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    SPA1 SPA (suppressor of phyA-105) protein family [ Arabidopsis thaliana (thale cress) ]

    Gene ID: 819242, updated on 18-Sep-2024

    Summary

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    Official Symbol
    SPA1
    Official Full Name
    SPA (suppressor of phyA-105) protein family
    Primary source
    TAIR:AT2G46340
    Locus tag
    AT2G46340
    See related
    Araport:AT2G46340
    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
    AT2G46350; F11C10.3; SUPPRESSOR OF PHYA-105 1
    Summary
    Encodes a member of the SPA (suppressor of phyA-105) protein family (SPA1-SPA4). SPA proteins contain an N-terminal serine/threonine kinase-like motif followed by a coiled-coil structure and a C-terminal WD-repeat domain. SPA1 is a PHYA signaling intermediate, putative regulator of PHYA signaling pathway. Light responsive repressor of photomorphogenesis. Involved in regulating circadian rhythms and flowering time in plants. Under constant light, the abundance of SPA1 protein exhibited circadian regulation, whereas under constant darkness, SPA1 protein levels remained unchanged. In addition, the spa1-3 mutation slightly shortened circadian period of CCA1, TOC1/PRR1 and SPA1 transcript accumulation under constant light.
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    Genomic context

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    See SPA1 in Genome Data Viewer
    Location:
    chromosome: 2
    Exon count:
    8
    Sequence:
    Chromosome: 2; NC_003071.7 (19022154..19027528, complement)

    Chromosome 2 - NC_003071.7Genomic Context describing neighboring genes Neighboring gene ncRNA Neighboring gene Mitochondrial substrate carrier family protein Neighboring gene arabinogalactan protein 16 Neighboring gene uncharacterized protein Neighboring gene Auxin-responsive GH3 family protein

    Genomic regions, transcripts, and products

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    Genomic Sequence:
    NC_003071.7

    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. Arabidopsis phytochromes A and B synergistically repress SPA1 under blue light. Jia X, et al. J Integr Plant Biol, 2023 Apr. PMID 36394421
    2. SPA1: a new genetic locus involved in phytochrome A-specific signal transduction. Hoecker U, et al. Plant Cell, 1998 Jan. PMID 9477570, Free PMC Article
    3. SPA1, a WD-repeat protein specific to phytochrome A signal transduction. Hoecker U, et al. Science, 1999 Apr 16. PMID 10205059
    4. The Arabidopsis SPA1 gene is required for circadian clock function and photoperiodic flowering. Ishikawa M, et al. Plant J, 2006 Jun. PMID 16709190
    5. The Arabidopsis repressor of light signaling SPA1 acts in the phloem to regulate seedling de-etiolation, leaf expansion and flowering time. Ranjan A, et al. Development, 2011 May. PMID 21447551

    See all (55) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Light-induced LLPS of the CRY2/SPA1/FIO1 complex regulating mRNA methylation and chlorophyll homeostasis in Arabidopsis.
      Title: Light-induced LLPS of the CRY2/SPA1/FIO1 complex regulating mRNA methylation and chlorophyll homeostasis in Arabidopsis.
    2. Arabidopsis phytochromes A and B synergistically repress SPA1 under blue light.
      Title: Arabidopsis phytochromes A and B synergistically repress SPA1 under blue light.
    3. Functional comparison of the WD-repeat domains of SPA1 and COP1 in suppression of photomorphogenesis.
      Title: Functional comparison of the WD-repeat domains of SPA1 and COP1 in suppression of photomorphogenesis.
    4. SPA1 acts as a serine/threonine kinase and directly phosphorylates PIF1 in vitro and in vivo.
      Title: A phyB-PIF1-SPA1 kinase regulatory complex promotes photomorphogenesis in Arabidopsis.
    5. The WD-repeat domain of SPA1 is necessary for the interaction between SPA1 and COL12.
      Title: The Transcription Factor COL12 Is a Substrate of the COP1/SPA E3 Ligase and Regulates Flowering Time and Plant Architecture.
    6. COP1/SPA complex associates with and stabilizes PHYTOCHROME INTERACTING FACTOR 3 (PIF3) to repress photomorphogenesis in the dark.
      Title: Noncanonical role of Arabidopsis COP1/SPA complex in repressing BIN2-mediated PIF3 phosphorylation and degradation in darkness.
    7. SPA proteins have a dual role: (1) they are required for light-responsiveness of COP1 subcellular localization, and (2) they promote COP1 activity in darkness in a fashion that is independent of the nuclear import/nuclear retention of COP1.
      Title: SPA Proteins Affect the Subcellular Localization of COP1 in the COP1/SPA Ubiquitin Ligase Complex during Photomorphogenesis.
    8. The N-terminal kinase-like domain is primarily responsible for the respective light-responsiveness of SPA1 and SPA2.
      Title: The functional divergence between SPA1 and SPA2 in Arabidopsis photomorphogenesis maps primarily to the respective N-terminal kinase-like domain.
    9. CUL4(COP1-SPA) E3 ubiquitin ligase is necessary for the light-induced degradation of PIF1 in Arabidopsis.
      Title: CUL4 forms an E3 ligase with COP1 and SPA to promote light-induced degradation of PIF1.
    10. Interaction of phyB with SPA1 promotes COP1-SPA1 dissociation and photomorphogenic development.
      Title: Red-light-dependent interaction of phyB with SPA1 promotes COP1-SPA1 dissociation and photomorphogenic development in Arabidopsis.
    Submit: New GeneRIF Correction See all GeneRIFs (30)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    NM_001337186.1
    NM_130197.5

    Gene Ontology Provided by TAIR

    Function Evidence Code Pubs
    enables identical protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein kinase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    acts_upstream_of_or_within chloroplast organization IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within negative regulation of photomorphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within photomorphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within red or far-red light signaling pathway IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within red, far-red light phototransduction IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    involved_in regulation of photoperiodism, flowering IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    acts_upstream_of_or_within regulation of photoperiodism, flowering IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in response to blue light IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in response to blue light IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within response to far red light IEP
    Inferred from Expression Pattern
    more info
    		 PubMed 
    acts_upstream_of_or_within response to red light IEP
    Inferred from Expression Pattern
    more info
    		 PubMed 
    acts_upstream_of_or_within short-day photoperiodism, flowering IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of Cul4-RING E3 ubiquitin ligase complex ISS
    Inferred from Sequence or Structural Similarity
    more info
    		 PubMed 
    located_in nuclear body IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    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
    SPA (suppressor of phyA-105) protein family
    NP_182157.2
    • SUPPRESSOR OF PHYA-105 1 (SPA1); CONTAINS InterPro DOMAIN/s: WD40 repeat 2 (InterPro:IPR019782), WD40 repeat, conserved site (InterPro:IPR019775), WD40 repeat (InterPro:IPR001680), Serine/threonine-protein kinase-like domain (InterPro:IPR017442), Protein kinase-like domain (InterPro:IPR011009), G-protein beta WD-40 repeat, region (InterPro:IPR020472), WD40 repeat-like-containing domain (InterPro:IPR011046), Protein kinase, catalytic domain (InterPro:IPR000719), WD40-repeat-containing domain (InterPro:IPR017986), WD40/YVTN repeat-like-containing domain (InterPro:IPR015943), WD40 repeat, subgroup (InterPro:IPR019781); BEST Arabidopsis thaliana protein match is: SPA1-related 2 (TAIR:AT4G11110.1); Has 31438 Blast hits to 19748 proteins in 684 species: Archae - 32; Bacteria - 4770; Metazoa - 12431; Fungi - 6743; Plants - 3442; Viruses - 2; Other Eukaryotes - 4018 (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_003071.7 Reference assembly

      Range
      19022154..19027528 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_130197.5 → NP_182157.2  SPA (suppressor of phyA-105) protein family [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_182157.2

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      Q0WUH3, Q56WP1, Q9SKE4, Q9SKE5, Q9SYX2
      UniProtKB/TrEMBL
      A0A178VSM9, A0A5S9X7G0, A0A654F7L9
      Conserved Domains (2) summary
      PLN00181
      Location:275 → 1029
      PLN00181; protein SPA1-RELATED; Provisional
      sd00039
      Location:721 → 764
      7WD40; WD40 repeat [structural motif]

    2. NM_001337186.1 → NP_001325255.1  SPA (suppressor of phyA-105) protein family [Arabidopsis thaliana]

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      Q0WUH3, Q56WP1, Q9SKE4, Q9SKE5, Q9SYX2
      UniProtKB/TrEMBL
      A0A178VSM9, A0A5S9X7G0, A0A654F7L9
      Conserved Domains (2) summary
      PLN00181
      Location:275 → 1029
      PLN00181; protein SPA1-RELATED; Provisional
      sd00039
      Location:721 → 764
      7WD40; WD40 repeat [structural motif]
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9SYX2.1

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