SUB1 / YMR039C Overview
- Standard Name
- SUB1 1
- Systematic Name
- YMR039C
- SGD ID
- SGD:S000004642
- Aliases
- TSP1
- Feature Type
- ORF , Verified
- Description
- Transcriptional regulator; facilitates elongation through factors that modify RNAP II; role in peroxide resistance involving Rad2p; role in nonhomologous end-joining (NHEJ) of ds breaks in plasmid DNA, but not chromosomal DNA; role in the hyperosmotic stress response through polymerase recruitment at RNAP II and RNAP III genes; negatively regulates sporulation; protein abundance increases in response to DNA replication stress; functionally complemented by human SUB1 (PC4) 2 3 4 5 6 7
- Name Description
- SUppressor of TFIIB mutations 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
- Protein abundance increases in response to DNA replication stress
- Length (a.a.)
- 292
- Mol. Weight (Da)
- 33096.8
- Isoelectric Point
- 5.3
- Median Abundance (molecules/cell)
- 3798 +/- 972
- Half-life (hr)
- 10.0
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. Click "YeastMine" to view all alleles in YeastMine.
View all SUB1 alleles in SGD search | YeastMine
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
- Chromatin binding transcription coactivator; involved in positive regulation of transcription by RNA polymerase II and III; contributes to assembly of RNA polymerase III transcriptional preinitiation complex, double-strand break repair via NHEJ, and hyperosmotic response; localizes to nucleus
View computational annotations
Molecular Function
- Manually Curated
- enables chromatin binding (IDA)
- enables G-quadruplex DNA binding (IDA)
- enables transcription coactivator activity (ISS)
Biological Process
- Manually Curated
- involved in cellular response to pheromone (IMP)
- involved in cellular response to stress (IMP, IDA, IGI)
- involved in double-strand break repair via nonhomologous end joining (IMP)
- involved in hyperosmotic response (IGI)
- involved in negative regulation of ascospore formation (IMP)
- involved in positive regulation of transcription by RNA polymerase II (IMP)
- involved in positive regulation of transcription by RNA polymerase III (IDA, IMP, IGI)
- involved in positive regulation of transcription elongation by RNA polymerase II (IMP)
- involved in regulation of transcription by RNA polymerase II (IDA, IMP, IGI)
- involved in RNA polymerase III preinitiation complex assembly (IDA)
- involved in termination of RNA polymerase II transcription (IGI)
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 displays heat sensitivity, increased mutation frequency, sensitivity to oxidative stress, abnormal phosphorylation of RNA polymerase II, and reduced tRNA levels; in large-scale studies, null mutant shows reduced competitive fitness and slow utilization of galactose; diploid homozygous null mutant shows increased chronological lifespan and sporulation efficiency, and decreased resistance to oxidative stress, UV, desiccation, and heat shock; null mutant shows altered resistance to a variety of chemicals
Classical Genetics
- null
- chemical compound accumulation: abnormal
- chronological lifespan: decreased
- chronological lifespan: increased
- competitive fitness: decreased
- desiccation resistance: decreased
- haploinsufficient
- heat sensitivity: increased
- innate thermotolerance: decreased
- oxidative stress resistance: decreased
- oxidative stress resistance: increased
- resistance to chemicals: decreased
- resistance to chemicals: increased
- sporulation efficiency: increased
- toxin resistance: increased
- transposable element transposition: decreased
- utilization of carbon source: decreased rate
- UV resistance: decreased
- vacuolar morphology: abnormal
- vegetative growth: decreased rate
- viable
- unspecified
- 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.
652 total interactions for 468 unique genes
Physical Interactions
- Affinity Capture-MS: 42
- Affinity Capture-RNA: 6
- Affinity Capture-Western: 12
- Biochemical Activity: 3
- Co-localization: 5
- Far Western: 4
- Reconstituted Complex: 9
- Two-hybrid: 2
Genetic Interactions
- Dosage Growth Defect: 2
- Dosage Lethality: 4
- Dosage Rescue: 5
- Negative Genetic: 414
- Phenotypic Enhancement: 22
- Phenotypic Suppression: 7
- Positive Genetic: 65
- Synthetic Growth Defect: 30
- Synthetic Lethality: 9
- Synthetic Rescue: 11
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
- SUB1 encodes a stress-response transcription reinitiation factor that plays both positive and negative roles in transcription initiation. Sub1p is also involved in transcription elongation, mRNA 3' end processing, and downstream transcription processes. Sub1p contains a unique conserved non-specific DNA-binding domain, can bind tightly to melted or single-stranded DNA, and is involved in other DNA-dependent processes including replication, DNA repair, and chromatin organization. Sub1p is present at some RNAPII-transcribed genes and at all RNAPIII-transcribed genes. Sub1p helps TFIIIB and TFIIIC to assemble on tRNA genes, possibly through direct interactions with both basal factors since Sub1p interacts with TFIIIB subunit Bdp1p and with two TFIIIC subunits. Sub1p participates in distinct steps of RNAPIII transcription by stimulating both RNAPIII initiation and reinitiation.
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.