (review evidence)

5) Downstream targets, pathways, and biological roles of OsEIL2

5.1 Abiotic stress sensitivity and senescence via BURP genes and cell-wall remodeling

5.2 Coleoptile elongation and direct-seeding emergence via ROS scavenging genes (2024)

6) Phenotypes of OsEIL2 perturbation (gain/loss of function)

6.1 OsEIL2 overexpression vs knockdown (stress/senescence module)

6.2 EIL1/EIL2 mutant context (coleoptile emergence module)

7) Expert opinions and analysis (authoritative synthesis)

8) Current applications and real-world implementations

8.1 Direct-seeded rice: improving emergence via OsEIL2-linked ROS scavenging

8.2 Stress resilience tradeoffs: OsEIL2 as a negative regulator of salt/drought tolerance

8.3 Regulatory intervention points beyond OsEIL2: translational control (MHZ9)

9) Statistics and data highlights (from recent studies)

10) Evidence summary table

11) Key limitations of this synthesis

References (URLs and publication dates)

Artifacts

Citations

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