VCS Transducin/WD40 repeat-like superfamily protein [Arabidopsis thaliana (thale cress)] - Gene

Summary

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Official Symbol: VCS
Official Full Name: Transducin/WD40 repeat-like superfamily protein
Primary source: TAIR:AT3G13300
Locus tag: AT3G13300
See related: Araport:AT3G13300
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: VARICOSE
Summary: Encodes VCS (VARICOSE). Involved in mRNA decapping. VCS forms a mRNA decapping complex with DCP1 (At1g08370) and DCP2 (At5g13570). Unlike DCP2, VCS itself does not have mRNA decapping activity in vitro. DCP1, DCP2 and VCS colocalize in cytoplasmic loci, which are putative Arabidopsis mRNA processing bodies. Null mutants of DCP1, DCP2, and VCS accumulate capped mRNAs with a reduced degradation rate. These mutants also share a similar lethal phenotype at the seedling cotyledon stage, with disorganized veins, swollen root hairs, and altered epidermal cell morphology. VCS is also required for leaf development.
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Genomic context

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See VCS in Genome Data Viewer

Location:: chromosome: 3

Exon count:: 11

Sequence:: Chromosome: 3; NC_003074.8 (4303822..4310275)

Chromosome 3 - NC_003074.8 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:: NC_003074.8

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Cauliflower mosaic virus transactivator protein (TAV) can suppress nonsense-mediated decay by targeting VARICOSE, a scaffold protein of the decapping complex.
Title: Cauliflower mosaic virus transactivator protein (TAV) can suppress nonsense-mediated decay by targeting VARICOSE, a scaffold protein of the decapping complex.
ABA-unresponsive subclass I SnRK2s and their downstream effector, VCS, regulate mRNA decay and mRNA accumulation and are required to maintain plant growth under osmotic stress conditions
Title: ABA-unresponsive SnRK2 protein kinases regulate mRNA decay under osmotic stress in plants.
Data suggest that specific motifs, secondary energy, and GC content of transcripts could play a role in their degradation by exoribonuclease4 (xrn4) and varicose (vcs).
Title: 5' to 3' mRNA Decay Contributes to the Regulation of Arabidopsis Seed Germination by Dormancy.
Seedling lethal phenotypes in dcp1, dcp2 and vcs mutants are caused the disruption of miRNA-mediated gene regulation.
Title: The role of decapping proteins in the miRNA accumulation in Arabidopsis thaliana.
DCP2 interacts in vitro and in vivo with DCP1 and VARICOSE (VCS), an Arabidopsis homolog of human Hedls/Ge-1, suggesting that the three proteins operate as a decapping complex.
Title: Arabidopsis DCP2, DCP1, and VARICOSE form a decapping complex required for postembryonic development.

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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_112175.3

Supported by ESTs:

NM_180245.2

Supported by ESTs:

Gene Ontology Provided by TAIR

Function	Evidence Code	Pubs
enables mRNA binding	HDA more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein homodimerization activity	IDA Inferred from Direct Assay more info	PubMed
enables protein homodimerization activity	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in cellular response to auxin stimulus	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within deadenylation-independent decapping of nuclear-transcribed mRNA	IDA Inferred from Direct Assay more info	PubMed
involved_in deadenylation-independent decapping of nuclear-transcribed mRNA	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within leaf morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within mRNA catabolic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in post-embryonic development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in primary shoot apical meristem specification	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in root meristem specification	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in P-body	IDA Inferred from Direct Assay more info	PubMed
located_in cytoplasmic stress granule	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: Transducin/WD40 repeat-like superfamily protein

NP_187938.2

VARICOSE (VCS); FUNCTIONS IN: protein homodimerization activity, nucleotide binding; INVOLVED IN: mRNA catabolic process, deadenylation-independent decapping of nuclear-transcribed mRNA, leaf morphogenesis; LOCATED IN: cytosol, nucleus, cytoplasmic mRNA processing body; EXPRESSED IN: whole plant, guard cell, cultured cell; CONTAINS InterPro DOMAIN/s: WD40 repeat-like-containing domain (InterPro:IPR011046), WD40 repeat 2 (InterPro:IPR019782), WD40-repeat-containing domain (InterPro:IPR017986), WD40 repeat (InterPro:IPR001680), WD40/YVTN repeat-like-containing domain (InterPro:IPR015943), WD40 repeat, subgroup (InterPro:IPR019781); BEST Arabidopsis thaliana protein match is: varicose-related (TAIR:AT3G13290.1); Has 1013 Blast hits to 919 proteins in 280 species: Archae - 4; Bacteria - 227; Metazoa - 270; Fungi - 225; Plants - 138; Viruses - 6; Other Eukaryotes - 143 (source: NCBI BLink).

NP_850576.1

VARICOSE (VCS); FUNCTIONS IN: protein homodimerization activity, nucleotide binding; INVOLVED IN: mRNA catabolic process, deadenylation-independent decapping of nuclear-transcribed mRNA, leaf morphogenesis; LOCATED IN: cytosol, nucleus, cytoplasmic mRNA processing body; EXPRESSED IN: whole plant, guard cell, cultured cell; CONTAINS InterPro DOMAIN/s: WD40 repeat-like-containing domain (InterPro:IPR011046), WD40 repeat 2 (InterPro:IPR019782), WD40-repeat-containing domain (InterPro:IPR017986), WD40/YVTN repeat-like-containing domain (InterPro:IPR015943), WD40 repeat (InterPro:IPR001680), WD40 repeat, subgroup (InterPro:IPR019781); BEST Arabidopsis thaliana protein match is: varicose-related (TAIR:AT3G13290.1); Has 885 Blast hits to 799 proteins in 264 species: Archae - 2; Bacteria - 218; Metazoa - 230; Fungi - 185; Plants - 114; Viruses - 4; Other Eukaryotes - 132 (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_003074.8 Reference assembly

Range

4303822..4310275

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001338042.1 → NP_001327264.1 Transducin/WD40 repeat-like superfamily protein [Arabidopsis thaliana]

Status: REVIEWED

UniProtKB/TrEMBL

A0A1I9LRS8, A0A5S9XC85
NM_112175.3 → NP_187938.2 Transducin/WD40 repeat-like superfamily protein [Arabidopsis thaliana]

See identical proteins and their annotated locations for NP_187938.2

Status: REVIEWED

UniProtKB/Swiss-Prot

F4JC94, Q0WLC5, Q56YT1, Q8L7N9, Q9LTT8

UniProtKB/TrEMBL

A0A5S9XC85

Conserved Domains (3) summary

pfam16529
Location:186 → 498

Ge1_WD40; WD40 region of Ge1, enhancer of mRNA-decapping protein

sd00039
Location:190 → 235

7WD40; WD40 repeat [structural motif]

cl02567
Location:229 → 456

WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
NM_180245.2 → NP_850576.1 Transducin/WD40 repeat-like superfamily protein [Arabidopsis thaliana]

See identical proteins and their annotated locations for NP_850576.1

Status: REVIEWED

UniProtKB/TrEMBL

A0A5S9XC85

Conserved Domains (3) summary

pfam16529
Location:151 → 463

Ge1_WD40; WD40 region of Ge1, enhancer of mRNA-decapping protein

sd00039
Location:155 → 200

7WD40; WD40 repeat [structural motif]

cl02567
Location:194 → 421

WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...