RPN4 / YDL020C Overview
- Standard Name
- RPN4 1
- Systematic Name
- YDL020C
- SGD ID
- SGD:S000002178
- Aliases
- SON1 7 , UFD5 8
- Feature Type
- ORF , Verified
- Description
- Transcription factor that stimulates expression of proteasome genes; Rpn4p levels are in turn regulated by the 26S proteasome in a negative feedback control mechanism; RPN4 is transcriptionally regulated by various stress responses; relative distribution to the nucleus increases upon DNA replication stress 2 3 4 5 6
- Name Description
- Regulatory Particle Non-ATPase 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.
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
- Relative distribution to the nucleus increases upon DNA replication stress
- Length (a.a.)
- 531
- Mol. Weight (Da)
- 60129.3
- Isoelectric Point
- 5.05
- Median Abundance (molecules/cell)
- 1487
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 RPN4 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
- Sequence specific DNA-binding, RNA polymerase II transcription factor involved in positive regulation of proteasome-mediated ubiquitin-dependent protein catabolism and transcription from RNA pol II promoters in response to stress; implicated in the regulation of DNA repair; localizes to the nucleus
View computational annotations
Molecular Function
- Manually Curated
Biological Process
- Manually Curated
- involved in cellular response to arsenic-containing substance (HMP, IMP)
- involved in cellular response to stress (HMP, IMP)
- involved in negative regulation of transcription by RNA polymerase II (HMP, IMP)
- involved in positive regulation of transcription by RNA polymerase II (HMP, IMP, IDA, IGI)
- involved in regulation of DNA repair (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
- Non-essential gene; null mutant has lower abundance of proteasome subunits and shows decreased proteolytic processing of reporters; null mutant has slow growth, increased sensitivity to metals; in systematic studies null mutants display increased sensitivity to multiple chemicals, including camptothecin, hydroxyurea, MMS, bleomycin, caffeine, cycloheximide, azoles
Classical Genetics
- null
- cell cycle progression: delayed
- chemical compound accumulation: increased
- growth in exponential phase: decreased rate
- metal resistance: decreased
- prion formation: increased
- protein activity: decreased
- protein/peptide accumulation: decreased
- protein/peptide accumulation: increased
- protein/peptide distribution: abnormal
- protein/peptide modification: decreased
- protein/peptide modification: increased
- replicative lifespan: decreased
- replicative lifespan: increased
- resistance to chemicals: decreased
- RNA accumulation: decreased
- small molecule transport: decreased
- stress resistance: decreased
- toxin resistance: decreased
- null
- acquired thermotolerance: decreased
- auxotrophy
- cell cycle progression through the G2/M phase transition: delayed
- chemical compound accumulation: abnormal
- competitive fitness: decreased
- competitive fitness: increased
- desiccation resistance: decreased
- fermentative growth: decreased rate
- haploinsufficient
- heat sensitivity: increased
- innate thermotolerance: increased
- liquid culture appearance: abnormal
- metal resistance: decreased
- mitotic recombination: decreased
- nutrient utilization: decreased
- protein activity: increased
- protein/peptide distribution: abnormal
- replicative lifespan: decreased
- resistance to chemicals: decreased
- resistance to chemicals: increased
- respiratory growth: increased rate
- stress resistance: decreased
- stress resistance: increased
- telomere length: decreased
- toxin resistance: decreased
- toxin resistance: increased
- transposable element transposition: decreased
- vegetative growth: decreased rate
- viable
- overexpression
Large-scale Survey
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.
1533 total interactions for 798 unique genes
Physical Interactions
- Affinity Capture-MS: 8
- Affinity Capture-RNA: 7
- Affinity Capture-Western: 11
- Biochemical Activity: 2
- Co-fractionation: 1
- Co-purification: 2
- Reconstituted Complex: 6
- Two-hybrid: 3
Genetic Interactions
- Dosage Growth Defect: 10
- Dosage Lethality: 1
- Dosage Rescue: 9
- Negative Genetic: 896
- Phenotypic Enhancement: 40
- Phenotypic Suppression: 58
- Positive Genetic: 129
- Synthetic Growth Defect: 255
- Synthetic Lethality: 80
- Synthetic Rescue: 15
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.
- Summary
- RPN4 encodes a zinc-coordinating proteasomal transcription factor of the beta-beta-alpha zinc finger family. Rpn4p contains a C2H2-type finger motif and two acidic domains. Rpn4p mediates expression of a majority of proteasome genes by binding proteasome-associated control elements (PACE; 5'-GGTGGCAAA-3') found in their promoters, and also in a number of promoters of genes related to the ubiquitin-proteasome pathway. Targets include PRE1, PRE3, PRE6, PRE7, PRE10, PUP3, RPN9, RPN12, ECM29, RPT2, RPT3, RPT4, SHP1, and OTU1. Rpn4p is also required for regulation of genes involved in DNA repair and other cellular processes, such as DNA damage-inducible genes MAG1 and DDI1. Upon oxidative stress, RPN4 transcripion is upregulated by Yap1p. The RPN4 promoter also has binding sites for other transcription factors, incuding Pdr1p/Pdr3p and Hsf1p. Rpn4p is a feedback regulator of YAP1 and PDR1, and plays a vital role in cellular tolerance to various stresses. Rpn4p is rapidly degraded by the proteasome, revealing a transcriptional feedback loop formulated to ensure proteasome activity.
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.
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.