ICS1 (also known as SID2 / SALICYLIC ACID INDUCTION DEFICIENT 2 and EDS16 / ENHANCED DISEASE SUSCEPTIBILITY 16; AtIcs1) is a chloroplast stroma-localized isochorismate synthase (EC 5.4.4.2) that catalyzes the Mg2+-dependent, reversible isomerization of chorismate to isochorismate. This reaction is the committed and rate-limiting step of pathogen- and stress-induced salicylic acid (SA) biosynthesis in Arabidopsis. SA produced via the ICS/isochorismate pathway is required for both local and systemic acquired resistance (SAR) against biotrophic pathogens and for the transcriptional induction of pathogenesis-related (PR) genes. ICS1 is a monofunctional isochorismate synthase: it converts chorismate to isochorismate but does not itself carry out the subsequent conversion of isochorismate to SA, which requires additional enzymes. Isochorismate generated by ICS1 also feeds into phylloquinone (vitamin K1) biosynthesis, an essential cofactor for Photosystem I. Arabidopsis has a paralog, ICS2, that is also plastid-localized and enzymatically active but contributes less to SA and phylloquinone pools (unequal redundancy); single ics1 mutants are viable with severely reduced inducible SA, while ics1 ics2 double mutants are seedling lethal due to loss of phylloquinone. ICS1 expression is strongly induced by pathogen infection and, after prolonged chilling, by cold; through its control of SA levels it is genetically required for diverse SA-dependent physiological outputs including stomatal immunity and pathogen- and drought-triggered leaf abscission.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0008909 isochorismate synthase activity | IEA GO_REF:0000120 | ACCEPT | Summary: Electronic annotation of the core catalytic activity, supported by InterPro family membership (isochorismate synthase / MenF-like), RHEA:18985 and EC 5.4.4.2. This is the well-established molecular function of ICS1 and is confirmed experimentally. Reason: The catalytic activity is directly demonstrated biochemically with purified protein and matches the InterPro/EC mapping. This is a core function. Supporting Evidence: PMID:17190832 AtICS1 acts as a monofunctional isochorismate synthase (ICS), catalyzing the conversion of chorismate to isochorismate (IC) in a reaction that operates near equilibrium (K(eq) = 0.89). file:ARATH/ICS1/ICS1-deep-research-falcon.md a plastid-derived metabolite at the branch point of aromatic compound biosynthesis |
| GO:0009507 chloroplast | IEA GO_REF:0000044 | ACCEPT | Summary: ICS1 carries an N-terminal chloroplast transit peptide (residues 1-45) and was shown by chloroplast import assays and immunolocalization to be a plastid stromal protein. Chloroplast localization is correct. Reason: Directly supported by import assays and immunolocalization; consistent with the transit peptide annotated in UniProt. Supporting Evidence: PMID:17190832 we show that AtICS1 is a plastid-localized, stromal protein using chloroplast import assays and immunolocalization. file:ARATH/ICS1/ICS1-deep-research-falcon.md the ICS step is the only SA-biosynthetic step occurring in chloroplasts |
| GO:0009536 plastid | IEA GO_REF:0000117 | ACCEPT | Summary: Plastid is the parent of chloroplast and is consistent with the experimentally demonstrated plastid stromal localization. Retained as a correct but less specific localization. Reason: Correct localization, though less specific than the chloroplast/stroma annotation. IEA mapping to a broader term is acceptable. Supporting Evidence: PMID:17190832 we show that AtICS1 is a plastid-localized, stromal protein using chloroplast import assays and immunolocalization. file:ARATH/ICS1/ICS1-deep-research-falcon.md the ICS step is the only SA-biosynthetic step occurring in chloroplasts |
| GO:0042372 phylloquinone biosynthetic process | IEA GO_REF:0000117 | KEEP AS NON CORE | Summary: ICS1 supplies isochorismate, the precursor of phylloquinone (vitamin K1). Isochorismate generated by ICS1 (and the paralog ICS2) feeds the PHYLLO pathway; ics1 ics2 double mutants are devoid of phylloquinone and seedling lethal. This is a genuine but non-core contribution given the redundancy with ICS2. Reason: ICS1 contributes precursor (isochorismate) to phylloquinone biosynthesis but acts redundantly with ICS2 and does not catalyze a phylloquinone-specific step; the inducible SA pathway is its primary role. Supporting Evidence: PMID:18451262 This unequal redundancy relationship was also observed for phylloquinone, another isochorismate-derived end product. PMID:16617180 enabled a metabolic branch from the phylloquinone biosynthetic route to independently regulate the synthesis of salicylic acid required for plant defense. |
| GO:0009697 salicylic acid biosynthetic process | IEA GO_REF:0000041 | ACCEPT | Summary: ICS1 catalyzes the committed step (chorismate to isochorismate) of the pathogen- and stress-induced SA biosynthesis pathway. This is the core biological process for ICS1. Reason: Directly supported; SA biosynthesis is the central inducible role of ICS1. UniPathway mapping (UPA00025) is appropriate. Supporting Evidence: PMID:11734859 SA is synthesized from chorismate by means of ICS, and that SA made by this pathway is required for LAR and SAR responses. file:ARATH/ICS1/ICS1-deep-research-falcon.md ICS1 contributes ~90% of pathogen-induced SA accumulation |
| GO:0008909 isochorismate synthase activity | EXP PMID:17190832 Arabidopsis isochorismate synthase functional in pathogen-in... | ACCEPT | Summary: Experimentally demonstrated isochorismate synthase activity with purified AtICS1, including kinetic parameters (Km 41.5 uM for chorismate, kcat 38.7 min-1) and demonstration that it is monofunctional (no IPL activity). Reason: Direct biochemical characterization of purified enzyme. Core molecular function. Supporting Evidence: PMID:17190832 we found that AtICS1 exhibits an apparent K(m) of 41.5 mum and k(cat) = 38.7 min(-1) for chorismate. |
| GO:0009507 chloroplast | ISM GO_REF:0000122 | ACCEPT | Summary: Predicted (sequence-based, AtSubP) chloroplast localization. Consistent with the experimentally confirmed plastid stromal localization. Reason: Prediction is corroborated by experimental import and immunolocalization data. Supporting Evidence: PMID:17190832 we show that AtICS1 is a plastid-localized, stromal protein using chloroplast import assays and immunolocalization. |
| GO:0050829 defense response to Gram-negative bacterium | IMP PMID:29253890 Leaf shedding as an anti-bacterial defense in Arabidopsis ca... | KEEP AS NON CORE | Summary: sid2 (ics1) mutants show reduced defense against the Gram-negative pathogen Pseudomonas syringae pv. tomato DC3000 in cauline leaves, reflecting the requirement for SA in antibacterial defense. ICS1 acts upstream by providing SA rather than acting directly on the bacterium. Reason: A genuine SA-dependent downstream defense phenotype, captured correctly with the acts_upstream_of_or_within qualifier, but a physiological consequence of SA production rather than the core enzymatic function. Supporting Evidence: PMID:29253890 sid2 mutants were the least compromised mutant tested in terms of both bacterial enumeration and cauline leaf abscission. |
| GO:0060866 leaf abscission | IMP PMID:29253890 Leaf shedding as an anti-bacterial defense in Arabidopsis ca... | KEEP AS NON CORE | Summary: sid2 mutants (and SA-deficient NahG plants) show quantitatively reduced pathogen-triggered cauline leaf abscission, indicating that SA produced by ICS1 contributes to the leaf-shedding defense response. ICS1 acts upstream via SA signaling, not as a direct effector of abscission. Reason: SA-dependent indirect contribution to abscission; correctly modeled with acts_upstream_of_or_within. Non-core downstream physiology. Supporting Evidence: PMID:29253890 We found that plants with reduced levels of SA, NahG and sid2, had quantitatively reduced abscission, with NahG being essentially qualitatively blocked in abscission |
| GO:0009409 response to cold | IMP PMID:23581962 Roles of CAMTA transcription factors and salicylic acid in c... | KEEP AS NON CORE | Summary: After prolonged chilling, SA accumulates via cold induction of ICS1 (and the ICS1 activators CBP60g and SARD1), and this cold-induced SA shapes the low-temperature transcriptome. ICS1 thus participates in the response to cold through SA production, though cold-induced SA did not contribute to freezing tolerance per se. Reason: Genuine but indirect role: ICS1 is cold-induced and supplies SA that configures the cold transcriptome. Downstream/conditional physiology, not the core function. Supporting Evidence: PMID:23581962 this chilling-induced SA biosynthesis proceeds through the isochorismate synthase (ICS) pathway, with cold induction of ICS1 (which encodes ICS) |
| GO:0008909 isochorismate synthase activity | ISA PMID:11734859 Isochorismate synthase is required to synthesize salicylic a... | ACCEPT | Summary: Sequence-analysis-based assignment of isochorismate synthase activity (with the ICS2 paralog as the comparator). This duplicates the experimentally supported core molecular function. Reason: Correct molecular function; corroborated by direct biochemical assays in PMID:17190832. Duplicate annotations of the same GO ID are acceptable. Supporting Evidence: PMID:17190832 AtICS1 acts as a monofunctional isochorismate synthase (ICS), catalyzing the conversion of chorismate to isochorismate (IC) |
| GO:0008909 isochorismate synthase activity | IMP PMID:18451262 Characterization and biological function of the ISOCHORISMAT... | ACCEPT | Summary: Genetic evidence (ics1 / ics2 / ics1 ics2 mutant series showing ICS1 and ICS2 encode functional ICS enzymes) supports that ICS1 has isochorismate synthase activity. Duplicates the core molecular function. Reason: Consistent with direct enzymology; ICS1 is a functional isochorismate synthase. Core molecular function. Supporting Evidence: PMID:18451262 We have shown that ICS2 encodes a functional ICS enzyme and that, similar to ICS1, ICS2 is targeted to the plastids. |
| GO:0009536 plastid | IDA PMID:18451262 Characterization and biological function of the ISOCHORISMAT... | ACCEPT | Summary: ICS1:GFP fusion shows ubiquitous stromal (plastid) localization, directly confirming plastid localization. Consistent with the chloroplast stromal localization shown by import assays. Reason: Direct experimental localization to the plastid stroma. Core location (though plastid is broader than chloroplast/stroma). Supporting Evidence: PMID:18451262 the ubiquitous stromal localization of both of the ICS:GFP fusions ( Fig. 3 ) indicates that neither ICS1 nor ICS2 is presumably restricted to these complexes. |
| GO:0042372 phylloquinone biosynthetic process | IMP PMID:18451262 Characterization and biological function of the ISOCHORISMAT... | KEEP AS NON CORE | Summary: Genetic analysis of ics1, ics2 and ics1 ics2 mutants shows ICS1 contributes precursor (isochorismate) for phylloquinone production; the double mutant is completely devoid of phylloquinone. ICS1 acts upstream by supplying isochorismate, redundantly with ICS2 (unequal redundancy). Reason: Real contribution to phylloquinone biosynthesis but redundant with ICS2 and limited to precursor supply; the inducible SA role is primary. Keep as non-core. Supporting Evidence: PMID:18451262 This unequal redundancy relationship was also observed for phylloquinone, another isochorismate-derived end product. |
| GO:0042372 phylloquinone biosynthetic process | IMP PMID:16617180 A plant locus essential for phylloquinone (vitamin K1) biosy... | KEEP AS NON CORE | Summary: Work on the PHYLLO locus established the phylloquinone biosynthetic pathway and the evolutionary branching of standalone menF-like ICS genes (ICS1/ICS2) that supply isochorismate for both phylloquinone and SA. Supports ICS1 involvement in phylloquinone biosynthesis via isochorismate supply. Reason: Confirms the phylloquinone-precursor role of ICS-type enzymes; redundant and non-core relative to SA biosynthesis. Supporting Evidence: PMID:16617180 enabled a metabolic branch from the phylloquinone biosynthetic route to independently regulate the synthesis of salicylic acid required for plant defense. |
| GO:0009627 systemic acquired resistance | IEP PMID:17419843 Pathogen-associated molecular pattern recognition rather tha... | KEEP AS NON CORE | Summary: SA biosynthesis and signaling mutants, which include ICS1/SID2, are impaired in establishing systemic acquired resistance triggered by non-host bacteria or PAMPs. ICS1-dependent SA accumulation is required upstream of SAR. Reason: SAR is an SA-dependent downstream defense outcome to which ICS1 contributes by producing SA; correctly modeled as upstream. Non-core relative to the enzymatic function. Supporting Evidence: PMID:17419843 a whole set of SAR-deficient Arabidopsis lines, including mutants in SA biosynthesis and signalling, are impaired in establishing the systemic resistance response triggered by non-host bacteria or PAMPs. file:ARATH/ICS1/ICS1-deep-research-falcon.md linking local-to-systemic signaling to renewed SA synthesis in distal tissue rather than relying solely on long-distance transport of SA from the infection site |
| GO:0050832 defense response to fungus | IMP PMID:17513501 ABA is an essential signal for plant resistance to pathogens... | MODIFY | Summary: In defense against Pythium irregulare, SA is one of the hormones required to limit disease progression, though much less important than jasmonic acid. P. irregulare is an oomycete (stramenopile), not a true fungus, so the original term "defense response to fungus" (GO:0050832) is taxonomically incorrect. The verified term "defense response to oomycetes" (GO:0002229) accurately describes this interaction. The contribution of ICS1-derived SA to defense against this pathogen is modest. Reason: The tested pathogen, Pythium irregulare, is an oomycete (stramenopile), not a true fungus, so GO:0050832 "defense response to fungus" is the wrong taxonomic term. It should be replaced with GO:0002229 "defense response to oomycetes". SA (and thus ICS1) plays only a minor SA-dependent role in this interaction, so this remains a non-core downstream defense contribution. Proposed replacements: defense response to oomycetes Supporting Evidence: PMID:17513501 both are required to prevent disease progression, although much less so than JA. |
| GO:0031348 negative regulation of defense response | IMP PMID:16732289 Conserved requirement for a plant host cell protein in powde... | REMOVE | Summary: This study shows that mlo-based powdery mildew resistance in Arabidopsis does NOT require salicylic acid (nor ethylene or jasmonic acid). It does not provide evidence that ICS1 negatively regulates defense; the annotation appears to be a misassignment from an epistasis experiment where the SA pathway was dispensable. Reason: The cited paper explicitly states mlo resistance does not involve SA, so it does not support a role for ICS1 in negative regulation of defense response. No positive evidence links ICS1 to negative regulation of defense. Supporting Evidence: PMID:16732289 mlo resistance in A. thaliana does not involve the signaling molecules ethylene, jasmonic acid or salicylic acid, but requires a syntaxin, glycosyl hydrolase and ABC transporter. |
| GO:0010118 stomatal movement | IMP PMID:16959575 Plant stomata function in innate immunity against bacterial ... | KEEP AS NON CORE | Summary: Stomatal closure is part of the innate immune response restricting bacterial entry, and SA is required for this stomatal defense; SA-deficient backgrounds are impaired in pathogen/PAMP-triggered stomatal closure. ICS1 contributes upstream by supplying SA. Reason: SA-dependent contribution to stomatal immunity, correctly modeled as upstream. Indirect, non-core physiology. Supporting Evidence: PMID:16959575 stomatal closure is part of a plant innate immune response to restrict bacterial invasion. |
| GO:0042742 defense response to bacterium | IMP PMID:16959575 Plant stomata function in innate immunity against bacterial ... | KEEP AS NON CORE | Summary: Stomatal innate immunity restricts bacterial invasion, and SA is required for the stomatal defense response; ICS1-derived SA therefore contributes to defense against bacteria. ICS1 acts upstream through SA, not directly on bacteria. Reason: Genuine SA-dependent antibacterial defense role captured with the upstream qualifier; downstream physiology, non-core. Supporting Evidence: PMID:16959575 stomata, as part of an integral innate immune system, act as a barrier against bacterial infection. |
| GO:0008909 isochorismate synthase activity | TAS PMID:11734859 Isochorismate synthase is required to synthesize salicylic a... | ACCEPT | Summary: Author statement that SID2/ICS1 encodes an isochorismate synthase that synthesizes SA from chorismate. Duplicates the core molecular function; corroborated by direct enzymology. Reason: Correct core molecular function; consistent with biochemical characterization. Supporting Evidence: PMID:11734859 SA is synthesized from chorismate by means of ICS |
| GO:0009536 plastid | ISS PMID:11734859 Isochorismate synthase is required to synthesize salicylic a... | ACCEPT | Summary: Sequence-similarity-based plastid localization assignment, consistent with the transit peptide and later experimentally confirmed stromal plastid localization. Reason: Correct localization; later confirmed by import assays and GFP fusions. Supporting Evidence: PMID:18451262 similar to ICS1, ICS2 is targeted to the plastids. |
| GO:0009617 response to bacterium | IMP PMID:15842626 Staphylococcus aureus pathogenicity on Arabidopsis thaliana ... | KEEP AS NON CORE | Summary: ics1 mutants (depleted in SA accumulation) are altered in resistance to Staphylococcus aureus, showing that ICS1-derived SA contributes to the response to bacteria. ICS1 acts upstream via SA. Reason: SA-dependent contribution to the response to bacteria, modeled upstream. Indirect, non-core physiology. Supporting Evidence: PMID:15842626 resistance of Arabidopsis to typical plant pathogens and the animal pathogen S. aureus is conserved and is mediated by SA. |
| GO:0009697 salicylic acid biosynthetic process | TAS PMID:15842626 Staphylococcus aureus pathogenicity on Arabidopsis thaliana ... | ACCEPT | Summary: Author statement that ics1 mutants are depleted in SA accumulation, consistent with ICS1 being required for SA biosynthesis. Duplicates the core SA-biosynthesis process annotation. Reason: Correct core biological process. (enables/involved_in framing would be preferable to acts_upstream_of_or_within for the enzyme's own pathway, but the term is appropriate.) Supporting Evidence: PMID:15842626 mutants ics1 (depleted in SA accumulation) |
| GO:0008909 isochorismate synthase activity | IMP PMID:11734859 Isochorismate synthase is required to synthesize salicylic a... | ACCEPT | Summary: Genetic (mutational) evidence from the original SID2 characterization that ICS1 is required for ICS-dependent SA synthesis, supporting the isochorismate synthase function. Duplicates the core molecular function. Reason: Correct core molecular function; consistent with direct enzymology in PMID:17190832. Supporting Evidence: PMID:11734859 SA is synthesized from chorismate by means of ICS |
| GO:0009627 systemic acquired resistance | IMP PMID:11734859 Isochorismate synthase is required to synthesize salicylic a... | KEEP AS NON CORE | Summary: SA produced via the ICS pathway is required for local and systemic acquired resistance; sid2/ics1 mutants are impaired in SAR. ICS1 acts upstream by providing SA. Reason: SAR is an SA-dependent downstream outcome to which ICS1 contributes by making SA; correctly modeled as upstream. Non-core relative to the enzyme activity. Supporting Evidence: PMID:11734859 SA made by this pathway is required for LAR and SAR responses. file:ARATH/ICS1/ICS1-deep-research-falcon.md linking local-to-systemic signaling to renewed SA synthesis in distal tissue rather than relying solely on long-distance transport of SA from the infection site |
| GO:0009697 salicylic acid biosynthetic process | IMP PMID:11734859 Isochorismate synthase is required to synthesize salicylic a... | ACCEPT | Summary: The defining genetic evidence: the SID2 mutation (in ICS1) blocks pathogen-induced SA accumulation, establishing ICS1 as required for SA biosynthesis. This is the core biological process for ICS1. Reason: Direct mutational evidence for the core SA-biosynthesis role of ICS1. Supporting Evidence: PMID:11734859 SA is synthesized from chorismate by means of ICS, and that SA made by this pathway is required for LAR and SAR responses. |
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Download this section (compressed HTML)Q: Which downstream enzyme(s) convert ICS1-derived isochorismate to salicylic acid in the Arabidopsis plastid/cytosol, and is the isochorismate channeled or freely diffusible?
Q: Does the isoform 2 (Q9S7H8-2, altered C-terminus) retain isochorismate synthase activity or have a distinct regulatory or localization role?
Q: To what extent does ICS1 contribute to constitutive versus inducible isochorismate pools for phylloquinone given the unequal redundancy with ICS2?
Experiment: Identify the Arabidopsis enzyme(s) converting ICS1-derived isochorismate to salicylic acid by genetic screens of EMS-mutagenized sid2 suppressor/enhancer lines combined with metabolomic tracking of 13C/15N-labeled chorismate flux through isochorismate to SA in plastid and cytosolic fractions.
Experiment: Express isoform 2 (Q9S7H8-2, altered C-terminus) in an ics1 ics2 double-mutant background under the native ICS1 promoter and assay isochorismate synthase activity, SA accumulation after pathogen challenge, and subcellular localization to test whether isoform 2 retains catalytic activity or instead has a regulatory or localization-only role.
Experiment: Quantify constitutive versus inducible isochorismate pools for phylloquinone and SA branches by comparing ics1, ics2, and ics1 ics2 plants for chorismate/isochorismate/SA/phylloquinone steady-state and pathogen-induced flux, dissecting ICS1's specific contribution to each branch.
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