PHD1 / YKL043W Overview
- Standard Name
- PHD1 1
- Systematic Name
- YKL043W
- SGD ID
- SGD:S000001526
- Feature Type
- ORF , Verified
- Description
- Transcriptional activator that enhances pseudohyphal growth; physically interacts with the Tup1-Cyc8 complex and recruits Tup1p to its targets; regulates expression of FLO11, an adhesin required for pseudohyphal filament formation; similar to StuA, an A. nidulans developmental regulator; potential Cdc28p substrate; PHD1 has a paralog, SOK2, that arose from the whole genome duplication 1 2 3 4 5
- Name Description
- PseudoHyphal Determinant 1
- Paralog
- SOK2 5
- 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
- PHD1 has a paralog, SOK2, that arose from the whole genome duplication
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.
- Length (a.a.)
- 366
- Mol. Weight (Da)
- 40651.5
- Isoelectric Point
- 9.3
- Median Abundance (molecules/cell)
- 1267 +/- 916
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 PHD1 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
- Nuclear DNA-binding transcription factor involved in activation of RNA Pol II transcription and pseudohyphal growth
View computational annotations
Molecular Function
- Manually Curated
- enables DNA-binding transcription factor activity (IMP)
- enables sequence-specific DNA binding (HDA)
Biological Process
- Manually Curated
- involved in positive regulation of pseudohyphal growth (IMP)
- involved in positive 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
- overexpression
- null
- null
- biofilm formation: increased
- competitive fitness: normal
- filamentous growth: decreased
- invasive growth: absent
- replicative lifespan: decreased
- replicative lifespan: increased
- resistance to chemicals: decreased
- transposable element transposition: increased
- utilization of nitrogen source: 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.
- Summary
- The phd1 null mutant is viable; the null mutant of paralog sok2 is viable; the phd1 sok2 double mutant displays negative genetic interactions.
112 total interactions for 103 unique genes
Physical Interactions
- Affinity Capture-MS: 2
- Affinity Capture-RNA: 8
- Affinity Capture-Western: 2
- Biochemical Activity: 2
- Co-purification: 2
- Two-hybrid: 2
Genetic Interactions
- Dosage Growth Defect: 3
- Dosage Lethality: 5
- Dosage Rescue: 6
- Negative Genetic: 63
- Phenotypic Enhancement: 2
- Phenotypic Suppression: 1
- Positive Genetic: 13
- Synthetic Growth Defect: 1
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
- PHD1 encodes a transcription factor that is a member of the KilA-N family. Phd1p binds to the promoters of many genes involved in filamentous growth, including FLO11, and genetic evidence indicates that it acts primarily as an activator. Phd1p interacts with the Tup1p-Cyc8p general transcriptional repressor complex, and may recruit Tup1p-Cyc8p to certain sites. PHD1 transcription is apparently controlled by six regulators of filamentous growth (Tec1p, Ste12p, Sok2p, Mga1p, Flo8p, and Phd1p itself) that bind to the PHD1 promoter region. Phd1p activity is regulated by the cAMP-protein kinase A (PKA) pathway, and the Yak1p protein kinase is a central player in this regulation.
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.