SSN3 / YPL042C Overview
- Standard Name
- SSN3 1
- Systematic Name
- YPL042C
- SGD ID
- SGD:S000005963
- Aliases
- CDK8 6 , RYE5 , GIG2 2 , NUT7 10 , SRB10 4 , UME5 7 , SSX7 8 , URR1 9
- Feature Type
- ORF , Verified
- EC Number
- 2.7.11.22, 2.7.11.23
- Description
- Component of the RNA polymerase II mediator complex; cyclin-dependent protein kinase involved in phosphorylation of the mediator component Pgd1p and suppression of transcription activation by RNA polymerase II; involved in glucose repression 2 3 4 5
- Name Description
- Suppressor of SNf1 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
- SSN3/YPL042C is located on the left arm of chromosome XVI between NOP4 and MRX11; coding sequence is 1668 nucleotides long with 9 SNPs, 2 of which cause amino acid polymorphisms
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 | CGD Synteny Browser
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
- Ssn3p is 555 amino acids long with 2 polymorphic residues, it is present at extremely low abundance.
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 SSN3 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
- Cyclin-dependent protein/serine threonine kinase; involved in phosphorylation of the RNA polymerase II C-terminal domain and regulation of transcription from RNA polymerase II promoters; involved in non-stop mRNA decay, protein destabilization, and negative regulation of filamentous growth; subunit of the mediator complex
View computational annotations
Molecular Function
- Manually Curated
- High-Throughput
- enables protein kinase activity (HDA)
Biological Process
- Manually Curated
- involved in negative regulation of filamentous growth (IMP, IGI)
- involved in negative regulation of transcription by RNA polymerase II (IPI, IMP)
- involved in nuclear-transcribed mRNA catabolic process, non-stop decay (IMP)
- involved in positive regulation of transcription by RNA polymerase II (IMP)
- involved in protein destabilization (IMP)
Cellular Component
- Manually Curated
- part of mediator complex (IDA)
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
- SSN3/YPL042C is a non-essential gene in reference strain S288C; null mutants are viable but display broad defects including decreased vegetative and respiratory growth and reduced competitive fitness. Cellular morphology and processes are altered, including abnormal vacuolar and lipid particle morphology, increased chitin deposition, enlarged cell size, and decreased endocytosis. Stress tolerance is compromised, with decreased resistance to UV, heat, desiccation, acidic pH, starvation, and metals. Developmental output is reduced, with lower sporulation efficiency. Genome-associated readouts include decreased transposable element transposition and increased telomere length.
Classical Genetics
- null
- chitin deposition: increased
- metal resistance: decreased
- protein/peptide accumulation: increased
- protein/peptide distribution: abnormal
- protein/peptide modification: increased
- resistance to chemicals: decreased
- resistance to chemicals: increased
- RNA accumulation: increased
- small molecule transport: increased
- vegetative growth: decreased
- unspecified
- null
- acid pH resistance: decreased
- cell size: increased
- chemical compound accumulation: abnormal
- chemical compound accumulation: increased
- chronological lifespan: decreased
- chronological lifespan: increased
- competitive fitness: decreased
- desiccation resistance: decreased
- endocytosis: decreased
- heat sensitivity: increased
- innate thermotolerance: decreased
- lipid particle morphology: abnormal
- metal resistance: decreased
- nutrient utilization: increased
- oxidative stress resistance: decreased
- oxidative stress resistance: increased
- protein/peptide accumulation: increased
- resistance to chemicals: decreased
- resistance to chemicals: increased
- respiratory growth: decreased rate
- RNA accumulation: increased
- sporulation efficiency: decreased
- starvation resistance: decreased
- stress resistance: decreased
- telomere length: increased
- toxin resistance: decreased
- transposable element transposition: decreased
- utilization of carbon source: decreased rate
- utilization of nitrogen source: decreased rate
- UV resistance: decreased
- vacuolar morphology: abnormal
- vegetative growth: decreased rate
- viable
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
- Ssn3p interacts physically with proteins involved in transcription; SSN3 interacts genetically with genes involved in transcription
604 total interactions for 396 unique genes
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
- SSN3 (also known as CDK8 or SRB10) encodes a subunit of the CDK8 kinase module (CKM) of the Mediator transcriptional regulation complex. The Mediator complex is highly conserved from yeast to human, and is a central player in the transcriptional regulation of protein-coding genes, being required for nearly all transcription by RNA polymerase II (RNAPII). Mediator bridges activators and the general transcription machinery. The core Mediator complex contains three distinct head, middle, and tail modules. The CKM is a dissociable subcomplex that represses basal transcription. The other three subunits of the CKM are encoded by SSN5/MED12/SRB8, SSN8/SRB11, and SSN2/MED13/SRB9. Formation of a Mediator-RNAPII holoenzyme is largely blocked by association of the CKM with the core Mediator complex. Interaction of the CKM with Mediator's middle module interferes with C-terminal domain (CTD)-dependent RNA polymerase II (RNAPII) binding and with the holoenzyme formation process. A combination of competitive interactions and conformational changes facilitate holoenzyme formation and underlie the mechanism of transcription regulation by Mediator. Obstruction of CTD-dependent RNAPII interaction with the middle module explains the repressive effect of the CKM on transcription.
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: 2026-01-27
All Curated Literature
All manually curated literature for the specified gene, shown as a count of references by year of publication followed by the most recent papers. Click "Literature Details" or "See all" to view all literature information for this locus, organized into topics according to their relevance to the gene (Primary Literature, Additional Literature, or Review).
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