HCM1 / YCR065W Overview
- Standard Name
- HCM1 1
- Systematic Name
- YCR065W
- SGD ID
- SGD:S000000661
- Feature Type
- ORF , Verified
- Description
- Forkhead transcription factor; drives S-phase activation of genes involved in chromosome segregation, spindle dynamics, budding; also activates genes involved in respiration, use of alternative energy sources, NAD synthesis, oxidative stress resistance; regulated by cell wall integrity checkpoint; key factor in early adaptation to nutrient deficiency and diauxic shift; suppressor of calmodulin mutants with specific SPB assembly defects; ortholog of C. elegans lifespan regulator PHA-4 1 2 3 4 5
- Name Description
- High-Copy suppressor of Calmodulin 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.
- Length (a.a.)
- 564
- Mol. Weight (Da)
- 63645.9
- Isoelectric Point
- 7.38
- Median Abundance (molecules/cell)
- 1160 +/- 931
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 HCM1 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 transcription factor involved in spindle pole body organization, mitochondrion organization, and the cellular response to oxidative stress
View computational annotations
Molecular Function
- Manually Curated
- enables DNA-binding transcription factor activity (IDA, IMP)
- enables mitochondrial transcription factor activity (IMP)
- enables sequence-specific DNA binding (HDA)
Biological Process
- Manually Curated
- involved in cellular response to oxidative stress (IMP)
- involved in mitochondrion organization (IMP)
- involved in positive regulation of transcription by RNA polymerase II (IDA)
- involved in regulation of mitochondrial transcription (IMP)
- involved in spindle pole body organization (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.
Classical Genetics
- null
- chromosome/plasmid maintenance: abnormal
- colony sectoring: increased
- innate thermotolerance: decreased
- oxidative stress resistance: decreased
- protein activity: decreased
- protein/peptide modification: increased
- replicative lifespan: decreased
- resistance to chemicals: decreased
- RNA accumulation: abnormal
- vegetative growth: decreased
- viable
- overexpression
- growth in exponential phase: decreased rate
- innate thermotolerance: increased
- mitochondrial genome maintenance: abnormal
- oxidative stress resistance: increased
- protein activity: decreased
- protein activity: increased
- protein/peptide accumulation: increased
- protein/peptide modification: decreased
- replicative lifespan: increased
- respiratory growth: increased rate
- null
- cell cycle progression through the G2/M phase transition: delayed
- cell size: increased
- chemical compound accumulation: abnormal
- chronological lifespan: decreased
- competitive fitness: decreased
- haploinsufficient
- haploproficient
- heat sensitivity: increased
- prion formation: increased
- replicative lifespan: decreased
- resistance to chemicals: decreased
- resistance to chemicals: increased
- respiratory growth: decreased rate
- telomere length: increased
- toxin resistance: increased
- 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.
564 total interactions for 306 unique genes
Physical Interactions
- Affinity Capture-MS: 7
- Affinity Capture-RNA: 9
- Affinity Capture-Western: 2
- Biochemical Activity: 7
- Co-localization: 1
- Co-purification: 1
- Two-hybrid: 3
Genetic Interactions
- Dosage Lethality: 1
- Dosage Rescue: 8
- Negative Genetic: 413
- Phenotypic Enhancement: 9
- Phenotypic Suppression: 1
- Positive Genetic: 65
- Synthetic Growth Defect: 21
- Synthetic Lethality: 11
- Synthetic Rescue: 5
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
- HCM1 is a member of the winged helix-turn-helix/forkhead family of transcription factors, and regulates the late S-phase specific expression of genes involved in chromosome segregation, spindle dynamics, and budding. The Hcm1p consensus site is 5'-ATAAACAA-3', and Hcm1p binds upstream of genes for such proteins as microtubule binder Ase1p, kinase Cdc15p, formin Bni1p, and tropomyosin Tpm1p. Hcm1p also drives the expression of FKH1, FKH2, and NDD1, which encode M-phase specific transcription factors required for the subsequent temporal wave of cell cycle regulated transcription, and two cell cycle specific transcriptional repressors WHI5 and YHP1. The HCM1 gene is cell cycle regulated, with peak expression in G1; abundance of Hcm1p reflects a similar periodicity. The HCM1 promoter contains binding sites for late G1 transcription factor complexes MBF (Swi4p-Swi6p) and SBF (Mbp1p-Swi6p), and is subject to redundant positive regulation by both. Hcm1p is also post-translationally regulated and is an efficient substrate of Cdc28p-Clb2p.
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: 2007-01-25
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.