acrA encodes ACR (also called ACB), the terminal-differentiation specific adenylate cyclase of Dictyostelium discoideum. It is a large (2123 aa) multidomain, multi-pass membrane protein comprising seven transmembrane helices, a degenerate histidine kinase region (HisKA plus HATPase-C domains), two receiver (response regulator) domains, and a C-terminal class III nucleotidyl cyclase catalytic domain that converts ATP to 3',5'-cyclic AMP (EC 4.6.1.1), using Mg2+ as cofactor and acting as a homodimer. ACR is expressed at low levels in growing cells and strongly induced during development, peaking during culmination and in prestalk regions of the fruiting body. Unlike the receptor-coupled aggregation adenylate cyclase ACA and the osmosensing spore-dormancy adenylate cyclase ACG, ACR provides the intracellular cAMP that activates cAMP-dependent protein kinase (PKA) at culmination, and is required for spore encapsulation/maturation and for formation of robust (non-thin) stalks. Rather than functioning as a phosphorelay signaling enzyme, its histidine-kinase-like and receiver domains have lost their canonical two-component signaling roles; the dimerizing HisKA subdomain instead serves to promote dimerization of the cyclase domain. Contrary to the plasma-membrane location of ACA, ACR localizes to the endoplasmic reticulum and nuclear envelope. It acts downstream of the cytokinin (discadenine) / DhkB signaling pathway that triggers rapid spore encapsulation.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
|
GO:0004016
adenylate cyclase activity
|
IBA
GO_REF:0000033 |
ACCEPT |
Summary: Adenylate cyclase activity is the core, experimentally established molecular function of ACR. The phylogenetic (IBA) inference is fully consistent with direct enzymatic evidence for this protein.
Reason: ACR is a bona fide class III adenylate cyclase whose ATP-to-cAMP activity has been directly demonstrated and dissected. This IBA annotation correctly captures the central molecular function.
Supporting Evidence:
PMID:10556070
we discovered a novel adenylyl cyclase gene, acrA, that is expressed at low levels in growing cells and at more than 25-fold higher levels during development
PMID:20966074
In addition to its cyclase (AC) domain, ACR harbors seven transmembrane helices, a histidine kinase domain, and two receiver domains
|
|
GO:0006171
cAMP biosynthetic process
|
IBA
GO_REF:0000033 |
ACCEPT |
Summary: ACR synthesizes cAMP, and cAMP biosynthesis is a core biological process for this enzyme, providing the second messenger that activates PKA during terminal differentiation.
Reason: The IBA inference of cAMP biosynthesis is directly supported by the catalytic activity of ACR and by the phenotype of acrA null cells, which fail to raise adenylyl cyclase activity after aggregation.
Supporting Evidence:
PMID:10556070
The increase in activity following aggregation fails to occur in acrA(-) cells
PMID:20966074
adenylate cyclase R (ACR), is essential for spore encapsulation
|
|
GO:0000160
phosphorelay signal transduction system
|
IEA
GO_REF:0000002 |
REMOVE |
Summary: This InterPro2GO annotation is inferred from the receiver (response-regulator) domain (IPR001789). However, functional dissection of ACR showed that its histidine kinase and receiver domains do NOT act as a phosphorelay to regulate the enzyme; the phosphoryl-accepting aspartates are largely dispensable and the domains have lost the switch-pair residues needed for phosphorylation-induced signaling.
Reason: The receiver/histidine-kinase domains are present by ancestry but their canonical phosphorelay function has eroded. Experimental evidence directly contradicts a role for ACR in phosphorelay signal transduction, so this domain-based electronic annotation is an over-annotation.
Supporting Evidence:
PMID:20966074
indicating that AC activity is not critically regulated by phosphorelay
PMID:20966074
This indicates that ACR is not regulated by its intramolecular histidine kinase activity
|
|
GO:0004016
adenylate cyclase activity
|
IEA
GO_REF:0000120 |
ACCEPT |
Summary: Electronic assignment of adenylate cyclase activity based on RHEA/EC mapping (EC 4.6.1.1). This is correct and redundant with the experimentally supported core molecular function.
Reason: The EC/RHEA-based inference matches the directly demonstrated ATP-to-cAMP catalytic activity of ACR.
Supporting Evidence:
PMID:10556070
we discovered a novel adenylyl cyclase gene, acrA, that is expressed at low levels in growing cells and at more than 25-fold higher levels during development
|
|
GO:0009190
cyclic nucleotide biosynthetic process
|
IEA
GO_REF:0000002 |
MODIFY |
Summary: InterPro2GO annotation from the cyclase domain (IPR001054). It is correct but overly general; ACR specifically synthesizes cAMP, so the more specific child term cAMP biosynthetic process is preferable.
Reason: ACR is an adenylate (not general nucleotidyl/guanylyl) cyclase, so the specific term cAMP biosynthetic process better represents its function than the parent cyclic nucleotide biosynthetic process.
Proposed replacements:
cAMP biosynthetic process
Supporting Evidence:
PMID:20966074
adenylate cyclase R (ACR), is essential for spore encapsulation
|
|
GO:0016020
membrane
|
IEA
GO_REF:0000044 |
KEEP AS NON CORE |
Summary: ACR is a multi-pass membrane protein with seven transmembrane helices, so a membrane location is correct. However, the specific experimentally determined locations are the endoplasmic reticulum and nuclear envelope, making the bare membrane term uninformative as a core location.
Reason: The generic membrane annotation is technically accurate for this multi-pass membrane protein but is subsumed by the more precise ER and nuclear-envelope localizations shown experimentally.
Supporting Evidence:
PMID:20966074
This strongly suggests that ACR localizes to the endoplasmic reticulum and nuclear envelope
PMID:20966074
In addition to its cyclase (AC) domain, ACR harbors seven transmembrane helices, a histidine kinase domain, and two receiver domains
|
|
GO:0016772
transferase activity, transferring phosphorus-containing groups
|
IEA
GO_REF:0000002 |
REMOVE |
Summary: This InterPro2GO annotation derives from the histidine-kinase-like C-terminal (HATPase) domain (IPR004358), implying phosphotransferase activity. But ACR is a lyase (adenylate cyclase, EC 4.6.1.1), and its histidine kinase domain is degenerate and catalytically non-functional, lacking the phospho-accepting histidine, and mutation of essential ATP-binding residues has no effect on activity.
Reason: ACR has no demonstrated phosphotransferase/kinase activity; the histidine-kinase-like domain is a pseudokinase used only for dimerization. Assigning transferase activity from this degenerate domain is a domain-based over-annotation contradicted by experimental evidence.
Supporting Evidence:
PMID:20966074
Mutation of three essential ATP-binding residues in the histidine kinase domain did not affect the AC activity or phenotypic rescue
PMID:20966074
the dimerizing histidine phosphoacceptor subdomain, which in ACR lacks the canonical histidine for autophosphorylation, was essential for AC activity
|
|
GO:0035556
intracellular signal transduction
|
IEA
GO_REF:0000002 |
KEEP AS NON CORE |
Summary: ACR produces intracellular cAMP that acts as a second messenger to activate PKA, so participation in intracellular signal transduction is correct. It is a broad process term subsumed by the more specific cAMP biosynthesis and developmental-differentiation annotations.
Reason: The annotation is biologically accurate (ACR generates a second-messenger signal) but too general to represent the specific evolved function; retained as non-core context.
Supporting Evidence:
PMID:10556070
Expression of many of the essential developmental genes in Dictyostelium discoideum are known to depend on PKA activity
|
|
GO:0009642
response to light intensity
|
HEP
PMID:41057014 Transcriptomic and metabolomic insights into light-mediated ... |
KEEP AS NON CORE |
Summary: This high-throughput expression (HEP) annotation reflects that acrA is a differentially expressed gene, downregulated in the dark, in a transcriptomic study of light-mediated development. It captures light-regulated expression of acrA rather than a direct functional role of the ACR protein in light responses.
Reason: The evidence is transcriptomic/correlative (acrA is a light-responsive DEG). This is peripheral to the core catalytic and developmental function and is retained as non-core.
Supporting Evidence:
PMID:41057014
Here we also observed that the adenylate cyclase gene acrA was downregulated under dark in the unicellular phase
|
|
GO:0005524
ATP binding
|
IC
PMID:10556070 An adenylyl cyclase that functions during late development o... |
ACCEPT |
Summary: ATP binding is curator-inferred (IC) from the adenylate cyclase activity, since ATP is the substrate of the ATP-to-cAMP reaction. This is a correct supporting molecular function.
Reason: ATP binding is a necessary component of the cyclase catalytic mechanism (ATP is converted to cAMP plus diphosphate) and is soundly inferred from the enzymatic activity.
Supporting Evidence:
PMID:10556070
we discovered a novel adenylyl cyclase gene, acrA, that is expressed at low levels in growing cells and at more than 25-fold higher levels during development
|
|
GO:0004016
adenylate cyclase activity
|
IDA
PMID:10556070 An adenylyl cyclase that functions during late development o... |
ACCEPT |
Summary: Direct experimental demonstration of adenylate cyclase activity for ACR, the core molecular function. Adenylyl cyclase activity increases through development and this increase is lost in acrA null cells.
Reason: This IDA annotation is the primary experimental evidence for the core catalytic function of ACR.
Supporting Evidence:
PMID:10556070
The increase in activity following aggregation fails to occur in acrA(-) cells
|
|
GO:0004016
adenylate cyclase activity
|
IDA
PMID:20966074 Functional dissection of adenylate cyclase R, an inducer of ... |
ACCEPT |
Summary: Direct measurement of cAMP production by an ACR-YFP fusion in acr- cells confirms adenylate cyclase activity and allowed domain-level dissection of the enzyme's catalytic requirements.
Reason: Independent IDA evidence for the core adenylate cyclase activity of ACR; the reconstituted enzyme produces cAMP and rescues the null phenotype.
Supporting Evidence:
PMID:20966074
the dimerizing histidine phosphoacceptor subdomain, which in ACR lacks the canonical histidine for autophosphorylation, was essential for AC activity
|
|
GO:0005635
nuclear envelope
|
IDA
PMID:20966074 Functional dissection of adenylate cyclase R, an inducer of ... |
ACCEPT |
Summary: ACR-YFP localizes to the nuclear envelope, shown by confocal microscopy and colocalization with the ER marker calnexin around the nuclei. This is a well-supported, distinctive localization for ACR.
Reason: Direct imaging evidence places ACR at the nuclear envelope, an unusual localization for a Dictyostelium adenylate cyclase and a core cellular-component annotation.
Supporting Evidence:
PMID:20966074
ACR is associated with the nuclear envelope and endoplasmic reticulum
PMID:20966074
This strongly suggests that ACR localizes to the endoplasmic reticulum and nuclear envelope
|
|
GO:0005783
endoplasmic reticulum
|
IDA
PMID:20966074 Functional dissection of adenylate cyclase R, an inducer of ... |
ACCEPT |
Summary: ACR-YFP colocalizes with the ER marker calnexin in a vesicular network throughout the cell, directly demonstrating endoplasmic reticulum localization.
Reason: Direct immunofluorescence/colocalization evidence supports ER localization; this is a core cellular-component annotation for ACR.
Supporting Evidence:
PMID:20966074
This strongly suggests that ACR localizes to the endoplasmic reticulum and nuclear envelope
|
|
GO:0030587
sorocarp development
|
HMP
PMID:17659086 High-throughput analysis of spatio-temporal dynamics in Dict... |
KEEP AS NON CORE |
Summary: High-throughput mutant phenotyping placed acrA among genes whose disruption produces phenotypes only at later (slug-to-culmination) stages of fruiting body (sorocarp) development. This general developmental term is correct but is captured more specifically by the sorocarp morphogenesis and spore-cell differentiation annotations.
Reason: The broad sorocarp development term is accurate for acrA but subsumed by more specific late-development annotations that better represent its role.
Supporting Evidence:
PMID:17659086
In contrast, dhkA and acrA show mutant phenotypes only at later stages consistent with their specific roles during slug to culmination stage
|
|
GO:0010468
regulation of gene expression
|
IMP
PMID:10556070 An adenylyl cyclase that functions during late development o... |
KEEP AS NON CORE |
Summary: ACR-derived cAMP activates PKA, and many essential developmental genes depend on PKA activity, so ACR acts upstream of developmental gene expression. This is an indirect, downstream effect mediated by the second-messenger/PKA cascade.
Reason: The influence of ACR on gene expression is real but indirect (via cAMP/PKA) and general; it is retained as non-core context rather than a direct molecular function.
Supporting Evidence:
PMID:10556070
Expression of many of the essential developmental genes in Dictyostelium discoideum are known to depend on PKA activity
|
|
GO:0031288
sorocarp morphogenesis
|
IMP
PMID:10556070 An adenylyl cyclase that functions during late development o... |
ACCEPT |
Summary: acrA null cells form unnaturally long, thin stalks, demonstrating a requirement for ACR in proper morphogenesis of the fruiting body (stalk) during culmination.
Reason: The stalk-morphogenesis defect of acrA mutants directly supports a core role in sorocarp morphogenesis at culmination.
Supporting Evidence:
PMID:10556070
Growth and development up to the slug stage are unaffected in acrA(-) mutant strains but the cells make almost no viable spores and produce unnaturally long stalks
PMID:10556070
As long as ACA is fully active, ACR is not required until culmination but then plays a critical role in sporulation and construction of the stalk
|
|
GO:0009736
cytokinin-activated signaling pathway
|
IMP
PMID:18216168 Cytokinins induce sporulation in Dictyostelium. |
ACCEPT |
Summary: AcrA is required, together with the histidine kinase DhkB, to transduce the cytokinin (discadenine/isopentenyladenine) signal that triggers rapid spore encapsulation. This annotation captures the Dictyostelium cytokinin signaling context in which ACR operates.
Reason: Genetic evidence shows AcrA is a required component of the cytokinin signal transduction pathway leading to sporulation, consistent with its role as the cAMP source that activates PKA for encapsulation.
Supporting Evidence:
PMID:18216168
DhkB and the adenylyl cyclase of late development, AcrA, are members of two component signal transduction families and both are required to transduce the cytokinin signal
|
|
GO:0031000
response to caffeine
|
IDA
PMID:16952277 Pharmacological profiling of the Dictyostelium adenylate cyc... |
KEEP AS NON CORE |
Summary: Pharmacological profiling showed that caffeine inhibits cAMP accumulation by ACB (ACR/acrA) in intact cells (an indirect effect, since caffeine does not inhibit basal ACB activity in lysates). This records a response of ACR-dependent cAMP output to caffeine.
Reason: The caffeine sensitivity is a pharmacological/experimental property of ACR-dependent cAMP accumulation rather than a core evolved function; retained as non-core.
Supporting Evidence:
PMID:16952277
Caffeine, which was previously used to specifically block ACA function, also inhibited cAMP accumulation by ACB and ACG
|
|
GO:0044671
sorocarp spore cell differentiation
|
IMP
PMID:20966074 Functional dissection of adenylate cyclase R, an inducer of ... |
ACCEPT |
Summary: ACR is essential for spore encapsulation; acr- cells develop to the fruiting body stage but fail to make viable, encapsulated spores, and ACR-YFP rescues this defect. This is a core developmental role of ACR.
Reason: Loss- and rescue-of-function evidence establishes ACR as required for spore cell differentiation/encapsulation during culmination.
Supporting Evidence:
PMID:20966074
adenylate cyclase R (ACR), is essential for spore encapsulation
PMID:10556070
As long as ACA is fully active, ACR is not required until culmination but then plays a critical role in sporulation and construction of the stalk
|
|
GO:0031288
sorocarp morphogenesis
|
IMP
PMID:20966074 Functional dissection of adenylate cyclase R, an inducer of ... |
ACCEPT |
Summary: A second IMP annotation for sorocarp morphogenesis, from the functional-dissection study in which acr- cells form thinner-than-wild-type stalks that are rescued by ACR-YFP.
Reason: Independent genetic evidence confirms a core role for ACR in proper stalk formation during fruiting-body morphogenesis.
Supporting Evidence:
PMID:20966074
adenylate cyclase R (ACR), is essential for spore encapsulation
|
id: Q55F68
gene_symbol: acrA
product_type: PROTEIN
status: COMPLETE
taxon:
id: NCBITaxon:44689
label: Dictyostelium discoideum
description: acrA encodes ACR (also called ACB), the terminal-differentiation
specific adenylate cyclase of Dictyostelium discoideum. It is a large (2123
aa) multidomain, multi-pass membrane protein comprising seven transmembrane
helices, a degenerate histidine kinase region (HisKA plus HATPase-C domains),
two receiver (response regulator) domains, and a C-terminal class III
nucleotidyl cyclase catalytic domain that converts ATP to 3',5'-cyclic AMP
(EC 4.6.1.1), using Mg2+ as cofactor and acting as a homodimer. ACR is
expressed at low levels in growing cells and strongly induced during
development, peaking during culmination and in prestalk regions of the
fruiting body. Unlike the receptor-coupled aggregation adenylate cyclase ACA
and the osmosensing spore-dormancy adenylate cyclase ACG, ACR provides the
intracellular cAMP that activates cAMP-dependent protein kinase (PKA) at
culmination, and is required for spore encapsulation/maturation and for
formation of robust (non-thin) stalks. Rather than functioning as a
phosphorelay signaling enzyme, its histidine-kinase-like and receiver domains
have lost their canonical two-component signaling roles; the dimerizing HisKA
subdomain instead serves to promote dimerization of the cyclase domain.
Contrary to the plasma-membrane location of ACA, ACR localizes to the
endoplasmic reticulum and nuclear envelope. It acts downstream of the
cytokinin (discadenine) / DhkB signaling pathway that triggers rapid spore
encapsulation.
existing_annotations:
- term:
id: GO:0004016
label: adenylate cyclase activity
evidence_type: IBA
original_reference_id: GO_REF:0000033
qualifier: enables
review:
summary: Adenylate cyclase activity is the core, experimentally established
molecular function of ACR. The phylogenetic (IBA) inference is fully
consistent with direct enzymatic evidence for this protein.
action: ACCEPT
reason: ACR is a bona fide class III adenylate cyclase whose ATP-to-cAMP
activity has been directly demonstrated and dissected. This IBA annotation
correctly captures the central molecular function.
supported_by:
- reference_id: PMID:10556070
supporting_text: we discovered a novel adenylyl cyclase gene, acrA, that
is expressed at low levels in growing cells and at more than 25-fold
higher levels during development
- reference_id: PMID:20966074
supporting_text: In addition to its cyclase (AC) domain, ACR harbors seven
transmembrane helices, a histidine kinase domain, and two receiver
domains
- term:
id: GO:0006171
label: cAMP biosynthetic process
evidence_type: IBA
original_reference_id: GO_REF:0000033
qualifier: involved_in
review:
summary: ACR synthesizes cAMP, and cAMP biosynthesis is a core biological
process for this enzyme, providing the second messenger that activates PKA
during terminal differentiation.
action: ACCEPT
reason: The IBA inference of cAMP biosynthesis is directly supported by the
catalytic activity of ACR and by the phenotype of acrA null cells, which
fail to raise adenylyl cyclase activity after aggregation.
supported_by:
- reference_id: PMID:10556070
supporting_text: The increase in activity following aggregation fails to
occur in acrA(-) cells
- reference_id: PMID:20966074
supporting_text: adenylate cyclase R (ACR), is essential for spore
encapsulation
- term:
id: GO:0000160
label: phosphorelay signal transduction system
evidence_type: IEA
original_reference_id: GO_REF:0000002
qualifier: involved_in
review:
summary: This InterPro2GO annotation is inferred from the receiver
(response-regulator) domain (IPR001789). However, functional dissection of
ACR showed that its histidine kinase and receiver domains do NOT act as a
phosphorelay to regulate the enzyme; the phosphoryl-accepting aspartates
are largely dispensable and the domains have lost the switch-pair residues
needed for phosphorylation-induced signaling.
action: REMOVE
reason: The receiver/histidine-kinase domains are present by ancestry but
their canonical phosphorelay function has eroded. Experimental evidence
directly contradicts a role for ACR in phosphorelay signal transduction,
so this domain-based electronic annotation is an over-annotation.
supported_by:
- reference_id: PMID:20966074
supporting_text: indicating that AC activity is not critically regulated
by phosphorelay
- reference_id: PMID:20966074
supporting_text: This indicates that ACR is not regulated by its
intramolecular histidine kinase activity
- term:
id: GO:0004016
label: adenylate cyclase activity
evidence_type: IEA
original_reference_id: GO_REF:0000120
qualifier: enables
review:
summary: Electronic assignment of adenylate cyclase activity based on
RHEA/EC mapping (EC 4.6.1.1). This is correct and redundant with the
experimentally supported core molecular function.
action: ACCEPT
reason: The EC/RHEA-based inference matches the directly demonstrated
ATP-to-cAMP catalytic activity of ACR.
supported_by:
- reference_id: PMID:10556070
supporting_text: we discovered a novel adenylyl cyclase gene, acrA, that
is expressed at low levels in growing cells and at more than 25-fold
higher levels during development
- term:
id: GO:0009190
label: cyclic nucleotide biosynthetic process
evidence_type: IEA
original_reference_id: GO_REF:0000002
qualifier: involved_in
review:
summary: InterPro2GO annotation from the cyclase domain (IPR001054). It is
correct but overly general; ACR specifically synthesizes cAMP, so the more
specific child term cAMP biosynthetic process is preferable.
action: MODIFY
reason: ACR is an adenylate (not general nucleotidyl/guanylyl) cyclase, so
the specific term cAMP biosynthetic process better represents its function
than the parent cyclic nucleotide biosynthetic process.
proposed_replacement_terms:
- id: GO:0006171
label: cAMP biosynthetic process
supported_by:
- reference_id: PMID:20966074
supporting_text: adenylate cyclase R (ACR), is essential for spore
encapsulation
- term:
id: GO:0016020
label: membrane
evidence_type: IEA
original_reference_id: GO_REF:0000044
qualifier: located_in
review:
summary: ACR is a multi-pass membrane protein with seven transmembrane
helices, so a membrane location is correct. However, the specific
experimentally determined locations are the endoplasmic reticulum and
nuclear envelope, making the bare membrane term uninformative as a core
location.
action: KEEP_AS_NON_CORE
reason: The generic membrane annotation is technically accurate for this
multi-pass membrane protein but is subsumed by the more precise ER and
nuclear-envelope localizations shown experimentally.
supported_by:
- reference_id: PMID:20966074
supporting_text: This strongly suggests that ACR localizes to the
endoplasmic reticulum and nuclear envelope
- reference_id: PMID:20966074
supporting_text: In addition to its cyclase (AC) domain, ACR harbors seven
transmembrane helices, a histidine kinase domain, and two receiver
domains
- term:
id: GO:0016772
label: transferase activity, transferring phosphorus-containing groups
evidence_type: IEA
original_reference_id: GO_REF:0000002
qualifier: enables
review:
summary: This InterPro2GO annotation derives from the histidine-kinase-like
C-terminal (HATPase) domain (IPR004358), implying phosphotransferase
activity. But ACR is a lyase (adenylate cyclase, EC 4.6.1.1), and its
histidine kinase domain is degenerate and catalytically non-functional,
lacking the phospho-accepting histidine, and mutation of essential
ATP-binding residues has no effect on activity.
action: REMOVE
reason: ACR has no demonstrated phosphotransferase/kinase activity; the
histidine-kinase-like domain is a pseudokinase used only for
dimerization. Assigning transferase activity from this degenerate domain
is a domain-based over-annotation contradicted by experimental evidence.
supported_by:
- reference_id: PMID:20966074
supporting_text: Mutation of three essential ATP-binding residues in the
histidine kinase domain did not affect the AC activity or phenotypic
rescue
- reference_id: PMID:20966074
supporting_text: the dimerizing histidine phosphoacceptor subdomain, which
in ACR lacks the canonical histidine for autophosphorylation, was
essential for AC activity
- term:
id: GO:0035556
label: intracellular signal transduction
evidence_type: IEA
original_reference_id: GO_REF:0000002
qualifier: involved_in
review:
summary: ACR produces intracellular cAMP that acts as a second messenger to
activate PKA, so participation in intracellular signal transduction is
correct. It is a broad process term subsumed by the more specific cAMP
biosynthesis and developmental-differentiation annotations.
action: KEEP_AS_NON_CORE
reason: The annotation is biologically accurate (ACR generates a
second-messenger signal) but too general to represent the specific evolved
function; retained as non-core context.
supported_by:
- reference_id: PMID:10556070
supporting_text: Expression of many of the essential developmental genes
in Dictyostelium discoideum are known to depend on PKA activity
- term:
id: GO:0009642
label: response to light intensity
evidence_type: HEP
original_reference_id: PMID:41057014
qualifier: acts_upstream_of_or_within
review:
summary: This high-throughput expression (HEP) annotation reflects that acrA
is a differentially expressed gene, downregulated in the dark, in a
transcriptomic study of light-mediated development. It captures
light-regulated expression of acrA rather than a direct functional role of
the ACR protein in light responses.
action: KEEP_AS_NON_CORE
reason: The evidence is transcriptomic/correlative (acrA is a
light-responsive DEG). This is peripheral to the core catalytic and
developmental function and is retained as non-core.
supported_by:
- reference_id: PMID:41057014
supporting_text: Here we also observed that the adenylate cyclase gene
acrA was downregulated under dark in the unicellular phase
- term:
id: GO:0005524
label: ATP binding
evidence_type: IC
original_reference_id: PMID:10556070
qualifier: enables
review:
summary: ATP binding is curator-inferred (IC) from the adenylate cyclase
activity, since ATP is the substrate of the ATP-to-cAMP reaction. This is
a correct supporting molecular function.
action: ACCEPT
reason: ATP binding is a necessary component of the cyclase catalytic
mechanism (ATP is converted to cAMP plus diphosphate) and is soundly
inferred from the enzymatic activity.
supported_by:
- reference_id: PMID:10556070
supporting_text: we discovered a novel adenylyl cyclase gene, acrA, that
is expressed at low levels in growing cells and at more than 25-fold
higher levels during development
- term:
id: GO:0004016
label: adenylate cyclase activity
evidence_type: IDA
original_reference_id: PMID:10556070
qualifier: enables
review:
summary: Direct experimental demonstration of adenylate cyclase activity for
ACR, the core molecular function. Adenylyl cyclase activity increases
through development and this increase is lost in acrA null cells.
action: ACCEPT
reason: This IDA annotation is the primary experimental evidence for the
core catalytic function of ACR.
supported_by:
- reference_id: PMID:10556070
supporting_text: The increase in activity following aggregation fails to
occur in acrA(-) cells
- term:
id: GO:0004016
label: adenylate cyclase activity
evidence_type: IDA
original_reference_id: PMID:20966074
qualifier: enables
review:
summary: Direct measurement of cAMP production by an ACR-YFP fusion in acr-
cells confirms adenylate cyclase activity and allowed domain-level
dissection of the enzyme's catalytic requirements.
action: ACCEPT
reason: Independent IDA evidence for the core adenylate cyclase activity of
ACR; the reconstituted enzyme produces cAMP and rescues the null
phenotype.
supported_by:
- reference_id: PMID:20966074
supporting_text: the dimerizing histidine phosphoacceptor subdomain, which
in ACR lacks the canonical histidine for autophosphorylation, was
essential for AC activity
- term:
id: GO:0005635
label: nuclear envelope
evidence_type: IDA
original_reference_id: PMID:20966074
qualifier: located_in
review:
summary: ACR-YFP localizes to the nuclear envelope, shown by confocal
microscopy and colocalization with the ER marker calnexin around the
nuclei. This is a well-supported, distinctive localization for ACR.
action: ACCEPT
reason: Direct imaging evidence places ACR at the nuclear envelope, an
unusual localization for a Dictyostelium adenylate cyclase and a core
cellular-component annotation.
supported_by:
- reference_id: PMID:20966074
supporting_text: ACR is associated with the nuclear envelope and
endoplasmic reticulum
- reference_id: PMID:20966074
supporting_text: This strongly suggests that ACR localizes to the
endoplasmic reticulum and nuclear envelope
- term:
id: GO:0005783
label: endoplasmic reticulum
evidence_type: IDA
original_reference_id: PMID:20966074
qualifier: located_in
review:
summary: ACR-YFP colocalizes with the ER marker calnexin in a vesicular
network throughout the cell, directly demonstrating endoplasmic reticulum
localization.
action: ACCEPT
reason: Direct immunofluorescence/colocalization evidence supports ER
localization; this is a core cellular-component annotation for ACR.
supported_by:
- reference_id: PMID:20966074
supporting_text: This strongly suggests that ACR localizes to the
endoplasmic reticulum and nuclear envelope
- term:
id: GO:0030587
label: sorocarp development
evidence_type: HMP
original_reference_id: PMID:17659086
qualifier: acts_upstream_of_or_within
review:
summary: High-throughput mutant phenotyping placed acrA among genes whose
disruption produces phenotypes only at later (slug-to-culmination) stages
of fruiting body (sorocarp) development. This general developmental term
is correct but is captured more specifically by the sorocarp morphogenesis
and spore-cell differentiation annotations.
action: KEEP_AS_NON_CORE
reason: The broad sorocarp development term is accurate for acrA but
subsumed by more specific late-development annotations that better
represent its role.
supported_by:
- reference_id: PMID:17659086
supporting_text: In contrast, dhkA and acrA show mutant phenotypes only at
later stages consistent with their specific roles during slug to
culmination stage
- term:
id: GO:0010468
label: regulation of gene expression
evidence_type: IMP
original_reference_id: PMID:10556070
qualifier: acts_upstream_of_or_within
review:
summary: ACR-derived cAMP activates PKA, and many essential developmental
genes depend on PKA activity, so ACR acts upstream of developmental gene
expression. This is an indirect, downstream effect mediated by the
second-messenger/PKA cascade.
action: KEEP_AS_NON_CORE
reason: The influence of ACR on gene expression is real but indirect (via
cAMP/PKA) and general; it is retained as non-core context rather than a
direct molecular function.
supported_by:
- reference_id: PMID:10556070
supporting_text: Expression of many of the essential developmental genes
in Dictyostelium discoideum are known to depend on PKA activity
- term:
id: GO:0031288
label: sorocarp morphogenesis
evidence_type: IMP
original_reference_id: PMID:10556070
qualifier: acts_upstream_of_or_within
review:
summary: acrA null cells form unnaturally long, thin stalks, demonstrating a
requirement for ACR in proper morphogenesis of the fruiting body (stalk)
during culmination.
action: ACCEPT
reason: The stalk-morphogenesis defect of acrA mutants directly supports a
core role in sorocarp morphogenesis at culmination.
supported_by:
- reference_id: PMID:10556070
supporting_text: Growth and development up to the slug stage are unaffected
in acrA(-) mutant strains but the cells make almost no viable spores and
produce unnaturally long stalks
- reference_id: PMID:10556070
supporting_text: As long as ACA is fully active, ACR is not required until
culmination but then plays a critical role in sporulation and
construction of the stalk
- term:
id: GO:0009736
label: cytokinin-activated signaling pathway
evidence_type: IMP
original_reference_id: PMID:18216168
qualifier: acts_upstream_of_or_within
review:
summary: AcrA is required, together with the histidine kinase DhkB, to
transduce the cytokinin (discadenine/isopentenyladenine) signal that
triggers rapid spore encapsulation. This annotation captures the
Dictyostelium cytokinin signaling context in which ACR operates.
action: ACCEPT
reason: Genetic evidence shows AcrA is a required component of the cytokinin
signal transduction pathway leading to sporulation, consistent with its
role as the cAMP source that activates PKA for encapsulation.
supported_by:
- reference_id: PMID:18216168
supporting_text: DhkB and the adenylyl cyclase of late development, AcrA,
are members of two component signal transduction families and both are
required to transduce the cytokinin signal
- term:
id: GO:0031000
label: response to caffeine
evidence_type: IDA
original_reference_id: PMID:16952277
qualifier: involved_in
review:
summary: Pharmacological profiling showed that caffeine inhibits cAMP
accumulation by ACB (ACR/acrA) in intact cells (an indirect effect, since
caffeine does not inhibit basal ACB activity in lysates). This records a
response of ACR-dependent cAMP output to caffeine.
action: KEEP_AS_NON_CORE
reason: The caffeine sensitivity is a pharmacological/experimental property
of ACR-dependent cAMP accumulation rather than a core evolved function;
retained as non-core.
supported_by:
- reference_id: PMID:16952277
supporting_text: Caffeine, which was previously used to specifically block
ACA function, also inhibited cAMP accumulation by ACB and ACG
- term:
id: GO:0044671
label: sorocarp spore cell differentiation
evidence_type: IMP
original_reference_id: PMID:20966074
qualifier: acts_upstream_of_or_within
review:
summary: ACR is essential for spore encapsulation; acr- cells develop to the
fruiting body stage but fail to make viable, encapsulated spores, and
ACR-YFP rescues this defect. This is a core developmental role of ACR.
action: ACCEPT
reason: Loss- and rescue-of-function evidence establishes ACR as required
for spore cell differentiation/encapsulation during culmination.
supported_by:
- reference_id: PMID:20966074
supporting_text: adenylate cyclase R (ACR), is essential for spore
encapsulation
- reference_id: PMID:10556070
supporting_text: As long as ACA is fully active, ACR is not required until
culmination but then plays a critical role in sporulation and
construction of the stalk
- term:
id: GO:0031288
label: sorocarp morphogenesis
evidence_type: IMP
original_reference_id: PMID:20966074
qualifier: acts_upstream_of_or_within
review:
summary: A second IMP annotation for sorocarp morphogenesis, from the
functional-dissection study in which acr- cells form
thinner-than-wild-type stalks that are rescued by ACR-YFP.
action: ACCEPT
reason: Independent genetic evidence confirms a core role for ACR in proper
stalk formation during fruiting-body morphogenesis.
supported_by:
- reference_id: PMID:20966074
supporting_text: adenylate cyclase R (ACR), is essential for spore
encapsulation
references:
- id: GO_REF:0000002
title: Gene Ontology annotation through association of InterPro records with GO
terms
findings: []
- id: GO_REF:0000033
title: Annotation inferences using phylogenetic trees
findings: []
- id: GO_REF:0000044
title: Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location
vocabulary mapping, accompanied by conservative changes to GO terms applied by
UniProt
findings: []
- id: GO_REF:0000120
title: Combined Automated Annotation using Multiple IEA Methods
findings: []
- id: PMID:10556070
title: An adenylyl cyclase that functions during late development of Dictyostelium.
findings:
- statement: acrA encodes a novel adenylyl cyclase expressed at low levels in
growth and induced more than 25-fold during development.
supporting_text: we discovered a novel adenylyl cyclase gene, acrA, that is
expressed at low levels in growing cells and at more than 25-fold higher
levels during development
- statement: acrA null cells develop normally to the slug stage but fail to make
viable spores and produce unnaturally long stalks.
supporting_text: Growth and development up to the slug stage are unaffected in
acrA(-) mutant strains but the cells make almost no viable spores and produce
unnaturally long stalks
- statement: ACR is dispensable until culmination when it is critical for
sporulation and stalk construction.
supporting_text: As long as ACA is fully active, ACR is not required until
culmination but then plays a critical role in sporulation and construction
of the stalk
reference_review:
relevance: HIGH
correctness: VERIFIED
review_notes: Primary discovery/characterization of acrA; abstract-only in
cache but establishes catalytic activity, developmental expression, and the
sporulation/stalk phenotype. Verified via PubMed title match.
- id: PMID:15875012
title: The genome of the social amoeba Dictyostelium discoideum.
findings: []
- id: PMID:16952277
title: Pharmacological profiling of the Dictyostelium adenylate cyclases ACA, ACB
and ACG.
findings:
- statement: Caffeine inhibits cAMP accumulation by ACB (acrA) as well as ACA and
ACG in intact cells.
supporting_text: Caffeine, which was previously used to specifically block ACA
function, also inhibited cAMP accumulation by ACB and ACG
- statement: ACB, encoded by the AcrA gene, is required for spore maturation.
supporting_text: ACB is required for the maturation of spores
reference_review:
relevance: MEDIUM
correctness: VERIFIED
review_notes: Full text available; supports the caffeine-response annotation
and confirms acrA=ACB identity and its spore-maturation role.
- id: PMID:17659086
title: High-throughput analysis of spatio-temporal dynamics in Dictyostelium.
findings:
- statement: acrA mutants show phenotypes only at later (slug-to-culmination)
developmental stages, consistent with a late-development role.
supporting_text: In contrast, dhkA and acrA show mutant phenotypes only at
later stages consistent with their specific roles during slug to culmination
stage
reference_review:
relevance: MEDIUM
correctness: VERIFIED
review_notes: Full text available; high-throughput phenotyping supporting the
late/culmination-stage sorocarp development annotation.
- id: PMID:18216168
title: Cytokinins induce sporulation in Dictyostelium.
findings:
- statement: AcrA and the histidine kinase DhkB are both required to transduce
the cytokinin (discadenine) signal that triggers spore encapsulation.
supporting_text: DhkB and the adenylyl cyclase of late development, AcrA, are
members of two component signal transduction families and both are required
to transduce the cytokinin signal
reference_review:
relevance: HIGH
correctness: VERIFIED
review_notes: Abstract-only in cache but the abstract explicitly names AcrA as
required for cytokinin signal transduction leading to sporulation.
- id: PMID:20966074
title: Functional dissection of adenylate cyclase R, an inducer of spore encapsulation.
findings:
- statement: ACR is essential for spore encapsulation and its multidomain
architecture includes seven TM helices, a histidine kinase domain, and two
receiver domains.
supporting_text: In addition to its cyclase (AC) domain, ACR harbors seven
transmembrane helices, a histidine kinase domain, and two receiver domains
- statement: ACR localizes to the endoplasmic reticulum and nuclear envelope.
supporting_text: This strongly suggests that ACR localizes to the endoplasmic
reticulum and nuclear envelope
- statement: ACR activity is not critically regulated by phosphorelay, and its
intramolecular histidine kinase activity is dispensable.
supporting_text: indicating that AC activity is not critically regulated by
phosphorelay
- statement: The degenerate HisKA subdomain lacks the canonical
autophosphorylation histidine yet is essential for AC activity, promoting
dimerization of the cyclase domain.
supporting_text: the dimerizing histidine phosphoacceptor subdomain, which in
ACR lacks the canonical histidine for autophosphorylation, was essential for
AC activity
reference_review:
relevance: HIGH
correctness: VERIFIED
review_notes: Full text available; the definitive domain-dissection and
localization study, and the basis for removing the phosphorelay and
transferase (histidine-kinase) domain-based IEA annotations.
- id: PMID:41057014
title: Transcriptomic and metabolomic insights into light-mediated unicellular-to-multicellular
transition in Dictyostelium discoideum.
findings:
- statement: acrA is a light-responsive differentially expressed gene,
downregulated in the dark in the unicellular phase.
supporting_text: Here we also observed that the adenylate cyclase gene acrA was
downregulated under dark in the unicellular phase
reference_review:
relevance: LOW
correctness: VERIFIED
review_notes: Full text available; supports only the expression-level (HEP)
light-response annotation, not a direct protein function.
core_functions:
- description: ACR is the terminal-differentiation-specific adenylate cyclase
that synthesizes cAMP (from ATP, EC 4.6.1.1) at the endoplasmic reticulum and
nuclear envelope during culmination. The cAMP it produces activates PKA to
drive spore encapsulation/maturation and proper stalk formation. Catalysis
requires homodimerization mediated by the degenerate histidine-kinase (HisKA)
domain rather than any phosphorelay or kinase activity.
molecular_function:
id: GO:0004016
label: adenylate cyclase activity
directly_involved_in:
- id: GO:0006171
label: cAMP biosynthetic process
- id: GO:0044671
label: sorocarp spore cell differentiation
- id: GO:0031288
label: sorocarp morphogenesis
locations:
- id: GO:0005783
label: endoplasmic reticulum
- id: GO:0005635
label: nuclear envelope
supported_by:
- reference_id: PMID:10556070
supporting_text: As long as ACA is fully active, ACR is not required until
culmination but then plays a critical role in sporulation and construction
of the stalk
- reference_id: PMID:20966074
supporting_text: adenylate cyclase R (ACR), is essential for spore
encapsulation
- reference_id: PMID:20966074
supporting_text: This strongly suggests that ACR localizes to the endoplasmic
reticulum and nuclear envelope