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

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_003071.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:: NC_003071.7

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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.
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.
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.
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.
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.

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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NM_001084502.2

Supported by ESTs:

NM_001336158.1

Supported by ESTs:

NM_001336159.1

Supported by ESTs:

NM_001336160.1

Supported by ESTs:

NM_179785.3

Supported by ESTs:

NM_179786.2

Supported by ESTs:

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 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: 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

NC_003071.7 Reference assembly

Range

12056213..12073279

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

Status: REVIEWED

UniProtKB/TrEMBL

A0A1P8B2Y3, A0A5S9X204
NM_001336159.1 → NP_001325348.1 P-loop containing nucleoside triphosphate hydrolases superfamily protein [Arabidopsis thaliana]

Status: REVIEWED

UniProtKB/TrEMBL

A0A178VTI3, A0A1P8B2X1, A0A384L3H2, A0A5S9X204