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    SIZ1 DNA-binding protein with MIZ/SP-RING zinc finger, PHD-finger and SAP domain-containing protein [ Arabidopsis thaliana (thale cress) ]

    Gene ID: 836163, updated on 30-Sep-2024

    Summary

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    Official Symbol
    SIZ1
    Official Full Name
    DNA-binding protein with MIZ/SP-RING zinc finger, PHD-finger and SAP domain-containing protein
    Primary source
    TAIR:AT5G60410
    Locus tag
    AT5G60410
    See related
    Araport:AT5G60410
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Arabidopsis thaliana (ecotype: Columbia)
    Lineage
    Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis
    Also known as
    AT5G60420; ATSIZ1; MUF9.5; MUF9_5
    Summary
    Encodes a plant small ubiquitin-like modifier (SUMO) E3 ligase that is a focal controller of Pi starvation-dependent responses. Also required for SA and PAD4-mediated R gene signalling, which in turn confers innate immunity in Arabidopsis. Also involved in the regulation of plant growth, drought responses and freezing tolerance. This latter effect is most likely due to SIZ1 dependent ABI5 sumoylation. Regulates leaf cell division and expansion through salicylic acid accumulation. signaling
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    Genomic context

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    See SIZ1 in Genome Data Viewer
    Location:
    chromosome: 5
    Exon count:
    18
    Sequence:
    Chromosome: 5; NC_003076.8 (24294704..24301157)

    Chromosome 5 - NC_003076.8Genomic Context describing neighboring genes Neighboring gene GTP binding Elongation factor Tu family protein Neighboring gene uncharacterized protein Neighboring gene ncRNA Neighboring gene antiporter/ drug transporter Neighboring gene AGAMOUS-like 62

    Genomic regions, transcripts, and products

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    Genomic Sequence:
    NC_003076.8

    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. The Arabidopsis SUMO E3 ligase SIZ1 controls phosphate deficiency responses. Miura K, et al. Proc Natl Acad Sci U S A, 2005 May 24. PMID 15894620, Free PMC Article
    2. SIZ1 small ubiquitin-like modifier E3 ligase facilitates basal thermotolerance in Arabidopsis independent of salicylic acid. Yoo CY, et al. Plant Physiol, 2006 Dec. PMID 17041025, Free PMC Article
    3. Salicylic acid-mediated innate immunity in Arabidopsis is regulated by SIZ1 SUMO E3 ligase. Lee J, et al. Plant J, 2007 Jan. PMID 17163880
    4. Specific domain structures control abscisic acid-, salicylic acid-, and stress-mediated SIZ1 phenotypes. Cheong MS, et al. Plant Physiol, 2009 Dec. PMID 19837819, Free PMC Article
    5. SIZ1 controls cell growth and plant development in Arabidopsis through salicylic acid. Miura K, et al. Plant Cell Physiol, 2010 Jan. PMID 20007967

    See all (55) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. E3 SUMO ligase SIZ1 splicing variants localize and function according to external conditions.
      Title: E3 SUMO ligase SIZ1 splicing variants localize and function according to external conditions.
    2. Complex genetic interaction between glucose sensor HXK1 and E3 SUMO ligase SIZ1 in regulating plant morphogenesis.
      Title: Complex genetic interaction between glucose sensor HXK1 and E3 SUMO ligase SIZ1 in regulating plant morphogenesis.
    3. Root responses to aluminium and iron stresses require the SIZ1 SUMO ligase to modulate the STOP1 transcription factor.
      Title: Root responses to aluminium and iron stresses require the SIZ1 SUMO ligase to modulate the STOP1 transcription factor.
    4. Arabidopsis SUMO E3 Ligase SIZ1 Interacts with HDA6 and Negatively Regulates HDA6 Function during Flowering.
      Title: Arabidopsis SUMO E3 Ligase SIZ1 Interacts with HDA6 and Negatively Regulates HDA6 Function during Flowering.
    5. SIZ1 regulates phosphate deficiency-induced inhibition of primary root growth of Arabidopsis by modulating Fe accumulation and ROS production in its roots.
      Title: SIZ1 regulates phosphate deficiency-induced inhibition of primary root growth of Arabidopsis by modulating Fe accumulation and ROS production in its roots.
    6. SIZ1-Mediated SUMO Modification of SEUSS Regulates Photomorphogenesis in Arabidopsis.
      Title: SIZ1-Mediated SUMO Modification of SEUSS Regulates Photomorphogenesis in Arabidopsis.
    7. The SUMO E3 ligase SIZ1 partially regulates STOP1 SUMOylation and stability in Arabidopsis thaliana.
      Title: The SUMO E3 ligase SIZ1 partially regulates STOP1 SUMOylation and stability in Arabidopsis thaliana.
    8. SIZ1-Mediated SUMOylation of ROS1 Enhances Its Stability and Positively Regulates Active DNA Demethylation in Arabidopsis.
      Title: SIZ1-Mediated SUMOylation of ROS1 Enhances Its Stability and Positively Regulates Active DNA Demethylation in Arabidopsis.
    9. The SUMO E3 Ligase SIZ1 Negatively Regulates Shoot Regeneration.
      Title: The SUMO E3 Ligase SIZ1 Negatively Regulates Shoot Regeneration.
    10. SUMO E3 Ligase SIZ1 stabilizes MYB75 to regulate anthocyanin accumulation under high light conditions in Arabidopsis.
      Title: SUMO E3 Ligase SIZ1 stabilizes MYB75 to regulate anthocyanin accumulation under high light conditions in Arabidopsis.
    Submit: New GeneRIF Correction See all GeneRIFs (47)

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    NM_001037031.1
    NM_001037032.2
    NM_001125993.1
    NM_001345415.1
    NM_125434.4
    NM_203240.3

    Gene Ontology Provided by TAIR

    Function Evidence Code Pubs
    enables SUMO binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables SUMO transferase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables SUMO transferase activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables zinc ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    acts_upstream_of_or_within cell division IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within cellular response to phosphate starvation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within detection of phosphate ion IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in developmental growth IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within embryo sac development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in heat acclimation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    NOT involved_in induced systemic resistance, jasmonic acid mediated signaling pathway IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within innate immune response-activating signaling pathway IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within negative regulation of flower development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in negative regulation of systemic acquired resistance IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within plant ovule development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within pollen tube guidance IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in protein sumoylation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in protein sumoylation IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within regulation of abscisic acid-activated signaling pathway IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within regulation of growth IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within regulation of nitrate assimilation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within regulation of response to water deprivation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within regulation of salicylic acid metabolic process IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within response to freezing IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in response to water deprivation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within shoot regeneration IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within unidimensional cell growth IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleus ISM
    Inferred from Sequence Model
    more info
    		  

    General protein information

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    Preferred Names
    DNA-binding protein with MIZ/SP-RING zinc finger, PHD-finger and SAP domain-containing protein
    NP_001032108.1
    • SIZ1; CONTAINS InterPro DOMAIN/s: Zinc finger, MIZ-type (InterPro:IPR004181), DNA-binding SAP (InterPro:IPR003034), Zinc finger, PHD-type, conserved site (InterPro:IPR019786), Zinc finger, PHD-type (InterPro:IPR001965), Zinc finger, FYVE/PHD-type (InterPro:IPR011011), Zinc finger, PHD-finger (InterPro:IPR019787); BEST Arabidopsis thaliana protein match is: RING/U-box superfamily protein (TAIR:AT5G41580.1); Has 1181 Blast hits to 1180 proteins in 204 species: Archae - 0; Bacteria - 0; Metazoa - 655; Fungi - 241; Plants - 117; Viruses - 0; Other Eukaryotes - 168 (source: NCBI BLink).
    NP_001032109.2
    • SIZ1; CONTAINS InterPro DOMAIN/s: Zinc finger, MIZ-type (InterPro:IPR004181), DNA-binding SAP (InterPro:IPR003034), Zinc finger, PHD-type, conserved site (InterPro:IPR019786), Zinc finger, PHD-type (InterPro:IPR001965), Zinc finger, FYVE/PHD-type (InterPro:IPR011011), Zinc finger, PHD-finger (InterPro:IPR019787); BEST Arabidopsis thaliana protein match is: RING/U-box superfamily protein (TAIR:AT5G41580.1); Has 1191 Blast hits to 1190 proteins in 207 species: Archae - 0; Bacteria - 6; Metazoa - 659; Fungi - 241; Plants - 117; Viruses - 0; Other Eukaryotes - 168 (source: NCBI BLink).
    NP_001119465.1
    • SIZ1; CONTAINS InterPro DOMAIN/s: DNA-binding SAP (InterPro:IPR003034), Zinc finger, MIZ-type (InterPro:IPR004181), Zinc finger, PHD-type, conserved site (InterPro:IPR019786), Zinc finger, PHD-type (InterPro:IPR001965), Zinc finger, FYVE/PHD-type (InterPro:IPR011011), Zinc finger, PHD-finger (InterPro:IPR019787); BEST Arabidopsis thaliana protein match is: RING/U-box superfamily protein (TAIR:AT5G41580.1); Has 30201 Blast hits to 17322 proteins in 780 species: Archae - 12; Bacteria - 1396; Metazoa - 17338; Fungi - 3422; Plants - 5037; Viruses - 0; Other Eukaryotes - 2996 (source: NCBI BLink).
    NP_200849.2
    • SIZ1; CONTAINS InterPro DOMAIN/s: DNA-binding SAP (InterPro:IPR003034), Zinc finger, MIZ-type (InterPro:IPR004181), Zinc finger, PHD-type, conserved site (InterPro:IPR019786), Zinc finger, PHD-type (InterPro:IPR001965), Zinc finger, FYVE/PHD-type (InterPro:IPR011011), Zinc finger, PHD-finger (InterPro:IPR019787); BEST Arabidopsis thaliana protein match is: RING/U-box superfamily protein (TAIR:AT5G41580.1); Has 1186 Blast hits to 1185 proteins in 207 species: Archae - 0; Bacteria - 6; Metazoa - 654; Fungi - 241; Plants - 117; Viruses - 0; Other Eukaryotes - 168 (source: NCBI BLink).
    NP_974969.1
    • SIZ1; CONTAINS InterPro DOMAIN/s: DNA-binding SAP (InterPro:IPR003034), Zinc finger, MIZ-type (InterPro:IPR004181), Zinc finger, PHD-type, conserved site (InterPro:IPR019786), Zinc finger, PHD-type (InterPro:IPR001965), Zinc finger, FYVE/PHD-type (InterPro:IPR011011), Zinc finger, PHD-finger (InterPro:IPR019787); BEST Arabidopsis thaliana protein match is: RING/U-box superfamily protein (TAIR:AT5G41580.1); Has 35333 Blast hits to 34131 proteins in 2444 species: Archae - 798; Bacteria - 22429; Metazoa - 974; Fungi - 991; Plants - 531; Viruses - 0; Other Eukaryotes - 9610 (source: NCBI BLink).

    NCBI Reference Sequences (RefSeq)

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    Genome Annotation

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference assembly

    Genomic

    1. NC_003076.8 Reference assembly

      Range
      24294704..24301157
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_125434.4 → NP_200849.2  DNA-binding protein with MIZ/SP-RING zinc finger, PHD-finger and SAP domain-containing protein [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_200849.2

      Status: REVIEWED

      UniProtKB/TrEMBL
      A0A178UAJ3, A0A5S9YI32, A0A654GD76
      Conserved Domains (3) summary
      smart00513
      Location:14 → 45
      SAP; Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation
      cd15570
      Location:114 → 165
      PHD_Bye1p_SIZ1_like; PHD domain found in Saccharomyces cerevisiae bypass of ESS1 protein 1 (Bye1p), the E3 Sumo Ligase SIZ1, and similar proteins
      cd16792
      Location:360 → 408
      SP-RING_Siz_plant; SP-RING finger found in Arabidopsis thaliana E3 SUMO-protein ligase SIZ1 (AtSIZ1) and similar proteins

    2. NM_203240.3 → NP_974969.1  DNA-binding protein with MIZ/SP-RING zinc finger, PHD-finger and SAP domain-containing protein [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_974969.1

      Status: REVIEWED

      UniProtKB/TrEMBL
      A0A178UAJ3, A0A7G2FHN3
      Conserved Domains (3) summary
      smart00513
      Location:14 → 45
      SAP; Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation
      cd15570
      Location:114 → 165
      PHD_Bye1p_SIZ1_like; PHD domain found in Saccharomyces cerevisiae bypass of ESS1 protein 1 (Bye1p), the E3 Sumo Ligase SIZ1, and similar proteins
      cd16792
      Location:360 → 408
      SP-RING_Siz_plant; SP-RING finger found in Arabidopsis thaliana E3 SUMO-protein ligase SIZ1 (AtSIZ1) and similar proteins

    3. NM_001345415.1 → NP_001332003.1  DNA-binding protein with MIZ/SP-RING zinc finger, PHD-finger and SAP domain-containing protein [Arabidopsis thaliana]

      Status: REVIEWED

      UniProtKB/TrEMBL
      A0A178UAJ3, A0A5S9YI32, A0A654GD76
      Conserved Domains (3) summary
      smart00513
      Location:14 → 45
      SAP; Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation
      cd15570
      Location:114 → 165
      PHD_Bye1p_SIZ1_like; PHD domain found in Saccharomyces cerevisiae bypass of ESS1 protein 1 (Bye1p), the E3 Sumo Ligase SIZ1, and similar proteins
      cd16792
      Location:360 → 408
      SP-RING_Siz_plant; SP-RING finger found in Arabidopsis thaliana E3 SUMO-protein ligase SIZ1 (AtSIZ1) and similar proteins

    4. NM_001125993.1 → NP_001119465.1  DNA-binding protein with MIZ/SP-RING zinc finger, PHD-finger and SAP domain-containing protein [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_001119465.1

      Status: REVIEWED

      UniProtKB/TrEMBL
      A0A178UAJ3, A0A7G2FHN3
      Conserved Domains (3) summary
      smart00513
      Location:14 → 45
      SAP; Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation
      cd15570
      Location:114 → 165
      PHD_Bye1p_SIZ1_like; PHD domain found in Saccharomyces cerevisiae bypass of ESS1 protein 1 (Bye1p), the E3 Sumo Ligase SIZ1, and similar proteins
      cd16792
      Location:360 → 408
      SP-RING_Siz_plant; SP-RING finger found in Arabidopsis thaliana E3 SUMO-protein ligase SIZ1 (AtSIZ1) and similar proteins

    5. NM_001037032.2 → NP_001032109.2  DNA-binding protein with MIZ/SP-RING zinc finger, PHD-finger and SAP domain-containing protein [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_001032109.2

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      B9DG12, Q56YS2, Q56ZS1, Q67ZL3, Q680Q4, Q9FKK4
      UniProtKB/TrEMBL
      A0A178UAJ3, A0A7G2FNS4
      Conserved Domains (3) summary
      smart00513
      Location:14 → 45
      SAP; Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation
      cd15570
      Location:114 → 165
      PHD_Bye1p_SIZ1_like; PHD domain found in Saccharomyces cerevisiae bypass of ESS1 protein 1 (Bye1p), the E3 Sumo Ligase SIZ1, and similar proteins
      cd16792
      Location:360 → 408
      SP-RING_Siz_plant; SP-RING finger found in Arabidopsis thaliana E3 SUMO-protein ligase SIZ1 (AtSIZ1) and similar proteins

    6. NM_001037031.1 → NP_001032108.1  DNA-binding protein with MIZ/SP-RING zinc finger, PHD-finger and SAP domain-containing protein [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_001032108.1

      Status: REVIEWED

      UniProtKB/TrEMBL
      A0A178UAJ3
      Conserved Domains (3) summary
      cd15570
      Location:114 → 165
      PHD_Bye1p_SIZ1_like; PHD domain found in Saccharomyces cerevisiae bypass of ESS1 protein 1 (Bye1p), the E3 Sumo Ligase SIZ1, and similar proteins
      pfam02037
      Location:11 → 45
      SAP; SAP domain
      pfam02891
      Location:359 → 408
      zf-MIZ; MIZ/SP-RING zinc finger
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q680Q4.2

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