ABF2 / YMR072W Overview
- Standard Name
- ABF2 1
- Systematic Name
- YMR072W
- SGD ID
- SGD:S000004676
- Aliases
- p19 8 , HM 9 , mtTFA 4
- Feature Type
- ORF , Verified
- Description
- Mitochondrial DNA-binding and packaging factor; mtDNA maintenance factor involved in mitochondrial DNA replication and recombination, regulating mtDNA copy number in opposition to DPI34; HMG1 DNA-binding protein family member containing two HMG-boxes; activity may be regulated by protein kinase A phosphorylation; ABF2 has a paralog, IXR1, that arose from the whole genome duplication; human homolog TFAM can complement yeast abf2 mutant, rescuing the loss-of-mitochondrial DNA phenotype 1 2 3 4 5 6 7
- Name Description
- ARS-Binding Factor 1
- Paralog
- IXR1 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
- ABF2 has a paralog, IXR1, 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.)
- 183
- Mol. Weight (Da)
- 21575.0
- Isoelectric Point
- 10.24
- Median Abundance (molecules/cell)
- 14668 +/- 6733
- Half-life (hr)
- 9.6
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 ABF2 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
- DNA binding protein involved in maintenance of mitochondrial genome; localizes to mitochondrial nucleoid
View computational annotations
Molecular Function
- Manually Curated
- enables DNA binding (IDA)
- enables DNA binding, bending (IDA)
Biological Process
- Manually Curated
- involved in mitochondrial chromosome packaging (IMP)
- involved in mitochondrial genome maintenance (IMP)
- involved in mitochondrion inheritance (IMP)
Cellular Component
- Manually Curated
- located in mitochondrial chromosome (IDA)
- located in mitochondrial nucleoid (IDA)
- located in mitochondrion (HDA)
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 is incapable of respiratory growth, sensitive to hyperosmotic stress, and shows defects in mitochondrial genome maintenance; overexpression causes abnormal budding and cell cycle progression through G2 phase
Classical Genetics
- null
- colony size: decreased
- hyperosmotic stress resistance: decreased
- metal resistance: increased
- mitochondrial genome maintenance: abnormal
- mitochondrial genome maintenance: absent
- mitochondrial morphology: abnormal
- petite
- resistance to chemicals: decreased
- respiratory growth: absent
- respiratory growth: decreased
- RNA accumulation: decreased
- vegetative growth: decreased rate
- overexpression
- reduction of function
- null
- cell cycle progression in G1 phase: delayed
- chemical compound accumulation: abnormal
- chemical compound accumulation: decreased
- chemical compound accumulation: increased
- chemical compound excretion: increased
- chronological lifespan: decreased
- competitive fitness: decreased
- desiccation resistance: decreased
- heat sensitivity: increased
- mitochondrial genome maintenance: absent
- mutation frequency: increased
- oxidative stress resistance: increased
- resistance to chemicals: decreased
- resistance to chemicals: increased
- respiratory growth: absent
- respiratory growth: decreased rate
- stress resistance: increased
- utilization of carbon source: decreased
- utilization of carbon source: decreased rate
- utilization of nitrogen source: decreased rate
- vegetative growth: 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 abf2 null mutant is viable; the null mutant of paralog ixr1 is viable; the abf2 ixr1 double mutant has not been annotated for phenotype.
230 total interactions for 198 unique genes
Physical Interactions
- Affinity Capture-MS: 111
- Affinity Capture-RNA: 6
- Affinity Capture-Western: 6
- Co-crystal Structure: 1
- Co-fractionation: 1
- Co-localization: 1
- Co-purification: 1
- Cross-Linking-MS (XL-MS): 1
- PCA: 1
- Reconstituted Complex: 2
Genetic Interactions
- Dosage Rescue: 6
- Negative Genetic: 66
- Phenotypic Enhancement: 3
- Phenotypic Suppression: 2
- Positive Genetic: 17
- Synthetic Growth Defect: 4
- Synthetic Rescue: 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
- ABF2 encodes a mitochondrial DNA (mtDNA)-binding histone-like protein that is a member of HMG1 DNA-binding protein family and has two HMG1-Box domains, HMG1-Box A and B. Abf2p functions in mitochondrial genome maintenance and packaging by introducing sharp bends and superhelical turns into the mtDNA, and associates with mitochondrial nucleoids under conditions of low respiration. Glucose repression activates the phosphorylation of the N-terminal segment of HMG1-Box A by cAMP-dependent protein kinase (PKA), which inhibits the binding of Abf2p to DNA. Mutant cells carrying the abf2-T47A/S48A unphosphorylatable allele have a severe defect in the regulation of mtDNA content during glucose repression. This suggests that the phosphorylation of Abf2p via PKA may regulate its functions for the control of mtDNA content during the shift from gluconeogenic to fermentative growth. ABF2 is up-regulated in cells overexpressing the HCM1 winged helix-turn-helix/forkhead transcription factor, which regulates the late S-phase specific expression of genes involved in chromosome segregation, spindle dynamics, and budding. Moderate increases in ABF2 expression lead to comparable increases in mtDNA copy number, and deletion of ABF2 results in ~50% reduction in mtDNA copy number. ABF2 has paralog IXR1, and ABF2 expression is decreased in ixr1 null mutants. Caloric restriction represses the synthesis of Abf2p. ABF2 is the ortholog of mammalian mitochondrial Transcription Factor A (TFAM).
- Regulators
- 5
- Targets
- 0
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.