PAD4

Existing Annotations Review

GO Term	Evidence	Action	Reason
GO:0001666 response to hypoxia	IMP PMID:18055613 Lysigenous aerenchyma formation in Arabidopsis is controlled...	KEEP AS NON CORE	Summary: PAD4 is genetically required for hypoxia-induced lysigenous aerenchyma and associated ROS signaling in the cited study. Reason: This is a real PAD4-dependent stress/developmental output, but it is downstream of the EDS1/PAD4 immune-redox signaling module rather than PAD4's core conserved role.
GO:0002213 defense response to insect	IMP PMID:17725549 Phloem-based resistance to green peach aphid is controlled b...	KEEP AS NON CORE	Summary: PAD4 contributes to Arabidopsis defense against the green peach aphid and limits phloem feeding or aphid population growth. Reason: The aphid-defense branch is experimentally supported and biologically important, but it is a specialized immune output rather than the central EDS1-PAD4 defense-signaling function.
GO:0009625 response to insect	IMP PMID:16299172 Premature leaf senescence modulated by the Arabidopsis PHYTO...	KEEP AS NON CORE	Summary: PAD4 contributes to Arabidopsis defense against the green peach aphid and limits phloem feeding or aphid population growth. Reason: The aphid-defense branch is experimentally supported and biologically important, but it is a specialized immune output rather than the central EDS1-PAD4 defense-signaling function.
GO:0009627 systemic acquired resistance	IEP PMID:17419843 Pathogen-associated molecular pattern recognition rather tha...	ACCEPT	Summary: PAD4 is a major positive regulator of salicylic-acid-associated systemic acquired resistance and defense amplification. Reason: PAD4 was cloned and characterized as required for SA accumulation/signaling and systemic resistance outputs, and later work places it in the EDS1-PAD4 immune signaling branch.
GO:0009862 systemic acquired resistance, salicylic acid mediated signaling pathway	TAS PMID:10557364 Arabidopsis thaliana PAD4 encodes a lipase-like gene that is...	ACCEPT	Summary: PAD4 is a major positive regulator of salicylic-acid-associated systemic acquired resistance and defense amplification. Reason: PAD4 was cloned and characterized as required for SA accumulation/signaling and systemic resistance outputs, and later work places it in the EDS1-PAD4 immune signaling branch.
GO:0009862 systemic acquired resistance, salicylic acid mediated signaling pathway	IMP PMID:11574472 Direct interaction between the Arabidopsis disease resistanc...	ACCEPT	Summary: PAD4 is a major positive regulator of salicylic-acid-associated systemic acquired resistance and defense amplification. Reason: PAD4 was cloned and characterized as required for SA accumulation/signaling and systemic resistance outputs, and later work places it in the EDS1-PAD4 immune signaling branch.
GO:0010150 leaf senescence	IMP PMID:16299172 Premature leaf senescence modulated by the Arabidopsis PHYTO...	KEEP AS NON CORE	Summary: PAD4 modulates premature leaf senescence induced by aphid feeding. Reason: This senescence annotation is supported in the aphid-defense context, but senescence is a downstream defense strategy rather than the core molecular role of PAD4.
GO:0010310 regulation of hydrogen peroxide metabolic process	IMP PMID:18055613 Lysigenous aerenchyma formation in Arabidopsis is controlled...	KEEP AS NON CORE	Summary: PAD4 is genetically required for hypoxia-induced lysigenous aerenchyma and associated ROS signaling in the cited study. Reason: This is a real PAD4-dependent stress/developmental output, but it is downstream of the EDS1/PAD4 immune-redox signaling module rather than PAD4's core conserved role.
GO:0010618 aerenchyma formation	IMP PMID:18055613 Lysigenous aerenchyma formation in Arabidopsis is controlled...	KEEP AS NON CORE	Summary: PAD4 is genetically required for hypoxia-induced lysigenous aerenchyma and associated ROS signaling in the cited study. Reason: This is a real PAD4-dependent stress/developmental output, but it is downstream of the EDS1/PAD4 immune-redox signaling module rather than PAD4's core conserved role.
GO:0031348 negative regulation of defense response	IMP PMID:16732289 Conserved requirement for a plant host cell protein in powde...	REMOVE	Summary: The cached text for the cited powdery-mildew MLO paper does not provide PAD4-specific support for negative regulation of defense response. Reason: PAD4 is predominantly a positive immune regulator; this citation does not substantiate PAD4 as a negative regulator of defense response.
GO:0042742 defense response to bacterium	IMP PMID:9136026 Phytoalexin-deficient mutants of Arabidopsis reveal that PAD...	ACCEPT	Summary: PAD4 positively regulates antibacterial defense, especially against Pseudomonas-associated disease contexts. Reason: Defense response to bacterium is a central biological process output of the EDS1-PAD4 immune signaling module.
GO:0050829 defense response to Gram-negative bacterium	IMP PMID:29253890 Leaf shedding as an anti-bacterial defense in Arabidopsis ca...	ACCEPT	Summary: PAD4 positively regulates antibacterial defense, especially against Pseudomonas-associated disease contexts. Reason: Defense response to bacterium is a central biological process output of the EDS1-PAD4 immune signaling module.
GO:0051707 response to other organism	IEP PMID:16531493 Salicylic acid-independent ENHANCED DISEASE SUSCEPTIBILITY1 ...	MODIFY	Summary: The cited expression-genomics study supports PAD4-dependent defense signaling after pathogen challenge, not a generic response to other organism. Reason: Replace the broad response-to-organism term with antibacterial defense regulation, which better captures PAD4 function. Proposed replacements: positive regulation of defense response to bacterium
GO:0060866 leaf abscission	IMP PMID:29253890 Leaf shedding as an anti-bacterial defense in Arabidopsis ca...	KEEP AS NON CORE	Summary: PAD4 is required for normal pathogen-triggered cauline leaf abscission in a bacterial defense context. Reason: The leaf-abscission phenotype is a tissue-level immune output mediated through salicylic-acid defense signaling, not a direct molecular function of PAD4.
GO:0005515 protein binding	IPI PMID:11574472 Direct interaction between the Arabidopsis disease resistanc...	MARK AS OVER ANNOTATED	Summary: PAD4 physically interacts with EDS1 in immune signaling contexts, but generic protein binding does not describe the functional role. Reason: The informative curation is EDS1 disease-resistance complex membership and signaling adaptor activity; protein binding alone is too generic for a core annotation.
GO:0005515 protein binding	IPI PMID:16040633 Arabidopsis SENESCENCE-ASSOCIATED GENE101 stabilizes and sig...	MARK AS OVER ANNOTATED	Summary: PAD4 physically interacts with EDS1 in immune signaling contexts, but generic protein binding does not describe the functional role. Reason: The informative curation is EDS1 disease-resistance complex membership and signaling adaptor activity; protein binding alone is too generic for a core annotation.
GO:0005515 protein binding	IPI PMID:21434927 Different roles of Enhanced Disease Susceptibility1 (EDS1) b...	MARK AS OVER ANNOTATED	Summary: PAD4 physically interacts with EDS1 in immune signaling contexts, but generic protein binding does not describe the functional role. Reason: The informative curation is EDS1 disease-resistance complex membership and signaling adaptor activity; protein binding alone is too generic for a core annotation.
GO:0005515 protein binding	IPI PMID:23275581 Natural variation in small molecule-induced TIR-NB-LRR signa...	MARK AS OVER ANNOTATED	Summary: PAD4 physically interacts with VICTR/TIR-NLR immune components in immune signaling contexts, but generic protein binding does not describe the functional role. Reason: The informative curation is EDS1 disease-resistance complex membership and signaling adaptor activity; protein binding alone is too generic for a core annotation.
GO:0005515 protein binding	IPI PMID:28555890 The dual role of LESION SIMULATING DISEASE 1 as a condition-...	MARK AS OVER ANNOTATED	Summary: This source is a broad LSD1 interaction/scaffold study with a GOA/IntAct PAD4-EDS1 IPI row, but generic protein binding does not describe PAD4's functional role. Reason: The informative curation is EDS1 disease-resistance complex membership and signaling adaptor activity; protein binding alone is too generic for a core annotation.
GO:0016298 lipase activity	ISS PMID:10557364 Arabidopsis thaliana PAD4 encodes a lipase-like gene that is...	REMOVE	Summary: PAD4 was initially annotated as lipase-like from sequence similarity, but no direct PAD4 lipase activity has been demonstrated. Reason: The cited paper describes predicted similarity to triacylglycerol lipases and explicitly leaves substrate/activity uncertain; later evidence favors pseudoenzymatic immune signaling.
GO:0006629 lipid metabolic process	IEA GO_REF:0000002	REMOVE	Summary: The InterPro lipid metabolic process transfer follows from a lipase-like domain but is not supported by PAD4 biology. Reason: PAD4 is an EDS1-family immune signaling protein; no direct lipid metabolic process or lipid substrate is established.
GO:0009617 response to bacterium	IDA PMID:10557364 Arabidopsis thaliana PAD4 encodes a lipase-like gene that is...	MODIFY	Summary: The cited PAD4 cloning paper supports antibacterial defense regulation, but response to bacterium is broader than the curated PAD4 role. Reason: Use a defense-response term that captures PAD4 as a positive immune regulator rather than a generic response term. Proposed replacements: positive regulation of defense response to bacterium
GO:0009625 response to insect	IDA PMID:21426427 TREHALOSE PHOSPHATE SYNTHASE11-dependent trehalose metabolis...	KEEP AS NON CORE	Summary: PAD4 contributes to Arabidopsis defense against the green peach aphid and limits phloem feeding or aphid population growth. Reason: The aphid-defense branch is experimentally supported and biologically important, but it is a specialized immune output rather than the central EDS1-PAD4 defense-signaling function.
GO:0009626 plant-type hypersensitive response	IMP PMID:16040633 Arabidopsis SENESCENCE-ASSOCIATED GENE101 stabilizes and sig...	KEEP AS NON CORE	Summary: PAD4 contributes to some TIR-NLR/EDS1-dependent hypersensitive-response and cell-death outputs. Reason: Hypersensitive response is a pathway output of immune signaling; PAD4 is not the dedicated cell-death effector and contemporary models separate the EDS1-PAD4 branch from the EDS1-SAG101-NRG1 cell-death branch.
GO:0009626 plant-type hypersensitive response	IMP PMID:19616764 Regulation of cell death and innate immunity by two receptor...	KEEP AS NON CORE	Summary: PAD4 contributes to some TIR-NLR/EDS1-dependent hypersensitive-response and cell-death outputs. Reason: Hypersensitive response is a pathway output of immune signaling; PAD4 is not the dedicated cell-death effector and contemporary models separate the EDS1-PAD4 branch from the EDS1-SAG101-NRG1 cell-death branch.
GO:0009626 plant-type hypersensitive response	NAS PMID:22072959 SAG101 forms a ternary complex with EDS1 and PAD4 and is req...	KEEP AS NON CORE	Summary: PAD4 contributes to some TIR-NLR/EDS1-dependent hypersensitive-response and cell-death outputs. Reason: Hypersensitive response is a pathway output of immune signaling; PAD4 is not the dedicated cell-death effector and contemporary models separate the EDS1-PAD4 branch from the EDS1-SAG101-NRG1 cell-death branch.
GO:0009751 response to salicylic acid	IDA PMID:10557364 Arabidopsis thaliana PAD4 encodes a lipase-like gene that is...	ACCEPT	Summary: PAD4 acts upstream of salicylic-acid accumulation and salicylic-acid-mediated defense signaling. Reason: SA amplification and SA-mediated defense regulation are central outputs of PAD4 immune signaling.
GO:0009862 systemic acquired resistance, salicylic acid mediated signaling pathway	IMP PMID:10796016 Arabidopsis thaliana EDS4 contributes to salicylic acid (SA)...	ACCEPT	Summary: PAD4 is a major positive regulator of salicylic-acid-associated systemic acquired resistance and defense amplification. Reason: PAD4 was cloned and characterized as required for SA accumulation/signaling and systemic resistance outputs, and later work places it in the EDS1-PAD4 immune signaling branch.
GO:0009862 systemic acquired resistance, salicylic acid mediated signaling pathway	NAS PMID:22072959 SAG101 forms a ternary complex with EDS1 and PAD4 and is req...	ACCEPT	Summary: PAD4 is a major positive regulator of salicylic-acid-associated systemic acquired resistance and defense amplification. Reason: PAD4 was cloned and characterized as required for SA accumulation/signaling and systemic resistance outputs, and later work places it in the EDS1-PAD4 immune signaling branch.
GO:0010105 negative regulation of ethylene-activated signaling pathway	IGI PMID:16813576 Arabidopsis MAP kinase 4 regulates salicylic acid- and jasmo...	KEEP AS NON CORE	Summary: PAD4 participates in defense hormone cross-talk involving SA, jasmonic acid, and ethylene pathways. Reason: Hormone cross-regulation is a downstream regulatory output of PAD4/EDS1 signaling rather than PAD4's core molecular role.
GO:0010225 response to UV-C	IMP PMID:11826312 EDS5, an essential component of salicylic acid-dependent sig...	KEEP AS NON CORE	Summary: PAD4 is required for EDS5 induction after UV-C exposure in the cited defense-signaling study. Reason: This abiotic stress annotation reflects shared defense/SA signaling circuitry and is not the central PAD4 immune-complex function.
GO:0042742 defense response to bacterium	IMP PMID:11826312 EDS5, an essential component of salicylic acid-dependent sig...	ACCEPT	Summary: PAD4 positively regulates antibacterial defense, especially against Pseudomonas-associated disease contexts. Reason: Defense response to bacterium is a central biological process output of the EDS1-PAD4 immune signaling module.
GO:0071327 cellular response to trehalose stimulus	IDA PMID:21426427 TREHALOSE PHOSPHATE SYNTHASE11-dependent trehalose metabolis...	KEEP AS NON CORE	Summary: Trehalose metabolism regulates PAD4 expression during aphid defense. Reason: This is a stimulus-response context feeding into the PAD4 aphid-defense branch, not the core EDS1-PAD4 immune signaling function.
GO:0080142 regulation of salicylic acid biosynthetic process	IMP PMID:9634589 PAD4 functions upstream from salicylic acid to control defen...	ACCEPT	Summary: PAD4 acts upstream of salicylic-acid accumulation and salicylic-acid-mediated defense signaling. Reason: SA amplification and SA-mediated defense regulation are central outputs of PAD4 immune signaling.
GO:0080151 positive regulation of salicylic acid mediated signaling pathway	IGI PMID:16813576 Arabidopsis MAP kinase 4 regulates salicylic acid- and jasmo...	ACCEPT	Summary: PAD4 acts upstream of salicylic-acid accumulation and salicylic-acid-mediated defense signaling. Reason: SA amplification and SA-mediated defense regulation are central outputs of PAD4 immune signaling.
GO:1900367 positive regulation of defense response to insect	IMP PMID:16299172 Premature leaf senescence modulated by the Arabidopsis PHYTO...	KEEP AS NON CORE	Summary: PAD4 contributes to Arabidopsis defense against the green peach aphid and limits phloem feeding or aphid population growth. Reason: The aphid-defense branch is experimentally supported and biologically important, but it is a specialized immune output rather than the central EDS1-PAD4 defense-signaling function.
GO:1900426 positive regulation of defense response to bacterium	IMP PMID:10557364 Arabidopsis thaliana PAD4 encodes a lipase-like gene that is...	ACCEPT	Summary: PAD4 positively regulates antibacterial defense, especially against Pseudomonas-associated disease contexts. Reason: Defense response to bacterium is a central biological process output of the EDS1-PAD4 immune signaling module.
GO:1900426 positive regulation of defense response to bacterium	IMP PMID:9634589 PAD4 functions upstream from salicylic acid to control defen...	ACCEPT	Summary: PAD4 positively regulates antibacterial defense, especially against Pseudomonas-associated disease contexts. Reason: Defense response to bacterium is a central biological process output of the EDS1-PAD4 immune signaling module.
GO:1901183 positive regulation of camalexin biosynthetic process	IMP PMID:10557364 Arabidopsis thaliana PAD4 encodes a lipase-like gene that is...	KEEP AS NON CORE	Summary: PAD4 positively regulates camalexin accumulation after pathogen infection. Reason: Camalexin biosynthesis is a supported defense output, but PAD4 is not itself a camalexin biosynthetic enzyme.
GO:2000022 regulation of jasmonic acid mediated signaling pathway	IGI PMID:16813576 Arabidopsis MAP kinase 4 regulates salicylic acid- and jasmo...	KEEP AS NON CORE	Summary: PAD4 participates in defense hormone cross-talk involving SA, jasmonic acid, and ethylene pathways. Reason: Hormone cross-regulation is a downstream regulatory output of PAD4/EDS1 signaling rather than PAD4's core molecular role.
GO:2000031 regulation of salicylic acid mediated signaling pathway	IMP PMID:10796016 Arabidopsis thaliana EDS4 contributes to salicylic acid (SA)...	ACCEPT	Summary: PAD4 acts upstream of salicylic-acid accumulation and salicylic-acid-mediated defense signaling. Reason: SA amplification and SA-mediated defense regulation are central outputs of PAD4 immune signaling.
GO:0005634 nucleus	IEA GO_REF:0000044	ACCEPT	Summary: PAD4-containing EDS1 complexes are supported in the nucleus and cytoplasm. Reason: Subcellular localization is experimentally supported for EDS1-PAD4 complexes and is consistent with nucleo-cytoplasmic immune signal relay.
GO:0005634 nucleus	ISM GO_REF:0000122	ACCEPT	Summary: PAD4-containing EDS1 complexes are supported in the nucleus and cytoplasm. Reason: Subcellular localization is experimentally supported for EDS1-PAD4 complexes and is consistent with nucleo-cytoplasmic immune signal relay.
GO:0005634 nucleus	IDA PMID:16040633 Arabidopsis SENESCENCE-ASSOCIATED GENE101 stabilizes and sig...	ACCEPT	Summary: PAD4-containing EDS1 complexes are supported in the nucleus and cytoplasm. Reason: Subcellular localization is experimentally supported for EDS1-PAD4 complexes and is consistent with nucleo-cytoplasmic immune signal relay.
GO:0005634 nucleus	IDA PMID:22072959 SAG101 forms a ternary complex with EDS1 and PAD4 and is req...	ACCEPT	Summary: PAD4-containing EDS1 complexes are supported in the nucleus and cytoplasm. Reason: Subcellular localization is experimentally supported for EDS1-PAD4 complexes and is consistent with nucleo-cytoplasmic immune signal relay.
GO:0005634 nucleus	NAS PMID:22072959 SAG101 forms a ternary complex with EDS1 and PAD4 and is req...	ACCEPT	Summary: PAD4-containing EDS1 complexes are supported in the nucleus and cytoplasm. Reason: Subcellular localization is experimentally supported for EDS1-PAD4 complexes and is consistent with nucleo-cytoplasmic immune signal relay.
GO:0005737 cytoplasm	IEA GO_REF:0000044	ACCEPT	Summary: PAD4-containing EDS1 complexes are supported in the nucleus and cytoplasm. Reason: Subcellular localization is experimentally supported for EDS1-PAD4 complexes and is consistent with nucleo-cytoplasmic immune signal relay.
GO:0005737 cytoplasm	IDA PMID:16040633 Arabidopsis SENESCENCE-ASSOCIATED GENE101 stabilizes and sig...	ACCEPT	Summary: PAD4-containing EDS1 complexes are supported in the nucleus and cytoplasm. Reason: Subcellular localization is experimentally supported for EDS1-PAD4 complexes and is consistent with nucleo-cytoplasmic immune signal relay.
GO:0005829 cytosol	IDA PMID:16040633 Arabidopsis SENESCENCE-ASSOCIATED GENE101 stabilizes and sig...	ACCEPT	Summary: PAD4-containing EDS1 complexes are supported in the cytosol/cytoplasmic fraction. Reason: Subcellular localization is experimentally supported for EDS1-PAD4 complexes and is consistent with nucleo-cytoplasmic immune signal relay.
GO:0106093 EDS1 disease-resistance complex	IDA PMID:11574472 Direct interaction between the Arabidopsis disease resistanc...	ACCEPT	Summary: PAD4 is a component of the EDS1 disease-resistance complex. Reason: EDS1-PAD4 complex membership is the best-supported cellular component annotation for PAD4 and reflects its core immune signaling role.
GO:0106093 EDS1 disease-resistance complex	NAS PMID:22072959 SAG101 forms a ternary complex with EDS1 and PAD4 and is req...	ACCEPT	Summary: PAD4 is a component of the EDS1 disease-resistance complex. Reason: EDS1-PAD4 complex membership is the best-supported cellular component annotation for PAD4 and reflects its core immune signaling role.
GO:0035591 signaling adaptor activity	IC file:ARATH/PAD4/PAD4-deep-research-falcon.md	NEW	Summary: PAD4 functions as a ligand-responsive EDS1-family immune signaling adaptor/scaffold rather than as a demonstrated lipase. Reason: Existing GOA rows capture EDS1 complex membership and defense outputs but not PAD4's current mechanistic role in ligand-responsive immune signal relay to ADR1-family helper NLRs. Supporting Evidence: file:ARATH/PAD4/PAD4-deep-research-falcon.md PAD4 forms an EDS1-PAD4 heterodimer that serves as a ligand-enabled receptor/scaffold for ADR1 file:ARATH/PAD4/PAD4-deep-research-falcon.md EDS1–PAD4–ADR1 heterotrimer bound to pRib-ADP PMID:11574472 EDS1 and PAD4 proteins interact in healthy and pathogen-challenged plant cells PMID:16040633 dynamic interactions of EDS1 and its signaling partners in multiple cell compartments are important for plant defense signal relay PMID:22072959 Co-IP of EDS1-90-MYC and PAD4-MYC with EDS1-80-FLAG

Core Functions

Ligand-responsive EDS1-PAD4 immune signaling adaptor. PAD4 forms an EDS1-PAD4 complex that amplifies salicylic-acid-associated antibacterial and systemic defense programs and, in current mechanistic models, helps connect TIR-derived immune signals to ADR1-family helper NLR activation.

Molecular Function:

signaling adaptor activity

Directly Involved In:

systemic acquired resistance, salicylic acid mediated signaling pathway positive regulation of defense response to bacterium

Cellular Locations:

nucleus cytoplasm

Supporting Evidence:

file:ARATH/PAD4/PAD4-deep-research-falcon.md
PAD4 forms an EDS1-PAD4 heterodimer that serves as a ligand-enabled receptor/scaffold for ADR1
file:ARATH/PAD4/PAD4-deep-research-falcon.md
EDS1–PAD4–ADR1 heterotrimer bound to **pRib-ADP**
PMID:11574472
EDS1 and PAD4 proteins interact in healthy and pathogen-challenged plant cells
file:ARATH/PAD4/PAD4-deep-research-falcon.md
PAD4 promotes defense transcriptional reprogramming and salicylic-acid-associated immunity rather than acting as the dedicated cell-death branch

References

GO_REF:0000002

Gene Ontology annotation through association of InterPro records with GO terms

GO_REF:0000044

Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location vocabulary mapping, accompanied by conservative changes to GO terms applied by UniProt

GO_REF:0000122

AtSubP analysis

PMID:10557364

Arabidopsis thaliana PAD4 encodes a lipase-like gene that is important for salicylic acid signaling.

PAD4 was cloned as a lipase-like gene required for salicylic-acid signaling, camalexin synthesis, PR-1 expression, and defense against Pseudomonas.

PMID:10796016

Arabidopsis thaliana EDS4 contributes to salicylic acid (SA)-dependent expression of defense responses: evidence for inhibition of jasmonic acid signaling by SA.

PMID:11574472

Direct interaction between the Arabidopsis disease resistance signaling proteins, EDS1 and PAD4.

This source directly supports physical interaction between Arabidopsis EDS1 and PAD4 and the EDS1-PAD4 disease-resistance complex.

PMID:11826312

EDS5, an essential component of salicylic acid-dependent signaling for disease resistance in Arabidopsis, is a member of the MATE transporter family.

PMID:16040633

Arabidopsis SENESCENCE-ASSOCIATED GENE101 stabilizes and signals within an ENHANCED DISEASE SUSCEPTIBILITY1 complex in plant innate immunity.

This source supports EDS1-PAD4 associations in nucleus and cytoplasm and notes that EDS1/PAD4 lipase-like proteins lack demonstrated esterase activity.

PMID:16299172

Premature leaf senescence modulated by the Arabidopsis PHYTOALEXIN DEFICIENT4 gene is associated with defense against the phloem-feeding green peach aphid.

PAD4 modulates aphid-induced premature leaf senescence and contributes to basal resistance to green peach aphid.

PMID:16531493

Salicylic acid-independent ENHANCED DISEASE SUSCEPTIBILITY1 signaling in Arabidopsis immunity and cell death is regulated by the monooxygenase FMO1 and the Nudix hydrolase NUDT7.

PMID:16732289

Conserved requirement for a plant host cell protein in powdery mildew pathogenesis.

Cached text does not provide PAD4-specific support for negative regulation of defense response.

PMID:16813576

Arabidopsis MAP kinase 4 regulates salicylic acid- and jasmonic acid/ethylene-dependent responses via EDS1 and PAD4.

PMID:17419843

Pathogen-associated molecular pattern recognition rather than development of tissue necrosis contributes to bacterial induction of systemic acquired resistance in Arabidopsis.

PMID:17725549

Phloem-based resistance to green peach aphid is controlled by Arabidopsis PHYTOALEXIN DEFICIENT4 without its signaling partner ENHANCED DISEASE SUSCEPTIBILITY1.

PAD4 controls phloem-based resistance to green peach aphid in an EDS1-independent branch.

PMID:18055613

Lysigenous aerenchyma formation in Arabidopsis is controlled by LESION SIMULATING DISEASE1.

LSD1, EDS1, and PAD4 regulate lysigenous aerenchyma formation in response to hypoxia through ethylene and reactive oxygen signaling.

PMID:19616764

Regulation of cell death and innate immunity by two receptor-like kinases in Arabidopsis.

PMID:21426427

TREHALOSE PHOSPHATE SYNTHASE11-dependent trehalose metabolism promotes Arabidopsis thaliana defense against the phloem-feeding insect Myzus persicae.

PMID:21434927

Different roles of Enhanced Disease Susceptibility1 (EDS1) bound to and dissociated from Phytoalexin Deficient4 (PAD4) in Arabidopsis immunity.

EDS1 forms molecularly distinct complexes with PAD4 or SAG101; EDS1-PAD4 complex formation supports basal resistance and SA defense mobilization.

PMID:22072959

SAG101 forms a ternary complex with EDS1 and PAD4 and is required for resistance signaling against turnip crinkle virus.

PMID:23275581

Natural variation in small molecule-induced TIR-NB-LRR signaling induces root growth arrest via EDS1- and PAD4-complexed R protein VICTR in Arabidopsis.

PMID:28555890

The dual role of LESION SIMULATING DISEASE 1 as a condition-dependent scaffold protein and transcription regulator.

PMID:29253890

Leaf shedding as an anti-bacterial defense in Arabidopsis cauline leaves.

PAD4 and other SA-defense components are required for pathogen-triggered cauline leaf abscission as an antibacterial defense response.

PMID:9136026

Phytoalexin-deficient mutants of Arabidopsis reveal that PAD4 encodes a regulatory factor and that four PAD genes contribute to downy mildew resistance.

PMID:9634589

PAD4 functions upstream from salicylic acid to control defense responses in Arabidopsis.

file:ARATH/PAD4/PAD4-deep-research-falcon.md

Falcon deep research for Arabidopsis PAD4

PAD4 is an EDS1-family lipase-like immune regulator forming EDS1-PAD4 complexes and acting downstream of TIR-NLR signaling.
Recent synthesis favors noncanonical/pseudoenzymatic immune signaling over demonstrated lipase catalysis.

file:ARATH/PAD4/PAD4-uniprot.txt

UniProt record for Arabidopsis PAD4

UniProt identifies PAD4/Q9S745 as lipase-like PAD4, also named enhanced disease susceptibility 9 and phytoalexin deficient 4, with nuclear and cytoplasmic localization annotations.

file:interpro/panther/PTHR47413/PTHR47413-entries.csv

PANTHER PTHR47413 plant innate immunity regulator family entries

PTHR47413 places Arabidopsis Q9S745/PAD4 in subfamily LIPASE-LIKE PAD4; the broader plant-innate-immunity family label is background context rather than evidence for a specific GO action.

Suggested Experiments

Experiment: Reconstitute Arabidopsis EDS1-PAD4 with candidate TIR-derived nucleotide ligands and ADR1-family helper NLRs to quantify PAD4-dependent complex assembly and signaling output.

Experiment: Test purified PAD4 and EDS1-PAD4 complexes against lipid and ester substrates alongside catalytic-site mutants to determine whether any physiologically relevant hydrolase activity exists.

Deep Research

Falcon

(PAD4-deep-research-falcon.md)

this with annotations you find in gene/protein databases, but these can be outdated or inaccurate. Falcon Edison Scientific Literature 24 citations 2026-05-07T01:36:20.356456

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: Arabidopsis thaliana PAD4 (UniProt Q9S745; gene PAD4/EDS9; At3g52430)

0) Scope and identity verification (critical)

The gene symbol PAD4 can refer to unrelated proteins in other organisms (e.g., mammalian PADI4/PAD4). The literature assembled here unambiguously concerns Arabidopsis thaliana PHYTOALEXIN DEFICIENT 4 (AtPAD4), which is repeatedly defined as a plant EDS1-family, “lipase-like” immune regulator forming an exclusive heterodimer with EDS1 and operating downstream of TIR-domain NLRs (TNLs). These properties match the UniProt target description (AB hydrolase–like/lipase-like + EP domain) provided by the user. (lapin2019acoevolvededs1sag101nrg1 pages 2-3, chen2024planttollinterleukin1receptorresistance pages 1-3)

A limitation of the retrieved full-text evidence is that the UniProt accession Q9S745 and locus At3g52430 are not explicitly printed in the passages available; mapping is therefore based on the user-provided UniProt identity plus the consistent Arabidopsis-specific nomenclature AtPAD4/PHYTOALEXIN DEFICIENT4 in the cited plant immunity studies. (lapin2019acoevolvededs1sag101nrg1 pages 2-3, chen2024planttollinterleukin1receptorresistance pages 1-3)

1) Key concepts and definitions (current understanding)

1.1 PAD4 as an EDS1-family “lipase-like” immune regulator

PAD4 belongs to the EDS1 family (EDS1, PAD4, SAG101), described as “lipase-like” proteins with (i) an N-terminal lipase-like domain (LLD) adopting an α/β-hydrolase fold and (ii) a C-terminal EP (EDS1–PAD4) domain that is characteristic of this family. (chen2024planttollinterleukin1receptorresistance pages 1-3, voss2022crucialstepson pages 66-72, lapin2019acoevolvededs1sag101nrg1 pages 2-3)

1.2 Modular immune signaling node: EDS1–PAD4 vs EDS1–SAG101

A central organizing concept in contemporary plant immunity is that EDS1 forms distinct heterodimers with PAD4 or SAG101, and these complexes connect upstream TIR signaling to downstream helper NLRs:
- EDS1–PAD4 cooperates with ADR1-family helper NLRs.
- EDS1–SAG101 cooperates with NRG1-family helper NLRs.
This division helps explain why some TIR-triggered outputs are biased toward defense gene induction/pathogen restriction (EDS1–PAD4–ADR1) versus cell death signaling (EDS1–SAG101–NRG1). (chen2024planttollinterleukin1receptorresistance pages 1-3, lapin2019acoevolvededs1sag101nrg1 pages 2-3, song2024substrateinducedcondensationactivates pages 1-2)

1.3 TIR enzymatic outputs as immune ligands

Plant TIR domains are enzymatic signaling modules (NADase/ribosyl-transferase activities) whose products act as immune signals. Recent work directly connects TIR-derived nucleotides to the EDS1–PAD4 node, with specific metabolites binding and enabling assembly of downstream signaling complexes. (yu2024activationofa pages 2-4, yu2024activationofa pages 4-5, song2024substrateinducedcondensationactivates pages 1-2)

2) Primary function of PAD4: what it does mechanistically

2.1 PAD4’s principal role is signaling, not proven lipase catalysis

Although PAD4 is “lipase-like” and retains sequence features suggestive of a catalytic triad across species, the most compelling recent mechanistic data support PAD4 functioning primarily as a noncanonical (pseudoenzymatic) immune signaling component rather than as a demonstrated hydrolase. A structural/biochemical analysis notes that, at least for Brassicaceae PAD4 proteins, sequence features may hinder classical oxyanion-hole formation; additionally, PAD4 catalytic triad residues can be dispensable for resistance in some pathogen contexts, which is inconsistent with an obligate catalytic mechanism. (voss2022crucialstepson pages 94-96)

2.2 PAD4 forms an EDS1–PAD4 heterodimer that serves as a ligand-enabled receptor/scaffold for ADR1

A major 2024 advance was the structural elucidation of how EDS1–PAD4 recruits ADR1:
- Yu et al. (Science, 20 Dec 2024) report a cryo-EM structure of an Arabidopsis EDS1–PAD4–ADR1 heterotrimer bound to pRib-ADP.
- Ligand binding induces an approximately 18° rotation of the PAD4 EP domain, creating an interaction cleft that enables stable association with ADR1. (yu2024activationofa pages 2-4)
- Two principal interaction interfaces with ADR1 were quantified with buried surface areas of 585.3 Å² (interface I-1) and 593.3 Å² (interface I-2). (yu2024activationofa pages 2-4)

These findings reposition EDS1–PAD4 from a genetically defined hub to a molecularly defined ligand-responsive complex that recruits helper NLRs. (yu2024activationofa pages 2-4, yu2024activationofa pages 1-2)

2.3 PAD4 transduces TIR-derived signals to downstream immunity

Yu et al. further connect TIR enzymatic products to the PAD4 branch:
- Specific TIR domains that generate 2′cADPR (rather than 3′cADPR) promote formation of the EDS1–PAD4–ADR1 complex and ADR1 oligomerization.
- Quantitatively, RPS4TIR produced ~6% and ~2.5% of the 2′cADPR yield of bacterial HopBY and AbTirTIR, respectively; an AbTirTIR variant produced ~2-fold more 2′cADPR than a catalytic control mutant. (yu2024activationofa pages 4-5)
- They also infer that pRib-AMP (an unstable metabolite whose detection required protection by ligand-free EDS1–PAD4) is a key activating species for the EPA complex, with 2′cADPR potentially serving as a storage form convertible to pRib-AMP. (yu2024activationofa pages 4-5)

3) Pathways and biological processes involving PAD4

3.1 TIR-NLR (TNL) effector-triggered immunity and transcriptional defense

Foundational work places PAD4 in TNL-triggered immunity where AtEDS1–AtPAD4 heterodimers promote defense transcription programs, including shifting responses toward salicylic-acid (SA)-associated defenses and away from antagonistic jasmonic-acid programs. (lapin2019acoevolvededs1sag101nrg1 pages 2-3)

3.2 Pattern-triggered immunity (PTI), receptor-like protein pathways, and stomatal immunity

PAD4 is also implicated beyond canonical TNL ETI.
- Chen et al. (iScience, 16 Feb 2024) provide evidence that plant TIR domains physically associate with PAD4 and other EDS1 family members in planta, and that TIR association occurs most strongly via the N-terminal lipase-like domain (LLD) rather than the EP domain. (chen2024planttollinterleukin1receptorresistance pages 7-8, chen2024planttollinterleukin1receptorresistance pages 6-7)
- A 2024 preprint focusing on stomatal immunity proposes a pathway where pathogen infection or flg22 triggers assembly of an EDS1–PAD4–ADR1 complex (including Arabidopsis components in Nicotiana assays), linking PRR/Ca2+ signaling to this intracellular node. (wang2024switchoftir pages 4-8)

4) Cellular and subcellular localization (evidence and gaps)

The retrieved evidence set contains limited explicit statements about PAD4’s subcellular localization (e.g., nucleus vs cytoplasm). One background source explicitly notes regulation of EDS1 nuclear import (via EIJ1), indicating that compartmental localization is functionally important for this node, but it does not explicitly localize PAD4 itself. (voss2022crucialstepson pages 20-22)

Several recent mechanistic models imply compartmentalization through partner functions (e.g., helper NLRs acting as plasma-membrane Ca2+ channels), but these do not constitute direct PAD4 localization evidence in the retrieved passages. (wang2024switchoftir pages 4-8, song2024substrateinducedcondensationactivates pages 1-2)

5) Recent developments (prioritizing 2023–2024)

5.1 2024: Structural basis of EDS1–PAD4–ADR1 activation by TIR-derived ligands

Yu et al. (Science, 20 Dec 2024) provide a high-impact synthesis of structural, biochemical, and genetic evidence showing how PAD4 contributes to ligand-enabled ADR1 recruitment and signaling, including quantitative interface metrics and conformational change (EP-domain rotation). (yu2024activationofa pages 2-4, yu2024activationofa pages 4-5)

To support the mechanistic claims visually, Figure 1 from this paper shows the domain architecture, the cryo-EM structure, and ligand density for pRib-ADP in the complex. (yu2024activationofa media 87d45877, yu2024activationofa media a568981a, yu2024activationofa media c7b81439)

5.2 2024: Physical association of plant TIRs with PAD4 and domain requirements

Chen et al. (iScience, 16 Feb 2024) use multiple orthogonal assays (Co-IP, split-luciferase, plant two-hybrid) to show TIR association with EDS1 family proteins including PAD4, with statistical analyses including one-way ANOVA with LSD (p < 0.05) and Student’s t-tests annotated up to ****P < 0.0001. (chen2024planttollinterleukin1receptorresistance pages 6-7, chen2024planttollinterleukin1receptorresistance pages 18-19)

They further show TIR association is strongest with the PAD4 LLD rather than the EP domain, clarifying how PAD4 receives upstream signals at the domain level. (chen2024planttollinterleukin1receptorresistance pages 7-8)

5.3 2024: Upstream mechanism—TIR substrate-induced condensation

Song et al. (Nature, Mar 2024) report that NAD+ and ATP can induce phase separation/condensation of plant TIR domain proteins in vitro and that similar condensation occurs in planta after pathogen inoculation, with disruption of condensates impairing TIR-triggered cell death. They frame EDS1–PAD4 (with ADR1) as key downstream components of TIR signaling. (song2024substrateinducedcondensationactivates pages 1-2)

6) Current applications and real-world implementations

6.1 Crop disease resistance engineering via the TIR→EDS1–PAD4→ADR1 node

The mechanistic definition of ligand-responsive EDS1–PAD4–ADR1 assemblies suggests practical strategies for crop protection: engineering TIR signaling, optimizing EDS1–PAD4–ADR1 compatibility, or manipulating signaling metabolite production/transfer to tune defense activation. These opportunities are underscored by the demonstration that bacterial TIRs producing 2′cADPR can activate the plant EDS1–PAD4–ADR1 complex. (yu2024activationofa pages 4-5, yu2024activationofa pages 2-4)

6.2 Immunity priming and stomatal defense

Stomatal immunity is a major determinant of resistance against foliar bacterial pathogens. Mechanistic evidence that PRR-triggered stomatal closure can require an intracellular EDS1–PAD4–ADR1 module provides a conceptual route to improve barrier immunity by targeting this node. (wang2024switchoftir pages 4-8)

7) Expert analysis and authoritative perspectives

A consistent expert-level interpretation across recent mechanistic papers is that PAD4’s “lipase-like” architecture supports protein–protein interactions and ligand-responsive conformational switching rather than classical lipid hydrolysis. The 2024 Science structure explicitly supports a model where a TIR-derived ligand triggers PAD4 EP-domain rearrangement to enable ADR1 engagement, establishing PAD4 as part of a bona fide receptor-like signaling module. (yu2024activationofa pages 2-4)

The 2024 iScience paper supports an additional expert model: activated TIR domains may physically interact with EDS1-family proteins to facilitate efficient delivery of low-abundance enzymatic products directly to EDS1–PAD4 heterodimers (channeling), providing an explanation for the difficulty of detecting free ligands in planta. (chen2023planttirdomains pages 1-4, chen2024planttollinterleukin1receptorresistance pages 7-8)

8) Key statistics and data highlights (recent)

EDS1–PAD4–ADR1 structure: PAD4 EP-domain rotates ~18° upon ligand binding; two EPA interfaces have buried surface areas 585.3 Å² and 593.3 Å². (yu2024activationofa pages 2-4)
TIR-product yields: RPS4TIR produces ~6% and 2.5% of HopBY and AbTirTIR 2′cADPR yields, respectively; an AbTirTIR variant produces ~2× more 2′cADPR than a catalytic mutant control. (yu2024activationofa pages 4-5)
Statistics and replication (TIR–PAD4 interaction assays): one-way ANOVA with LSD p < 0.05; Student’s t-test with annotations up to *P < 0.0001*; Co-IP repeated ≥5 times and most infiltrations repeated ≥3 times with 3–4 plants**. (chen2024planttollinterleukin1receptorresistance pages 6-7, chen2024planttollinterleukin1receptorresistance pages 18-19, chen2024planttollinterleukin1receptorresistance pages 4-6)

9) Evidence summary table

Functional role/claim	Mechanistic details (partners, ligands, pathway)	Key quantitative/statistical data (if any)	Primary supporting source with publication year + URL
Arabidopsis PAD4 is the correct target protein: an EDS1-family lipase-like immune regulator rather than mammalian PADI4/PAD4	AtPAD4/PHYTOALEXIN DEFICIENT 4 is described in Arabidopsis immunity literature as an EDS1-family protein with an N-terminal lipase-like/αβ-hydrolase fold and a C-terminal EP domain; it forms exclusive heterodimers with EDS1 and acts downstream of TIR-NLR signaling. This matches the UniProt target Q9S745 / At3g52430 context. (lapin2019acoevolvededs1sag101nrg1 pages 2-3, chen2024planttollinterleukin1receptorresistance pages 1-3, voss2022crucialstepson pages 66-72)	No locus/UniProt number explicitly given in retrieved passages, but Arabidopsis-specific AtPAD4 nomenclature and domain architecture are consistent across sources.	Chen et al., iScience (2024), https://doi.org/10.1016/j.isci.2024.108817; Lapin et al., Plant Cell (2019), https://doi.org/10.1105/tpc.19.00118
PAD4 is a core signaling component of the EDS1–PAD4–ADR1 branch of plant immunity	EDS1–PAD4 heterocomplexes cooperate with ADR1 helper NLRs, whereas EDS1–SAG101 cooperates with NRG1. This defines a mechanistic split in TIR signaling outputs: PAD4 is associated mainly with defense activation/pathogen restriction, while SAG101–NRG1 is more tightly linked to cell death. TIR domains can physically associate with PAD4/EDS1-family proteins in planta. (chen2024planttollinterleukin1receptorresistance pages 1-3, chen2023planttirdomains pages 1-4, lapin2019acoevolvededs1sag101nrg1 pages 2-3)	In split-luciferase / two-hybrid assays, TIR–PAD4 interactions were statistically supported; figure legend reports one-way ANOVA with LSD test p < 0.05 and Student’s t-test significance up to **P < 0.0001. (chen2024planttollinterleukin1receptorresistance pages 6-7)	Chen et al., iScience (2024), https://doi.org/10.1016/j.isci.2024.108817; Chen et al., bioRxiv (2023), https://doi.org/10.1101/2023.08.02.551391
PAD4 participates directly in ligand-enabled assembly of the Arabidopsis EDS1–PAD4–ADR1 (“EPA”) complex	Cryo-EM in Arabidopsis resolved an EDS1–PAD4–ADR1 heterotrimer bound to a ribosylated TIR-product ligand. PAD4 contributes to the EP-domain interface that recognizes ADR1 after ligand binding, supporting a receptor-like role for the EDS1–PAD4 heterodimer in downstream signaling. (yu2024activationofa pages 1-2, yu2024activationofa pages 2-4, yu2024activationofa media 87d45877)	Ligand binding causes an approximately 18° rotation of the PAD4 EP domain; interface I-1 buried surface area 585.3 Å² and interface I-2 593.3 Å². Pull-down assays were repeated 3 times. (yu2024activationofa pages 2-4)	Yu et al., Science (2024), https://doi.org/10.1126/science.adr3150
PAD4-containing EDS1 complexes are activated by TIR-derived nucleotide signals	TIR NADase/ribosyl-transferase activities generate immune metabolites that allosterically activate downstream EDS1-family complexes. In the 2024 Science study, pRib-ADP was visualized in the EPA complex, and the authors conclude that pRib-AMP activates EDS1–PAD4–ADR1 signaling; 2′cADPR can be hydrolyzed to pRib-AMP and thereby activate EPA. (yu2024activationofa pages 1-2, yu2024activationofa pages 4-5, song2024substrateinducedcondensationactivates pages 1-2)	RPS4TIR accumulated about 6% and 2.5% of the 2′cADPR yield produced by HopBY and AbTirTIR, respectively; an AbTirTIR variant produced about 2-fold more 2′cADPR than a catalytic mutant control. Detection of pRib-AMP required protection by ligand-free EDS1–PAD4, indicating instability. (yu2024activationofa pages 4-5)	Yu et al., Science (2024), https://doi.org/10.1126/science.adr3150; Song et al., Nature (2024), https://doi.org/10.1038/s41586-024-07183-9
PAD4 functions beyond canonical TNL ETI, including PTI-linked stomatal immunity	In stomatal immunity, a Ca²⁺ sensor/TIR-only pathway promotes EDS1–PAD4–ADR1 complex assembly after pathogen infection or flg22 treatment. PAD4 therefore contributes to a PTI-associated immune branch linking PRR/Ca²⁺ signals to intracellular RNL activation. (wang2024switchoftir pages 1-4, wang2024switchoftir pages 4-8, voss2022crucialstepson pages 20-22)	In Nicotiana assays complemented with Arabidopsis proteins, AtEDS1 + AtPAD4 + AtADR1-L2 restored stomatal closure in eds1 leaves; complex formation was induced by Pst DC3000 hrcC−, flg22, and active NbSTIR1 but not NbSTIR1 E109A. (wang2024switchoftir pages 4-8)	Wang et al., bioRxiv (2024), https://doi.org/10.1101/2024.10.29.620780
PAD4 promotes defense transcriptional reprogramming and salicylic-acid-associated immunity rather than acting as the dedicated cell-death branch	Foundational genetics distinguish EDS1–PAD4 from EDS1–SAG101: AtEDS1–AtPAD4 steers host transcription toward SA-induced defense and away from JA-antagonistic programs, strongly restricting bacterial growth; by contrast, EDS1–SAG101–NRG1 is the coevolved TNL cell-death module. (lapin2019acoevolvededs1sag101nrg1 pages 1-2, lapin2019acoevolvededs1sag101nrg1 pages 2-3)	No recent numerical effect size in retrieved excerpt, but the genetic separation of PAD4 vs SAG101 functions is explicit; AtPAD4 was reported dispensable for some TNL-triggered cell death in N. benthamiana while contributing strongly to pathogen growth restriction in Arabidopsis. (lapin2019acoevolvededs1sag101nrg1 pages 2-3)	Lapin et al., Plant Cell (2019), https://doi.org/10.1105/tpc.19.00118
PAD4 is “lipase-like,” but current evidence favors a noncanonical/pseudoenzymatic signaling role over demonstrated hydrolase catalysis	PAD4 retains a catalytic triad and α/β-hydrolase fold, yet direct lipase activity has not been convincingly demonstrated. Structural/background analysis notes that, like EDS1, Brassicaceae PAD4 proteins may have oxyanion-hole-disfavoring features; Arabidopsis PAD4 catalytic residues are not generally required for resistance to some pathogens, arguing that signaling/scaffolding is primary. (voss2022crucialstepson pages 94-96, voss2022crucialstepson pages 20-22)	Recombinant vvPAD4 showed no clear lipase activity in initial chromogenic assays; mutation of PAD4 catalytic Ser or Asp affected green peach aphid defense, but His mutation did not, arguing against a straightforward classical lipase mechanism. (voss2022crucialstepson pages 94-96, voss2022crucialstepson pages 20-22)	Voß, thesis (2022), URL not available in retrieved metadata; cited context from thesis text (voss2022crucialstepson pages 94-96, voss2022crucialstepson pages 20-22)
PAD4’s relevant structural region for downstream signaling is the EP domain as well as the lipase-like domain used in heterodimerization	EDS1 binds PAD4 via a convex–concave interface where the EDS1 α-H helix inserts into a hydrophobic pocket on PAD4; TIR association in planta is strongest with the lipase-like domain fragments, whereas ADR1 engagement in the EPA complex depends heavily on the ligand-repositioned PAD4 EP domain. (chen2024planttollinterleukin1receptorresistance pages 1-3, chen2024planttollinterleukin1receptorresistance pages 6-7, yu2024activationofa pages 2-4)	Statistical annotation for TIR–PAD4 interaction assays includes one-way ANOVA/LSD p < 0.05 and t-test significance levels from P < 0.05 to **P < 0.0001. (chen2024planttollinterleukin1receptorresistance pages 6-7)	Chen et al., iScience (2024), https://doi.org/10.1016/j.isci.2024.108817; Yu et al., Science (2024), https://doi.org/10.1126/science.adr3150
TIR substrate-induced condensation provides an upstream biochemical framework for PAD4 activation	Plant TIR domains undergo NAD⁺/ATP-driven phase separation; these condensates are required for robust TIR signaling and are proposed to promote production/transfer of metabolites that activate EDS1–PAD4 and EDS1–SAG101 branches. This refines the current model of how PAD4 receives upstream signals. (song2024substrateinducedcondensationactivates pages 1-2)	Nature 2024 excerpt is qualitative in the retrieved text; it reports that disrupting TIR condensates impairs cell-death activity but does not provide numeric values in the available passage.	Song et al., Nature (2024), https://doi.org/10.1038/s41586-024-07183-9

Table: This table summarizes functional annotation evidence for Arabidopsis thaliana PAD4, emphasizing recent 2023–2024 mechanistic studies and key foundational sources. It is useful for mapping PAD4’s validated role, pathway partners, signaling ligands, and the current view that PAD4 is a lipase-like immune regulator with primarily noncanonical signaling functions.

10) References (prioritizing 2023–2024; publication dates and URLs)

Yu H. et al. “Activation of a helper NLR by plant and bacterial TIR immune signaling.” Science 386:1413–1420. 20 Dec 2024. https://doi.org/10.1126/science.adr3150 (yu2024activationofa pages 1-2, yu2024activationofa pages 2-4, yu2024activationofa pages 4-5)
Chen J. et al. “Plant Toll/interleukin-1 receptor/resistance protein domains physically associate with enhanced disease susceptibility1 family proteins in immune signaling.” iScience 27:108817. 16 Feb 2024. https://doi.org/10.1016/j.isci.2024.108817 (chen2024planttollinterleukin1receptorresistance pages 1-3, chen2024planttollinterleukin1receptorresistance pages 6-7, chen2024planttollinterleukin1receptorresistance pages 7-8, chen2024planttollinterleukin1receptorresistance pages 18-19)
Song W. et al. “Substrate-induced condensation activates plant TIR domain proteins.” Nature 627:847–853. Mar 2024. https://doi.org/10.1038/s41586-024-07183-9 (song2024substrateinducedcondensationactivates pages 1-2)
Chen J. et al. “Plant TIR domains physically interact with EDS1 family proteins to propagate immune signalling.” bioRxiv Aug 2023. https://doi.org/10.1101/2023.08.02.551391 (chen2023planttirdomains pages 1-4)
Wang H. et al. “Switch of TIR signaling by a Ca2+ sensor activates ADR1 recognition of pRib-AMP-EDS1-PAD4 for stomatal immunity.” bioRxiv posted 2 Nov 2024. https://doi.org/10.1101/2024.10.29.620780 (wang2024switchoftir pages 4-8)
Lapin D. et al. “A Coevolved EDS1-SAG101-NRG1 Module Mediates Cell Death Signaling by TIR-Domain Immune Receptors.” The Plant Cell 31:2430–2455. Jul 2019. https://doi.org/10.1105/tpc.19.00118 (lapin2019acoevolvededs1sag101nrg1 pages 2-3)

11) Explicitly unresolved items (based on retrieved evidence)

Direct biochemical substrate specificity for PAD4 as an enzyme: no conclusive hydrolase reaction/substrate is established in the retrieved primary literature; the dominant model is noncanonical signaling. (voss2022crucialstepson pages 94-96, yu2024activationofa pages 2-4)
Direct PAD4 subcellular localization: explicit nucleus/cytoplasm/membrane localization statements for PAD4 were not captured in the retrieved excerpts and should be addressed by targeted retrieval of localization studies (e.g., PAD4-GFP experiments) if required. (voss2022crucialstepson pages 20-22)

References

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(voss2022crucialstepson pages 66-72): M Voß. Crucial steps on the way to a comprehensive structural understanding of the plant proteins eds1 and pad4 and their role in innate immunity. Unknown journal, 2022.
(song2024substrateinducedcondensationactivates pages 1-2): Wen Song, Li Liu, Dongli Yu, Hanna Bernardy, Jan Jirschitzka, Shijia Huang, Aolin Jia, Wictoria Jemielniak, Julia Acker, Henriette Laessle, Junli Wang, Qiaochu Shen, Weijie Chen, Pilong Li, Jane E. Parker, Zhifu Han, Paul Schulze-Lefert, and Jijie Chai. Substrate-induced condensation activates plant tir domain proteins. Nature, 627:847-853, Mar 2024. URL: https://doi.org/10.1038/s41586-024-07183-9, doi:10.1038/s41586-024-07183-9. This article has 69 citations and is from a highest quality peer-reviewed journal.
(yu2024activationofa pages 2-4): Hua Yu, Weiying Xu, Sisi Chen, Xiaoxian Wu, Weiwei Rao, Xiaoxiao Liu, Xiaoyan Xu, Jingqi Chen, Marc T. Nishimura, Yu Zhang, and Li Wan. Activation of a helper nlr by plant and bacterial tir immune signaling. Science, 386:1413-1420, Dec 2024. URL: https://doi.org/10.1126/science.adr3150, doi:10.1126/science.adr3150. This article has 70 citations and is from a highest quality peer-reviewed journal.
(yu2024activationofa pages 4-5): Hua Yu, Weiying Xu, Sisi Chen, Xiaoxian Wu, Weiwei Rao, Xiaoxiao Liu, Xiaoyan Xu, Jingqi Chen, Marc T. Nishimura, Yu Zhang, and Li Wan. Activation of a helper nlr by plant and bacterial tir immune signaling. Science, 386:1413-1420, Dec 2024. URL: https://doi.org/10.1126/science.adr3150, doi:10.1126/science.adr3150. This article has 70 citations and is from a highest quality peer-reviewed journal.
(voss2022crucialstepson pages 94-96): M Voß. Crucial steps on the way to a comprehensive structural understanding of the plant proteins eds1 and pad4 and their role in innate immunity. Unknown journal, 2022.
(yu2024activationofa pages 1-2): Hua Yu, Weiying Xu, Sisi Chen, Xiaoxian Wu, Weiwei Rao, Xiaoxiao Liu, Xiaoyan Xu, Jingqi Chen, Marc T. Nishimura, Yu Zhang, and Li Wan. Activation of a helper nlr by plant and bacterial tir immune signaling. Science, 386:1413-1420, Dec 2024. URL: https://doi.org/10.1126/science.adr3150, doi:10.1126/science.adr3150. This article has 70 citations and is from a highest quality peer-reviewed journal.
(chen2024planttollinterleukin1receptorresistance pages 7-8): Jian Chen, Xiaoxiao Zhang, Maud Bernoux, John P. Rathjen, and Peter N. Dodds. Plant toll/interleukin-1 receptor/resistance protein domains physically associate with enhanced disease susceptibility1 family proteins in immune signaling. iScience, 27:108817, Feb 2024. URL: https://doi.org/10.1016/j.isci.2024.108817, doi:10.1016/j.isci.2024.108817. This article has 11 citations and is from a peer-reviewed journal.
(chen2024planttollinterleukin1receptorresistance pages 6-7): Jian Chen, Xiaoxiao Zhang, Maud Bernoux, John P. Rathjen, and Peter N. Dodds. Plant toll/interleukin-1 receptor/resistance protein domains physically associate with enhanced disease susceptibility1 family proteins in immune signaling. iScience, 27:108817, Feb 2024. URL: https://doi.org/10.1016/j.isci.2024.108817, doi:10.1016/j.isci.2024.108817. This article has 11 citations and is from a peer-reviewed journal.
(wang2024switchoftir pages 4-8): Hanling Wang, Jiaxin Tan, Xiulin Cui, Yuhan Bai, Shang Gao, Brian Staskawicz, Susheng Song, Chuangye Yan, and Tiancong Qi. Switch of tir signaling by a ca2+ sensor activates adr1 recognition of prib-amp-eds1-pad4 for stomatal immunity. bioRxiv, Nov 2024. URL: https://doi.org/10.1101/2024.10.29.620780, doi:10.1101/2024.10.29.620780. This article has 7 citations.
(voss2022crucialstepson pages 20-22): M Voß. Crucial steps on the way to a comprehensive structural understanding of the plant proteins eds1 and pad4 and their role in innate immunity. Unknown journal, 2022.
(yu2024activationofa media 87d45877): Hua Yu, Weiying Xu, Sisi Chen, Xiaoxian Wu, Weiwei Rao, Xiaoxiao Liu, Xiaoyan Xu, Jingqi Chen, Marc T. Nishimura, Yu Zhang, and Li Wan. Activation of a helper nlr by plant and bacterial tir immune signaling. Science, 386:1413-1420, Dec 2024. URL: https://doi.org/10.1126/science.adr3150, doi:10.1126/science.adr3150. This article has 70 citations and is from a highest quality peer-reviewed journal.
(yu2024activationofa media a568981a): Hua Yu, Weiying Xu, Sisi Chen, Xiaoxian Wu, Weiwei Rao, Xiaoxiao Liu, Xiaoyan Xu, Jingqi Chen, Marc T. Nishimura, Yu Zhang, and Li Wan. Activation of a helper nlr by plant and bacterial tir immune signaling. Science, 386:1413-1420, Dec 2024. URL: https://doi.org/10.1126/science.adr3150, doi:10.1126/science.adr3150. This article has 70 citations and is from a highest quality peer-reviewed journal.
(yu2024activationofa media c7b81439): Hua Yu, Weiying Xu, Sisi Chen, Xiaoxian Wu, Weiwei Rao, Xiaoxiao Liu, Xiaoyan Xu, Jingqi Chen, Marc T. Nishimura, Yu Zhang, and Li Wan. Activation of a helper nlr by plant and bacterial tir immune signaling. Science, 386:1413-1420, Dec 2024. URL: https://doi.org/10.1126/science.adr3150, doi:10.1126/science.adr3150. This article has 70 citations and is from a highest quality peer-reviewed journal.
(chen2024planttollinterleukin1receptorresistance pages 18-19): Jian Chen, Xiaoxiao Zhang, Maud Bernoux, John P. Rathjen, and Peter N. Dodds. Plant toll/interleukin-1 receptor/resistance protein domains physically associate with enhanced disease susceptibility1 family proteins in immune signaling. iScience, 27:108817, Feb 2024. URL: https://doi.org/10.1016/j.isci.2024.108817, doi:10.1016/j.isci.2024.108817. This article has 11 citations and is from a peer-reviewed journal.
(chen2023planttirdomains pages 1-4): Jian Chen, Xiaoxiao Zhang, Maud Bernoux, John P. Rathjen, and Peter N. Dodds. Plant tir domains physically interact with eds1 family proteins to propagate immune signalling. bioRxiv, Aug 2023. URL: https://doi.org/10.1101/2023.08.02.551391, doi:10.1101/2023.08.02.551391. This article has 0 citations.
(chen2024planttollinterleukin1receptorresistance pages 4-6): Jian Chen, Xiaoxiao Zhang, Maud Bernoux, John P. Rathjen, and Peter N. Dodds. Plant toll/interleukin-1 receptor/resistance protein domains physically associate with enhanced disease susceptibility1 family proteins in immune signaling. iScience, 27:108817, Feb 2024. URL: https://doi.org/10.1016/j.isci.2024.108817, doi:10.1016/j.isci.2024.108817. This article has 11 citations and is from a peer-reviewed journal.
(wang2024switchoftir pages 1-4): Hanling Wang, Jiaxin Tan, Xiulin Cui, Yuhan Bai, Shang Gao, Brian Staskawicz, Susheng Song, Chuangye Yan, and Tiancong Qi. Switch of tir signaling by a ca2+ sensor activates adr1 recognition of prib-amp-eds1-pad4 for stomatal immunity. bioRxiv, Nov 2024. URL: https://doi.org/10.1101/2024.10.29.620780, doi:10.1101/2024.10.29.620780. This article has 7 citations.
(lapin2019acoevolvededs1sag101nrg1 pages 1-2): Dmitry Lapin, Viera Kovacova, Xinhua Sun, Joram A. Dongus, Deepak Bhandari, Patrick von Born, Jaqueline Bautor, Nina Guarneri, Jakub Rzemieniewski, Johannes Stuttmann, Andreas Beyer, and Jane E. Parker. A coevolved eds1-sag101-nrg1 module mediates cell death signaling by tir-domain immune receptors. The Plant Cell, 31:2430-2455, Jul 2019. URL: https://doi.org/10.1105/tpc.19.00118, doi:10.1105/tpc.19.00118. This article has 315 citations.

Citations

voss2022crucialstepson pages 94-96
yu2024activationofa pages 2-4
yu2024activationofa pages 4-5
wang2024switchoftir pages 4-8
voss2022crucialstepson pages 20-22
song2024substrateinducedcondensationactivates pages 1-2
chen2023planttirdomains pages 1-4
voss2022crucialstepson pages 66-72
yu2024activationofa pages 1-2
wang2024switchoftir pages 1-4
https://doi.org/10.1016/j.isci.2024.108817;
https://doi.org/10.1105/tpc.19.00118
https://doi.org/10.1101/2023.08.02.551391
https://doi.org/10.1126/science.adr3150
https://doi.org/10.1126/science.adr3150;
https://doi.org/10.1038/s41586-024-07183-9
https://doi.org/10.1101/2024.10.29.620780
https://doi.org/10.1016/j.isci.2024.108817
https://doi.org/10.1105/tpc.19.00118,
https://doi.org/10.1016/j.isci.2024.108817,
https://doi.org/10.1038/s41586-024-07183-9,
https://doi.org/10.1126/science.adr3150,
https://doi.org/10.1101/2024.10.29.620780,
https://doi.org/10.1101/2023.08.02.551391,

📄 View Raw YAML

id: Q9S745
gene_symbol: PAD4
product_type: PROTEIN
status: COMPLETE
taxon:
  id: NCBITaxon:3702
  label: Arabidopsis thaliana
description: PAD4 is an Arabidopsis EDS1-family, lipase-like immune signaling regulator. It forms EDS1-PAD4 complexes in nucleus and cytoplasm, amplifies salicylic-acid-associated defense programs, and contributes to systemic acquired resistance, antibacterial defense, TIR-NLR signaling, and selected aphid, hypoxia, and leaf-abscission outputs. Despite AB-hydrolase/lipase-like domains, direct lipase activity is not established; current mechanistic evidence favors a pseudoenzymatic adaptor/scaffold role in immune signaling.
existing_annotations:
- term:
    id: GO:0001666
    label: response to hypoxia
  evidence_type: IMP
  original_reference_id: PMID:18055613
  review:
    summary: PAD4 is genetically required for hypoxia-induced lysigenous aerenchyma and associated ROS signaling in the cited study.
    action: KEEP_AS_NON_CORE
    reason: This is a real PAD4-dependent stress/developmental output, but it is downstream of the EDS1/PAD4 immune-redox signaling module rather than PAD4's core conserved role.
- term:
    id: GO:0002213
    label: defense response to insect
  evidence_type: IMP
  original_reference_id: PMID:17725549
  review:
    summary: PAD4 contributes to Arabidopsis defense against the green peach aphid and limits phloem feeding or aphid population growth.
    action: KEEP_AS_NON_CORE
    reason: The aphid-defense branch is experimentally supported and biologically important, but it is a specialized immune output rather than the central EDS1-PAD4 defense-signaling function.
- term:
    id: GO:0009625
    label: response to insect
  evidence_type: IMP
  original_reference_id: PMID:16299172
  review:
    summary: PAD4 contributes to Arabidopsis defense against the green peach aphid and limits phloem feeding or aphid population growth.
    action: KEEP_AS_NON_CORE
    reason: The aphid-defense branch is experimentally supported and biologically important, but it is a specialized immune output rather than the central EDS1-PAD4 defense-signaling function.
- term:
    id: GO:0009627
    label: systemic acquired resistance
  evidence_type: IEP
  original_reference_id: PMID:17419843
  review:
    summary: PAD4 is a major positive regulator of salicylic-acid-associated systemic acquired resistance and defense amplification.
    action: ACCEPT
    reason: PAD4 was cloned and characterized as required for SA accumulation/signaling and systemic resistance outputs, and later work places it in the EDS1-PAD4 immune signaling branch.
- term:
    id: GO:0009862
    label: systemic acquired resistance, salicylic acid mediated signaling pathway
  evidence_type: TAS
  original_reference_id: PMID:10557364
  review:
    summary: PAD4 is a major positive regulator of salicylic-acid-associated systemic acquired resistance and defense amplification.
    action: ACCEPT
    reason: PAD4 was cloned and characterized as required for SA accumulation/signaling and systemic resistance outputs, and later work places it in the EDS1-PAD4 immune signaling branch.
- term:
    id: GO:0009862
    label: systemic acquired resistance, salicylic acid mediated signaling pathway
  evidence_type: IMP
  original_reference_id: PMID:11574472
  review:
    summary: PAD4 is a major positive regulator of salicylic-acid-associated systemic acquired resistance and defense amplification.
    action: ACCEPT
    reason: PAD4 was cloned and characterized as required for SA accumulation/signaling and systemic resistance outputs, and later work places it in the EDS1-PAD4 immune signaling branch.
- term:
    id: GO:0010150
    label: leaf senescence
  evidence_type: IMP
  original_reference_id: PMID:16299172
  review:
    summary: PAD4 modulates premature leaf senescence induced by aphid feeding.
    action: KEEP_AS_NON_CORE
    reason: This senescence annotation is supported in the aphid-defense context, but senescence is a downstream defense strategy rather than the core molecular role of PAD4.
- term:
    id: GO:0010310
    label: regulation of hydrogen peroxide metabolic process
  evidence_type: IMP
  original_reference_id: PMID:18055613
  review:
    summary: PAD4 is genetically required for hypoxia-induced lysigenous aerenchyma and associated ROS signaling in the cited study.
    action: KEEP_AS_NON_CORE
    reason: This is a real PAD4-dependent stress/developmental output, but it is downstream of the EDS1/PAD4 immune-redox signaling module rather than PAD4's core conserved role.
- term:
    id: GO:0010618
    label: aerenchyma formation
  evidence_type: IMP
  original_reference_id: PMID:18055613
  review:
    summary: PAD4 is genetically required for hypoxia-induced lysigenous aerenchyma and associated ROS signaling in the cited study.
    action: KEEP_AS_NON_CORE
    reason: This is a real PAD4-dependent stress/developmental output, but it is downstream of the EDS1/PAD4 immune-redox signaling module rather than PAD4's core conserved role.
- term:
    id: GO:0031348
    label: negative regulation of defense response
  evidence_type: IMP
  original_reference_id: PMID:16732289
  review:
    summary: The cached text for the cited powdery-mildew MLO paper does not provide PAD4-specific support for negative regulation of defense response.
    action: REMOVE
    reason: PAD4 is predominantly a positive immune regulator; this citation does not substantiate PAD4 as a negative regulator of defense response.
- term:
    id: GO:0042742
    label: defense response to bacterium
  evidence_type: IMP
  original_reference_id: PMID:9136026
  review:
    summary: PAD4 positively regulates antibacterial defense, especially against Pseudomonas-associated disease contexts.
    action: ACCEPT
    reason: Defense response to bacterium is a central biological process output of the EDS1-PAD4 immune signaling module.
- term:
    id: GO:0050829
    label: defense response to Gram-negative bacterium
  evidence_type: IMP
  original_reference_id: PMID:29253890
  review:
    summary: PAD4 positively regulates antibacterial defense, especially against Pseudomonas-associated disease contexts.
    action: ACCEPT
    reason: Defense response to bacterium is a central biological process output of the EDS1-PAD4 immune signaling module.
- term:
    id: GO:0051707
    label: response to other organism
  evidence_type: IEP
  original_reference_id: PMID:16531493
  review:
    summary: The cited expression-genomics study supports PAD4-dependent defense signaling after pathogen challenge, not a generic response to other organism.
    action: MODIFY
    reason: Replace the broad response-to-organism term with antibacterial defense regulation, which better captures PAD4 function.
    proposed_replacement_terms:
    - id: GO:1900426
      label: positive regulation of defense response to bacterium
- term:
    id: GO:0060866
    label: leaf abscission
  evidence_type: IMP
  original_reference_id: PMID:29253890
  review:
    summary: PAD4 is required for normal pathogen-triggered cauline leaf abscission in a bacterial defense context.
    action: KEEP_AS_NON_CORE
    reason: The leaf-abscission phenotype is a tissue-level immune output mediated through salicylic-acid defense signaling, not a direct molecular function of PAD4.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:11574472
  review:
    summary: PAD4 physically interacts with EDS1 in immune signaling contexts, but generic protein binding does not describe the functional role.
    action: MARK_AS_OVER_ANNOTATED
    reason: The informative curation is EDS1 disease-resistance complex membership and signaling adaptor activity; protein binding alone is too generic for a core annotation.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:16040633
  review:
    summary: PAD4 physically interacts with EDS1 in immune signaling contexts, but generic protein binding does not describe the functional role.
    action: MARK_AS_OVER_ANNOTATED
    reason: The informative curation is EDS1 disease-resistance complex membership and signaling adaptor activity; protein binding alone is too generic for a core annotation.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:21434927
  review:
    summary: PAD4 physically interacts with EDS1 in immune signaling contexts, but generic protein binding does not describe the functional role.
    action: MARK_AS_OVER_ANNOTATED
    reason: The informative curation is EDS1 disease-resistance complex membership and signaling adaptor activity; protein binding alone is too generic for a core annotation.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:23275581
  review:
    summary: PAD4 physically interacts with VICTR/TIR-NLR immune components in immune signaling contexts, but generic protein binding does not describe the functional role.
    action: MARK_AS_OVER_ANNOTATED
    reason: The informative curation is EDS1 disease-resistance complex membership and signaling adaptor activity; protein binding alone is too generic for a core annotation.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:28555890
  review:
    summary: This source is a broad LSD1 interaction/scaffold study with a GOA/IntAct PAD4-EDS1 IPI row, but generic protein binding does not describe PAD4's functional role.
    action: MARK_AS_OVER_ANNOTATED
    reason: The informative curation is EDS1 disease-resistance complex membership and signaling adaptor activity; protein binding alone is too generic for a core annotation.
- term:
    id: GO:0016298
    label: lipase activity
  evidence_type: ISS
  original_reference_id: PMID:10557364
  review:
    summary: PAD4 was initially annotated as lipase-like from sequence similarity, but no direct PAD4 lipase activity has been demonstrated.
    action: REMOVE
    reason: The cited paper describes predicted similarity to triacylglycerol lipases and explicitly leaves substrate/activity uncertain; later evidence favors pseudoenzymatic immune signaling.
- term:
    id: GO:0006629
    label: lipid metabolic process
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  review:
    summary: The InterPro lipid metabolic process transfer follows from a lipase-like domain but is not supported by PAD4 biology.
    action: REMOVE
    reason: PAD4 is an EDS1-family immune signaling protein; no direct lipid metabolic process or lipid substrate is established.
- term:
    id: GO:0009617
    label: response to bacterium
  evidence_type: IDA
  original_reference_id: PMID:10557364
  review:
    summary: The cited PAD4 cloning paper supports antibacterial defense regulation, but response to bacterium is broader than the curated PAD4 role.
    action: MODIFY
    reason: Use a defense-response term that captures PAD4 as a positive immune regulator rather than a generic response term.
    proposed_replacement_terms:
    - id: GO:1900426
      label: positive regulation of defense response to bacterium
- term:
    id: GO:0009625
    label: response to insect
  evidence_type: IDA
  original_reference_id: PMID:21426427
  review:
    summary: PAD4 contributes to Arabidopsis defense against the green peach aphid and limits phloem feeding or aphid population growth.
    action: KEEP_AS_NON_CORE
    reason: The aphid-defense branch is experimentally supported and biologically important, but it is a specialized immune output rather than the central EDS1-PAD4 defense-signaling function.
- term:
    id: GO:0009626
    label: plant-type hypersensitive response
  evidence_type: IMP
  original_reference_id: PMID:16040633
  review:
    summary: PAD4 contributes to some TIR-NLR/EDS1-dependent hypersensitive-response and cell-death outputs.
    action: KEEP_AS_NON_CORE
    reason: Hypersensitive response is a pathway output of immune signaling; PAD4 is not the dedicated cell-death effector and contemporary models separate the EDS1-PAD4 branch from the EDS1-SAG101-NRG1 cell-death branch.
- term:
    id: GO:0009626
    label: plant-type hypersensitive response
  evidence_type: IMP
  original_reference_id: PMID:19616764
  review:
    summary: PAD4 contributes to some TIR-NLR/EDS1-dependent hypersensitive-response and cell-death outputs.
    action: KEEP_AS_NON_CORE
    reason: Hypersensitive response is a pathway output of immune signaling; PAD4 is not the dedicated cell-death effector and contemporary models separate the EDS1-PAD4 branch from the EDS1-SAG101-NRG1 cell-death branch.
- term:
    id: GO:0009626
    label: plant-type hypersensitive response
  evidence_type: NAS
  original_reference_id: PMID:22072959
  review:
    summary: PAD4 contributes to some TIR-NLR/EDS1-dependent hypersensitive-response and cell-death outputs.
    action: KEEP_AS_NON_CORE
    reason: Hypersensitive response is a pathway output of immune signaling; PAD4 is not the dedicated cell-death effector and contemporary models separate the EDS1-PAD4 branch from the EDS1-SAG101-NRG1 cell-death branch.
- term:
    id: GO:0009751
    label: response to salicylic acid
  evidence_type: IDA
  original_reference_id: PMID:10557364
  review:
    summary: PAD4 acts upstream of salicylic-acid accumulation and salicylic-acid-mediated defense signaling.
    action: ACCEPT
    reason: SA amplification and SA-mediated defense regulation are central outputs of PAD4 immune signaling.
- term:
    id: GO:0009862
    label: systemic acquired resistance, salicylic acid mediated signaling pathway
  evidence_type: IMP
  original_reference_id: PMID:10796016
  review:
    summary: PAD4 is a major positive regulator of salicylic-acid-associated systemic acquired resistance and defense amplification.
    action: ACCEPT
    reason: PAD4 was cloned and characterized as required for SA accumulation/signaling and systemic resistance outputs, and later work places it in the EDS1-PAD4 immune signaling branch.
- term:
    id: GO:0009862
    label: systemic acquired resistance, salicylic acid mediated signaling pathway
  evidence_type: NAS
  original_reference_id: PMID:22072959
  review:
    summary: PAD4 is a major positive regulator of salicylic-acid-associated systemic acquired resistance and defense amplification.
    action: ACCEPT
    reason: PAD4 was cloned and characterized as required for SA accumulation/signaling and systemic resistance outputs, and later work places it in the EDS1-PAD4 immune signaling branch.
- term:
    id: GO:0010105
    label: negative regulation of ethylene-activated signaling pathway
  evidence_type: IGI
  original_reference_id: PMID:16813576
  review:
    summary: PAD4 participates in defense hormone cross-talk involving SA, jasmonic acid, and ethylene pathways.
    action: KEEP_AS_NON_CORE
    reason: Hormone cross-regulation is a downstream regulatory output of PAD4/EDS1 signaling rather than PAD4's core molecular role.
- term:
    id: GO:0010225
    label: response to UV-C
  evidence_type: IMP
  original_reference_id: PMID:11826312
  review:
    summary: PAD4 is required for EDS5 induction after UV-C exposure in the cited defense-signaling study.
    action: KEEP_AS_NON_CORE
    reason: This abiotic stress annotation reflects shared defense/SA signaling circuitry and is not the central PAD4 immune-complex function.
- term:
    id: GO:0042742
    label: defense response to bacterium
  evidence_type: IMP
  original_reference_id: PMID:11826312
  review:
    summary: PAD4 positively regulates antibacterial defense, especially against Pseudomonas-associated disease contexts.
    action: ACCEPT
    reason: Defense response to bacterium is a central biological process output of the EDS1-PAD4 immune signaling module.
- term:
    id: GO:0071327
    label: cellular response to trehalose stimulus
  evidence_type: IDA
  original_reference_id: PMID:21426427
  review:
    summary: Trehalose metabolism regulates PAD4 expression during aphid defense.
    action: KEEP_AS_NON_CORE
    reason: This is a stimulus-response context feeding into the PAD4 aphid-defense branch, not the core EDS1-PAD4 immune signaling function.
- term:
    id: GO:0080142
    label: regulation of salicylic acid biosynthetic process
  evidence_type: IMP
  original_reference_id: PMID:9634589
  review:
    summary: PAD4 acts upstream of salicylic-acid accumulation and salicylic-acid-mediated defense signaling.
    action: ACCEPT
    reason: SA amplification and SA-mediated defense regulation are central outputs of PAD4 immune signaling.
- term:
    id: GO:0080151
    label: positive regulation of salicylic acid mediated signaling pathway
  evidence_type: IGI
  original_reference_id: PMID:16813576
  review:
    summary: PAD4 acts upstream of salicylic-acid accumulation and salicylic-acid-mediated defense signaling.
    action: ACCEPT
    reason: SA amplification and SA-mediated defense regulation are central outputs of PAD4 immune signaling.
- term:
    id: GO:1900367
    label: positive regulation of defense response to insect
  evidence_type: IMP
  original_reference_id: PMID:16299172
  review:
    summary: PAD4 contributes to Arabidopsis defense against the green peach aphid and limits phloem feeding or aphid population growth.
    action: KEEP_AS_NON_CORE
    reason: The aphid-defense branch is experimentally supported and biologically important, but it is a specialized immune output rather than the central EDS1-PAD4 defense-signaling function.
- term:
    id: GO:1900426
    label: positive regulation of defense response to bacterium
  evidence_type: IMP
  original_reference_id: PMID:10557364
  review:
    summary: PAD4 positively regulates antibacterial defense, especially against Pseudomonas-associated disease contexts.
    action: ACCEPT
    reason: Defense response to bacterium is a central biological process output of the EDS1-PAD4 immune signaling module.
- term:
    id: GO:1900426
    label: positive regulation of defense response to bacterium
  evidence_type: IMP
  original_reference_id: PMID:9634589
  review:
    summary: PAD4 positively regulates antibacterial defense, especially against Pseudomonas-associated disease contexts.
    action: ACCEPT
    reason: Defense response to bacterium is a central biological process output of the EDS1-PAD4 immune signaling module.
- term:
    id: GO:1901183
    label: positive regulation of camalexin biosynthetic process
  evidence_type: IMP
  original_reference_id: PMID:10557364
  review:
    summary: PAD4 positively regulates camalexin accumulation after pathogen infection.
    action: KEEP_AS_NON_CORE
    reason: Camalexin biosynthesis is a supported defense output, but PAD4 is not itself a camalexin biosynthetic enzyme.
- term:
    id: GO:2000022
    label: regulation of jasmonic acid mediated signaling pathway
  evidence_type: IGI
  original_reference_id: PMID:16813576
  review:
    summary: PAD4 participates in defense hormone cross-talk involving SA, jasmonic acid, and ethylene pathways.
    action: KEEP_AS_NON_CORE
    reason: Hormone cross-regulation is a downstream regulatory output of PAD4/EDS1 signaling rather than PAD4's core molecular role.
- term:
    id: GO:2000031
    label: regulation of salicylic acid mediated signaling pathway
  evidence_type: IMP
  original_reference_id: PMID:10796016
  review:
    summary: PAD4 acts upstream of salicylic-acid accumulation and salicylic-acid-mediated defense signaling.
    action: ACCEPT
    reason: SA amplification and SA-mediated defense regulation are central outputs of PAD4 immune signaling.
- term:
    id: GO:0005634
    label: nucleus
  evidence_type: IEA
  original_reference_id: GO_REF:0000044
  review:
    summary: PAD4-containing EDS1 complexes are supported in the nucleus and cytoplasm.
    action: ACCEPT
    reason: Subcellular localization is experimentally supported for EDS1-PAD4 complexes and is consistent with nucleo-cytoplasmic immune signal relay.
- term:
    id: GO:0005634
    label: nucleus
  evidence_type: ISM
  original_reference_id: GO_REF:0000122
  review:
    summary: PAD4-containing EDS1 complexes are supported in the nucleus and cytoplasm.
    action: ACCEPT
    reason: Subcellular localization is experimentally supported for EDS1-PAD4 complexes and is consistent with nucleo-cytoplasmic immune signal relay.
- term:
    id: GO:0005634
    label: nucleus
  evidence_type: IDA
  original_reference_id: PMID:16040633
  review:
    summary: PAD4-containing EDS1 complexes are supported in the nucleus and cytoplasm.
    action: ACCEPT
    reason: Subcellular localization is experimentally supported for EDS1-PAD4 complexes and is consistent with nucleo-cytoplasmic immune signal relay.
- term:
    id: GO:0005634
    label: nucleus
  evidence_type: IDA
  original_reference_id: PMID:22072959
  review:
    summary: PAD4-containing EDS1 complexes are supported in the nucleus and cytoplasm.
    action: ACCEPT
    reason: Subcellular localization is experimentally supported for EDS1-PAD4 complexes and is consistent with nucleo-cytoplasmic immune signal relay.
- term:
    id: GO:0005634
    label: nucleus
  evidence_type: NAS
  original_reference_id: PMID:22072959
  review:
    summary: PAD4-containing EDS1 complexes are supported in the nucleus and cytoplasm.
    action: ACCEPT
    reason: Subcellular localization is experimentally supported for EDS1-PAD4 complexes and is consistent with nucleo-cytoplasmic immune signal relay.
- term:
    id: GO:0005737
    label: cytoplasm
  evidence_type: IEA
  original_reference_id: GO_REF:0000044
  review:
    summary: PAD4-containing EDS1 complexes are supported in the nucleus and cytoplasm.
    action: ACCEPT
    reason: Subcellular localization is experimentally supported for EDS1-PAD4 complexes and is consistent with nucleo-cytoplasmic immune signal relay.
- term:
    id: GO:0005737
    label: cytoplasm
  evidence_type: IDA
  original_reference_id: PMID:16040633
  review:
    summary: PAD4-containing EDS1 complexes are supported in the nucleus and cytoplasm.
    action: ACCEPT
    reason: Subcellular localization is experimentally supported for EDS1-PAD4 complexes and is consistent with nucleo-cytoplasmic immune signal relay.
- term:
    id: GO:0005829
    label: cytosol
  evidence_type: IDA
  original_reference_id: PMID:16040633
  review:
    summary: PAD4-containing EDS1 complexes are supported in the cytosol/cytoplasmic fraction.
    action: ACCEPT
    reason: Subcellular localization is experimentally supported for EDS1-PAD4 complexes and is consistent with nucleo-cytoplasmic immune signal relay.
- term:
    id: GO:0106093
    label: EDS1 disease-resistance complex
  evidence_type: IDA
  original_reference_id: PMID:11574472
  review:
    summary: PAD4 is a component of the EDS1 disease-resistance complex.
    action: ACCEPT
    reason: EDS1-PAD4 complex membership is the best-supported cellular component annotation for PAD4 and reflects its core immune signaling role.
- term:
    id: GO:0106093
    label: EDS1 disease-resistance complex
  evidence_type: NAS
  original_reference_id: PMID:22072959
  review:
    summary: PAD4 is a component of the EDS1 disease-resistance complex.
    action: ACCEPT
    reason: EDS1-PAD4 complex membership is the best-supported cellular component annotation for PAD4 and reflects its core immune signaling role.
- term:
    id: GO:0035591
    label: signaling adaptor activity
  evidence_type: IC
  original_reference_id: file:ARATH/PAD4/PAD4-deep-research-falcon.md
  review:
    summary: PAD4 functions as a ligand-responsive EDS1-family immune signaling adaptor/scaffold rather than as a demonstrated lipase.
    action: NEW
    reason: Existing GOA rows capture EDS1 complex membership and defense outputs but not PAD4's current mechanistic role in ligand-responsive immune signal relay to ADR1-family helper NLRs.
    additional_reference_ids:
    - PMID:11574472
    - PMID:16040633
    - PMID:22072959
    supported_by:
    - reference_id: file:ARATH/PAD4/PAD4-deep-research-falcon.md
      supporting_text: PAD4 forms an EDS1-PAD4 heterodimer that serves as a ligand-enabled receptor/scaffold for ADR1
    - reference_id: file:ARATH/PAD4/PAD4-deep-research-falcon.md
      supporting_text: EDS1–PAD4–ADR1 heterotrimer bound to **pRib-ADP**
    - reference_id: PMID:11574472
      supporting_text: EDS1 and PAD4 proteins interact in healthy and pathogen-challenged plant cells
    - reference_id: PMID:16040633
      supporting_text: dynamic interactions of EDS1 and its signaling partners in multiple cell compartments are important for plant defense signal relay
    - reference_id: PMID:22072959
      supporting_text: Co-IP of EDS1-90-MYC and PAD4-MYC with EDS1-80-FLAG
references:
- id: GO_REF:0000002
  title: Gene Ontology annotation through association of InterPro records with GO terms
  findings: []
- id: GO_REF:0000044
  title: Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location vocabulary mapping, accompanied by conservative changes to GO terms applied by UniProt
  findings: []
- id: GO_REF:0000122
  title: AtSubP analysis
  findings: []
- id: PMID:10557364
  title: Arabidopsis thaliana PAD4 encodes a lipase-like gene that is important for salicylic acid signaling.
  findings:
  - statement: PAD4 was cloned as a lipase-like gene required for salicylic-acid signaling, camalexin synthesis, PR-1 expression, and defense against Pseudomonas.
- id: PMID:10796016
  title: 'Arabidopsis thaliana EDS4 contributes to salicylic acid (SA)-dependent expression of defense responses: evidence for inhibition of jasmonic acid signaling by SA.'
  findings: []
- id: PMID:11574472
  title: Direct interaction between the Arabidopsis disease resistance signaling proteins, EDS1 and PAD4.
  findings:
  - statement: This source directly supports physical interaction between Arabidopsis EDS1 and PAD4 and the EDS1-PAD4 disease-resistance complex.
- id: PMID:11826312
  title: EDS5, an essential component of salicylic acid-dependent signaling for disease resistance in Arabidopsis, is a member of the MATE transporter family.
  findings: []
- id: PMID:16040633
  title: Arabidopsis SENESCENCE-ASSOCIATED GENE101 stabilizes and signals within an ENHANCED DISEASE SUSCEPTIBILITY1 complex in plant innate immunity.
  findings:
  - statement: This source supports EDS1-PAD4 associations in nucleus and cytoplasm and notes that EDS1/PAD4 lipase-like proteins lack demonstrated esterase activity.
- id: PMID:16299172
  title: Premature leaf senescence modulated by the Arabidopsis PHYTOALEXIN DEFICIENT4 gene is associated with defense against the phloem-feeding green peach aphid.
  findings:
  - statement: PAD4 modulates aphid-induced premature leaf senescence and contributes to basal resistance to green peach aphid.
- id: PMID:16531493
  title: Salicylic acid-independent ENHANCED DISEASE SUSCEPTIBILITY1 signaling in Arabidopsis immunity and cell death is regulated by the monooxygenase FMO1 and the Nudix hydrolase NUDT7.
  findings: []
- id: PMID:16732289
  title: Conserved requirement for a plant host cell protein in powdery mildew pathogenesis.
  findings:
  - statement: Cached text does not provide PAD4-specific support for negative regulation of defense response.
- id: PMID:16813576
  title: Arabidopsis MAP kinase 4 regulates salicylic acid- and jasmonic acid/ethylene-dependent responses via EDS1 and PAD4.
  findings: []
- id: PMID:17419843
  title: Pathogen-associated molecular pattern recognition rather than development of tissue necrosis contributes to bacterial induction of systemic acquired resistance in Arabidopsis.
  findings: []
- id: PMID:17725549
  title: Phloem-based resistance to green peach aphid is controlled by Arabidopsis PHYTOALEXIN DEFICIENT4 without its signaling partner ENHANCED DISEASE SUSCEPTIBILITY1.
  findings:
  - statement: PAD4 controls phloem-based resistance to green peach aphid in an EDS1-independent branch.
- id: PMID:18055613
  title: Lysigenous aerenchyma formation in Arabidopsis is controlled by LESION SIMULATING DISEASE1.
  findings:
  - statement: LSD1, EDS1, and PAD4 regulate lysigenous aerenchyma formation in response to hypoxia through ethylene and reactive oxygen signaling.
- id: PMID:19616764
  title: Regulation of cell death and innate immunity by two receptor-like kinases in Arabidopsis.
  findings: []
- id: PMID:21426427
  title: TREHALOSE PHOSPHATE SYNTHASE11-dependent trehalose metabolism promotes Arabidopsis thaliana defense against the phloem-feeding insect Myzus persicae.
  findings: []
- id: PMID:21434927
  title: Different roles of Enhanced Disease Susceptibility1 (EDS1) bound to and dissociated from Phytoalexin Deficient4 (PAD4) in Arabidopsis immunity.
  findings:
  - statement: EDS1 forms molecularly distinct complexes with PAD4 or SAG101; EDS1-PAD4 complex formation supports basal resistance and SA defense mobilization.
- id: PMID:22072959
  title: SAG101 forms a ternary complex with EDS1 and PAD4 and is required for resistance signaling against turnip crinkle virus.
  findings: []
- id: PMID:23275581
  title: Natural variation in small molecule-induced TIR-NB-LRR signaling induces root growth arrest via EDS1- and PAD4-complexed R protein VICTR in Arabidopsis.
  findings: []
- id: PMID:28555890
  title: The dual role of LESION SIMULATING DISEASE 1 as a condition-dependent scaffold protein and transcription regulator.
  findings: []
- id: PMID:29253890
  title: Leaf shedding as an anti-bacterial defense in Arabidopsis cauline leaves.
  findings:
  - statement: PAD4 and other SA-defense components are required for pathogen-triggered cauline leaf abscission as an antibacterial defense response.
- id: PMID:9136026
  title: Phytoalexin-deficient mutants of Arabidopsis reveal that PAD4 encodes a regulatory factor and that four PAD genes contribute to downy mildew resistance.
  findings: []
- id: PMID:9634589
  title: PAD4 functions upstream from salicylic acid to control defense responses in Arabidopsis.
  findings: []
- id: file:ARATH/PAD4/PAD4-deep-research-falcon.md
  title: Falcon deep research for Arabidopsis PAD4
  findings:
  - statement: PAD4 is an EDS1-family lipase-like immune regulator forming EDS1-PAD4 complexes and acting downstream of TIR-NLR signaling.
  - statement: Recent synthesis favors noncanonical/pseudoenzymatic immune signaling over demonstrated lipase catalysis.
- id: file:ARATH/PAD4/PAD4-uniprot.txt
  title: UniProt record for Arabidopsis PAD4
  findings:
  - statement: UniProt identifies PAD4/Q9S745 as lipase-like PAD4, also named enhanced disease susceptibility 9 and phytoalexin deficient 4, with nuclear and cytoplasmic localization annotations.
- id: file:interpro/panther/PTHR47413/PTHR47413-entries.csv
  title: PANTHER PTHR47413 plant innate immunity regulator family entries
  findings:
  - statement: PTHR47413 places Arabidopsis Q9S745/PAD4 in subfamily LIPASE-LIKE PAD4; the broader plant-innate-immunity family label is background context rather than evidence for a specific GO action.
core_functions:
- description: Ligand-responsive EDS1-PAD4 immune signaling adaptor. PAD4 forms an EDS1-PAD4 complex that amplifies salicylic-acid-associated antibacterial and systemic defense programs and, in current mechanistic models, helps connect TIR-derived immune signals to ADR1-family helper NLR activation.
  molecular_function:
    id: GO:0035591
    label: signaling adaptor activity
  directly_involved_in:
  - id: GO:0009862
    label: systemic acquired resistance, salicylic acid mediated signaling pathway
  - id: GO:1900426
    label: positive regulation of defense response to bacterium
  locations:
  - id: GO:0005634
    label: nucleus
  - id: GO:0005737
    label: cytoplasm
  supported_by:
  - reference_id: file:ARATH/PAD4/PAD4-deep-research-falcon.md
    supporting_text: PAD4 forms an EDS1-PAD4 heterodimer that serves as a ligand-enabled receptor/scaffold for ADR1
  - reference_id: file:ARATH/PAD4/PAD4-deep-research-falcon.md
    supporting_text: EDS1–PAD4–ADR1 heterotrimer bound to **pRib-ADP**
  - reference_id: PMID:11574472
    supporting_text: EDS1 and PAD4 proteins interact in healthy and pathogen-challenged plant cells
  - reference_id: file:ARATH/PAD4/PAD4-deep-research-falcon.md
    supporting_text: PAD4 promotes defense transcriptional reprogramming and salicylic-acid-associated immunity rather than acting as the dedicated cell-death branch
proposed_new_terms: []
suggested_questions:
- question: Should GO add a more specific molecular function term for ligand-responsive EDS1-family immune adaptor activity, distinct from generic protein-containing complex binding?
- question: Should older PAD4 lipase-activity annotations be retired or replaced systematically for EDS1-family proteins unless direct hydrolase activity is demonstrated?
suggested_experiments:
- description: Reconstitute Arabidopsis EDS1-PAD4 with candidate TIR-derived nucleotide ligands and ADR1-family helper NLRs to quantify PAD4-dependent complex assembly and signaling output.
- description: Test purified PAD4 and EDS1-PAD4 complexes against lipid and ester substrates alongside catalytic-site mutants to determine whether any physiologically relevant hydrolase activity exists.

Gene Description

Existing Annotations Review

Core Functions

Ligand-responsive EDS1-PAD4 immune signaling adaptor. PAD4 forms an EDS1-PAD4 complex that amplifies salicylic-acid-associated antibacterial and systemic defense programs and, in current mechanistic models, helps connect TIR-derived immune signals to ADR1-family helper NLR activation.

References

Suggested Questions for Experts

Suggested Experiments

Deep Research

Falcon

Research report: Arabidopsis thaliana PAD4 (UniProt Q9S745; gene PAD4/EDS9; At3g52430)

0) Scope and identity verification (critical)

1) Key concepts and definitions (current understanding)

1.1 PAD4 as an EDS1-family “lipase-like” immune regulator

1.2 Modular immune signaling node: EDS1–PAD4 vs EDS1–SAG101

1.3 TIR enzymatic outputs as immune ligands

2) Primary function of PAD4: what it does mechanistically

2.1 PAD4’s principal role is signaling, not proven lipase catalysis

2.2 PAD4 forms an EDS1–PAD4 heterodimer that serves as a ligand-enabled receptor/scaffold for ADR1

2.3 PAD4 transduces TIR-derived signals to downstream immunity

3) Pathways and biological processes involving PAD4

3.1 TIR-NLR (TNL) effector-triggered immunity and transcriptional defense

3.2 Pattern-triggered immunity (PTI), receptor-like protein pathways, and stomatal immunity

4) Cellular and subcellular localization (evidence and gaps)

5) Recent developments (prioritizing 2023–2024)

5.1 2024: Structural basis of EDS1–PAD4–ADR1 activation by TIR-derived ligands

5.2 2024: Physical association of plant TIRs with PAD4 and domain requirements

5.3 2024: Upstream mechanism—TIR substrate-induced condensation

6) Current applications and real-world implementations

6.1 Crop disease resistance engineering via the TIR→EDS1–PAD4→ADR1 node

6.2 Immunity priming and stomatal defense

7) Expert analysis and authoritative perspectives

8) Key statistics and data highlights (recent)

9) Evidence summary table

10) References (prioritizing 2023–2024; publication dates and URLs)

11) Explicitly unresolved items (based on retrieved evidence)

Citations

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