VPS1 / YKR001C Overview
- Standard Name
- VPS1 1 2 3
- Systematic Name
- YKR001C
- SGD ID
- SGD:S000001709
- Aliases
- GRD1 6 , LAM1 11 , SPO15 12 , VPL1 13 , VPT26 2
- Feature Type
- ORF , Verified
- Description
- Dynamin-like GTPase required for vacuolar sorting; promotes fission of retrograde transport carriers from endosome; also involved in actin cytoskeleton organization, endocytosis, late Golgi-retention of some proteins, regulation of peroxisome biogenesis 4 5 6 7 8 9 10
- Name Description
- Vacuolar Protein Sorting 2 3
- Comparative Info
-
Sequence
The S. cerevisiae Reference Genome sequence is derived from laboratory strain S288C. Download DNA or protein sequence, view genomic context and coordinates. Click "Sequence Details" to view all sequence information for this locus, including that for other strains.
- Summary
- VPS1 is located on the right arm of Chromosome XI between the centromere and PAP1 poly(A) polymerase; coding sequence is 2115 nucleotides long with 11 SNPs, 9 of which are silent, 1 of which produces a K/Q polymorphism at residue 141, and 1 of which leads to a Q/H polymorphism at residue 254
Analyze Sequence
S288C only
BLASTN | BLASTP | Design Primers | Restriction Fragment Map | Restriction Fragment Sizes | Six-Frame Translation
S288C vs. other species
BLASTN vs. fungi | BLASTP at NCBI | BLASTP vs. fungi
S288C vs. other strains
Protein
Basic sequence-derived (length, molecular weight, isoelectric point) and experimentally-determined (median abundance, median absolute deviation) protein information. Click "Protein Details" for further information about the protein such as half-life, abundance, domains, domains shared with other proteins, protein sequence retrieval for various strains, physico-chemical properties, protein modification sites, and external identifiers for the protein.
- Summary
- Vps1p is 704 amino acids long with 6 dynamin signature domains, a GTPase domain near N-terminus, a central stalk, and a GTPase effector domain (GED) near C-terminus; shares domains with other proteins involved in mitochondrion organization; undergoes various post-translational modifications, including acetylation, phosphorylation, and ubiquitinylation at 15 residues
- Length (a.a.)
- 704
- Mol. Weight (Da)
- 78738.3
- Isoelectric Point
- 8.18
- Median Abundance (molecules/cell)
- 15358 +/- 6640
- Half-life (hr)
- 12.0
Alleles
Curated mutant alleles for the specified gene, listed alphabetically. Click on the allele name to open the allele page. Click "SGD search" to view all alleles in search results.
View all VPS1 alleles in SGD search
Gene Ontology
GO Annotations consist of four mandatory components: a gene product, a term from one of the three Gene Ontology (GO) controlled vocabularies (Molecular Function, Biological Process, and Cellular Component), a reference, and an evidence code. SGD has manually curated and high-throughput GO Annotations, both derived from the literature, as well as computational, or predicted, annotations. Click "Gene Ontology Details" to view all GO information and evidence for this locus as well as biological processes it shares with other genes.
- Summary
- GTPase involved in vacuolar protein sorting, protein retention in Golgi apparatus, peroxisome organization and fission, endocytosis, and actin cytoskeleton organization; localizes to the vacuole membrane, late endosome, peroxisome, and actin cortical patch; necessary for efficient trafficking of CoQ6 to mitochondria
View computational annotations
Molecular Function
- Manually Curated
- enables actin filament binding (IDA)
- enables GTPase activity (IDA)
Biological Process
- Manually Curated
- involved in actin cytoskeleton organization (IMP)
- involved in actin filament bundle assembly (IMP)
- involved in autophagosome assembly (IMP)
- involved in autophagy (IMP)
- involved in endocytosis (IGI, IMP)
- involved in lipid tube assembly (IDA)
- involved in peroxisome fission (IMP)
- involved in peroxisome organization (IMP, IDA)
- involved in protein localization to phagophore assembly site (IMP)
- involved in protein retention in Golgi apparatus (IMP)
- involved in protein targeting to vacuole (IMP)
- involved in vacuolar transport (IMP)
Cellular Component
- Manually Curated
- located in actin cortical patch (IDA)
- located in cytosol (HDA)
- located in fungal-type vacuole membrane (IDA)
- located in late endosome (IDA)
- located in mitochondrial outer membrane (HDA)
- located in mitochondrion (HDA)
- located in peroxisome (IDA)
- is active in phagophore assembly site (IMP)
Phenotype
Phenotype annotations for a gene are curated single mutant phenotypes that require an observable (e.g., "cell shape"), a qualifier (e.g., "abnormal"), a mutant type (e.g., null), strain background, and a reference. In addition, annotations are classified as classical genetics or high-throughput (e.g., large scale survey, systematic mutation set). Whenever possible, allele information and additional details are provided. Click "Phenotype Details" to view all phenotype annotations and evidence for this locus as well as phenotypes it shares with other genes.
- Summary
- VPS1/YKR001C is a non-essential gene; null mutant is defective in vacuolar protein sorting, resulting in decreased processing, missorting, and secretion of hydrolases; null mutant displays decreased endocytosis, a fragmented vacuolar morphology, fewer but enlarged peroxisomes and an altered endocytic vesicle distribution; null mutant is temperature sensitive and exhibits decreased ionic, oxidative and hyperosmotic stress resistance; null mutant has a respiratory growth defect, a reduced rate of nitrogen utilization and increased starvation induced mitophagy
Classical Genetics
- null
- actin cytoskeleton morphology: abnormal
- autophagy: decreased
- chemical compound accumulation: increased
- endocytosis: decreased
- metal resistance: decreased
- metal resistance: increased
- peroxisomal morphology: abnormal
- protein/peptide distribution: abnormal
- protein/peptide modification: decreased
- resistance to chemicals: decreased
- vacuolar morphology: abnormal
- vesicle distribution: abnormal
- reduction of function
- dominant negative
- overexpression
- null
- acid pH resistance: decreased
- chemical compound accumulation: abnormal
- chemical compound accumulation: decreased
- chemical compound accumulation: increased
- chemical compound excretion: increased
- chronological lifespan: decreased
- chronological lifespan: increased
- competitive fitness: decreased
- endocytosis: decreased
- heat sensitivity: increased
- hyperosmotic stress resistance: decreased
- metal resistance: decreased
- mitophagy: increased
- oxidative stress resistance: decreased
- protein/peptide accumulation: decreased
- protein/peptide distribution: abnormal
- protein/peptide modification: decreased
- resistance to chemicals: decreased
- resistance to chemicals: increased
- resistance to enzymatic treatment: decreased
- respiratory growth: absent
- respiratory growth: decreased rate
- stress resistance: decreased
- toxin resistance: decreased
- utilization of carbon source: decreased rate
- utilization of nitrogen source: decreased rate
- vacuolar morphology: abnormal
- vegetative growth: decreased
- vegetative growth: decreased rate
- viable
Large-scale Survey
Disease
Disease Annotations consist of three mandatory components: a gene product, a term from the Disease Ontology (DO) controlled vocabulary and an evidence code. SGD provides manually curated DO Annotations derived from the literature. Click "Disease Details" to view all Disease information and evidence for this locus as well as diseases it shares with other genes.
- Summary
- Yeast VPS1 is homologous to human DYNAMIN1 (DNM1) and has been used to study mutations found in patients with epileptic encephalopathy; yeast VPS1 is also homologous to human DYNAMIN2 (DNM2) and has been used to study mutations found in patients with microcytic anemia, centronuclear myopathy, Charcot-Marie-Tooth disease, and lethal congenital contracture syndrome
Interaction
Interaction annotations are curated by BioGRID and include physical or genetic interactions observed between at least two genes. An interaction annotation is composed of the interaction type, name of the interactor, assay type (e.g., Two-Hybrid), annotation type (e.g., manual or high-throughput), and a reference, as well as other experimental details. Click "Interaction Details" to view all interaction annotations and evidence for this locus, including an interaction visualization.
- Summary
- Vps1p interacts physically with proteins involved in transcription and protein targeting; VPS1 interacts genetically with genes involved in Golgi vesicle transport
882 total interactions for 586 unique genes
Physical Interactions
- Affinity Capture-MS: 132
- Affinity Capture-RNA: 3
- Affinity Capture-Western: 10
- Biochemical Activity: 2
- Co-fractionation: 2
- Co-localization: 1
- Co-purification: 1
- Far Western: 1
- FRET: 3
- PCA: 5
- Proximity Label-MS: 6
- Reconstituted Complex: 4
- Two-hybrid: 13
Genetic Interactions
- Dosage Growth Defect: 4
- Dosage Lethality: 1
- Dosage Rescue: 6
- Negative Genetic: 389
- Phenotypic Enhancement: 50
- Phenotypic Suppression: 108
- Positive Genetic: 50
- Synthetic Growth Defect: 46
- Synthetic Haploinsufficiency: 1
- Synthetic Lethality: 37
- Synthetic Rescue: 7
Regulation
The number of putative Regulators (genes that regulate it) and Targets (genes it regulates) for the given locus, based on experimental evidence. This evidence includes data generated through high-throughput techniques. Click "Regulation Details" to view all regulation annotations, shared GO enrichment among regulation Targets, and a regulator/target diagram for the locus.
- Regulators
- 3
- Targets
- 0
Expression
Expression data are derived from records contained in the Gene Expression Omnibus (GEO), and are first log2 transformed and normalized. Referenced datasets may contain one or more condition(s), and as a result there may be a greater number of conditions than datasets represented in a single clickable histogram bar. The histogram division at 0.0 separates the down-regulated (green) conditions and datasets from those that are up-regulated (red). Click "Expression Details" to view all expression annotations and details for this locus, including a visualization of genes that share a similar expression pattern.
Summary Paragraph
A summary of the locus, written by SGD Biocurators following a thorough review of the literature. Links to gene names and curated GO terms are included within the Summary Paragraphs.
Last Updated: 2024-05-31
Literature
All manually curated literature for the specified gene, organized into topics according to their relevance to the gene (Primary Literature, Additional Literature, or Review). Click "Literature Details" to view all literature information for this locus, including shared literature between genes.