TOD6 / YBL054W Overview
- Standard Name
- TOD6 1 2
- Systematic Name
- YBL054W
- SGD ID
- SGD:S000000150
- Aliases
- PBF1 4
- Feature Type
- ORF , Verified
- Description
- PAC motif binding protein involved in rRNA and ribosome biogenesis; subunit of the RPD3L histone deacetylase complex; Myb-like HTH transcription factor; hypophosphorylated by rapamycin treatment in a Sch9p-dependent manner; activated in stochastic pulses of nuclear localization 1 2 3 4 5 6
- Name Description
- Twin Of Dot6p 2
- Paralog
- DOT6 6
- 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
- PAC motif binding protein involved in rRNA and ribosome biogenesis; subunit of the RPD3L histone deacetylase complex; hypophosphorylated by rapamycin treatment in a Sch9p-dependent manner; activated in stochastic pulses of nuclear localization
- Length (a.a.)
- 525
- Mol. Weight (Da)
- 59239.9
- Isoelectric Point
- 9.93
- Median Abundance (molecules/cell)
- 2059 +/- 1047
- Half-life (hr)
- 3.3
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 TOD6 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 protein involved in regulation of RNA polymerase II transcription; subunit of the Rpd3L-Expanded chromatin remodeling histone deacetylase complex
View computational annotations
Molecular Function
- Manually Curated
- enables sequence-specific DNA binding (IDA, HDA)
Biological Process
- Manually Curated
- involved in regulation of transcription by RNA polymerase II (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.
Classical Genetics
- null
- 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.
- Summary
- The tod6 null mutant is viable; the null mutant of paralog dot6 is viable; the tod6 dot6 double mutant displays a phenotypic enhancement.
100 total interactions for 90 unique genes
Physical Interactions
- Affinity Capture-MS: 18
- Affinity Capture-RNA: 6
- Affinity Capture-Western: 2
- Biochemical Activity: 1
- Co-localization: 1
- Co-purification: 2
- Proximity Label-MS: 3
- Two-hybrid: 1
Genetic Interactions
- Dosage Growth Defect: 2
- Dosage Rescue: 6
- Negative Genetic: 42
- Phenotypic Enhancement: 1
- Phenotypic Suppression: 1
- Positive Genetic: 6
- Synthetic Growth Defect: 4
- Synthetic Lethality: 1
- Synthetic Rescue: 3
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
- TOD6 encodes transcription factor that binds PAC (RNA Pol A and C) motifs of the form 5'-GCGATGAGMT-3', which are present in roughly half of all promoters of genes involved in ribosome biogenesis. PAC sites function as Dot6p/Tod6p-dependent repressor elements under stress or poor nutrient conditions. Tod6p functions as a transcriptional repressor whose repressive activity is alleviated by phosphorylation in response to nitrogen availability. Sch9p responds to nitrogen availability and phosphorylates Tod6p. Nitrogen deprivation is thereby sufficient to cause repression of ribosome biogenesis. Tod6p appears to effect repression of ribosome biogenesis gene expression at least in part by recruitment of the Rpd3L histone deacetylase complex to ribosome biogenesis gene promoters. The TOR complex I (TORC1) regulates ribosome biogenesis through modulation of Sch9p activity, which affects Tod6p binding to ribosome biogenesis gene promoters.
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.