PUB1 / YNL016W Overview
- Standard Name
- PUB1 1
- Systematic Name
- YNL016W
- SGD ID
- SGD:S000004961
- Aliases
- RNP1 9
- Feature Type
- ORF , Verified
- Description
- Poly (A)+ RNA-binding protein; abundant mRNP-component protein that binds cell wall mRNAs; required for stability of many mRNAs; component of glucose deprivation induced stress granules, involved in P-body-dependent granule assembly; implicated in regulation of translation; carries Q/N-rich domain at C- terminus, identified as candidate prion; ribosome-bound Pub1p modulates stop codon decoding during translation termination 1 2 3 4 5 6 7 8
- Name Description
- PolyUridylate Binding 1
- 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
- PUB1 is located on the left arm of chromosome XIV near the telomere, between tRNA-Ile and PBI2 vacuolar proteinase B inhibitor; coding sequence is 1362 nucleotides long with 12 SNPs, 3 of which lead to amino acid polymorphisms, and an insertion of 12 nucleotides near the C-terminus in strain SK1
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
- Pub1p is 453 amino acids long, longer lived, and abundant; contains 3 RNA recognition motif domains, methylated on Arg260; string of 12 glutamines at C-terminus is 16 glutamines in strain SK1
- Length (a.a.)
- 453
- Mol. Weight (Da)
- 50748.6
- Isoelectric Point
- 4.73
- Median Abundance (molecules/cell)
- 22861 +/- 7024
- Half-life (hr)
- 12.8
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 PUB1 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
- Protein that binds to poly(U) RNA and mRNA; involved in nonsense-mediated mRNA decay, regulation of mRNA stability, and stress granule assembly; localizes to the nucleus and cytoplasm, and to both cytoplasmic stress granules and mRNA processing bodies
View computational annotations
Molecular Function
- Manually Curated
- enables mRNA binding (IDA, IMP, HDA)
- enables poly(U) RNA binding (IDA)
- enables ribosome binding (IDA)
Biological Process
- Manually Curated
- involved in cellular response to glucose starvation (IMP)
- involved in nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (IDA)
- involved in regulation of mRNA stability (IMP)
- involved in stress granule assembly (IMP)
- involved in translational termination (IMP, IPI)
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
- Non-essential gene; null shows small defect in vacuolar fragmentation, decreased utilization of glutamine as nitrogen source, altered transposable element transposition, decreased ethanol resistance, sensitivity to zinc starvation, increased resistance to fluconazole and to caffeine, decreased resistance to camptothecin, increased oxidative stress resistance, decreased endocytosis, increased chronological lifespan; overexpression slows growth
Classical Genetics
- null
- chromosome/plasmid maintenance: decreased
- competitive fitness: decreased
- endocytosis: decreased
- haploinsufficient
- metal resistance: decreased
- oxidative stress resistance: increased
- resistance to chemicals: decreased
- resistance to chemicals: increased
- stress resistance: decreased
- transposable element transposition: decreased
- transposable element transposition: increased
- utilization of nitrogen source: decreased rate
- vacuolar morphology: abnormal
- 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 PUB1 is homologous to human TIA1, and has been used to study amyotrophic lateral sclerosis type 26
Manually Curated
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
- Pub1p interacts physically with proteins involved in mitochondrial translation; PUB1 interacts genetically with genes involved in transcription
867 total interactions for 720 unique genes
Physical Interactions
- Affinity Capture-MS: 524
- Affinity Capture-RNA: 7
- Affinity Capture-Western: 6
- Co-fractionation: 2
- Co-localization: 1
- PCA: 15
- Proximity Label-MS: 4
- Reconstituted Complex: 6
- Two-hybrid: 5
Genetic Interactions
- Dosage Rescue: 1
- Negative Genetic: 242
- Phenotypic Suppression: 1
- Positive Genetic: 39
- Synthetic Growth Defect: 12
- Synthetic Lethality: 2
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
- 6
- 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: 2024-06-11
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.