ActC is one of the proteins encoded by the act operon of Myxococcus xanthus, a single transcription unit (actA-actE) that sets the level and the timing of C-signal production during starvation-induced fruiting-body development. The C-signal is the cell-surface morphogen encoded by csgA; it coordinates cell aggregation and the differentiation of myxospores, with sporulation genes requiring a higher C-signal threshold than aggregation genes. Within the operon actA and actB fix how high the C-signal can rise, while actC and actD govern when it rises. ActC is the brake: cells lacking actC begin accumulating CsgA about 15 hours earlier than wild type, reach the normal maximum, express C-signal-dependent aggregation and sporulation genes prematurely, and form many small fruiting bodies ahead of schedule, while early C-signal-independent development is unaffected. ActC therefore restrains the rise of csgA expression and, through it, the schedule of C-signal-dependent development; one proposal has the ActD protease degrading ActC to release that inhibition at the appropriate time. The 437-residue protein combines an N-terminal NAD(P)-binding Rossmann-like domain with a C-terminal GNAT (GCN5-related N-acetyltransferase) domain, but no catalytic activity, substrate, acetylation target or binding partner has been assayed, so the molecular mechanism of the inhibition is unknown.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0004029 aldehyde dehydrogenase (NAD+) activity | IEA GO_REF:0000118 | REMOVE | Summary: TreeGrafter graft onto PANTHER ancestral node PTN005180820, asserting the EC 1.2.1.3 activity. ActC has no ALDH-superfamily signature; its NAD(P)-binding domain is the Rossmann-like fold shared by short-chain dehydrogenases/reductases and NAD-dependent epimerases/dehydratases, and its only other domain is GNAT. The node emits this one term pair to ~1,300 proteins. Reason: An over-propagated electronic inference that can be argued against on fold grounds, which is the sanctioned ground for REMOVE on an IEA row. NAD+-dependent aldehyde dehydrogenases belong to the ALDH superfamily (Pfam PF00171 Aldedh, SUPFAM SSF53720) and Q93P57 matches none of those signatures: it carries Gene3D 3.40.50.720 / SUPFAM SSF51735, the NAD(P)-binding Rossmann-like fold, plus a GNAT domain. PANTHER itself names the family PTHR48079 "PROTEIN YEEZ", whose InterPro integration IPR051783 is a family of ketoreductases, epimerases and dehydratases with no aldehyde dehydrogenase among its listed members. This is not a judgement about whether the Rossmann domain binds NAD(P) - it very likely does - but about the specific reaction asserted. Note that the error is systematic rather than specific to this gene: QuickGO serves 2,648 annotations from PTN005180820, all of them this term or cytoplasm, so the node projects an aldehyde-dehydrogenase assertion onto roughly 1,324 proteins. The companion cytoplasm row from the same node is sound and is kept. Supporting Evidence: file:MYXXA/actC/actC-uniprot.txt SUPFAM; SSF51735; NAD(P)-binding Rossmann-fold domains; 1. file:MYXXA/actC/actC-uniprot.txt Gene3D; 3.40.50.720; NAD(P)-binding Rossmann-like Domain; 1. file:MYXXA/actC/actC-uniprot.txt PANTHER; PTHR48079; PROTEIN YEEZ; 1. file:MYXXA/actC/actC-uniprot.txt PROSITE; PS51186; GNAT; 1. file:MYXXA/actC/actC-bioinformatics/RESULTS.md NAD+-dependent aldehyde dehydrogenases (EC 1.2.1.3) are the ALDH superfamily (Pfam PF00171, SUPFAM SSF53720), and Q93P57 matches none of those signatures file:MYXXA/actC/actC-bioinformatics/RESULTS.md QuickGO served `numberOfHits: 2648` for `withFrom=PANTHER:PTN005180820`, the ancestral node behind Q93P57's TreeGrafter rows. |
| GO:0005737 cytoplasm | IEA GO_REF:0000118 | ACCEPT | Summary: Soluble-cytoplasmic location from the same TreeGrafter graft. ActC has no transmembrane segment, no signal peptide and no lipoprotein motif in the record, and it acts on the expression of a chromosomal gene, so the cytoplasm is where its activity must happen. Reason: The claim is sound even though the node that supplies it also supplies a wrong molecular function: the two assertions are independent, and the location one is the generic consequence of the protein being soluble. For a bacterium, cytoplasm is as precise as the evidence (sequence-based, no sub-compartment resolvable) allows and is not a root organelle term, so no sub-compartment is proposed. The record shows no membrane or export feature of any kind - the only FT line is the N-acetyltransferase domain - and ActC's demonstrated action, restraining csgA expression, is necessarily intracellular. Supporting Evidence: file:MYXXA/actC/actC-uniprot.txt DOMAIN 273..437 PMID:17189369 Since deletion of actC leads to precocious C-signal-dependent gene expression, actC protein appears to inhibit the rise of csgA expression |
| GO:0009966 regulation of signal transduction | IMP PMID:11359579 The act operon controls the level and time of C-signal produ... | MODIFY | Summary: CACAO row. The cited paper shows that the act operon regulates production of the C-signal, the CsgA morphogen that drives fruiting-body assembly and myxospore differentiation, and that actC specifically sets the time pattern of CsgA production: an actC null mutant raises CsgA 15 h earlier than wild type while reaching the same maximum. Regulating the C-signal does regulate C-signalling, so the term is true of actC; the direction is known and the term does not state it. Reason: Right claim, unsigned term. Every reported actC phenotype is a release of a restraint: the null mutant produces CsgA 15 h early (PMID:11359579) and expresses C-signal-dependent aggregation and sporulation reporters prematurely (PMID:11807078), and the authors draw the conclusion explicitly in PMID:17189369 - actC inhibits the rise of csgA expression. ActC therefore reduces the rate at which C-signalling increases, which is negative regulation, and GO:0009968 is the is_a child of this term that says so. This is the standard sign refinement, not a change of claim. Two points in favour of keeping the row in this neighbourhood at all: the paper's readout is the signal's own production rather than any step inside a receiving cell, which would argue for the regulation-of-signaling branch, but the act operon is itself part of a C-signal-responsive positive feedback loop (ActA relays C-signal to the sigma-54 activator ActB, which drives act and csgA expression), so actC modulates a signal transduction pathway it also sits inside, and GO:0009968 remains defensible as well as more informative. The student's choice of a regulation-of term rather than a bare signalling term was correct: ActC performs the regulation and the C-signalling cascade performs the transduction. Proposed replacements: negative regulation of signal transduction Supporting Evidence: PMID:11359579 The C-signal is a morphogen that controls the assembly of fruiting bodies and the differentiation of myxospores PMID:11359579 Production of this signal, which is encoded by the csgA gene, is regulated by the act operon of four genes that are co-transcribed from the same start site PMID:11359579 An act C null mutant raises CsgA production 15 h earlier than the wild type, whereas an act D null mutant does so 6 h later than wild type PMID:17189369 Since deletion of actC leads to precocious C-signal-dependent gene expression, actC protein appears to inhibit the rise of csgA expression PMID:11807078 The other act null mutations caused either premature expression to wild-type levels (actC) or delayed expression (actD), which ultimately rose to wild-type levels |
| GO:0016407 acetyltransferase activity | IEA GO_REF:0000104 | MODIFY | Summary: UniRule inference from the GNAT domain that occupies residues 273-437 of ActC. The domain match is genuine, but no acetyltransferase activity, acetyl donor or acceptor has ever been assayed for this protein, and the term stops one level above what the signature actually specifies. Reason: The GNAT match is real: the UniProt record carries a 273-437 N-acetyltransferase domain feature, PROSITE PS51186 (GNAT) and Pfam PF00583. The domain family is specifically an N-acetyltransferase, transferring acetyl to a nitrogen acceptor, which GO:0008080 states and the annotated term does not. GO:0008080 is an is_a child of this term, so this is a refinement to the specificity the evidence carries, with the evidence unchanged - it remains a domain-level prediction on a PE 4 (Predicted) entry, not a measured activity, and the review does not place it among the core functions. Keeping it rather than removing it is right: a GNAT domain is a positive, well-defined structural prediction and the protein's unknown mechanism may well run through it. The one caution worth recording is that domain presence does not establish catalysis; several GNAT-fold proteins are non-catalytic binding modules, and only an assay can settle whether ActC acetylates anything. Proposed replacements: N-acetyltransferase activity Supporting Evidence: file:MYXXA/actC/actC-uniprot.txt DOMAIN 273..437 file:MYXXA/actC/actC-uniprot.txt /note="N-acetyltransferase" file:MYXXA/actC/actC-uniprot.txt PROSITE; PS51186; GNAT; 1. file:MYXXA/actC/actC-uniprot.txt Pfam; PF00583; Acetyltransf_1; 1. file:MYXXA/actC/actC-uniprot.txt PE 4: Predicted; |
| GO:0016740 transferase activity | IEA GO_REF:0000104 | TOO GENERAL | Summary: The EC-class-2 root, from the same UniRule as the acetyltransferase row. True if the GNAT prediction is true, and uninformative either way. Reason: Not a claim this review doubts: it is entailed by GO:0008080 N-acetyltransferase activity, which the two more specific transferase rows are modified to. GO:0008080 is a descendant of GO:0016740 through GO:0016746 and GO:0016747, so asserting the specific term already asserts this one, and a bare "transferase activity" on a protein whose predicted domain is a defined N-acetyltransferase adds nothing a reader or a downstream pipeline can use. TOO_GENERAL rather than REMOVE because the term is not false and its removal would not be a correction. Supporting Evidence: file:MYXXA/actC/actC-uniprot.txt PROSITE; PS51186; GNAT; 1. file:MYXXA/actC/actC-uniprot.txt Pfam; PF00583; Acetyltransf_1; 1. |
| GO:0016747 acyltransferase activity, transferring groups other than amino-acyl groups | IEA GO_REF:0000002 | MODIFY | Summary: InterPro2GO mapping of IPR000182 (GNAT domain), the same domain that drives the UniRule rows. Correct genus, two levels above what the signature specifies. Reason: The GNAT match is real: the UniProt record carries a 273-437 N-acetyltransferase domain feature, PROSITE PS51186 (GNAT) and Pfam PF00583. The domain family is specifically an N-acetyltransferase, transferring acetyl to a nitrogen acceptor, which GO:0008080 states and the annotated term does not. GO:0008080 is a descendant of this term through GO:0016407, so the refinement loses nothing and the mapping itself is not at fault - IPR000182 is a domain entry and a conservative generic mapping is reasonable at the InterPro level. The action is kept identical to the GO:0016407 row because the two rows make the same claim from the same domain by different routes, and a review must not split them. As there, the activity stays a prediction, not a core function: nothing about ActC's catalysis has been measured. Proposed replacements: N-acetyltransferase activity Supporting Evidence: file:MYXXA/actC/actC-uniprot.txt DOMAIN 273..437 file:MYXXA/actC/actC-uniprot.txt /note="N-acetyltransferase" file:MYXXA/actC/actC-uniprot.txt Pfam; PF00583; Acetyltransf_1; 1. file:MYXXA/actC/actC-uniprot.txt PE 4: Predicted; |
| GO:0031155 regulation of reproductive fruiting body development | IMP PMID:11359579 The act operon controls the level and time of C-signal produ... | ACCEPT | Summary: CACAO row, and the best-grounded of the three. The cited paper's actC null mutant forms many small fruiting bodies prematurely - a morphological phenotype of the fruiting-body programme itself, which the same authors later restate while citing this paper. The mechanism is the 15 h advance in CsgA production that the same mutant shows. Reason: The claim, the gene and the paper all match, and the term is at the right altitude. PMID:17189369 attributes the morphology to this reference in terms: deletion of actC led to the premature formation of many small fruiting bodies. That is modulation of the rate and pattern of fruiting-body development, which is what GO:0031155 asserts, and it is a regulation-of term rather than the developmental process itself, which is the correct device here - ActC performs the regulation, while the C-signalling cascade executes the morphogenesis. The granularity question is worth stating because it is the obvious objection: the paper's primary actC measurement is csgA/CsgA timing, which is a step upstream, so one could argue the row is a phenotype read as a process. It is not, for two reasons. First, the fruiting-body phenotype is itself reported, not inferred. Second, C-signal is the direct and sufficient determinant of fruiting-body timing and size in this organism, so modulating its rise is modulating fruiting-body development rather than something several steps removed. The direct claim the paper also supports - negative regulation of csgA expression - is absent from GOA and is added as a NEW row rather than substituted for this one. Supporting Evidence: PMID:17189369 deletion of the actC gene led to the premature formation of many small fruiting bodies PMID:11359579 An act C null mutant raises CsgA production 15 h earlier than the wild type, whereas an act D null mutant does so 6 h later than wild type PMID:11359579 The C-signal is a morphogen that controls the assembly of fruiting bodies and the differentiation of myxospores PMID:11807078 These mutations changed the expression of four gene reporters that are related to aggregation and sporulation and are expressed at 6 h or later in development |
| GO:0043937 regulation of sporulation | IMP PMID:11359579 The act operon controls the level and time of C-signal produ... | MODIFY | Summary: CACAO row. Sporulation in Myxococcus xanthus is triggered by the highest C-signal levels, so a gene that sets when C-signal rises does modulate when sporulation is induced; the companion paper shows the actC null expresses sporulation-related reporters prematurely. But the sporulation phenotypes named in the cited abstract are actA's and actB's, not actC's, and no actC sporulation defect is reported in anything readable here. Reason: The claim is defensible but sits a step further out than the fruiting-body row and is timing-only, which is what makes it non-core rather than core. What the cited abstract attributes to actC is the time pattern of CsgA production at an unchanged maximum level; the sporulation phenotype it names belongs to the other two genes - the actA and actB mutants aggregate and neither sporulates. The actC-specific sporulation evidence is in the companion paper PMID:11807078, where the actC null expresses aggregation- and sporulation-related reporters prematurely but those reporters ultimately reach wild-type levels, so the effect is on scheduling and not on sporulation competence. Keeping the row is nevertheless right on the biology, since C-signal is essential for sporulation and sporulation genes have a higher C-signal threshold than aggregation genes, which is precisely the threshold whose crossing time actC sets. It is also right under the curator-deference rule: PMID:11359579 is not open access and our cache is abstract-only, the full text very likely reports spore yields for all four act mutants, and REMOVE on an IMP row from an abstract would be exactly the error this project has warned about. Peripheral, not over-annotated: the claim is not inflated, it is simply a step away from ActC's own job of restraining csgA expression, and that judgement is recorded here rather than by action, because the action has to carry the refinement. GO:0043937 is one level too general for this organism whoever makes the spore: Myxococcus xanthus makes myxospores, which are cellular spores, so the supported term is the child GO:0042173, and the sibling actA review refines the same term from the same paper on exactly that ground. The taxon argument is gene-independent, so applying it to actA and not here would have been an inconsistency rather than a judgement about this gene; per CLAUDE.md a correct-but-general term is MODIFY and KEEP_AS_NON_CORE is only for terms already as precise as the evidence allows. Proposed replacements: regulation of sporulation resulting in formation of a cellular spore Supporting Evidence: PMID:11807078 These mutations changed the expression of four gene reporters that are related to aggregation and sporulation and are expressed at 6 h or later in development PMID:11807078 The other act null mutations caused either premature expression to wild-type levels (actC) or delayed expression (actD), which ultimately rose to wild-type levels PMID:17189369 The cell-surface-associated, nondiffusible C signal is essential for both fruiting body formation and sporulation PMID:17189369 Sporulation genes have a higher threshold of C-signal intensity than genes for aggregation PMID:11359579 The act A and act B mutants have the same developmental phenotype: both aggregate, neither sporulates, both prolong rippling |
| GO:0010629 negative regulation of gene expression | IMP PMID:11359579 The act operon controls the level and time of C-signal produ... | NEW | Summary: ActC restrains the rise of csgA expression. Deleting it makes CsgA appear about 15 h early, at the normal maximum level, and makes C-signal-dependent reporters fire prematurely; the authors state the inference directly, that ActC inhibits the rise of csgA expression. Reason: This is ActC's own action and GOA states only its consequences. Three rows cover the downstream developmental and signalling effects; none says what the protein does, which is to hold csgA expression down until the right time. The participation test is satisfied by the entity question rather than by the knockout: the process is a decrease in the expression of a gene, and the entity that decreases it is ActC, not the C-signalling cascade that executes the development downstream. The polarity is unambiguous across three papers from the same group - precocious CsgA production (PMID:11359579), precocious C-signal-dependent reporter expression at unchanged final levels (PMID:11807078), and the explicit conclusion in PMID:17189369 - and it is specific rather than a general developmental delay, because early C-signal-independent expression is untouched in all four act mutants. Chosen deliberately at GO:0010629 rather than at GO:0045892 negative regulation of DNA-templated transcription: the reporters are transcriptional and the authors speak of csgA transcription, but ActC is a GNAT/Rossmann protein with no demonstrated DNA binding and the proposed mechanism has it acting as a labile inhibitor removed by the ActD protease, so the level at which it intervenes is not established and a transcription-specific term would assert more than is known. Proposed as the single missing term; no additional regulatory or metabolic terms are proposed, since nothing else about ActC's activity has been measured. Supporting Evidence: PMID:11359579 The act C and act D genes regulate the time pattern of CsgA production, while achieving the same maximum level PMID:11359579 An act C null mutant raises CsgA production 15 h earlier than the wild type, whereas an act D null mutant does so 6 h later than wild type PMID:17189369 Since deletion of actC leads to precocious C-signal-dependent gene expression, actC protein appears to inhibit the rise of csgA expression PMID:11807078 Earlier work has shown that transcription of the csgA gene, which encodes the C-signal, is directed by four genes of the act operon PMID:11807078 Neither the time of first expression nor the rate of expression increase was changed in actA, actB, actC, or actD mutant strains |
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Download this section (compressed HTML)Q: Does ActC have acetyltransferase activity at all, and if so what does it acetylate? The GNAT domain is the only molecular handle on the protein, and whether it is a catalytic domain or a non-catalytic binding module decides whether the molecular-function rows in GOA mean anything.
Suggested experts: Gronewold TM, Kaiser D
Q: Is the proposed ActD-mediated degradation of ActC real? The scheme in PMID:17189369 - comparable amounts of ActC and ActD made from one operon, ActC inhibiting csgA expression, the ActD caspase-like protease removing ActC to let csgA rise - is a hypothesis with no direct evidence, and it is the mechanism that would explain the opposite timing phenotypes of the two mutants.
Suggested experts: Gronewold TM, Kaiser D
Q: What does actE do, and should the act operon's GO annotations be revisited as a five-gene unit? actE was described after the 2001 paper that every current act annotation cites, and PMID:17189369 reports no homologues and no phenotype for it.
Q: Does ActC act on the csgA promoter, on another act product, or on a C-signal-responsive regulator? This is what decides whether negative regulation of DNA-templated transcription is the right term rather than the gene-expression parent used here.
Experiment: Express and purify full-length ActC and the isolated GNAT domain (residues 273-437), and assay acetyl-CoA-dependent acetyltransferase activity against a candidate panel - ActA, ActB, CsgA, FruA - and against M. xanthus developmental cell lysate, reading out by CoA release and by anti-acetyllysine immunoblot. Confirm any hit by mass spectrometry of the modified site and by mutating the conserved GNAT acetyl-CoA-binding motif in the chromosomal copy, which should reproduce the premature-CsgA phenotype of the null if catalysis is the relevant activity.
Hypothesis: The GNAT domain of ActC is catalytically active and acetylates a protein of the C-signalling or act circuit.
Type: in vitro enzyme assay with targeted mutagenesis
Experiment: Raise antibodies against ActC or tag the chromosomal copy, and follow ActC protein levels through development in wild type and in an actD null by immunoblot. The prediction is that ActC disappears at the time csgA expression rises in wild type and persists in the actD mutant, matching that mutant's 6 h delay. Pair this with an in vitro cleavage assay using purified ActD and ActC, and with the ActD catalytic-dyad mutant as a negative control.
Hypothesis: ActC is degraded during development by the ActD protease, and this is what releases csgA expression on schedule.
Type: developmental time-course immunoblot and in vitro proteolysis
Experiment: Test purified ActC for binding to the csgA promoter region by electrophoretic mobility shift and by DNase I footprinting, and in parallel map ActC occupancy genome-wide during development by ChIP-seq on a tagged chromosomal allele. A negative result on both would move the mechanism downstream of transcription initiation and would justify keeping the review's process term at the gene-expression level rather than refining it to a transcription term.
Hypothesis: ActC lowers csgA expression by acting at or near the csgA promoter.
Type: DNA-binding assays and ChIP-seq
Experiment: Score sporulation quantitatively in the actC null against DK1622 over a full developmental time course - heat- and sonication-resistant spore counts at 12, 18, 24, 48 and 72 h - rather than at a single endpoint. This directly tests the reading taken here, that the sporulation row is a timing effect at unchanged final competence, and it supplies the actC-specific sporulation datum that the cited paper's abstract does not state.
Hypothesis: actC regulates the timing of sporulation but not sporulation competence.
Type: quantitative sporulation time course
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