VTS1 Vts1p [Saccharomyces cerevisiae S288C] - Gene

Summary

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Official Symbol: VTS1
Official Full Name: Vts1p
Primary source: SGD:S000005886
Locus tag: YOR359W
See related: AllianceGenome:SGD:S000005886; FungiDB:YOR359W; VEuPathDB:YOR359W
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Saccharomyces cerevisiae S288C (strain: S288C)
Lineage: Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces
Summary: Enables RNA binding activity and flap-structured DNA binding activity. Involved in nuclear-transcribed mRNA poly(A) tail shortening and positive regulation of DNA metabolic process. Located in P-body; cytosol; and nucleus. Orthologous to human SAMD4A (sterile alpha motif domain containing 4A) and SAMD4B (sterile alpha motif domain containing 4B). [provided by Alliance of Genome Resources, Jan 2025]
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Genomic context

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See VTS1 in Genome Data Viewer

Location:: chromosome: XV

Exon count:: 1

Sequence:: Chromosome: XV; NC_001147.6 (1011189..1012760)

Chromosome XV - NC_001147.6 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:: NC_001147.6

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Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

The work couples transcriptome-wide measurements of binding affinity, sequence, and structural determinants of binding, and phenotypic outcomes to provide a comprehensive portrait of Vts1 function. Notably, the impact of Vts1 on transcript abundance was largely independent of where it bound within an mRNA, challenging prevailing assumptions about how this RBP drives RNA degradation.
Title: Comprehensive and quantitative mapping of RNA-protein interactions across a transcribed eukaryotic genome.
the influence of SUP35 and VTS1 on [NSI+]
Title: [Interactions of [NSI+] determinant with SUP35 and VTS1 genes in Saccharomyces cerevisiae].
the interaction of Vts1p with Eap1p at target mRNAs stimulates decapping and transcript decay
Title: The eIF4E-binding protein Eap1p functions in Vts1p-mediated transcript decay.
VTS1 gene modulates nonsense suppression and vegetative growth in S. cerevisiae
Title: [NSI+] determinant has a pleiotropic phenotypic manifestation that is modulated by SUP35, SUP45, and VTS1 genes.
VTS1 is a multi-copy suppressor of dna2-K1080E, a lethal mutant allele of DNA2 that lacks DNA helicase activity.
Title: Involvement of Vts1, a structure-specific RNA-binding protein, in Okazaki fragment processing in yeast.
Using RNA reporters that recapitulate Vts1p-mediated decay in vivo, study demonstrates that Vts1p stimulates mRNA degradation through deadenylation mediated by the Ccr4p-Pop2p-Not deadenylase complex.
Title: S. cerevisiae Vts1p induces deadenylation-dependent transcript degradation and interacts with the Ccr4p-Pop2p-Not deadenylase complex.
Results describe the 1.6 Angstroms X-ray crystal structure of the Vts1 SAM domain in its unliganded state, and the NMR solution structure of this domain in its RNA-bound state.
Title: The NMR and X-ray structures of the Saccharomyces cerevisiae Vts1 SAM domain define a surface for the recognition of RNA hairpins.
identified several genes in S. cerevisiae that seem to be regulated by Vts1p and contain one or more copies of the Smaug response element
Title: Shape-specific recognition in the structure of the Vts1p SAM domain with RNA.
present the NMR structures of the Vts1p-Smaug recognition element (SRE) complex and the free SRE
Title: RNA recognition by the Vts1p SAM domain.
2.0-A X-ray structure of the Vts1p SAM domain bound to a high-affinity RNA ligand
Title: Sequence-specific recognition of RNA hairpins by the SAM domain of Vts1p.

Submit: New GeneRIF Correction See all GeneRIFs (11)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Homology

Orthologs from OrthoDB

Gene Ontology Provided by SGD

Function	Evidence Code	Pubs
enables RNA binding	IDA Inferred from Direct Assay more info	PubMed
enables RNA binding	IEA Inferred from Electronic Annotation more info
enables flap-structured DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables mRNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables mRNA binding	IEA Inferred from Electronic Annotation more info
enables nucleotide binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in nuclear-transcribed mRNA catabolic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in nuclear-transcribed mRNA poly(A) tail shortening	IBA Inferred from Biological aspect of Ancestor more info
involved_in nuclear-transcribed mRNA poly(A) tail shortening	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in nuclear-transcribed mRNA poly(A) tail shortening	IPI Inferred from Physical Interaction more info	PubMed
involved_in positive regulation of DNA metabolic process	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of DNA metabolic process	IPI Inferred from Physical Interaction more info	PubMed
involved_in protein transport	IEA Inferred from Electronic Annotation more info
involved_in regulation of mRNA stability	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
is_active_in P-body	IBA Inferred from Biological aspect of Ancestor more info
located_in P-body	IDA Inferred from Direct Assay more info	PubMed
located_in P-body	IEA Inferred from Electronic Annotation more info
located_in cytoplasm	IEA Inferred from Electronic Annotation more info
located_in cytosol	IDA Inferred from Direct Assay more info	PubMed
located_in cytosol	IEA Inferred from Electronic Annotation more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: Vts1p

NP_015004.3

Flap-structured DNA-binding and RNA-binding protein; stimulates deadenylation-dependent mRNA degradation mediated by the CCR4-NOT deadenylase complex; member of the Smaug (Smg) family of post-transcriptional regulators which bind RNA through a conserved sterile alpha motif (SAM) domain that interacts with Smg recognition element (SREs) containing transcripts; stimulates Dna2p endonuclease activity; forms [SMAUG+] prion

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_001147.6 Reference assembly

Range

1011189..1012760

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001183779.3 → NP_015004.3 TPA: Vts1p [Saccharomyces cerevisiae S288C]

See identical proteins and their annotated locations for NP_015004.3

Status: REVIEWED

UniProtKB/Swiss-Prot

D6W354, Q08831

UniProtKB/TrEMBL

A6ZPI9, B3LK16, C7GNQ9, G2WNM0, N1NX26

Conserved Domains (1) summary

cd09556
Location:448 → 516

SAM_VTS1_fungal; SAM domain of VTS1 RNA-binding proteins