RPD3 / YNL330C Overview
- Standard Name
- RPD3 1
- Systematic Name
- YNL330C
- SGD ID
- SGD:S000005274
- Aliases
- MOF6 23 , REC3 21 , SDI2 24 , SDS6 25 26
- Feature Type
- ORF , Verified
- Description
- Histone deacetylase, component of both Rpd3S and Rpd3L complexes; regulates transcription, silencing, autophagy and other processes by influencing chromatin remodeling; forms at least two different complexes which have distinct functions and members; Rpd3(L) recruitment to the subtelomeric region is regulated by interaction with the Hmt1p methyltransferase; delays late firing of single copy origins by opposing the Fkh1/2 origin activation pathway 2 3 4 5 6 7 8 9 10 11 12 13
- Name Description
- Reduced Potassium Dependency 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
- Rpd3p is 433 amino acids long, low in abundance, of average half-life; ubiquitinylated on K412, phosphorylated on 10 residues
- Length (a.a.)
- 433
- Mol. Weight (Da)
- 48887.5
- Isoelectric Point
- 5.2
- Median Abundance (molecules/cell)
- 3850 +/- 1138
- Half-life (hr)
- 10.6
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 RPD3 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
- Histone deacetylase subunit of the Rpd3S, Rpd3L and Snt2C complexes; functions as both a transcription coactivator and corepressor; regulates transcription by RNA polymerases I and II through chromatin silencing; involved in mitosis, meiosis, macroautophagy, and aging
View computational annotations
Molecular Function
- Manually Curated
- enables histone deacetylase activity (IMP, IDA)
- enables transcription coactivator activity (IMP, IPI)
- enables transcription corepressor activity (IPI, IMP)
- enables zinc ion binding (RCA)
Biological Process
- Manually Curated
- involved in cellular response to heat (IMP)
- involved in cellular response to nitrogen starvation (IMP)
- involved in G1/S transition of mitotic cell cycle (IPI, IGI)
- involved in G2/M transition of mitotic cell cycle (IGI)
- involved in meiotic cell cycle (IMP)
- involved in negative regulation of rDNA heterochromatin formation (IMP)
- involved in negative regulation of reciprocal meiotic recombination (IMP)
- involved in negative regulation of silent mating-type cassette heterochromatin formation (IMP)
- involved in negative regulation of transcription by RNA polymerase I (IMP)
- involved in negative regulation of transcription by RNA polymerase II (IMP, IGI, IPI)
- involved in nucleophagy (IMP)
- involved in positive regulation of macroautophagy (IMP)
- involved in positive regulation of transcription by RNA polymerase II (IMP, IGI)
- involved in protein localization to nucleolar rDNA repeats (IMP)
- involved in rDNA chromatin condensation (IMP)
- involved in regulation of DNA-templated DNA replication initiation (IMP, IGI)
- involved in regulation of transcription by RNA polymerase II (IGI, IPI)
- involved in transcription elongation by RNA polymerase II (IGI)
Cellular Component
- Manually Curated
- part of histone deacetylase complex (IDA)
- located in nuclear periphery (IDA)
- part of Rpd3L complex (IDA, HDA)
- part of Rpd3L-Expanded complex (HDA)
- part of Rpd3S complex (IDA)
- part of Sin3-type complex (IDA)
- part of Snt2C complex (HDA)
Complex
Macromolecular complex annotations are imported from the Complex Portal. These annotations have been derived from physical molecular interaction evidence extracted from the literature and cross-referenced in the entry, or by curator inference from information on homologs in closely related species or by inference from scientific background.
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 mutants grow slowly, have abnormal vacuolar morphology, altered silencing, are impaired in respiration, mitotic recombination, mating, and are sensitive to heat and anoxia; null mutants also show increased recombination at hotspots
Classical Genetics
- null
- autophagy: increased
- chemical compound excretion: increased
- endocytosis: premature
- innate thermotolerance: decreased
- mating efficiency: decreased
- meiotic recombination: increased
- mitophagy: delayed
- mitotic recombination: decreased
- nutrient uptake: decreased rate
- oxidative stress resistance: increased
- protein/peptide accumulation: decreased
- protein/peptide modification: decreased
- protein/peptide modification: increased
- replicative lifespan: increased
- resistance to chemicals: decreased
- respiratory growth: absent
- RNA accumulation: decreased
- silencing: decreased
- silencing: increased
- vacuolar transport: decreased
- vegetative growth: decreased
- unspecified
- null
- anaerobic growth: decreased
- chemical compound accumulation: decreased
- chemical compound excretion: increased
- heat sensitivity: increased
- metal resistance: increased
- resistance to chemicals: decreased
- transposable element transposition: increased
- vacuolar morphology: abnormal
- vegetative growth: decreased rate
- viable
- reduction of function
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.
- Summary
- Rpd3p interacts physically with proteins involved in transcription; RPD3 interacts genetically with genes involved in transcription
2089 total interactions for 1061 unique genes
Physical Interactions
- Affinity Capture-MS: 215
- Affinity Capture-RNA: 8
- Affinity Capture-Western: 53
- Biochemical Activity: 6
- Co-localization: 6
- Co-purification: 5
- Reconstituted Complex: 8
- Two-hybrid: 3
Genetic Interactions
- Dosage Growth Defect: 4
- Dosage Lethality: 497
- Dosage Rescue: 3
- Negative Genetic: 601
- Phenotypic Enhancement: 36
- Phenotypic Suppression: 65
- Positive Genetic: 219
- Synthetic Growth Defect: 175
- Synthetic Lethality: 115
- Synthetic Rescue: 70
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
- Rpd3p is a histone deactylase of the Rpd3 class I histone deacetylase complex (HDAC). The Rpd3 complex deacetylates histones and regulates gene expression by limiting the accessibility of transcriptional factors to bind the underlying DNA. Deletion of RPD3 increases histone acetylation and thus gene expression, in vivo, particularly at histone H4 lysine positions 5 and 12, increases telomeric repression of transcription and plays a role in life span extension. Rpd3 negatively regulates meiosis and is required for repression of certain meiotic genes during vegetative growth. In diploid cells, mutations in RPD3 cause defects in mitotic recombination and in sporulation. Two distinct Rpd3 complexes have been identified: a small Rpd3S complex and a large Rpd3L complex. These two complexes share the three subunits, Rpd3p, Sin3p, and Ume1p in common.
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: 2000-01-06
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.