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    SPY Tetratricopeptide repeat (TPR)-like superfamily protein [ Arabidopsis thaliana (thale cress) ]

    Gene ID: 820327, updated on 18-Sep-2024

    Summary

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    Official Symbol
    SPY
    Official Full Name
    Tetratricopeptide repeat (TPR)-like superfamily protein
    Primary source
    TAIR:AT3G11540
    Locus tag
    AT3G11540
    See related
    Araport:AT3G11540
    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
    SPINDLY
    Summary
    Encodes a N-acetyl glucosamine transferase that may glycosylate other molecules involved in GA signaling. Contains a tetratricopeptide repeat region, and a novel carboxy-terminal region. SPY acts as both a repressor of GA responses and as a positive regulation of cytokinin signalling. SPY may be involved in reducing ROS accumulation in response to stress.
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    Genomic context

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    See SPY in Genome Data Viewer
    Location:
    chromosome: 3
    Exon count:
    18
    Sequence:
    Chromosome: 3; NC_003074.8 (3631887..3638100)

    Chromosome 3 - NC_003074.8Genomic Context describing neighboring genes Neighboring gene ncRNA Neighboring gene Vacuolar protein sorting 55 (VPS55) family protein Neighboring gene Uncharacterized protein family (UPF0497) Neighboring gene LETM1-like protein Neighboring gene ncRNA

    Genomic regions, transcripts, and products

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    Genomic Sequence:
    NC_003074.8

    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. SPINDLY O-fucosylates nuclear and cytoplasmic proteins involved in diverse cellular processes in plants. Zentella R, et al. Plant Physiol, 2023 Mar 17. PMID 36740243, Free PMC Article
    2. Gibberellin signal transduction presents ellipsisthe SPY who O-GlcNAc'd me. Thornton TM, et al. Trends Plant Sci, 1999 Nov. PMID 10529823
    3. SPINDLY's role in the gibberellin response pathway. Jacobsen SE, et al. Symp Soc Exp Biol, 1998. PMID 10645426
    4. Ectopic expression of the tetratricopeptide repeat domain of SPINDLY causes defects in gibberellin response. Tseng TS, et al. Plant Physiol, 2001 Jul. PMID 11457975, Free PMC Article
    5. SPINDLY is a nuclear-localized repressor of gibberellin signal transduction expressed throughout the plant. Swain SM, et al. Plant Physiol, 2002 Jun. PMID 12068105, Free PMC Article

    See all (23) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. SPINDLY mediates O-fucosylation of hundreds of proteins and sugar-dependent growth in Arabidopsis.
      Title: SPINDLY mediates O-fucosylation of hundreds of proteins and sugar-dependent growth in Arabidopsis.
    2. Structure and dynamics of the Arabidopsis O-fucosyltransferase SPINDLY.
      Title: Structure and dynamics of the Arabidopsis O-fucosyltransferase SPINDLY.
    3. SPINDLY O-fucosylates nuclear and cytoplasmic proteins involved in diverse cellular processes in plants.
      Title: SPINDLY O-fucosylates nuclear and cytoplasmic proteins involved in diverse cellular processes in plants.
    4. Structural insights into mechanism and specificity of the plant protein O-fucosyltransferase SPINDLY.
      Title: Structural insights into mechanism and specificity of the plant protein O-fucosyltransferase SPINDLY.
    5. The Arabidopsis O-fucosyltransferase SPINDLY regulates root hair patterning independently of gibberellin signaling.
      Title: The Arabidopsis O-fucosyltransferase SPINDLY regulates root hair patterning independently of gibberellin signaling.
    6. Nuclear Localized O-Fucosyltransferase SPY Facilitates PRR5 Proteolysis to Fine-Tune the Pace of Arabidopsis Circadian Clock.
      Title: Nuclear Localized O-Fucosyltransferase SPY Facilitates PRR5 Proteolysis to Fine-Tune the Pace of Arabidopsis Circadian Clock.
    7. posttranslational modification of TCP14/15 by SPY inhibits their proteolysis.
      Title: The Putative O-Linked N-Acetylglucosamine Transferase SPINDLY Inhibits Class I TCP Proteolysis to Promote Sensitivity to Cytokinin.
    8. The study revealed that SPY-dependent protein O-fucosylation plays a key role in regulating plant development.
      Title: The Arabidopsis O-fucosyltransferase SPINDLY activates nuclear growth repressor DELLA.
    9. SPINDLY regulates cortex proliferation by maintaining cellular redox homeostasis
      Title: SPINDLY, ERECTA, and its ligand STOMAGEN have a role in redox-mediated cortex proliferation in the Arabidopsis root.
    10. SPY plays a negative role in plant abiotic stress tolerance, probably by integrating environmental stress signals via gibberellic acid and Cytokinins cross talk.
      Title: SPINDLY, a negative regulator of gibberellic acid signaling, is involved in the plant abiotic stress response.
    Submit: New GeneRIF Correction See all GeneRIFs (14)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    NM_111987.4
    NM_202557.2

    Gene Ontology Provided by TAIR

    Function Evidence Code Pubs
    enables glycosyltransferase activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables peptide-O-fucosyltransferase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein N-acetylglucosaminyltransferase activity TAS
    Traceable Author Statement
    more info
    		 PubMed 
    enables protein O-acetylglucosaminyltransferase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    acts_upstream_of_or_within cytokinin-activated signaling pathway IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within gibberellic acid mediated signaling pathway TAS
    Traceable Author Statement
    more info
    		 PubMed 
    acts_upstream_of_or_within negative regulation of gibberellic acid mediated signaling pathway IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    involved_in protein O-linked fucosylation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in protein glycosylation IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within regulation of reactive oxygen species metabolic process IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in cytoplasm 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
    		  
    located_in nucleus TAS
    Traceable Author Statement
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    Tetratricopeptide repeat (TPR)-like superfamily protein
    NP_187761.1
    • SPINDLY (SPY); CONTAINS InterPro DOMAIN/s: Tetratricopeptide TPR-1 (InterPro:IPR001440), Tetratricopeptide-like helical (InterPro:IPR011990), Tetratricopeptide repeat-containing (InterPro:IPR013026), Tetratricopeptide repeat (InterPro:IPR019734), Sel1-like (InterPro:IPR006597); BEST Arabidopsis thaliana protein match is: Tetratricopeptide repeat (TPR)-like superfamily protein (TAIR:AT3G04240.1); Has 77055 Blast hits to 28756 proteins in 2442 species: Archae - 2374; Bacteria - 35241; Metazoa - 12084; Fungi - 2779; Plants - 2385; Viruses - 3; Other Eukaryotes - 22189 (source: NCBI BLink).
    NP_974286.1
    • SPINDLY (SPY); CONTAINS InterPro DOMAIN/s: Tetratricopeptide TPR-1 (InterPro:IPR001440), Tetratricopeptide-like helical (InterPro:IPR011990), Tetratricopeptide repeat-containing (InterPro:IPR013026), Tetratricopeptide repeat (InterPro:IPR019734); BEST Arabidopsis thaliana protein match is: Tetratricopeptide repeat (TPR)-like superfamily protein (TAIR:AT3G04240.1); 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_003074.8 Reference assembly

      Range
      3631887..3638100
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_111987.4 → NP_187761.1  Tetratricopeptide repeat (TPR)-like superfamily protein [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_187761.1

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      Q56YX8, Q96301
      UniProtKB/TrEMBL
      A0A178VPY6, A0A5S9XB37, A0A654F7U9, W8QNP6
      Conserved Domains (5) summary
      sd00006
      Location:329 → 357
      TPR; TPR repeat [structural motif]
      pfam00515
      Location:220 → 253
      TPR_1; Tetratricopeptide repeat
      pfam13414
      Location:329 → 394
      TPR_11; TPR repeat
      pfam13424
      Location:107 → 183
      TPR_12; Tetratricopeptide repeat
      cl10013
      Location:485 → 841
      Glycosyltransferase_GTB_type; Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can be a lipid, a protein, a heterocyclic compound, or another carbohydrate ...

    2. NM_202557.2 → NP_974286.1  Tetratricopeptide repeat (TPR)-like superfamily protein [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_974286.1

      Status: REVIEWED

      UniProtKB/TrEMBL
      A0A178VPY6, A0A5S9XB37, A0A654F7U9, F4J7C7
      Conserved Domains (6) summary
      smart00028
      Location:220 → 247
      TPR; Tetratricopeptide repeats
      sd00006
      Location:152 → 180
      TPR; TPR repeat [structural motif]
      pfam00515
      Location:186 → 212
      TPR_1; Tetratricopeptide repeat
      pfam13414
      Location:186 → 246
      TPR_11; TPR repeat
      pfam13424
      Location:107 → 183
      TPR_12; Tetratricopeptide repeat
      cl10013
      Location:303 → 659
      Glycosyltransferase_GTB_type; Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can be a lipid, a protein, a heterocyclic compound, or another carbohydrate ...
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q96301.1

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