SIZ1

Existing Annotations Review

GO Term	Evidence	Action	Reason
GO:0000785 chromatin	IBA GO_REF:0000033	KEEP AS NON CORE	Summary: PAINT IBA placing SIZ1 on chromatin, inherited from the Siz/PIAS node (yeast Siz1/Siz2, fly Su(var)2-10, worm GEI-17). SIZ1 carries the N-terminal SAP (scaffold attachment) DNA/chromatin-binding domain typical of the family and sumoylates chromatin-associated substrates such as the bromodomain protein GTE3 and the FLC regulator FLD, but no study in the cache directly shows plant SIZ1 bound to chromatin. Reason: The family-level inference is phylogenetically reasonable (SAP domain conserved; chromatin substrates) and there is no evidence of loss in the plant clade, so the IBA is retained. It is non-core because the primary, experimentally established compartment is nuclear foci/speckles, and chromatin association has not been tested directly for AtSIZ1. Supporting Evidence: PMID:19837819 Four conserved motifs in SIZ1 include SAP (for scaffold attachment factor A/B/acinus/PIAS domain) PMID:18502747 Modification of GTE3 modulates its capacity to bind acetyl-histone H3 in vitro.
GO:0002758 innate immune response-activating signaling pathway	IMP PMID:17163880 Salicylic acid-mediated innate immunity in Arabidopsis is re...	MODIFY	Summary: Lee et al. 2007 showed siz1 mutants have constitutive SA accumulation, elevated PR gene expression and enhanced resistance to Pst DC3000, reverted by NahG; SIZ1 acts epistatically with PAD4. This places SIZ1 as a regulator (in loss-of-function, a repressor) of SA/PAD4-dependent immune signaling, not as a component of a receptor-to-response activating pathway. Reason: The original term (a ligand-receptor signaling pathway that activates innate immunity) does not match the data, which show that SIZ1 loss derepresses SA-dependent immunity. The evidence supports regulation of salicylic acid mediated signaling. GO has no "negative regulation of SA mediated signaling pathway" term, so the regulation parent GO:2000031 is proposed. Later work (PMID:41986387) shows SIZ1 overaccumulation can also potentiate immune condensate signaling, further favouring a neutral "regulation" term over a directional or pathway-component term. Proposed replacements: regulation of salicylic acid mediated signaling pathway Supporting Evidence: PMID:17163880 Mutant siz1 plants exhibit constitutive systemic-acquired resistance (SAR) characterized by elevated accumulation of salicylic acid (SA), increased expression of pathogenesis-related (PR) genes PMID:17163880 SIZ1 interacts epistatically with PAD4 to regulate PR expression and disease resistance. PMID:41986387 SIZ1 overaccumulation unexpectedly activates robust immune responses and cell death, dependent on its E3 ligase activity file:ARATH/SIZ1/SIZ1-deep-research-openscientist.md SIZ1 therefore both restrains basal SA immunity and reinforces activated immune condensates in a dose- and context-dependent manner.
GO:0005515 protein binding	IPI PMID:18502747 The PHD domain of plant PIAS proteins mediates sumoylation o...	MODIFY	Summary: IPI with SCE1 (Q42551, the sole Arabidopsis SUMO E2). Garcia-Dominguez et al. showed the SIZ1 PHD domain binds AtSCE1 and contributes to ligase function; SIZ1 also sumoylates SCE1. Binding the E2 is the mechanistic basis of SP-RING/PHD E3 activity. Reason: Generic protein binding is uninformative. The paper supports a specific interaction with the SUMO-conjugating enzyme, which GO captures as ubiquitin-like protein conjugating enzyme binding. Proposed replacements: ubiquitin-like protein conjugating enzyme binding Supporting Evidence: PMID:18502747 We found that the PHD domain binds AtSCE1 and contributes to the SUMO ligase function PMID:18502747 The importance of SP-RING relies on its capacity to bind the E2 enzyme of the pathway.
GO:0005515 protein binding	IPI PMID:18502747 The PHD domain of plant PIAS proteins mediates sumoylation o...	REMOVE	Summary: IPI with GTE5 (Q8H1D7), a bromodomain GTE protein. UniProt records interaction of the SIZ1 PHD domain with GTE3 and GTE5, and SIZ1 sumoylates these bromodomain proteins; GTE5 is a SIZ1 substrate. Reason: Generic protein binding is uninformative. The interaction is real but reflects enzyme-substrate engagement already captured by the SUMO transferase/ligase activity and protein sumoylation annotations; there is no more specific MF term for binding a sumoylation substrate. Removal does not dispute the interaction. Supporting Evidence: file:ARATH/SIZ1/SIZ1-uniprot.txt Interacts (via PHD domain) with SCE1, GTE3 and GTE5.
GO:0005515 protein binding	IPI PMID:18502747 The PHD domain of plant PIAS proteins mediates sumoylation o...	REMOVE	Summary: IPI with GTE3 (Q9S7T1), a bromodomain protein that interacts with SIZ1 and is sumoylated by it; GTE3 sumoylation absolutely requires the SIZ1 PHD domain. Reason: Generic protein binding is uninformative. The interaction is an enzyme-substrate interaction already represented by the SUMO transferase activity (IDA, same paper) and protein sumoylation annotations; no informative binding MF applies. Removal does not dispute the interaction. Supporting Evidence: PMID:18502747 describe self-sumoylation and AtSIZ1-mediated sumoylation of the E2 enzyme AtSCE1 and GTE3, a bromodomain protein interacting with AtSIZ1
GO:0005634 nucleus	IDA PMID:15894620 The Arabidopsis SUMO E3 ligase SIZ1 controls phosphate defic...	ACCEPT	Summary: AtSIZ1-GFP localizes to nuclear foci/speckles; SP-RING mutation disrupts nuclear localization. Most SIZ1-dependent SUMO conjugates accumulate in the nucleus. Reason: Direct localization evidence, consistent with the nuclear substrate set (PHR1, ICE1, ABI5, FLD, MYB30, NF-YC10). Supporting Evidence: PMID:15894620 AtSIZ1-GFP was localized to nuclear foci. PMID:19837819 Domain SP-RING is required for SUMO conjugation activity and nuclear localization of SIZ1.
GO:0005634 nucleus	ISM GO_REF:0000122	ACCEPT	Summary: AtSubP sequence-based prediction of nuclear localization. Reason: Consistent with direct experimental evidence for nuclear localization. Supporting Evidence: PMID:15894620 AtSIZ1-GFP was localized to nuclear foci.
GO:0005654 nucleoplasm	IBA GO_REF:0000033	ACCEPT	Summary: PAINT IBA for nucleoplasm from the Siz/PIAS family node (human PIAS1-4, mouse Pias, yeast Siz). SIZ1 itself is one of the descendant evidences (AGI_LocusCode:AT5G60410). Reason: Nuclear (non-nucleolar) localization in foci/speckles is experimentally established for AtSIZ1 and is the ancestral location for the family; nuclear speck is part of nucleoplasm. Supporting Evidence: PMID:15894620 AtSIZ1 localizes to nuclear speckles PMID:17644626 This increase involves SUMO1 and SUMO2 and is mainly driven by the SUMO protein ligase SIZ1, with most of the conjugates accumulating in the nucleus.
GO:0008270 zinc ion binding	IEA GO_REF:0000002	KEEP AS NON CORE	Summary: InterPro2GO mapping from the PHD-type zinc finger (IPR004181 Znf_MIZ / SP-RING). SIZ1 has a PHD zinc finger (aa 112-168) and an SP-RING zinc finger (aa 346-429) with annotated Zn ligands. Reason: Correct structurally (zinc-coordinating SP-RING and PHD fingers; mutating Cys-379 abolishes E3 activity) but zinc binding is a structural cofactor property, not the evolved function, which is SUMO ligase activity. Supporting Evidence: PMID:19837819 Our results indicate that an intact zinc finger motif in the SP-RING domain is a major contributor to SUMOylation capability of SIZ1
GO:0009414 response to water deprivation	IMP PMID:17905899 The Arabidopsis E3 SUMO ligase SIZ1 regulates plant growth a...	KEEP AS NON CORE	Summary: Catala et al. 2007 showed siz1-3 has lower drought tolerance, drought-induced SUMO conjugate accumulation is partly SIZ1-dependent, and SIZ1 mediates drought induction of ~300 genes independently of DREB2A and ABA. Reason: SIZ1 contributes to the drought response through stress-induced sumoylation, but the specific substrates mediating drought tolerance are not identified in this paper; this is a pleiotropic stress-physiology role rather than the core molecular function. Supporting Evidence: PMID:17905899 Drought stress induces the accumulation of SUMO-protein conjugates, which is in part dependent on SIZ1 but not on abscisic acid (ABA). Mutant plants of siz1-3 have significantly lower tolerance to drought stress.
GO:0009553 embryo sac development	IMP PMID:22253727 Mutation in SUMO E3 ligase, SIZ1, disrupts the mature female...	KEEP AS NON CORE	Summary: Ling et al. 2012 found that some siz1-2 embryo sacs degenerate after stage FG7, with reduced seed set of maternal origin; expression of known female gametophyte genes was unchanged. Reason: The phenotype supports a requirement for SIZ1 in maintaining the mature female gametophyte (acts upstream of or within), but no substrate or mechanism is identified and siz1 is highly pleiotropic. Retained as a non-core developmental role. Supporting Evidence: PMID:22253727 Some of the embryo sacs of ovules in siz1-2 were also disrupted quickly after stage FG7. PMID:22253727 our results suggest that SIZ1 sustains the stability and normal function of the mature female gametophyte which is necessary for pollen tube guidance.
GO:0009787 regulation of abscisic acid-activated signaling pathway	IMP PMID:19276109 Sumoylation of ABI5 by the Arabidopsis SUMO E3 ligase SIZ1 n...	MODIFY	Summary: siz1 mutants are ABA hypersensitive; SIZ1 sumoylates ABI5 at K391 and abi5-4 is epistatic to siz1; ABI5(K391R) causes greater ABA hypersensitivity. MYB30 is a second SIZ1 substrate in ABA signaling (K283). SIZ1 therefore directly attenuates ABA signaling by sumoylating pathway transcription factors. Reason: The annotation is correct in essence and well supported by a direct substrate mechanism, but the direction is established (SIZ1-dependent sumoylation of ABI5 attenuates ABA signaling), so the more specific negative regulation term is preferable. Proposed replacements: negative regulation of abscisic acid-activated signaling pathway Supporting Evidence: PMID:19276109 Together, these results establish that SIZ1-dependent sumoylation of ABI5 attenuates ABA signaling. PMID:19276109 A K391R substitution in ABI5 [ABI5(K391R)] blocked SIZ1-mediated sumoylation of the transcription factor in vitro and in Arabidopsis protoplasts PMID:22814374 A K283R substitution in MYB30 blocks its SUMO E3 ligase SIZ1-mediated sumoylation in Arabidopsis protoplasts
GO:0009826 unidimensional cell growth	IMP PMID:20007967 SIZ1 controls cell growth and plant development in Arabidops...	MARK AS OVER ANNOTATED	Summary: Miura et al. 2010 attributed the siz1 dwarf shoot to reduced leaf cell volume and number; these defects, and reduced XTH8/XTH31 expression, are suppressed by NahG, i.e. they are secondary to SA hyperaccumulation. Reason: The phenotype is leaf cell expansion that is reversed by removing SA, so it is an indirect consequence of the autoimmune SA accumulation of siz1 rather than SIZ1 acting in cell growth. Moreover "unidimensional cell growth" (polarized, single-axis growth as in root hairs or pollen tubes) is a poor fit for leaf cell volume. Not core. Supporting Evidence: PMID:20007967 Mature siz1-2 and siz1-3 plants exhibited a dwarf-like shoot phenotype that is attributable to decreased leaf cell volume and number relative to the wild type. Cell division and expansion defects caused by siz1 were also suppressed by the expression of nahG.
GO:0009864 induced systemic resistance, jasmonic acid mediated signaling pathway	IMP NOT PMID:17163880 Salicylic acid-mediated innate immunity in Arabidopsis is re...	ACCEPT	Summary: NOT annotation. Lee et al. 2007 found that JA-induced PDF1.2 expression and susceptibility to Botrytis cinerea were unaltered in siz1, indicating SIZ1 does not act in the JA-mediated defense arm. Reason: The negative result is explicitly reported and supports the NOT qualifier; UniProt likewise states SIZ1 is probably not involved in JA-mediated defense. Supporting Evidence: PMID:17163880 Jasmonic acid (JA)-induced PDF1.2 expression and susceptibility to Botrytis cinerea were unaltered in siz1 plants. file:ARATH/SIZ1/SIZ1-uniprot.txt Probably not involved in jasmonic acid (JA)-mediated defense response.
GO:0009910 negative regulation of flower development	IMP PMID:18069938 The SUMO E3 ligase, AtSIZ1, regulates flowering by controlli...	ACCEPT	Summary: siz1 flowers early under short days. SIZ1 represses flowering through two routes - suppressing SA-dependent floral promotion and maintaining FLC expression by sumoylating and repressing the autonomous-pathway protein FLD (FLDK3R reduces FLC transcription and H4 acetylation). Reason: The FLD sumoylation mechanism shows SIZ1 doing work in this regulation (modifying a regulator of FLC), not merely an indirect phenotype. GO uses regulation of flower development for flowering-time control. The SA-dependent part is indirect, but the term is supported. Supporting Evidence: PMID:18069938 the results suggest that SIZ1 is a floral repressor that not only represses the SA-dependent pathway, but also promotes FLC expression by repressing FLD activity through sumoylation PMID:18069938 SIZ1 facilitates sumoylation of FLD that can be suppressed by mutations in three predicted sumoylation motifs in FLD
GO:0010113 negative regulation of systemic acquired resistance	IMP PMID:17163880 Salicylic acid-mediated innate immunity in Arabidopsis is re...	KEEP AS NON CORE	Summary: siz1 shows constitutive SAR with SA accumulation, PR expression and enhanced Pst resistance, all reverted by NahG; SIZ1 acts with PAD4. UniProt describes SIZ1 as an upstream negative regulator of SA accumulation and SAR signaling. Reason: Well supported by genetics, but the direct SIZ1 substrates responsible for SAR repression are not defined in this paper, and later work shows a context-dependent positive immune role (PMID:41986387). Retained as a physiological, non-core role. Supporting Evidence: PMID:17163880 Transfer of the NahG gene to siz1 plants results in reversal of these phenotypes back to wild-type. file:ARATH/SIZ1/SIZ1-uniprot.txt Functions as an upstream negative regulator of salicylic acid (SA) accumulation and subsequent SA-mediated systemic acquired resistance (SAR) signaling.
GO:0010183 pollen tube guidance	IMP PMID:22253727 Mutation in SUMO E3 ligase, SIZ1, disrupts the mature female...	MARK AS OVER ANNOTATED	Summary: Funicular and micropylar pollen tube guidance was arrested in siz1-2, but SIZ1 is expressed in female organs and not in pollen, and the authors attribute the guidance defect to degeneration of the mature female gametophyte. Reason: The guidance failure is a downstream consequence of embryo sac collapse (captured by the embryo sac development row); SIZ1 is not shown to generate or perceive guidance signals. Annotating pollen tube guidance overstates SIZ1's role. Supporting Evidence: PMID:22253727 SIZ1 showed enhanced expression in female organs, but was not detected in the anther or pollen. PMID:22253727 our results suggest that SIZ1 sustains the stability and normal function of the mature female gametophyte which is necessary for pollen tube guidance.
GO:0010247 detection of phosphate ion	IDA PMID:21156857 SIZ1 regulation of phosphate starvation-induced root archite...	MODIFY	Summary: Miura et al. 2011 show SIZ1 negatively regulates Pi starvation-induced root architecture remodeling through control of auxin patterning. Earlier work showed siz1 plants have wild-type intracellular Pi, and SIZ1 acts by sumoylating the transcription factor PHR1. Reason: The term detection of phosphate ion (reception of the Pi stimulus and its conversion to a signal) implies a sensor role, which no data support; SIZ1 modulates the downstream starvation response (PHR1 sumoylation, auxin patterning). The essence - SIZ1 acting in the phosphate starvation response - is sound, so the annotation is modified to the regulation term rather than removed. Proposed replacements: regulation of cellular response to phosphate starvation Supporting Evidence: PMID:21156857 these results suggest that SIZ1 negatively regulates Pi starvation-induced root architecture remodeling through the control of auxin patterning. PMID:15894620 even though intracellular Pi levels in siz1 plants were similar to wild type
GO:0010286 heat acclimation	IMP PMID:17041025 SIZ1 small ubiquitin-like modifier E3 ligase facilitates bas...	MODIFY	Summary: Yoo et al. 2006 showed siz1 mutations cause basal, but not acquired, thermosensitivity; siz1 seedlings acquire thermotolerance like wild type after a sublethal pretreatment. Heat-induced SUMO1/2 conjugation is largely SIZ1-dependent. Reason: Heat acclimation is the acquired (pretreatment-induced) increase in heat tolerance, which this paper explicitly shows is not affected by siz1. The data support a role in the basal response to heat, so response to heat is the appropriate term. Proposed replacements: response to heat Supporting Evidence: PMID:17041025 Together, these results indicate that SIZ1 controls basal, but not acquired, thermotolerance PMID:17041025 siz1 - 2 and siz1 - 3 seedlings exhibited a similar capacity for acquired thermotolerance as wild type
GO:0010337 regulation of salicylic acid metabolic process	IMP PMID:20007967 SIZ1 controls cell growth and plant development in Arabidops...	KEEP AS NON CORE	Summary: siz1 plants accumulate SA, and the dwarf, cell-growth phenotypes are suppressed by NahG; SIZ1 thus restrains SA accumulation. Reason: SIZ1 negatively regulates SA levels (consistently shown across several papers, and dependent on the SP-RING and SXS domains), but the mechanism is via upstream immune regulators rather than SA-metabolic enzymes. Retained as non-core. Supporting Evidence: PMID:20007967 These results indicate that SIZ1 regulates cell growth and plant development with regulation of SA accumulation. PMID:19837819 The SXS domain also controlled SA accumulation
GO:0016036 cellular response to phosphate starvation	IMP PMID:21156857 SIZ1 regulation of phosphate starvation-induced root archite...	ACCEPT	Summary: siz1 mutants show exaggerated Pi-starvation root architecture remodeling linked to auxin patterning; SIZ1 sumoylates PHR1, the MYB activator of Pi-starvation genes AtIPS1/AtRNS1. Reason: SIZ1 acts in the phosphate starvation response directly, by sumoylating PHR1 (K261/K372), and genetically controls multiple Pi-deficiency responses. This is one of the best-characterised SIZ1 roles. Supporting Evidence: PMID:21156857 The siz1 mutations caused greater PR growth inhibition and LR development of seedlings in response to Pi limitation. PMID:15894620 PHR1, a MYB transcriptional activator of AtIPS1 and AtRNS1, is an AtSIZ1 sumoylation target.
GO:0016607 nuclear speck	EXP PMID:15894620 The Arabidopsis SUMO E3 ligase SIZ1 controls phosphate defic...	ACCEPT	Summary: Functional AtSIZ1-GFP compartmentalizes to nuclear speckles, like mammalian PIAS proteins. Reason: Direct imaging evidence; UniProt subcellular location is nucleus speckle. Supporting Evidence: PMID:15894620 These results indicate that AtSIZ1-GFP is functional and that AtSIZ1 compartmentalizes to nuclear speckles, as do PIAS proteins
GO:0016607 nuclear speck	IEA GO_REF:0000044	ACCEPT	Summary: UniProt SubCell mapping (SL-0186 nucleus speckle). Reason: Derived from the experimentally supported UniProt location. Supporting Evidence: PMID:15894620 AtSIZ1 localizes to nuclear speckles
GO:0016925 protein sumoylation	IBA GO_REF:0000033	ACCEPT	Summary: PAINT IBA from the Siz/PIAS node; SIZ1 itself is among the experimental descendants. Reason: Core process for an SP-RING SUMO E3; experimentally established for SIZ1. Supporting Evidence: PMID:15894620 AtSIZ1 has SUMO E3 ligase activity in vitro, and immunoblot analysis revealed that the protein sumoylation profile is impaired in siz1 plants. file:ARATH/SIZ1/SIZ1-deep-research-openscientist.md SAP + PINIT + SP-RING + PHD domain architecture all match the primary experimental literature
GO:0016925 protein sumoylation	IDA PMID:18069938 The SUMO E3 ligase, AtSIZ1, regulates flowering by controlli...	ACCEPT	Summary: SIZ1 facilitates SUMO1 modification of FLD in protoplasts; mutation of three FLD sumoylation motifs (FLDK3R) suppresses it. Reason: Direct evidence of SIZ1-dependent substrate sumoylation. Supporting Evidence: PMID:18069938 SIZ1 facilitates sumoylation of FLD that can be suppressed by mutations in three predicted sumoylation motifs in FLD
GO:0016925 protein sumoylation	IDA PMID:18502747 The PHD domain of plant PIAS proteins mediates sumoylation o...	ACCEPT	Summary: SIZ1 mediates self-sumoylation and sumoylation of SCE1 and GTE3; the PHD domain is required. Reason: Direct biochemical evidence of SIZ1-mediated sumoylation. Supporting Evidence: PMID:18502747 describe self-sumoylation and AtSIZ1-mediated sumoylation of the E2 enzyme AtSCE1 and GTE3
GO:0016925 protein sumoylation	IEA GO_REF:0000120	ACCEPT	Summary: Combined automated annotation (ARBA, UniPathway protein sumoylation). Reason: Consistent with experimental evidence. Supporting Evidence: file:ARATH/SIZ1/SIZ1-uniprot.txt PATHWAY: Protein modification; protein sumoylation.
GO:0019789 SUMO transferase activity	IDA PMID:15894620 The Arabidopsis SUMO E3 ligase SIZ1 controls phosphate defic...	ACCEPT	Summary: Recombinant GST-AtSIZ1 functions as a SUMO E3 in vitro (substituting for yeast Siz2 on Cdc3) and facilitates PHR1 sumoylation; PHR1 K261R/K372R prevents modification. Reason: Direct in vitro evidence of E3 SUMO ligase activity. Supporting Evidence: PMID:15894620 AtSIZ1 can replace ScSiz2 to sumoylate the substrate ScCdc3 in an in vitro assay, providing evidence of its SUMO E3 ligase activity PMID:15894620 AtSIZ1 facilitated the sumoylation of PHR1
GO:0019789 SUMO transferase activity	IDA PMID:18069938 The SUMO E3 ligase, AtSIZ1, regulates flowering by controlli...	ACCEPT	Summary: SIZ1-dependent SUMO1 modification of FLD in protoplasts (wild type vs siz1-2). Reason: Supports SIZ1 E3 activity toward a specific substrate in vivo. Supporting Evidence: PMID:18069938 However, we also found that SIZ1 facilitates sumoylation of FLD, which represses FLD activity.
GO:0019789 SUMO transferase activity	IDA PMID:18502747 The PHD domain of plant PIAS proteins mediates sumoylation o...	ACCEPT	Summary: In vitro SIZ1-mediated sumoylation of SCE1, GTE3 and self; the PHD domain binds SCE1 and is required for ligase function. Reason: Direct biochemical evidence. Supporting Evidence: PMID:18502747 the PHD domain binds AtSCE1 and contributes to the SUMO ligase function, being partially and absolutely required for AtSCE1 and GTE3 sumoylation, respectively
GO:0019789 SUMO transferase activity	IDA PMID:19837819 Specific domain structures control abscisic acid-, salicylic...	ACCEPT	Summary: Structure-function analysis showing the SP-RING domain is required for SUMO conjugation activity, and PHD/PINIT mutations affect in vivo SUMOylation. Reason: Direct evidence linking the SP-RING catalytic domain to SUMO conjugation activity. Supporting Evidence: PMID:19837819 Domain SP-RING is required for SUMO conjugation activity and nuclear localization of SIZ1. PMID:19837819 Mutations of the PHD zinc finger domain and the PINIT motif affected in vivo SUMOylation.
GO:0019789 SUMO transferase activity	IEA GO_REF:0000117	ACCEPT	Summary: ARBA machine-learning annotation. Reason: Consistent with abundant experimental evidence. Supporting Evidence: PMID:15894620 AtSIZ1 has SUMO E3 ligase activity in vitro
GO:0019789 SUMO transferase activity	IMP PMID:17905899 The Arabidopsis E3 SUMO ligase SIZ1 regulates plant growth a...	ACCEPT	Summary: Drought-induced accumulation of SUMO-protein conjugates is partly SIZ1-dependent in siz1-3. Reason: Loss-of-function reduction of stress-induced conjugates is weaker evidence for an MF than biochemistry, but it is consistent with the established in vitro E3 activity and the curator read the full text. Supporting Evidence: PMID:17905899 Drought stress induces the accumulation of SUMO-protein conjugates, which is in part dependent on SIZ1
GO:0032183 SUMO binding	IPI PMID:24255109 Identification of Arabidopsis SUMO-interacting proteins that...	KEEP AS NON CORE	Summary: Large-scale yeast two-hybrid screens with three Arabidopsis SUMO isoforms; the annotation records a SIZ1-SUMO1 (AT4G26840) interaction. The cached abstract does not mention SIZ1 (full text not available). Reason: Non-covalent SUMO binding is plausible for an SP-RING E3 (PIAS proteins use SUMO-interacting motifs to engage the E2~SUMO thioester), and the curator had the full text, so the annotation is retained. It is a supporting property of the ligase mechanism rather than an independent core function. Supporting Evidence: PMID:24255109 large-scale yeast two-hybrid screens repeatedly identified a surprisingly small number of proteins that interacted with three Arabidopsis SUMO isoforms
GO:0040008 regulation of growth	IMP PMID:17905899 The Arabidopsis E3 SUMO ligase SIZ1 regulates plant growth a...	KEEP AS NON CORE	Summary: siz1-3 null plants are smaller, attributed to reduced expression of brassinosteroid biosynthesis and signaling genes. Reason: SIZ1 influences overall growth, but via pleiotropic effects (BR gene expression; SA accumulation in other studies) rather than a defined substrate mechanism. Non-core. Supporting Evidence: PMID:17905899 the null mutant siz1-3 is smaller in stature because of reduced expression of genes involved in brassinosteroid biosynthesis and signaling
GO:0048481 plant ovule development	IMP PMID:22253727 Mutation in SUMO E3 ligase, SIZ1, disrupts the mature female...	KEEP AS NON CORE	Summary: siz1-2 shows reduced seed set from the maternal side and degeneration of some mature embryo sacs after FG7. Reason: Supported phenotypically as acts upstream of or within, overlapping the embryo sac development row; mechanism unknown. Non-core developmental role. Supporting Evidence: PMID:22253727 A defect in the siz1-2 maternal source resulted in reduced seed-set regardless of high SA concentration within the plant.
GO:0048589 developmental growth	IMP PMID:17905899 The Arabidopsis E3 SUMO ligase SIZ1 regulates plant growth a...	MARK AS OVER ANNOTATED	Summary: Same evidence as the regulation of growth row - siz1-3 is smaller because of reduced BR gene expression. Reason: The involved_in claim that SIZ1 executes developmental growth overstates the evidence; SIZ1 is a regulator whose loss reduces growth indirectly. The regulation of growth annotation from the same paper captures this appropriately. Supporting Evidence: PMID:17905899 From these results, we conclude that SIZ1 regulates Arabidopsis growth
GO:0050826 response to freezing	IMP PMID:17416732 SIZ1-mediated sumoylation of ICE1 controls CBF3/DREB1A expre...	ACCEPT	Summary: siz1-2 and siz1-3 are freezing and chilling sensitive (complemented by SIZ1); SIZ1 sumoylates ICE1 at K393, stabilizing it against polyubiquitination and promoting CBF3/DREB1A expression. Reason: Genetic and biochemical evidence with a mapped substrate site shows SIZ1 does work in the cold/freezing response pathway. Supporting Evidence: PMID:17416732 siz1-2 and siz1-3 T-DNA insertion alleles that caused freezing and chilling sensitivities were complemented genetically by expressing SIZ1 PMID:17416732 A K393R substitution in ICE1 [ICE1(K393R)] blocked SIZ1-mediated sumoylation in vitro and in protoplasts identifying the K393 residue as the principal site of SUMO conjugation.
GO:0051301 cell division	IMP PMID:20007967 SIZ1 controls cell growth and plant development in Arabidops...	MARK AS OVER ANNOTATED	Summary: Reduced leaf cell number in siz1 contributes to dwarfism; the defect is suppressed by NahG. Reason: The cell-number defect is a secondary consequence of SA hyperaccumulation, and SIZ1 is not shown to act in the cell division machinery. Annotating cell division overstates SIZ1's role. Supporting Evidence: PMID:20007967 Cell division and expansion defects caused by siz1 were also suppressed by the expression of nahG.
GO:0061665 SUMO ligase activity	IBA GO_REF:0000033	ACCEPT	Summary: PAINT IBA from the Siz/PIAS node, seeded by yeast Siz1/Siz2, human PIAS1-4, and the Arabidopsis paralogs. Reason: Correct and at the right specificity; SIZ1 is the archetypal plant SP-RING SUMO E3 with direct in vitro E3 activity. Supporting Evidence: PMID:15894620 AtSIZ1 has SUMO E3 ligase activity in vitro PMID:38497423 SIZ1 and all SSVs exhibited similar E3 SUMO ligase activities and preferred SUMO1 and SUMO2 for their E3 ligase activity
GO:0062210 shoot regeneration	IMP PMID:32611787 The SUMO E3 Ligase SIZ1 Negatively Regulates Shoot Regenerat...	KEEP AS NON CORE	Summary: siz1 mutants overproduce shoot meristems in tissue culture (rescued by pSIZ1::SIZ1), with hyper-induction of wound-responsive genes including WIND1/WIND2. Reason: SIZ1 negatively regulates in vitro shoot regeneration by repressing wound-induced reprogramming; the SUMO substrates involved are not identified. Supported, but a pleiotropic, non-core role. Supporting Evidence: PMID:32611787 In this study, we demonstrate that the SUMO E3 ligase SIZ1 negatively regulates in vitro shoot regeneration in Arabidopsis
GO:0090352 regulation of nitrate assimilation	IMP PMID:21772271 Arabidopsis nitrate reductase activity is stimulated by the ...	ACCEPT	Summary: siz1-2 has decreased nitrate reductase activity, low N and high nitrate; NIA1 and NIA2 are sumoylated by SIZ1 in an E1/E2-dependent reaction, which dramatically increases their activity; ammonium rescues siz1 phenotypes. Reason: SIZ1 does work in this regulation by directly sumoylating and activating the nitrate reductases. Supporting Evidence: PMID:21772271 The nitrate reductases, NIA1 and NIA2, are sumoylated by AtSIZ1, which dramatically increases their activity. PMID:21772271 Our results indicate that AtSIZ1 positively controls nitrogen assimilation by promoting sumoylation of NRs in Arabidopsis.
GO:2000070 regulation of response to water deprivation	IMP PMID:17905899 The Arabidopsis E3 SUMO ligase SIZ1 regulates plant growth a...	KEEP AS NON CORE	Summary: SIZ1 mediates drought induction of ~300 genes independently of DREB2A and ABA, and siz1-3 is drought sensitive. Reason: Supported regulatory role in the drought response, but no specific substrate is identified in this study; non-core stress physiology. Supporting Evidence: PMID:17905899 SIZ1 mediating the expression of 300 of them by a pathway independent of DREB2A and ABA

Gene Description

Existing Annotations Review

Core Functions

SP-RING-type SUMO E3 ligase: binds the SUMO E2 SCE1 (via the PHD finger and SP-RING) and promotes transfer of SUMO1/SUMO2 to lysine residues of substrate proteins, driving bulk stress-induced (heat, drought) sumoylation of predominantly nuclear proteins in nuclear foci/speckles.

Sumoylation of the MYB transcription factor PHR1 (K261/K372), the central activator of phosphate-starvation genes such as AtIPS1 and AtRNS1, modulating phosphate-starvation responses including root architecture remodeling.

Sumoylation of the bHLH transcription factor ICE1 at K393, which reduces ICE1 polyubiquitination and promotes cold induction of CBF3/DREB1A while repressing MYB15, conferring chilling and freezing tolerance.

Sumoylation of the ABA-pathway transcription factors ABI5 (K391) and MYB30 (K283), attenuating abscisic acid signaling during seed germination and seedling growth.

Sumoylation of the nitrate reductases NIA1 and NIA2, which strongly increases their enzymatic activity and promotes nitrate assimilation.

Sumoylation of the autonomous-pathway LSD1-like histone demethylase FLD, repressing FLD activity so as to maintain FLC expression and repress the floral transition.

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