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SYD P-loop containing nucleoside triphosphate hydrolases superfamily protein [ Arabidopsis thaliana (thale cress) ]

Gene ID: 817375, updated on 18-Sep-2024

Summary

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Official Symbol
SYD
Official Full Name
P-loop containing nucleoside triphosphate hydrolases superfamily protein
Primary source
TAIR:AT2G28290
Locus tag
AT2G28290
See related
Araport:AT2G28290
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
CHR3; CHROMATIN REMODELING COMPLEX SUBUNIT R; CHROMATIN REMODELING COMPLEX SUBUNIT R 3; SPLAYED
Summary
Encodes a SWI2/SNF2-like protein in the SNF2 subclass. Homozygous plants with null mutations exhibit premature termination of the meristem and carpelloid structures from the inflorescence meristem. Co-activator of floral homeotic gene expression. Acts with LFY to regulate shoot apical meristem identity. Required for meristem maintenance. Regulates flowering under a non-inductive photoperiod. It promotes the expression of CUC2 during cotyledon boundary formation. Affects reproductive shoot apical meristem function by regulating the expression of WUS. In CHiP experiments SYD binds to WUS promoter. Present as two forms in the nucleus, full-length and truncated, with the latter apparently lacking the C-terminal domain. The ratio of the two forms differs in juvenile and in adult tissues. The C-terminal domain is not required for activity.
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Genomic context

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See SYD in Genome Data Viewer
Location:
chromosome: 2
Exon count:
35
Sequence:
Chromosome: 2; NC_003071.7 (12056213..12073279)

Chromosome 2 - NC_003071.7Genomic Context describing neighboring genes Neighboring gene Cysteine/Histidine-rich C1 domain family protein Neighboring gene miscRNA Neighboring gene Putative lysine decarboxylase family protein Neighboring gene trimethylguanosine synthase (DUF707)

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. SPLAYED, a novel SWI/SNF ATPase homolog, controls reproductive development in Arabidopsis. Wagner D, et al. Curr Biol, 2002 Jan 22. PMID 11818058
  2. WUSCHEL is a primary target for transcriptional regulation by SPLAYED in dynamic control of stem cell fate in Arabidopsis. Kwon CS, et al. Genes Dev, 2005 Apr 15. PMID 15833920, Free PMC Article
  3. The chromatin remodeler SPLAYED regulates specific stress signaling pathways. Walley JW, et al. PLoS Pathog, 2008 Dec. PMID 19079584, Free PMC Article
  4. The Chromatin Remodeler SPLAYED Negatively Regulates SNC1-Mediated Immunity. Johnson KC, et al. Plant Cell Physiol, 2015 Aug. PMID 26063389
  5. The N-terminal ATPase AT-hook-containing region of the Arabidopsis chromatin-remodeling protein SPLAYED is sufficient for biological activity. Su Y, et al. Plant J, 2006 May. PMID 16640604

See all (19) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Transcription elongator SPT6L regulates the occupancies of the SWI2/SNF2 chromatin remodelers SYD/BRM and nucleosomes at transcription start sites in Arabidopsis.
    Title: Transcription elongator SPT6L regulates the occupancies of the SWI2/SNF2 chromatin remodelers SYD/BRM and nucleosomes at transcription start sites in Arabidopsis.
  2. SYD plays a subtle, specific role in the regulation of SNC1 expression and SNC1-mediated immunity. SYD may work with other proteins at the chromatin level to repress SNC1 transcription.
    Title: The Chromatin Remodeler SPLAYED Negatively Regulates SNC1-Mediated Immunity.
  3. The SWI2/SNF2 chromatin-remodeling ATPases SPLAYED (SYD) and BRAHMA (BRM) are redundantly required for flower patterning and for the activation of AP3 and AG.
    Title: SWI2/SNF2 chromatin remodeling ATPases overcome polycomb repression and control floral organ identity with the LEAFY and SEPALLATA3 transcription factors.
  4. study found that the chromatin remodeling protein, SPLAYED, is required for gene expression within specific biotic stress signaling networks
    Title: The chromatin remodeler SPLAYED regulates specific stress signaling pathways.
  5. Results describe overlapping functions for the two SWI/SNF ATPases, SPLAYED and BRAHMA, and indicate that these proteins exhibit remarkable regulatory specificity.
    Title: Unique, shared, and redundant roles for the Arabidopsis SWI/SNF chromatin remodeling ATPases BRAHMA and SPLAYED.
  6. SYD is recruited to the WUS promoter and is involved in regulation of the stem cell pool maintenance via direct transcriptional control of this master regulator.
    Title: WUSCHEL is a primary target for transcriptional regulation by SPLAYED in dynamic control of stem cell fate in Arabidopsis.
  7. The N-terminal ATPase AT-hook-containing region of the SYD protein is responsible for its biological activity.
    Title: The N-terminal ATPase AT-hook-containing region of the Arabidopsis chromatin-remodeling protein SPLAYED is sufficient for biological activity.
Submit: New GeneRIF Correction

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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NM_001084502.2
NM_001336158.1
NM_001336159.1
NM_001336160.1
NM_179785.3
NM_179786.2

Gene Ontology Provided by TAIR

Function Evidence Code Pubs
enables ATP hydrolysis activity ISS
Inferred from Sequence or Structural Similarity
more info
 PubMed 
enables ATP-dependent chromatin remodeler activity IEA
Inferred from Electronic Annotation
more info
  
enables chromatin binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables histone binding 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 epigenetic regulation of gene expression IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within flower development IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within organ boundary specification between lateral organs and the meristem IGI
Inferred from Genetic Interaction
more info
 PubMed 
involved_in regulation of DNA-templated transcription IEA
Inferred from Electronic Annotation
more info
  
involved_in regulation of defense response to fungus IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in regulation of ethylene-activated signaling pathway IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in regulation of jasmonic acid mediated signaling pathway IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within response to wounding IEP
Inferred from Expression Pattern
more info
 PubMed 
involved_in response to wounding TAS
Traceable Author Statement
more info
 PubMed 
Component Evidence Code Pubs
located_in cytosol HDA 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
P-loop containing nucleoside triphosphate hydrolases superfamily protein
NP_001077971.1
  • SPLAYED (SYD); CONTAINS InterPro DOMAIN/s: DEAD-like helicase, N-terminal (InterPro:IPR014001), DNA/RNA helicase, C-terminal (InterPro:IPR001650), Helicase/SANT-associated, DNA binding (InterPro:IPR014012), Helicase, superfamily 1/2, ATP-binding domain (InterPro:IPR014021), SNF2-related (InterPro:IPR000330); BEST Arabidopsis thaliana protein match is: Homeotic gene regulator (TAIR:AT3G06010.1); Has 38598 Blast hits to 29293 proteins in 2471 species: Archae - 323; Bacteria - 8462; Metazoa - 11641; Fungi - 6683; Plants - 2383; Viruses - 257; Other Eukaryotes - 8849 (source: NCBI BLink).
NP_850116.1
  • SPLAYED (SYD); CONTAINS InterPro DOMAIN/s: DEAD-like helicase, N-terminal (InterPro:IPR014001), DNA/RNA helicase, C-terminal (InterPro:IPR001650), Helicase/SANT-associated, DNA binding (InterPro:IPR014012), Helicase, superfamily 1/2, ATP-binding domain (InterPro:IPR014021), SNF2-related (InterPro:IPR000330); BEST Arabidopsis thaliana protein match is: Homeotic gene regulator (TAIR:AT3G06010.1); Has 37832 Blast hits to 28961 proteins in 2437 species: Archae - 315; Bacteria - 8243; Metazoa - 11351; Fungi - 6777; Plants - 2369; Viruses - 253; Other Eukaryotes - 8524 (source: NCBI BLink).
NP_850117.1
  • SPLAYED (SYD); CONTAINS InterPro DOMAIN/s: DEAD-like helicase, N-terminal (InterPro:IPR014001), DNA/RNA helicase, C-terminal (InterPro:IPR001650), Helicase/SANT-associated, DNA binding (InterPro:IPR014012), Helicase, superfamily 1/2, ATP-binding domain (InterPro:IPR014021), SNF2-related (InterPro:IPR000330); BEST Arabidopsis thaliana protein match is: Homeotic gene regulator (TAIR:AT3G06010.1); Has 37993 Blast hits to 29119 proteins in 2440 species: Archae - 313; Bacteria - 8300; Metazoa - 11402; Fungi - 6833; Plants - 2357; Viruses - 252; Other Eukaryotes - 8536 (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
    12056213..12073279
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_179786.2 → NP_850117.1  P-loop containing nucleoside triphosphate hydrolases superfamily protein [Arabidopsis thaliana]

    See identical proteins and their annotated locations for NP_850117.1

    Status: REVIEWED

    UniProtKB/TrEMBL
    A0A5S9X204
    Conserved Domains (6) summary
    smart00951
    Location:277 → 310
    QLQ; QLQ is named after the conserved Gln, Leu, Gln motif
    PLN03142
    Location:603 → 1215
    PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional
    PHA03307
    Location:1490 → 1818
    PHA03307; transcriptional regulator ICP4; Provisional
    COG5271
    Location:2213 → 2589
    MDN1; Midasin, AAA ATPase with vWA domain, involved in ribosome maturation [Translation, ribosomal structure and biogenesis]
    PRK10811
    Location:3167 → 3336
    rne; ribonuclease E; Reviewed
    pfam14619
    Location:1282 → 1368
    SnAC; Snf2-ATP coupling, chromatin remodelling complex

  2. NM_001084502.2 → NP_001077971.1  P-loop containing nucleoside triphosphate hydrolases superfamily protein [Arabidopsis thaliana]

    See identical proteins and their annotated locations for NP_001077971.1

    Status: REVIEWED

    UniProtKB/TrEMBL
    A0A178VTN0, A0A5S9X204
    Conserved Domains (6) summary
    smart00951
    Location:277 → 310
    QLQ; QLQ is named after the conserved Gln, Leu, Gln motif
    PLN03142
    Location:603 → 1215
    PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional
    PHA03307
    Location:1490 → 1818
    PHA03307; transcriptional regulator ICP4; Provisional
    COG5271
    Location:2213 → 2589
    MDN1; Midasin, AAA ATPase with vWA domain, involved in ribosome maturation [Translation, ribosomal structure and biogenesis]
    PRK10811
    Location:3167 → 3336
    rne; ribonuclease E; Reviewed
    pfam14619
    Location:1282 → 1368
    SnAC; Snf2-ATP coupling, chromatin remodelling complex

  3. NM_179785.3 → NP_850116.1  P-loop containing nucleoside triphosphate hydrolases superfamily protein [Arabidopsis thaliana]

    See identical proteins and their annotated locations for NP_850116.1

    Status: REVIEWED

    UniProtKB/Swiss-Prot
    F4IHS2, F4IHS3, F4IHS4, Q5BN47, Q8L9D7, Q9AUB4, Q9SL27
    UniProtKB/TrEMBL
    A0A178VWG9, A0A5S9X204
    Conserved Domains (6) summary
    smart00951
    Location:277 → 310
    QLQ; QLQ is named after the conserved Gln, Leu, Gln motif
    PLN03142
    Location:603 → 1215
    PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional
    PHA03307
    Location:1490 → 1818
    PHA03307; transcriptional regulator ICP4; Provisional
    COG5271
    Location:2213 → 2589
    MDN1; Midasin, AAA ATPase with vWA domain, involved in ribosome maturation [Translation, ribosomal structure and biogenesis]
    PRK10811
    Location:3167 → 3341
    rne; ribonuclease E; Reviewed
    pfam14619
    Location:1306 → 1368
    SnAC; Snf2-ATP coupling, chromatin remodelling complex

  4. NM_001336158.1 → NP_001325347.1  P-loop containing nucleoside triphosphate hydrolases superfamily protein [Arabidopsis thaliana]

    Status: REVIEWED

    UniProtKB/TrEMBL
    A0A178VTN0, A0A5S9X204
    Conserved Domains (6) summary
    smart00951
    Location:277 → 310
    QLQ; QLQ is named after the conserved Gln, Leu, Gln motif
    PLN03142
    Location:603 → 1215
    PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional
    PHA03307
    Location:1490 → 1818
    PHA03307; transcriptional regulator ICP4; Provisional
    COG5271
    Location:2213 → 2589
    MDN1; Midasin, AAA ATPase with vWA domain, involved in ribosome maturation [Translation, ribosomal structure and biogenesis]
    PRK10811
    Location:3167 → 3336
    rne; ribonuclease E; Reviewed
    pfam14619
    Location:1282 → 1368
    SnAC; Snf2-ATP coupling, chromatin remodelling complex

  5. NM_001336160.1 → NP_001325349.1  P-loop containing nucleoside triphosphate hydrolases superfamily protein [Arabidopsis thaliana]

    Status: REVIEWED

    UniProtKB/TrEMBL
    A0A1P8B2Y3, A0A5S9X204

  6. NM_001336159.1 → NP_001325348.1  P-loop containing nucleoside triphosphate hydrolases superfamily protein [Arabidopsis thaliana]

    Status: REVIEWED

    UniProtKB/TrEMBL
    A0A178VTI3, A0A1P8B2X1, A0A384L3H2, A0A5S9X204
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
F4IHS2.1

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