HAP2 (YGL237C) is the NF-YA-type subunit of the budding yeast CCAAT-binding factor (Hap2/3/4/5 complex). It is a nuclear protein of 265 residues. A conserved core contains a subunit-association domain and a short basic DNA-recognition region, and the rest of the protein is largely disordered. HAP2 assembles with HAP3 (NF-YB type) and HAP5 (NF-YC type) in a one-step pathway into a heterotrimer that recognises the 5'-CCAAT-3' box in upstream activation sites such as UAS2 of CYC1. Short regions of HAP2 and HAP3 together form a hybrid DNA-binding domain, and none of the three subunits binds DNA alone. The DNA-bound heterotrimer recruits the activation subunit HAP4, which supplies the transcriptional activation domains. The assembled complex activates RNA polymerase II transcription of genes for mitochondrial electron transport and respiration when cells grow on nonfermentable carbon sources. hap2 mutants have reduced levels of all cytochromes and grow slowly on glycerol.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0000978 RNA polymerase II cis-regulatory region sequence-specific DNA binding | IDA PMID:7828851 Cloning of yeast HAP5: a novel subunit of a heterotrimeric c... | ACCEPT | Summary: Purified recombinant HAP2, HAP3 and HAP5 together reconstitute CCAAT-binding activity in mobility-shift assays, and all three subunits are required. The contributes_to qualifier is the right one, because HAP2 recognises the CCAAT box only within the heterotrimer. Reason: Direct biochemical evidence in S. cerevisiae shows that HAP2 contributes to sequence-specific binding of Pol II promoter CCAAT elements (UAS2 of CYC1). Mutagenesis maps a 21-residue HAP2 DNA-binding region in which R199L changes the sequence specificity (PMID:8223474). This is the core molecular contribution of HAP2. Supporting Evidence: PMID:7828851 purified recombinant HAP2, HAP3, and HAP5 are able to reconstitute CCAAT-binding activity in mobility shift analysis PMID:7828851 the HAP2/3/5 heterotrimer represents a unique DNA-binding factor in which all three subunits of the complex are absolutely required for DNA-binding activity PMID:8223474 Mutation of an arginine at position 199 to leucine alters the DNA-binding specificity of the complex to favor CCAAC over CCAAT. |
| GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific | IBA GO_REF:0000033 | ACCEPT | Summary: This IBA comes from PAINT node PTN000290575 (NF-YA/HAP2), whose experimental donors include yeast HAP2 itself, human NFYA and mouse Nfya. PANTHER 19 places HAP2 in PTHR12632:SF6 with human NFYA. Reason: The node placement is sound. Every characterised NF-YA/HAP2 subunit acts as part of a sequence-specific Pol II transcription factor, and HAP2 carries its own experimental evidence for this activity (IDA, contributes_to GO:0001228). HAP2 does not bind DNA alone, so its contribution is as a subunit, as the IDA rows record. That HAP2 appears in the WITH/FROM list is expected, not circular. The PAINT curator placed the generic activity term at this node rather than the activator-specific child, which fits NF-Y acting as both activator and repressor across the family. Supporting Evidence: file:yeast/HAP2/HAP2-bioinformatics/RESULTS.md HAP2, NCU03033 and human NFYA are all placed in the same PANTHER subfamily, PMID:7828851 the HAP2/3/5 heterotrimer represents a unique DNA-binding factor in which all three subunits of the complex are absolutely required for DNA-binding activity |
| GO:0001228 DNA-binding transcription activator activity, RNA polymerase II-specific | IDA PMID:2832951 Yeast HAP2 and HAP3: transcriptional activators in a heterom... | ACCEPT | Summary: HAP2 and HAP3 copurify with UAS2-binding activity and form a multisubunit activation complex without DNA. In S. cerevisiae this complex activates CYC1 UAS2 and other respiratory genes. Reason: This is the core activity of the yeast complex. The contributes_to qualifier is appropriate. HAP4 supplies the activation domains (PMID:16278450, PMID:15075264), and UniProt describes HAP2 as primarily structural, so HAP2 contributes the DNA-recognition and assembly functions of an activator complex. The activator direction is established in yeast. It should not be transferred automatically to relatives that lack a HAP4-type subunit. Supporting Evidence: PMID:2832951 HAP2 and HAP3 associate in the absence of DNA to form a multisubunit activation complex PMID:16278450 The Hap4p subunit contains the transcriptional activation domain necessary for stimulating transcription after interacting with Hap2p/Hap3p/Hap5p. file:yeast/HAP2/HAP2-uniprot.txt HAP2 has primarily a structural role in the HAP |
| GO:0003677 DNA binding | IEA GO_REF:0000002 | TOO GENERAL | Summary: InterPro2GO mapping from the CCAAT-binding factor conserved-site signature. Reason: The claim is true at the level of the complex, but the accepted GO:0000978 RNA polymerase II cis-regulatory region sequence-specific DNA binding (contributes_to, IDA) already entails it. HAP2 does not bind DNA as an isolated polypeptide. Supporting Evidence: PMID:7828851 all three subunits of the complex are absolutely required for DNA-binding activity |
| GO:0003700 DNA-binding transcription factor activity | IEA GO_REF:0000002 | TOO GENERAL | Summary: InterPro2GO mapping from the NFYA family signature (IPR001289). Reason: The term is correct for the complex HAP2 belongs to. It is entailed by GO:0000981 (IBA, accepted) and GO:0001228 (IDA, accepted), which specify Pol II and the activator role. Supporting Evidence: file:yeast/HAP2/HAP2-uniprot.txt Belongs to the NFYA/HAP2 subunit family. |
| GO:0005515 protein binding | IPI PMID:10688190 A comprehensive analysis of protein-protein interactions in ... | REMOVE | Summary: HAP2 interacts with HAP5 (Q02516) in a genome-wide yeast two-hybrid screen. Reason: Generic protein binding is uninformative. The HAP2-HAP5 interaction is real. It reflects assembly of the CCAAT-binding heterotrimer, which the accepted GO:0016602 CCAAT-binding factor complex annotations already capture. Removal does not mean the interaction is false. |
| GO:0005515 protein binding | IPI PMID:11805837 Systematic identification of protein complexes in Saccharomy... | REMOVE | Summary: HAP2 copurifies with HAP5 in a high-throughput affinity purification and mass-spectrometry survey of yeast complexes. Reason: Generic protein binding is uninformative. The interaction reflects subunit assembly of the CCAAT-binding factor, which GO:0016602 captures. |
| GO:0005515 protein binding | IPI PMID:16278450 Assembly of the Hap2p/Hap3p/Hap4p/Hap5p-DNA complex in Sacch... | REMOVE | Summary: McNabb and Pinto (2005) showed that Hap2p, Hap3p and Hap5p assemble in a one-step pathway that requires all three subunits at once. Reason: Generic protein binding is uninformative. The assembly data show heterotrimer formation, and the IPI-based GO:0016602 CCAAT-binding factor complex row from the same paper records it. No more specific MF term, such as a bridging or adaptor activity, is warranted. Supporting Evidence: PMID:16278450 Hap2p, Hap3p, and Hap5p assemble via a one-step pathway requiring all three subunits simultaneously |
| GO:0005515 protein binding | IPI PMID:16429126 Proteome survey reveals modularity of the yeast cell machine... | REMOVE | Summary: HAP2 copurifies with HAP5 in a proteome-wide TAP-MS survey. Reason: Generic protein binding is uninformative. The complex membership is captured by GO:0016602. |
| GO:0005515 protein binding | IPI PMID:21179020 Defining the budding yeast chromatin-associated interactome. | REMOVE | Summary: A chromatin-associated interactome affinity-purification survey detected HAP2 with HAP5. Reason: Generic protein binding is uninformative. The complex membership is captured by GO:0016602. |
| GO:0005634 nucleus | HDA PMID:11914276 Subcellular localization of the yeast proteome. | ACCEPT | Summary: A proteome-wide localisation screen places HAP2 in the nucleus. Reason: The screen agrees with the early single-gene study in which a HAP2-beta-galactosidase fusion localised to the nucleus. A nuclear location fits a CCAAT-binding transcription factor subunit. Supporting Evidence: PMID:3547076 a bifunctional HAP2-beta-galactosidase fusion gene was localized to the yeast nucleus |
| GO:0005634 nucleus | IEA GO_REF:0000044 | ACCEPT | Summary: UniProt subcellular-location mapping (Nucleus). Reason: The experimental nuclear localisation of a HAP2 fusion in yeast agrees with this mapping. Supporting Evidence: PMID:3547076 a bifunctional HAP2-beta-galactosidase fusion gene was localized to the yeast nucleus |
| GO:0006109 regulation of carbohydrate metabolic process | NAS PMID:16278450 Assembly of the Hap2p/Hap3p/Hap4p/Hap5p-DNA complex in Sacch... | KEEP AS NON CORE | Summary: This curator statement reflects that the HAP complex activates genes in response to growth on nonfermentable carbon sources. Reason: The yeast CCAAT-binding factor mediates carbon-source-dependent derepression, but its documented targets are mainly respiratory and mitochondrial electron transport genes rather than carbohydrate-metabolism enzymes as such. The term is a broad physiological consequence of the transcriptional activity, not a separate function. I keep it as non-core and yeast-specific. It is not a candidate for transfer by homology. Supporting Evidence: PMID:7828851 The CCAAT-binding factor of Saccharomyces cerevisiae activates the transcription of these genes in response to growth in a nonfermentable carbon source. |
| GO:0006355 regulation of DNA-templated transcription | IEA GO_REF:0000002 | MODIFY | Summary: InterPro2GO mapping from the NFYA family signature. Reason: The term is correct but general. HAP2 has experimental support (IDA) for the more specific GO:0045944 positive regulation of transcription by RNA polymerase II, which the gene already carries. Proposed replacements: positive regulation of transcription by RNA polymerase II Supporting Evidence: PMID:2832951 HAP2 and HAP3 associate in the absence of DNA to form a multisubunit activation complex |
| GO:0006355 regulation of DNA-templated transcription | NAS PMID:16278450 Assembly of the Hap2p/Hap3p/Hap4p/Hap5p-DNA complex in Sacch... | MODIFY | Summary: This curator statement is based on HAP2 being a subunit of the CCAAT-binding transcriptional activator. Reason: The term is correct but general. The gene already carries the more specific GO:0045944 positive regulation of transcription by RNA polymerase II (IDA). Proposed replacements: positive regulation of transcription by RNA polymerase II Supporting Evidence: PMID:16278450 The CCAAT-binding factor (CBF) is an evolutionarily conserved multimeric transcriptional activator in eukaryotes. |
| GO:0006357 regulation of transcription by RNA polymerase II | IBA GO_REF:0000033 | MODIFY | Summary: This IBA comes from PAINT node PTN000290575, with donors that include yeast HAP2, human NFYA, mouse Nfya and a C. elegans member. Reason: The node placement and term are correct for the family. The PAINT curator chose the direction-neutral term, consistent with NF-Y acting as both activator and repressor in other lineages. For S. cerevisiae HAP2 itself, though, the evidence supports the more specific GO:0045944 positive regulation of transcription by RNA polymerase II (IDA), which the gene already carries. The general IBA term remains the right level for transfer to relatives in PTHR12632:SF6, such as N. crassa NCU03033. Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN000290575 SUPPORTS TRANSFER The NF-YA/HAP2 ancestral node is correctly placed, and HAP2 is an experimental donor to it. The MODIFY only refines the yeast gene to the activator-specific child term and does not dispute the inheritance. Proposed replacements: positive regulation of transcription by RNA polymerase II Supporting Evidence: file:yeast/HAP2/HAP2-bioinformatics/RESULTS.md HAP2, NCU03033 and human NFYA are all placed in the same PANTHER subfamily, PMID:2832951 HAP2 and HAP3 associate in the absence of DNA to form a multisubunit activation complex |
| GO:0016602 CCAAT-binding factor complex | IBA GO_REF:0000033 | ACCEPT | Summary: This IBA comes from PAINT node PTN000290576, with donors from yeast, human, rat, fly and worm NF-YA members. Reason: Membership of the NF-Y/HAP CCAAT-binding complex is the defining, ancestral property of NF-YA/HAP2 subunits. HAP2 has its own IDA and IPI support for this location, and it belongs to the same PANTHER subfamily (SF6) as human NFYA. Supporting Evidence: file:yeast/HAP2/HAP2-bioinformatics/RESULTS.md HAP2, NCU03033 and human NFYA are all placed in the same PANTHER subfamily, PMID:16278450 The Hap2p/Hap3p/Hap5p heterotrimer is the DNA-binding component of the complex |
| GO:0016602 CCAAT-binding factor complex | IDA PMID:2832951 Yeast HAP2 and HAP3: transcriptional activators in a heterom... | ACCEPT | Summary: LexA-HAP2 copurifies with HAP3-beta-galactosidase and UAS2-binding activity. Reason: This is direct biochemical evidence that HAP2 is a subunit of the yeast CCAAT-binding factor. Supporting Evidence: PMID:2832951 The copurification of LexA-HAP2, HAP3 beta-galactosidase, and UAS2 binding activity shows that HAP2 and HAP3 associate in the absence of DNA |
| GO:0016602 CCAAT-binding factor complex | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro2GO mapping from the CCAAT-binding factor conserved-site signature. Reason: The mapping agrees with the experimental evidence for complex membership. Supporting Evidence: PMID:7828851 These data suggest that the HAP2/3/5 heterotrimer represents a unique DNA-binding factor |
| GO:0016602 CCAAT-binding factor complex | IPI PMID:16278450 Assembly of the Hap2p/Hap3p/Hap4p/Hap5p-DNA complex in Sacch... | ACCEPT | Summary: The paper reconstructs assembly of the Hap2/3/5 heterotrimer and the DNA-dependent recruitment of Hap4. Reason: This is direct evidence for HAP2 as a core subunit of the four-subunit yeast CCAAT-binding factor. Supporting Evidence: PMID:16278450 In Saccharomyces cerevisiae, the CCAAT-binding factor is composed of four subunits, termed Hap2p, Hap3p, Hap4p, and Hap5p. PMID:16278450 the interaction of Hap4p with Hap2p/Hap3p/Hap5p requires DNA binding as a prerequisite |
| GO:0016602 CCAAT-binding factor complex | IPI PMID:2832951 Yeast HAP2 and HAP3: transcriptional activators in a heterom... | ACCEPT | Summary: HAP2 associates with HAP3 (SGD:S000000117) in the absence of DNA. Reason: HAP2-HAP3 association is the founding evidence for the heteromeric CCAAT-binding complex. Supporting Evidence: PMID:2832951 HAP2 and HAP3 associate in the absence of DNA to form a multisubunit activation complex |
| GO:0043457 regulation of cellular respiration | IMP PMID:2182199 Effects of hap mutations on heme and cytochrome formation in... | KEEP AS NON CORE | Summary: hap2 mutants have all cytochromes reduced to about 40-50% of wild type, grow very slowly on glycerol and show a high frequency of [rho-] cells. Reason: The phenotype is real and is an expected consequence of HAP2's transcriptional activation of respiratory genes. It is established experimentally in S. cerevisiae only. The mechanism is captured by the transcription-activation terms. PAINT did not propagate this term to the NF-YA node, and the respiratory regulon depends on the HAP4 activation subunit, so this annotation should not be transferred to orthologs without species-specific evidence. Supporting Evidence: PMID:2182199 In hap2 and hap3 strains all cytochromes were decreased proportionally to about 40-50% of wild type values. PMID:2182199 whereas hap2 and hap3 mutants grew very slowly |
| GO:0045944 positive regulation of transcription by RNA polymerase II | IDA PMID:2832951 Yeast HAP2 and HAP3: transcriptional activators in a heterom... | ACCEPT | Summary: HAP2 is required, with HAP3, for activity of the CYC1 UAS2 and forms an activation complex with HAP3. A lexA-HAP2 fusion activates transcription from a lexA operator. Reason: This is the core biological process of HAP2 in yeast, positive regulation of Pol II transcription from CCAAT-containing UASs, with direct experimental support. Supporting Evidence: PMID:2832951 Activity of UAS2 requires both the HAP2 and HAP3 activators, which bind to UAS2 in an interdependent manner. PMID:3547076 a lexA-HAP2 fusion gene was capable of activating transcription when bound to a lexA operator site |
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Download this section (compressed HTML)Q: Does HAP2 also act in repression complexes (for example with HAP4-independent cofactors), as NF-YA does in metazoans, or is the yeast complex exclusively an activator?
Q: Is the CCAAT-binding factor that UniProt describes, citing PMID:11390369 (a Hap complex associated with Elongator), the same assembly as HAP2/3/5, or a differently named complex?
Experiment: Genome-wide ChIP-exo of HAP2 under fermentative and respiratory growth, in wild type and hap4 deletion strains. This would separate HAP4-independent CCAAT occupancy and transcriptional effects from HAP4-dependent activation.
Type: ChIP-seq
Subunit of the Hap2p/3p/4p/5p CCAAT-binding complex; complex is heme-activated and glucose-repressed; complex is a transcriptional activator and global regulator of respiratory gene expression; contains sequences sufficient for both complex assembly and DNA binding; respiratory defect of the null mutant is functionally complemented by human NFYA
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