BCY1 encodes the cAMP-binding regulatory subunit of budding-yeast protein kinase A. Bcy1 homodimerizes and binds Tpk1, Tpk2, and Tpk3 catalytic subunits to form the inactive PKA holoenzyme; cAMP binding relieves that inhibition and releases active catalytic kinase. Bcy1 is distributed between the nucleus and cytosol in a carbon-source- and phosphorylation-regulated manner, with additional chromatin and plasma-membrane-associated pools, and it gates Ras/cAMP/PKA signaling outputs that control nutrient-responsive growth, stress physiology, starvation responses, P-body assembly, and transcriptional programs. By keeping PKA inactive, Bcy1 is needed for entry into meiosis: bcy1 homozygous diploids undergo no premeiotic DNA replication and form no spores, and cells with a single copy of BCY1 commit to meiosis less well.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0000785 chromatin | IDA PMID:26403272 PKA-chromatin association at stress responsive target genes ... | KEEP AS NON CORE | Summary: PKA regulatory and catalytic subunits associate with stress-responsive promoters and coding regions in a stress-dependent manner. Reason: The chromatin row is supported by direct ChIP assays, but the chromatin-associated pool is a regulated nuclear pool rather than the defining Bcy1 activity. Supporting Evidence: PMID:26403272 PKA catalytic and regulatory subunits are associated with |
| GO:0004862 cAMP-dependent protein kinase inhibitor activity | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT places cAMP-dependent protein kinase inhibitor activity at the PTHR11635 root node, which correctly covers budding-yeast Bcy1. Reason: This is the conserved core molecular function of PKA regulatory subunits: Bcy1 binds Tpk catalytic subunits in an inactive PKA holoenzyme and cAMP binding releases active kinase. Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN004280545 · PTHR11635 root PKA regulatory-chain IBD SUPPORTS TRANSFER The PTHR11635 root carries the conserved inhibitor, cAMP-binding, PKA-catalytic-subunit-binding, and PKA-complex assertions. Bcy1 is the experimentally characterized S. cerevisiae member. Supporting Evidence: PMID:3037314 encodes a regulatory subunit of the cyclic AMP-dependent protein kinase |
| GO:0004862 cAMP-dependent protein kinase inhibitor activity | IDA PMID:3037314 Cloning and characterization of BCY1, a locus encoding a reg... | ACCEPT | Summary: The original cloning paper established BCY1 as the yeast PKA regulatory-subunit gene. Reason: The cloned BCY1 locus encodes the cAMP-dependent PKA regulatory subunit that inhibits the catalytic subunits in the inactive holoenzyme. Supporting Evidence: PMID:3037314 encodes a regulatory subunit of the cyclic AMP-dependent protein kinase |
| GO:0004862 cAMP-dependent protein kinase inhibitor activity | IMP PMID:6292221 Characterization of cyclic AMP-requiring yeast mutants alter... | ACCEPT | Summary: The CYR3/BCY1 mutant had altered cAMP responsiveness of PKA, supporting BCY1 as the PKA regulatory subunit. Reason: The CYR3/BCY1 phenotype resulted from a structural mutation in the gene encoding the PKA regulatory subunit; altered activation by cAMP is the expected behavior for impaired regulatory-subunit inhibition. Supporting Evidence: PMID:6292221 the CYR3 gene coding for the regulatory subunit |
| GO:0005515 protein binding | IPI PMID:10688190 A comprehensive analysis of protein-protein interactions in ... | MODIFY | Summary: The reported binding partner is Tpk3, a PKA catalytic subunit, so the row should not remain at generic protein binding. Reason: Bcy1 binding to Tpk catalytic subunits is a specific conserved activity used to form the inactive PKA holoenzyme. Replace this generic high-throughput interaction row with protein kinase A catalytic subunit binding. Proposed replacements: protein kinase A catalytic subunit binding Supporting Evidence: file:yeast/BCY1/BCY1-uniprot.txt CC P07278; P05986: TPK3; NbExp=5; IntAct=EBI-9475, EBI-9470; |
| GO:0005515 protein binding | IPI PMID:11805837 Systematic identification of protein complexes in Saccharomy... | MODIFY | Summary: The HMS-PCI row reports Bcy1 association with the Tpk3 PKA catalytic subunit. Reason: The interaction is the PKA regulatory-subunit to PKA catalytic-subunit association; the narrower PKA catalytic subunit binding term captures the same molecular function more informatively. Proposed replacements: protein kinase A catalytic subunit binding Supporting Evidence: file:yeast/BCY1/BCY1-uniprot.txt CC P07278; P05986: TPK3; NbExp=5; IntAct=EBI-9475, EBI-9470; |
| GO:0005515 protein binding | IPI PMID:11805837 Systematic identification of protein complexes in Saccharomy... | MODIFY | Summary: The HMS-PCI row reports Bcy1 association with the Tpk1 PKA catalytic subunit. Reason: Tpk1 is one of the three PKA catalytic subunits bound by the Bcy1 regulatory subunit. This row should use PKA catalytic subunit binding rather than an uninformative parent interaction term. Proposed replacements: protein kinase A catalytic subunit binding Supporting Evidence: PMID:16924114 PKA is an inactive tetramer composed of two regulatory subunits and two catalytic subunits |
| GO:0005515 protein binding | IPI PMID:11805837 Systematic identification of protein complexes in Saccharomy... | MODIFY | Summary: The HMS-PCI row reports Bcy1 association with the Tpk2 PKA catalytic subunit. Reason: Tpk2 is a PKA catalytic subunit, so this physical interaction is a direct instance of the PKA catalytic subunit binding function inherited through PAINT for this family. Proposed replacements: protein kinase A catalytic subunit binding Supporting Evidence: file:yeast/BCY1/BCY1-uniprot.txt CC P07278; P06245: TPK2; NbExp=7; IntAct=EBI-9475, EBI-9465; |
| GO:0005515 protein binding | IPI PMID:11805837 Systematic identification of protein complexes in Saccharomy... | REMOVE | Summary: The reported Ess1 co-complex interaction is generic and does not identify a specific Bcy1 molecular function. Reason: Ess1 is not a PKA catalytic subunit, and this high-throughput physical interaction does not support any more informative Bcy1 activity. Removing the generic protein binding row rejects an uninformative GO molecular function, not the existence of an Ess1 edge. Supporting Evidence: file:yeast/BCY1/BCY1-uniprot.txt CC P07278; P22696: ESS1; NbExp=2; IntAct=EBI-9475, EBI-6679; |
| GO:0005515 protein binding | IPI PMID:16429126 Proteome survey reveals modularity of the yeast cell machine... | MODIFY | Summary: The AP-MS row reports Bcy1 association with the Tpk1 PKA catalytic subunit. Reason: Bcy1's interaction with Tpk1 is the specific regulatory-subunit to catalytic-subunit association of the PKA holoenzyme; GO:0034236 captures that function better than generic protein binding. Proposed replacements: protein kinase A catalytic subunit binding Supporting Evidence: PMID:16924114 PKA is an inactive tetramer composed of two regulatory subunits and two catalytic subunits |
| GO:0005515 protein binding | IPI PMID:16429126 Proteome survey reveals modularity of the yeast cell machine... | MODIFY | Summary: The AP-MS row reports Bcy1 association with the Tpk2 PKA catalytic subunit. Reason: Tpk2 is a PKA catalytic subunit. Bcy1's interaction with Tpk2 is therefore the specific catalytic-subunit-binding activity that enables holoenzyme-mediated PKA inhibition. Proposed replacements: protein kinase A catalytic subunit binding Supporting Evidence: file:yeast/BCY1/BCY1-uniprot.txt CC P07278; P06245: TPK2; NbExp=7; IntAct=EBI-9475, EBI-9465; |
| GO:0005515 protein binding | IPI PMID:16606443 Comparative analysis of Saccharomyces cerevisiae WW domains ... | REMOVE | Summary: This protein-microarray row reports binding to the prolyl isomerase Ess1, not to a PKA catalytic subunit. Reason: The Ess1 edge from the WW-domain screen is not evidence of Bcy1's conserved PKA regulatory activity and provides no more specific molecular-function term. Generic protein binding should be removed rather than retained as a Bcy1 function. Supporting Evidence: PMID:16606443 the interaction between Ess1 and Bcy1, a regulatory subunit of cAMP-dependent protein kinase A |
| GO:0005515 protein binding | IPI PMID:16924114 Kelch-repeat proteins interacting with the Galpha protein Gp... | MODIFY | Summary: The Gpa2/Krh study directly assayed regulation of the Bcy1-Tpk1 association. Reason: This paper specifically tests the Bcy1-Tpk1 interaction. Replace the generic physical-interaction term with the precise PKA catalytic subunit binding term. Proposed replacements: protein kinase A catalytic subunit binding Supporting Evidence: PMID:16924114 absence of Krh1/2 reduces the interaction between the catalytic and regulatory subunits of PKA in vivo |
| GO:0005515 protein binding | IPI PMID:18467557 An in vivo map of the yeast protein interactome. | MODIFY | Summary: The PCA row reports Bcy1 association with the Tpk1 PKA catalytic subunit. Reason: The physical interaction is between the PKA regulatory subunit and a PKA catalytic subunit, so it should be represented as GO:0034236 rather than generic protein binding. Proposed replacements: protein kinase A catalytic subunit binding Supporting Evidence: file:yeast/BCY1/BCY1-uniprot.txt CC P07278; P06244: TPK1; NbExp=8; IntAct=EBI-9475, EBI-9458; |
| GO:0005515 protein binding | IPI PMID:18467557 An in vivo map of the yeast protein interactome. | MODIFY | Summary: The PCA row reports Bcy1 association with the Tpk2 PKA catalytic subunit. Reason: The supporting partner is a PKA catalytic subunit. Narrow the generic row to PKA catalytic subunit binding. Proposed replacements: protein kinase A catalytic subunit binding Supporting Evidence: file:yeast/BCY1/BCY1-uniprot.txt CC P07278; P06245: TPK2; NbExp=7; IntAct=EBI-9475, EBI-9465; |
| GO:0005515 protein binding | IPI PMID:18719252 High-quality binary protein interaction map of the yeast int... | MODIFY | Summary: The high-throughput Y2H row reports Bcy1 binding to Tpk2. Reason: Tpk2 is a PKA catalytic subunit, so this binary interaction maps onto the same specific catalytic-subunit-binding activity that defines Bcy1's role in the PKA holoenzyme. Proposed replacements: protein kinase A catalytic subunit binding Supporting Evidence: file:yeast/BCY1/BCY1-uniprot.txt CC P07278; P06245: TPK2; NbExp=7; IntAct=EBI-9475, EBI-9465; |
| GO:0005515 protein binding | IPI PMID:20489023 A global protein kinase and phosphatase interaction network ... | MODIFY | Summary: The KPI row reports Bcy1 association with the Tpk3 PKA catalytic subunit. Reason: Bcy1 binding to Tpk3 is a regulatory-subunit to catalytic-subunit interaction of the PKA holoenzyme and should be curated as PKA catalytic subunit binding. Proposed replacements: protein kinase A catalytic subunit binding Supporting Evidence: file:yeast/BCY1/BCY1-uniprot.txt CC P07278; P05986: TPK3; NbExp=5; IntAct=EBI-9475, EBI-9470; |
| GO:0005515 protein binding | IPI PMID:20489023 A global protein kinase and phosphatase interaction network ... | MODIFY | Summary: The KPI row reports Bcy1 association with the Tpk1 PKA catalytic subunit. Reason: The Bcy1-Tpk1 edge is a specific PKA regulatory-subunit interaction. Replace generic protein binding with the catalytic-subunit binding term. Proposed replacements: protein kinase A catalytic subunit binding Supporting Evidence: file:yeast/BCY1/BCY1-uniprot.txt CC P07278; P06244: TPK1; NbExp=8; IntAct=EBI-9475, EBI-9458; |
| GO:0005515 protein binding | IPI PMID:20489023 A global protein kinase and phosphatase interaction network ... | MODIFY | Summary: The KPI row reports Bcy1 association with the Tpk2 PKA catalytic subunit. Reason: Tpk2 is a catalytic PKA subunit. Bcy1's interaction with Tpk2 is therefore the specific catalytic-subunit-binding activity that enables holoenzyme-mediated PKA inhibition. Proposed replacements: protein kinase A catalytic subunit binding Supporting Evidence: file:yeast/BCY1/BCY1-uniprot.txt CC P07278; P06245: TPK2; NbExp=7; IntAct=EBI-9475, EBI-9465; |
| GO:0005515 protein binding | IPI PMID:37968396 The social and structural architecture of the yeast protein ... | MODIFY | Summary: The AE-MS row reports Bcy1 association with the Tpk3 PKA catalytic subunit. Reason: The curated partner is the PKA catalytic subunit Tpk3; replace generic protein binding with the family-appropriate PKA catalytic subunit binding term. Proposed replacements: protein kinase A catalytic subunit binding Supporting Evidence: file:yeast/BCY1/BCY1-uniprot.txt CC P07278; P05986: TPK3; NbExp=5; IntAct=EBI-9475, EBI-9470; |
| GO:0005515 protein binding | IPI PMID:37968396 The social and structural architecture of the yeast protein ... | MODIFY | Summary: The AE-MS row reports Bcy1 association with the Tpk1 PKA catalytic subunit. Reason: The high-throughput Bcy1-TPK1 edge describes the PKA regulatory subunit binding a PKA catalytic subunit; this should use GO:0034236. Proposed replacements: protein kinase A catalytic subunit binding Supporting Evidence: file:yeast/BCY1/BCY1-uniprot.txt CC P07278; P06244: TPK1; NbExp=8; IntAct=EBI-9475, EBI-9458; |
| GO:0005515 protein binding | IPI PMID:37968396 The social and structural architecture of the yeast protein ... | MODIFY | Summary: The AE-MS row reports Bcy1 association with the Tpk2 PKA catalytic subunit. Reason: The interaction partner is a PKA catalytic subunit, making GO:0034236 the precise term for this Bcy1 row. Proposed replacements: protein kinase A catalytic subunit binding Supporting Evidence: file:yeast/BCY1/BCY1-uniprot.txt CC P07278; P06245: TPK2; NbExp=7; IntAct=EBI-9475, EBI-9465; |
| GO:0005634 nucleus | HDA PMID:11914276 Subcellular localization of the yeast proteome. | ACCEPT | Summary: The proteome-scale localization survey assigned Bcy1 to the nucleus, in agreement with direct Bcy1 immunofluorescence and live-cell imaging. Reason: Nuclear localization is an experimentally established, carbon-source-regulated location for budding-yeast Bcy1. Supporting Evidence: PMID:11134339 In glucose-grown cells, Bcy1 is almost exclusively nuclear |
| GO:0005634 nucleus | HDA PMID:22842922 Dissecting DNA damage response pathways by analysing protein... | ACCEPT | Summary: The replication-stress GFP screen assigned Bcy1 to the nucleus, matching targeted Bcy1 localization studies. Reason: This high-throughput nuclear row is consistent with several direct Bcy1 nuclear-localization studies. Supporting Evidence: PMID:18417610 The nuclear shift of Bcy1p requires the presence of Ksp1p, Kss1p, and Sks1p. |
| GO:0005634 nucleus | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT places nuclear activity on a fungal PKA-regulatory-subunit node, which fits the direct budding-yeast Bcy1 localization record. Reason: The PTN000908765 node is restricted to fungal descendants and is seeded by CGD, PomBase, and SGD members of PTHR11635. Bcy1 has direct organism-specific evidence for nuclear localization under glucose growth and filamentous-growth conditions. Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN000908765 · fungal PKA regulatory-chain nucleus IBD SUPPORTS TRANSFER The PAINT nucleus assertion is scoped to a fungal PKA regulatory-subunit node and agrees with direct S. cerevisiae evidence. Supporting Evidence: PMID:11134339 In glucose-grown cells, Bcy1 is almost exclusively nuclear |
| GO:0005634 nucleus | IDA PMID:11134339 Nucleocytoplasmic distribution of budding yeast protein kina... | ACCEPT | Summary: Bcy1 was almost exclusively nuclear during glucose growth. Reason: Live-cell Bcy1-GFP imaging directly established nuclear localization of Bcy1 and showed that its distribution changes with carbon source. Supporting Evidence: PMID:11134339 In glucose-grown cells, Bcy1 is almost exclusively nuclear |
| GO:0005634 nucleus | IDA PMID:18417610 Analysis of the yeast kinome reveals a network of regulated ... | ACCEPT | Summary: Bcy1 shifts from a diffuse nuclear/cytoplasmic distribution to predominant nuclear localization during filamentous growth. Reason: The kinase-localization study independently supports nuclear localization as a regulated Bcy1 state. Supporting Evidence: PMID:18417610 The nuclear shift of Bcy1p requires the presence of Ksp1p, Kss1p, and Sks1p. |
| GO:0005634 nucleus | IDA PMID:3288487 Localization of the regulatory subunit of cAMP-dependent pro... | ACCEPT | Summary: Subcellular fractionation and immunofluorescence detected the cAMP-binding PKA regulatory subunit in the nuclear fraction. Reason: This early study used the bcy1 mutant as a control and directly supports Bcy1 nuclear localization. Supporting Evidence: PMID:3288487 The regulatory subunit was concentrated in a nuclear fraction in addition to a cytoplasmic fraction. |
| GO:0005634 nucleus | IEA GO_REF:0000120 | ACCEPT | Summary: The automated UniProt nuclear row is consistent with direct Bcy1 localization evidence. Reason: Direct immunofluorescence and Bcy1-GFP imaging place Bcy1 in the nucleus, so the automated nuclear location is appropriate. Supporting Evidence: PMID:11134339 In glucose-grown cells, Bcy1 is almost exclusively nuclear |
| GO:0005737 cytoplasm | HDA PMID:11914276 Subcellular localization of the yeast proteome. | ACCEPT | Summary: The proteome-scale localization survey assigned Bcy1 to the cytoplasm, a location supported by targeted Bcy1 studies. Reason: Bcy1 is cytoplasmic as well as nuclear, with phosphorylation of its N-terminal domain promoting cytoplasmic distribution in carbon-source-derepressed cells. Supporting Evidence: PMID:11134339 phosphorylation of its N-terminal domain directs Bcy1 to the cytoplasm |
| GO:0005737 cytoplasm | HDA PMID:22842922 Dissecting DNA damage response pathways by analysing protein... | ACCEPT | Summary: The replication-stress GFP screen assigned Bcy1 to the cytoplasm, which matches the established cytoplasmic Bcy1 pool. Reason: Direct Bcy1-GFP and biochemical data place a phosphorylated pool of Bcy1 in the cytoplasm. Supporting Evidence: PMID:11134339 phosphorylation of its N-terminal domain directs Bcy1 to the cytoplasm |
| GO:0005737 cytoplasm | IDA PMID:11134339 Nucleocytoplasmic distribution of budding yeast protein kina... | ACCEPT | Summary: Carbon-source derepression redistributes Bcy1 from a mostly nuclear pool toward the cytoplasm. Reason: The paper directly showed that phosphorylated Bcy1 is cytoplasmic and that N-terminal phosphorylation promotes cytoplasmic localization. Supporting Evidence: PMID:11134339 phosphorylation of its N-terminal domain directs Bcy1 to the cytoplasm |
| GO:0005737 cytoplasm | IEA GO_REF:0000120 | ACCEPT | Summary: The automated cytoplasm call agrees with direct Bcy1 fractionation and Bcy1-GFP localization experiments. Reason: Bcy1 is a soluble regulatory subunit with a cytoplasmic pool. Direct work supports cytoplasmic localization, so the IEA is sound. Supporting Evidence: PMID:3288487 The regulatory subunit was concentrated in a nuclear fraction in addition to a cytoplasmic fraction. |
| GO:0005829 cytosol | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT places cytosolic localization on a broad PKA regulatory-chain node. Reason: The cytosol inference is appropriate for Bcy1, a soluble regulatory subunit of the PKA holoenzyme with direct evidence for a cytoplasmic pool. Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN000180782 · broad PKA regulatory-chain cytosol IBD SUPPORTS TRANSFER The PTN000180782 cytosol placement is broader than fungi and fits Bcy1's regulated cytoplasmic distribution. Supporting Evidence: PMID:11134339 phosphorylation of its N-terminal domain directs Bcy1 to the cytoplasm |
| GO:0005886 plasma membrane | IDA PMID:2831892 Yeast cAMP-dependent protein kinase can be associated to the... | KEEP AS NON CORE | Summary: Purified plasma-membrane preparations contained the PKA regulatory subunit and cAMP-dependent PKA activity. Reason: The old biochemical study supports a plasma-membrane-associated Bcy1 pool, but this is peripheral to Bcy1's dominant soluble nuclear/cytosolic PKA regulatory role. Supporting Evidence: PMID:2831892 associated form of the regulatory subunit |
| GO:0005952 cAMP-dependent protein kinase complex | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT places PKA complex membership at the PTHR11635 root, correctly covering the Bcy1 regulatory subunit. Reason: Bcy1's defining role is to form the inactive PKA holoenzyme with Tpk catalytic subunits. The PTN004280545 complex placement captures that conserved role. Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN004280545 · PTHR11635 root PKA regulatory-chain IBD SUPPORTS TRANSFER PTHR11635 root placement for cAMP-dependent protein kinase regulatory subunits in the PKA holoenzyme. Supporting Evidence: PMID:16924114 PKA is an inactive tetramer composed of two regulatory subunits and two catalytic subunits |
| GO:0005952 cAMP-dependent protein kinase complex | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro maps the PKA regulatory-subunit family signatures to membership in the cAMP-dependent protein kinase complex. Reason: Bcy1 matches the PKA regulatory-chain family signatures and direct yeast evidence shows that Bcy1 is the regulatory subunit of the PKA holoenzyme. Supporting Evidence: file:yeast/BCY1/BCY1-uniprot.txt DR InterPro; IPR012198; cAMP_dep_PK_reg_su. file:yeast/BCY1/BCY1-uniprot.txt DR InterPro; IPR050503; cAMP-dep_PK_reg_su-like. |
| GO:0005952 cAMP-dependent protein kinase complex | NAS PMID:3037314 Cloning and characterization of BCY1, a locus encoding a reg... | ACCEPT | Summary: The BCY1 gene product is the regulatory subunit of cAMP-dependent PKA. Reason: The cloning paper identified BCY1 as the locus encoding the yeast cAMP-dependent PKA regulatory subunit, which functions as part of the PKA holoenzyme. Supporting Evidence: PMID:3037314 encodes a regulatory subunit of the cyclic AMP-dependent protein kinase |
| GO:0006995 cellular response to nitrogen starvation | IMP PMID:26947009 The signaling pathways underlying starvation-induced upregul... | KEEP AS NON CORE | Summary: PKA and TORC1 regulate Ams1 activity under nitrogen starvation, placing BCY1 in a starvation-response context. Reason: This row reflects a downstream nutrient-signaling output of Bcy1-mediated PKA regulation. It is plausible for BCY1 but secondary to the core cAMP-binding, Tpk-binding, and PKA-inhibitory activities. Supporting Evidence: PMID:26947009 protein kinase A and the target of rapamycin complex 1 pathways |
| GO:0007189 adenylate cyclase-activating G protein-coupled receptor signaling pathway | IBA GO_REF:0000033 | MODIFY | Summary: The PAINT-inherited process is biologically related to cAMP signaling but scopes Bcy1 onto the upstream GPCR-to-adenylate-cyclase arm. Reason: BCY1 acts downstream of Ras, Gpr1/Gpa2, and adenylate cyclase: cAMP binds Bcy1 and relieves PKA inhibition. The more precise process is negative regulation of cAMP/PKA signal transduction, not activation of adenylate cyclase by a GPCR. Propagation Review Root cause: TERM SCOPING PROBLEM Failure modes: GRANULARITY MISMATCH ROLE CONFLATION Sources checked: PANTHER:PTN000180782 · broad PKA regulatory-chain GPCR-pathway IBD SUPPORTS SOURCE BUT NOT TARGET The PTN000180782 placement groups genuine cAMP/PKA signaling genes, but GO:0007189 names an upstream receptor-to-adenylate-cyclase step. Proposed replacements: negative regulation of cAMP/PKA signal transduction Supporting Evidence: PMID:3037314 encodes a regulatory subunit of the cyclic AMP-dependent protein kinase |
| GO:0008603 cAMP-dependent protein kinase regulator activity | IEA GO_REF:0000120 | MODIFY | Summary: The automated row assigns a true but unnecessarily broad parent of Bcy1's specific PKA inhibitor activity. Reason: Bcy1 is not merely some kind of PKA regulator; it is the cAMP-binding regulatory subunit that inhibits PKA catalytic activity until cAMP binding releases the catalytic subunits. Propagation Review Root cause: TERM SCOPING PROBLEM Failure modes: GRANULARITY MISMATCH Sources checked: InterPro:IPR012198 SUPPORTS TRANSFER The PKA regulatory-subunit family source identifies the correct biology but maps only to a parent molecular-function term. Proposed replacements: cAMP-dependent protein kinase inhibitor activity Supporting Evidence: file:yeast/BCY1/BCY1-uniprot.txt DR InterPro; IPR012198; cAMP_dep_PK_reg_su. |
| GO:0009267 cellular response to starvation | IEA GO_REF:0000117 | MODIFY | Summary: The ARBA row points to a real starvation-response signaling context but stops at an overly broad starvation parent. Reason: BCY1 has direct SGD rows to glucose- and nitrogen-starvation responses through PKA control of P-body assembly and Ams1 regulation. Those children are more informative than the generic ARBA parent. Propagation Review Root cause: TERM SCOPING PROBLEM Failure modes: GRANULARITY MISMATCH SOURCE EVIDENCE WEAK Sources checked: ARBA:ARBA00034565 SOURCE WEAK OR INFERRED The ARBA mapping is an inferred generic parent, while BCY1 already has experimentally grounded child rows for glucose and nitrogen starvation contexts. Proposed replacements: cellular response to glucose starvation cellular response to nitrogen starvation Supporting Evidence: PMID:26947009 protein kinase A and the target of rapamycin complex 1 pathways |
| GO:0010603 regulation of cytoplasmic mRNA processing body assembly | IMP PMID:21925385 The cAMP-dependent protein kinase signaling pathway is a key... | KEEP AS NON CORE | Summary: The cAMP-PKA pathway inhibits larger P-body aggregate formation through Pat1 phosphorylation. Reason: Because Bcy1 restrains PKA catalytic activity, loss of BCY1 can affect this P-body assembly branch. The annotation is retained as a downstream glucose-starvation context rather than as Bcy1's core activity. Supporting Evidence: PMID:21925385 specifically inhibits the formation of the larger P body aggregates |
| GO:0016020 membrane | IEA GO_REF:0000117 | MODIFY | Summary: The generic membrane IEA is too broad for the old direct evidence of a peripheral plasma-membrane Bcy1 pool. Reason: Bcy1 is not an integral generic membrane protein. The available direct membrane evidence specifically describes the PKA regulatory subunit associated with purified plasma-membrane preparations, so plasma membrane is the better replacement term. Propagation Review Root cause: TERM SCOPING PROBLEM Failure modes: GRANULARITY MISMATCH SOURCE EVIDENCE WEAK Sources checked: ARBA:ARBA00028763 SOURCE WEAK OR INFERRED The ARBA inference is a generic membrane parent; the yeast-specific evidence points to plasma membrane. Proposed replacements: plasma membrane Supporting Evidence: PMID:2831892 associated form of the regulatory subunit |
| GO:0030552 cAMP binding | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT places cAMP binding on the PTHR11635 root node for PKA regulatory chains. Reason: Bcy1 contains two cyclic-nucleotide binding domains and is the yeast cAMP receptor within the PKA holoenzyme. The root PTN004280545 cAMP binding placement correctly transfers to Bcy1. Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN004280545 · PTHR11635 root PKA regulatory-chain IBD SUPPORTS TRANSFER cAMP binding is a conserved activity of PKA regulatory subunits in PTHR11635. Supporting Evidence: file:yeast/BCY1/BCY1-uniprot.txt DR Pfam; PF00027; cNMP_binding; 2. |
| GO:0034236 protein kinase A catalytic subunit binding | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT places PKA catalytic-subunit binding at the PTHR11635 root. Reason: Tpk1, Tpk2, and Tpk3 binding is the core interaction through which Bcy1 forms and inhibits the inactive PKA holoenzyme; the root PAINT placement correctly captures this conserved function. Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN004280545 · PTHR11635 root PKA regulatory-chain IBD SUPPORTS TRANSFER The root PTHR11635 PAINT node captures the PKA catalytic-subunit-binding activity used by regulatory chains to form the inactive holoenzyme. Supporting Evidence: PMID:16924114 PKA is an inactive tetramer composed of two regulatory subunits and two catalytic subunits |
| GO:0042149 cellular response to glucose starvation | IMP PMID:21925385 The cAMP-dependent protein kinase signaling pathway is a key... | KEEP AS NON CORE | Summary: PKA regulation controls P-body foci formation during glucose starvation. Reason: The P-body assembly phenotype is a plausible outcome of Bcy1-mediated PKA regulation during glucose starvation. It is kept as a non-core process rather than elevated to the main evolved activity. Supporting Evidence: PMID:21925385 specifically inhibits the formation of the larger P body aggregates |
| GO:0042149 cellular response to glucose starvation | IMP PMID:26947009 The signaling pathways underlying starvation-induced upregul... | KEEP AS NON CORE | Summary: PKA and TORC1 signaling regulate Ams1 induction after glucose depletion and nitrogen starvation. Reason: The Ams1 response connects Bcy1 to starvation signaling through the PKA pathway, but it is a downstream nutrient-response branch rather than the direct molecular function of the regulatory subunit. Supporting Evidence: PMID:26947009 protein kinase A and the target of rapamycin complex 1 pathways |
| GO:0042802 identical protein binding | IPI PMID:16683188 The zinc containing pro-apoptotic protein siva interacts wit... | UNDECIDED | Summary: The cited PMID resolves to an abstract-only Siva/PMP22 paper, leaving the yeast Bcy1 self-interaction evidence unverified. Reason: The cached abstract foregrounds a human heart cDNA-library screen and a Siva/PMP22 interaction, while the full text is unavailable; the IntAct bait or control evidence for Bcy1 self-interaction cannot be adjudicated from the locally cached abstract. Supporting Evidence: PMID:16683188 By screening a human heart cDNA library |
| GO:0042802 identical protein binding | IPI PMID:18467557 An in vivo map of the yeast protein interactome. | KEEP AS NON CORE | Summary: The PCA self-interaction row is compatible with Bcy1 homodimerization in the PKA holoenzyme. Reason: PKA regulatory subunits homodimerize as part of the inactive PKA tetramer. The specific PKA inhibitor, cAMP-binding, catalytic-subunit-binding, and PKA-complex rows are more informative, so the generic identical-binding row is retained as non-core. Supporting Evidence: PMID:16924114 PKA is an inactive tetramer composed of two regulatory subunits and two catalytic subunits |
| GO:0042802 identical protein binding | IPI PMID:18719252 High-quality binary protein interaction map of the yeast int... | KEEP AS NON CORE | Summary: The Y2H self-interaction row is compatible with Bcy1 homodimerization in the PKA holoenzyme. Reason: Regulatory-subunit dimerization is a real component of the PKA holoenzyme, but the generic identical protein binding term is less informative than the direct PKA molecular-function and complex rows. Supporting Evidence: file:yeast/BCY1/BCY1-uniprot.txt CC P07278; P07278: BCY1; NbExp=3; IntAct=EBI-9475, EBI-9475; |
| GO:0045944 positive regulation of transcription by RNA polymerase II | IMP PMID:26947009 The signaling pathways underlying starvation-induced upregul... | MARK AS OVER ANNOTATED | Summary: The Ams1 starvation study reflects an indirect PKA/Msn2/4 transcriptional output. Reason: Bcy1 controls PKA activity upstream of starvation-induced transcriptional changes, but it is not itself an RNA polymerase II transcriptional regulator. The broad transcription row overstates the directness of the evidence. Supporting Evidence: PMID:26947009 protein kinase A and the target of rapamycin complex 1 pathways |
| GO:0046580 negative regulation of Ras protein signal transduction | IDA PMID:3037314 Cloning and characterization of BCY1, a locus encoding a reg... | MODIFY | Summary: The Ras-signaling row points to the right cAMP/PKA pathway but to the wrong upstream step. Reason: Bcy1 is downstream of Ras and cAMP: it inhibits Tpk catalytic subunits until cAMP binds. Negative regulation of cAMP/PKA signal transduction preserves the sign and pathway while removing the incorrect implication that Bcy1 regulates Ras itself. Proposed replacements: negative regulation of cAMP/PKA signal transduction Supporting Evidence: PMID:3037314 encodes a regulatory subunit of the cyclic AMP-dependent protein kinase |
| GO:0046580 negative regulation of Ras protein signal transduction | IMP PMID:3037314 Cloning and characterization of BCY1, a locus encoding a reg... | MODIFY | Summary: The mutant phenotype establishes negative control of PKA signaling rather than direct negative regulation of Ras. Reason: Disruption of BCY1 bypasses upstream Ras/cAMP signaling by releasing PKA catalytic activity downstream. The better GO process term is negative regulation of cAMP/PKA signal transduction. Proposed replacements: negative regulation of cAMP/PKA signal transduction Supporting Evidence: PMID:3037314 encodes a regulatory subunit of the cyclic AMP-dependent protein kinase |
| GO:0097271 protein localization to bud neck | IGI PMID:12782684 Ras recruits mitotic exit regulator Lte1 to the bud cortex i... | REMOVE | Summary: The paper identifies Ras-dependent Lte1 bud-cortex localization; bcy1 is only a bypass background used to keep ras1 ras2 cells viable. Reason: A bcy1 deletion alone did not disrupt Lte1 localization. The bud-cortex recruitment step is executed by Ras proteins, not by the PKA regulatory subunit that bypasses the essential Ras-cAMP branch in the experimental background. Supporting Evidence: PMID:12782684 In the Δras1, Δras2, or Δbcy1 cells, Lte1–2HA protein localized properly |
| GO:0097271 protein localization to bud neck | IGI PMID:12782684 Ras recruits mitotic exit regulator Lte1 to the bud cortex i... | REMOVE | Summary: The paper identifies Ras-dependent Lte1 bud-cortex localization; bcy1 is only a bypass background used to keep ras1 ras2 cells viable. Reason: BCY1 deletion bypasses lethality caused by simultaneous loss of RAS1 and RAS2, but Ras1/Ras2 are the actors upstream of Lte1 localization. The genetic background should not be converted into a direct Bcy1 function. Supporting Evidence: PMID:12782684 the deletion of the BCY1 gene rescues the lethality |
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Download this section (compressed HTML)Q: How are the stress- and carbon-source-specific Bcy1 pools at chromatin, the plasma membrane, the nucleus, and the cytosol coupled to different Tpk catalytic isoforms and substrate sets?
Q: Does Bcy1 homodimer composition or post-translational modification state bias the holoenzyme toward Tpk1, Tpk2, or Tpk3 during glucose depletion, nitrogen starvation, osmotic stress, and heat stress?
Experiment: Quantify endogenous Bcy1-Tpk1, Bcy1-Tpk2, and Bcy1-Tpk3 holoenzymes by affinity purification/mass spectrometry across glucose-rich, glucose-depleted, nitrogen-starved, heat-stressed, and osmotic-stress conditions.
Type: affinity purification and mass spectrometry
Experiment: Combine phosphosite-mutant Bcy1 alleles with live-cell imaging and phosphoproteomics to map which Bcy1 phosphorylation clusters control nuclear, cytosolic, plasma-membrane, and chromatin-associated PKA outputs.
Type: phosphosite mutagenesis and live-cell imaging
Regulatory subunit of the cyclic AMP-dependent protein kinase (PKA); PKA is a component of a signaling pathway that controls a variety of cellular processes, including metabolism, cell cycle, stress response, stationary phase, and sporulation; regulator of meiotic commitment
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