id: Q93P57 gene_symbol: actC product_type: PROTEIN status: COMPLETE taxon: id: NCBITaxon:34 label: Myxococcus xanthus description: '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.' existing_annotations: - term: id: GO:0004029 label: aldehyde dehydrogenase (NAD+) activity evidence_type: IEA original_reference_id: GO_REF:0000118 qualifier: enables supporting_entities: - PANTHER:PTN005180820 review: 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. action: REMOVE 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.' supported_by: - reference_id: file:MYXXA/actC/actC-uniprot.txt supporting_text: SUPFAM; SSF51735; NAD(P)-binding Rossmann-fold domains; 1. record_section: - DR:SUPFAM - reference_id: file:MYXXA/actC/actC-uniprot.txt supporting_text: Gene3D; 3.40.50.720; NAD(P)-binding Rossmann-like Domain; 1. record_section: - DR:Gene3D - reference_id: file:MYXXA/actC/actC-uniprot.txt supporting_text: PANTHER; PTHR48079; PROTEIN YEEZ; 1. record_section: - DR:PANTHER - reference_id: file:MYXXA/actC/actC-uniprot.txt supporting_text: PROSITE; PS51186; GNAT; 1. record_section: - DR:PROSITE - reference_id: file:MYXXA/actC/actC-bioinformatics/RESULTS.md supporting_text: 'NAD+-dependent aldehyde dehydrogenases (EC 1.2.1.3) are the ALDH superfamily (Pfam PF00171, SUPFAM SSF53720), and Q93P57 matches none of those signatures' - reference_id: file:MYXXA/actC/actC-bioinformatics/RESULTS.md supporting_text: 'QuickGO served `numberOfHits: 2648` for `withFrom=PANTHER:PTN005180820`, the ancestral node behind Q93P57''s TreeGrafter rows.' source_defects: - defect_type: WRONG_TERM resource: PANTHER record: PANTHER:PTN005180820 slot: GO_ID requested_change: REPOINT asserted_value: GO:0004029 corrected_value: GO:0004022 corrected_label: alcohol dehydrogenase (NAD+) activity cause: OVER_PROPAGATION confidence: CONFIRMED explanation: >- Resource is PANTHER: the defect is the node's own GO association, which UniProt's TreeGrafter emits as GO_REF:0000118. Not GO_CENTRAL - PAINT owns a separate node, PTN002449572, dealt with below. PANTHER node PTN005180820, in family PTHR48079 (InterPro IPR051783, "NAD(P)-dependent Metabolic Enzyme"), asserts GO:0004029 aldehyde dehydrogenase (NAD+) activity, and QuickGO serves 2,648 annotations whose WITH/FROM is that node, i.e. 1,324 proteins across 1,277 taxa carrying GO:0004029 and the same number carrying GO:0005737 (checked 2026-11-01). Tracing the term to its origin identifies a single seed: of the 56 proteins in GOA with an experimental GO:0004029 annotation, 29 are in PTHR11699, the real ALDH family, and exactly one is in PTHR48079 - UniProtKB:Q12177 (YLL056C, S. cerevisiae), whose IDA cites PMID:28265724. That paper is titled "YLL056C from Saccharomyces cerevisiae encodes a novel protein with aldehyde reductase activity" and reports "an NADH-dependent aldehyde reductase, which can reduce at least seven aldehyde compounds". A reductase takes an aldehyde to an alcohol; GO:0004029 is defined as aldehyde + H2O + NAD+ = carboxylate, the opposite direction with a different product and a different EC class. So the seed annotation states the wrong reaction, and the node inherits the error rather than introducing it. The corrected value given here, GO:0004022 alcohol dehydrogenase (NAD+) activity, is what the paper supports for the seed written in GO's oxidative direction; GO:0018455 may suit better given the substrate breadth. The family-level claim is doubtful independently of the term: the recipients are PTHR48079:SF6 while the seed is SF9, and spot-checking them returns dTDP-glucose 4,6-dehydratase, GDP-fucose synthase, GDP-mannose 4,6-dehydratase, sterol-4alpha-carboxylate 3-dehydrogenase and many copies of E. coli YeeZ - extended-SDR Rossmann enzymes carrying Pfam PF01370 or PF13460, not the ALDH superfamily fold (PF00171, SSF53720). Myxococcus xanthus ActC (UniProtKB:Q93P57) matches none of the ALDH signatures either; its only domains are a Rossmann-like NAD(P)-binding domain and a GNAT N-acetyltransferase domain. This is not a donor-count objection: a one-donor node can be sound, and the complaint is the content of the seed's term, not how many donors support it. Fix order is SGD first, then the PAINT IBD at PTN002449572 (63 IBA rows), then this node (1,324 TreeGrafter rows). The REPOINT recorded here is the MINIMUM ask, not the preferred one: repointing substitutes one family-level catalytic claim for another across the same 1,324 proteins, and a node spanning SF6 and SF9 over dTDP-glucose 4,6-dehydratase, GDP-fucose synthase and YeeZ copies arguably should assert no specific catalytic MF at all. Deletion of the node's MF association is therefore the preferred outcome. It is stated in prose rather than as a second defect entry because the two are alternatives on one record, not two independent asks, and requested_change is single-valued; filing both would double-count the defect. Written up in projects/CACAO/upstream-panther-aldh-propagation.md. supported_by: - reference_id: file:MYXXA/actC/actC-bioinformatics/RESULTS.md supporting_text: 'QuickGO served `numberOfHits: 2648` for `withFrom=PANTHER:PTN005180820`, the ancestral node behind Q93P57''s TreeGrafter rows.' - reference_id: file:MYXXA/actC/actC-bioinformatics/RESULTS.md supporting_text: 'NAD+-dependent aldehyde dehydrogenases (EC 1.2.1.3) are the ALDH superfamily (Pfam PF00171, SUPFAM SSF53720), and Q93P57 matches none of those signatures' - reference_id: file:MYXXA/actC/actC-uniprot.txt supporting_text: PANTHER; PTHR48079; PROTEIN YEEZ; 1. record_section: - DR:PANTHER - term: id: GO:0005737 label: cytoplasm evidence_type: IEA original_reference_id: GO_REF:0000118 qualifier: located_in supporting_entities: - PANTHER:PTN005180820 review: 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. action: ACCEPT 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.' supported_by: - reference_id: file:MYXXA/actC/actC-uniprot.txt supporting_text: DOMAIN 273..437 record_section: - FT:DOMAIN - reference_id: PMID:17189369 supporting_text: Since deletion of actC leads to precocious C-signal-dependent gene expression, actC protein appears to inhibit the rise of csgA expression reference_section_type: DISCUSSION - term: id: GO:0009966 label: regulation of signal transduction evidence_type: IMP original_reference_id: PMID:11359579 qualifier: involved_in review: 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.' action: MODIFY 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_replacement_terms: - id: GO:0009968 label: negative regulation of signal transduction additional_reference_ids: - PMID:11807078 - PMID:17189369 supported_by: - reference_id: PMID:11359579 supporting_text: The C-signal is a morphogen that controls the assembly of fruiting bodies and the differentiation of myxospores reference_section_type: ABSTRACT - reference_id: PMID:11359579 supporting_text: 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 reference_section_type: ABSTRACT - reference_id: PMID:11359579 supporting_text: 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 reference_section_type: ABSTRACT - reference_id: PMID:17189369 supporting_text: Since deletion of actC leads to precocious C-signal-dependent gene expression, actC protein appears to inhibit the rise of csgA expression reference_section_type: DISCUSSION - reference_id: PMID:11807078 supporting_text: 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 reference_section_type: ABSTRACT - term: id: GO:0016407 label: acetyltransferase activity evidence_type: IEA original_reference_id: GO_REF:0000104 qualifier: enables supporting_entities: - UniRule:UR000414522 review: 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. action: MODIFY 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_replacement_terms: - id: GO:0008080 label: N-acetyltransferase activity supported_by: - reference_id: file:MYXXA/actC/actC-uniprot.txt supporting_text: DOMAIN 273..437 record_section: - FT:DOMAIN - reference_id: file:MYXXA/actC/actC-uniprot.txt supporting_text: /note="N-acetyltransferase" record_section: - FT:DOMAIN - reference_id: file:MYXXA/actC/actC-uniprot.txt supporting_text: PROSITE; PS51186; GNAT; 1. record_section: - DR:PROSITE - reference_id: file:MYXXA/actC/actC-uniprot.txt supporting_text: Pfam; PF00583; Acetyltransf_1; 1. record_section: - DR:Pfam - reference_id: file:MYXXA/actC/actC-uniprot.txt supporting_text: 'PE 4: Predicted;' record_section: - PE - term: id: GO:0016740 label: transferase activity evidence_type: IEA original_reference_id: GO_REF:0000104 qualifier: enables supporting_entities: - UniRule:UR000414522 review: 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. action: TOO_GENERAL 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.' supported_by: - reference_id: file:MYXXA/actC/actC-uniprot.txt supporting_text: PROSITE; PS51186; GNAT; 1. record_section: - DR:PROSITE - reference_id: file:MYXXA/actC/actC-uniprot.txt supporting_text: Pfam; PF00583; Acetyltransf_1; 1. record_section: - DR:Pfam - term: id: GO:0016747 label: acyltransferase activity, transferring groups other than amino-acyl groups evidence_type: IEA original_reference_id: GO_REF:0000002 qualifier: enables supporting_entities: - InterPro:IPR000182 review: summary: InterPro2GO mapping of IPR000182 (GNAT domain), the same domain that drives the UniRule rows. Correct genus, two levels above what the signature specifies. action: MODIFY 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_replacement_terms: - id: GO:0008080 label: N-acetyltransferase activity supported_by: - reference_id: file:MYXXA/actC/actC-uniprot.txt supporting_text: DOMAIN 273..437 record_section: - FT:DOMAIN - reference_id: file:MYXXA/actC/actC-uniprot.txt supporting_text: /note="N-acetyltransferase" record_section: - FT:DOMAIN - reference_id: file:MYXXA/actC/actC-uniprot.txt supporting_text: Pfam; PF00583; Acetyltransf_1; 1. record_section: - DR:Pfam - reference_id: file:MYXXA/actC/actC-uniprot.txt supporting_text: 'PE 4: Predicted;' record_section: - PE - term: id: GO:0031155 label: regulation of reproductive fruiting body development evidence_type: IMP original_reference_id: PMID:11359579 qualifier: involved_in review: 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. action: ACCEPT 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.' additional_reference_ids: - PMID:17189369 - PMID:11807078 supported_by: - reference_id: PMID:17189369 supporting_text: deletion of the actC gene led to the premature formation of many small fruiting bodies reference_section_type: INTRODUCTION - reference_id: PMID:11359579 supporting_text: 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 reference_section_type: ABSTRACT - reference_id: PMID:11359579 supporting_text: The C-signal is a morphogen that controls the assembly of fruiting bodies and the differentiation of myxospores reference_section_type: ABSTRACT - reference_id: PMID:11807078 supporting_text: 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 reference_section_type: ABSTRACT source_defects: - defect_type: OTHER resource: UNIPROT record: Q93P57 requested_change: CHECK asserted_value: UniProtKB:Q93P57 corrected_value: UniProtKB:Q1D7F7 corrected_label: ActC (MXAN_3215), Myxococcus xanthus DK1622 reference proteome cause: OTHER confidence: CONFIRMED explanation: 'UniProtKB holds two entries for this protein. Q93P57 (NCBI taxon 34, Myxococcus xanthus) comes from GenBank AF350253, the sequence submitted with PMID:11359579, whose own RC line records STRAIN=DK1622. Q1D7F7 (NCBI taxon 246197, M. xanthus strain DK1622) comes from the DK1622 genome CP000113. The two sequences are byte-identical over 437 residues (md5 35f6afd6eb648ed125515102dc4ef8c1, verified by fetching both on 2026-11-01) and share RefSeq WP_011553262.1, so they are the same protein of the same strain. The consequences are not cosmetic. Only Q1D7F7 is in reference proteome UP000002402, so it is the ActC reached through the proteome, STRING, KEGG and EnsemblBacteria - yet all three experimental developmental annotations (GO:0031155, GO:0009966, GO:0043937, each IMP from PMID:11359579) sit on Q93P57, and Q1D7F7 carries only three IEA rows. The same redundancy splits the operon: actA and actC are annotated on the taxon-34 entries, actB on the DK1622 entry Q1D7F8, because actB has a GN Name only on the DK1622 side and actC only on the taxon-34 side (Q1D7F7 has no GN Name at all). Requests, in order of value: merge the redundant pair, or failing that add GN Name=actC to Q1D7F7 so the gene is findable on the proteome entry. The same duplication affects actA (Q93P59/Q1D7F9, which differ at 2 of 342 residues) and actB (Q93P58/Q1D7F8, identical).' supported_by: - reference_id: file:MYXXA/actC/actC-bioinformatics/RESULTS.md supporting_text: '| length / sequence md5 | 437 / `35f6afd6eb648ed125515102dc4ef8c1` | 437 / `35f6afd6eb648ed125515102dc4ef8c1` |' - reference_id: file:MYXXA/actC/actC-bioinformatics/RESULTS.md supporting_text: '| reference proteome | none | `UP000002402` |' - reference_id: file:MYXXA/actC/actC-bioinformatics/RESULTS.md supporting_text: 'carries only the three IEA rows (`GO:0005737`, `GO:0016747`, `GO:0004029`) and none of the experimental ones.' - reference_id: file:MYXXA/actC/actC-bioinformatics/RESULTS.md supporting_text: '`actB` is a `GN Name` only on the DK1622 side, `actC` only on the taxon-34 side' - reference_id: file:MYXXA/actC/actC-uniprot.txt supporting_text: STRAIN=DK1622 record_section: - REF - reference_id: PMID:17189369 supporting_text: The entire sequence was verified in the complete sequence of the M. xanthus genome, GenBank accession number CP000113 reference_section_type: RESULTS - term: id: GO:0043937 label: regulation of sporulation evidence_type: IMP original_reference_id: PMID:11359579 qualifier: involved_in review: 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. action: MODIFY proposed_replacement_terms: - id: GO:0042173 label: regulation of sporulation resulting in formation of a cellular spore 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.' additional_reference_ids: - PMID:11807078 - PMID:17189369 supported_by: - reference_id: PMID:11807078 supporting_text: 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 reference_section_type: ABSTRACT - reference_id: PMID:11807078 supporting_text: 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 reference_section_type: ABSTRACT - reference_id: PMID:17189369 supporting_text: The cell-surface-associated, nondiffusible C signal is essential for both fruiting body formation and sporulation reference_section_type: INTRODUCTION - reference_id: PMID:17189369 supporting_text: Sporulation genes have a higher threshold of C-signal intensity than genes for aggregation reference_section_type: INTRODUCTION - reference_id: PMID:11359579 supporting_text: 'The act A and act B mutants have the same developmental phenotype: both aggregate, neither sporulates, both prolong rippling' reference_section_type: ABSTRACT - term: id: GO:0010629 label: negative regulation of gene expression evidence_type: IMP original_reference_id: PMID:11359579 qualifier: involved_in review: action: 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.' additional_reference_ids: - PMID:11807078 - PMID:17189369 supported_by: - reference_id: PMID:11359579 supporting_text: The act C and act D genes regulate the time pattern of CsgA production, while achieving the same maximum level reference_section_type: ABSTRACT - reference_id: PMID:11359579 supporting_text: 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 reference_section_type: ABSTRACT - reference_id: PMID:17189369 supporting_text: Since deletion of actC leads to precocious C-signal-dependent gene expression, actC protein appears to inhibit the rise of csgA expression reference_section_type: DISCUSSION - reference_id: PMID:11807078 supporting_text: Earlier work has shown that transcription of the csgA gene, which encodes the C-signal, is directed by four genes of the act operon reference_section_type: ABSTRACT - reference_id: PMID:11807078 supporting_text: Neither the time of first expression nor the rate of expression increase was changed in actA, actB, actC, or actD mutant strains reference_section_type: ABSTRACT core_functions: - description: 'Timing brake on C-signal production during fruiting-body development: ActC, expressed from the act operon, holds down the rise of csgA expression so that the CsgA morphogen accumulates on schedule. In its absence CsgA rises about 15 h early to the same maximum, C-signal-dependent aggregation and sporulation genes are expressed prematurely, and many small fruiting bodies form ahead of time, while C-signal-independent early development is unchanged. No molecular_function term is asserted: the protein carries a GNAT N-acetyltransferase domain and an NAD(P)-binding Rossmann-like domain, but no activity, acceptor substrate or target has been assayed, so the predicted N-acetyltransferase activity is a domain-level inference rather than an established core activity.' directly_involved_in: - id: GO:0010629 label: negative regulation of gene expression - id: GO:0031155 label: regulation of reproductive fruiting body development locations: - id: GO:0005737 label: cytoplasm supported_by: - reference_id: PMID:11359579 supporting_text: The act C and act D genes regulate the time pattern of CsgA production, while achieving the same maximum level reference_section_type: ABSTRACT - reference_id: PMID:11359579 supporting_text: 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 reference_section_type: ABSTRACT - reference_id: PMID:17189369 supporting_text: deletion of the actC gene led to the premature formation of many small fruiting bodies reference_section_type: INTRODUCTION - reference_id: PMID:17189369 supporting_text: Since deletion of actC leads to precocious C-signal-dependent gene expression, actC protein appears to inhibit the rise of csgA expression reference_section_type: DISCUSSION - reference_id: PMID:11807078 supporting_text: 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 reference_section_type: ABSTRACT - reference_id: file:MYXXA/actC/actC-uniprot.txt supporting_text: /note="N-acetyltransferase" record_section: - FT:DOMAIN knowledge_gaps: - gap_statement: 'ActC''s molecular activity and its target are undetermined: whether the GNAT domain acetylates anything, what the acceptor is, whether the NAD(P)-binding Rossmann domain binds a dinucleotide or catalyses a reaction, and by what step the protein lowers csgA expression.' boundary: 'What is firmly established is genetic and quantitative: actC is co-transcribed with the other act genes, its null mutant advances CsgA accumulation by about 15 h without changing the maximum, advances C-signal-dependent aggregation and sporulation gene expression, and produces many small fruiting bodies prematurely, while leaving C-signal-independent early development untouched. The domain architecture is also established from signatures.' gap_kind: - BIOLOGY dark_aspect: MF_DARK significance: ActC is the only identified negative component of the act timing circuit, and the circuit is the clock that sets fruiting-body number and size through C-signal kinetics. Without its activity the mechanism of developmental timing in this organism stops at a genetic epistasis and cannot be modelled biochemically; it also leaves the GNAT domain prediction, which is the only molecular handle on the protein, untestable. resolution: 'Assay purified ActC for acetyl-CoA-dependent acetyltransferase activity and identify its acceptor, and test whether it binds the csgA promoter region or acts through another act product. The only mechanism on offer is a proposal (PMID:17189369): ActC and ActD made in comparable amounts from one operon, ActC inhibiting csgA expression, and the ActD caspase-like protease degrading ActC to release the inhibition on schedule.' references: - id: GO_REF:0000002 title: Gene Ontology annotation through association of InterPro records with GO terms findings: [] reference_review: relevance: LOW correctness: VERIFIED review_notes: InterPro2GO mapping of IPR000182 (GNAT domain) to GO:0016747. The domain match is real; the mapping is conservative and two levels above the N-acetyltransferase specificity the signature carries, so the row is modified rather than removed. - id: GO_REF:0000104 title: Electronic Gene Ontology annotations created by transferring manual GO annotations between related proteins based on shared sequence features findings: [] reference_review: relevance: LOW correctness: VERIFIED review_notes: UniRule UR000414522, driven by PROSITE-ProRule PRU00532 on the GNAT domain. Source of the acetyltransferase and transferase rows; sound as a domain-level prediction, uninformative at the transferase root. - id: GO_REF:0000118 title: TreeGrafter-generated GO annotations findings: [] reference_review: relevance: LOW correctness: MISCITED review_notes: 'The TreeGrafter graft onto PANTHER node PTN005180820 supplies two rows of very different quality. Cytoplasm is sound. Aldehyde dehydrogenase (NAD+) activity is not: the node''s family PTHR48079 is one of NAD(P)-binding Rossmann-fold ketoreductases, epimerases and dehydratases, not of ALDH-superfamily enzymes, and Q93P57 matches no ALDH signature. The node emits the same term pair to roughly 1,324 proteins (QuickGO, 2026-11-01), so the defect is systematic rather than specific to this gene. Filed as a source defect against PANTHER, whose node association TreeGrafter propagates, not GO Central: PAINT owns a separate node (PTN002449572).' - id: PMID:11359579 title: The act operon controls the level and time of C-signal production for Myxococcus xanthus development. findings: - statement: The act operon, four co-transcribed genes at the time of this paper, regulates production of the CsgA C-signal, the morphogen controlling fruiting-body assembly and myxospore differentiation. supporting_text: 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 reference_section_type: ABSTRACT - statement: actC and actD control the timing rather than the magnitude of CsgA production; the actC null mutant raises CsgA 15 h early at the same maximum level. supporting_text: The act C and act D genes regulate the time pattern of CsgA production, while achieving the same maximum level reference_section_type: ABSTRACT - statement: The sporulation and aggregation phenotypes reported in the abstract belong to actA and actB, not to actC. supporting_text: 'The act A and act B mutants have the same developmental phenotype: both aggregate, neither sporulates, both prolong rippling' reference_section_type: ABSTRACT full_text_unavailable: true reference_review: relevance: HIGH correctness: VERIFIED review_notes: 'Verified against PubMed and Europe PMC: Gronewold & Kaiser, Mol Microbiol 40:744-756 (2001), the paper all three CACAO rows cite, and the source of GenBank AF350253 from which UniProt Q93P57 derives. Not open access (Europe PMC isOpenAccess N, inEPMC N, no PMCID) and abstract-only in our cache, so the full text was not read; the abstract is nonetheless explicit about actC, and the actC fruiting-body phenotype is restated from this paper in PMID:17189369. The strain is DK1622, recorded on the entry''s own RC line and confirmed by the follow-up paper''s statement that the submitted sequence matches the DK1622 genome CP000113.' - id: PMID:11807078 title: act operon control of developmental gene expression in Myxococcus xanthus. findings: - statement: Loss-of-function mutations in each act gene leave C-signal-independent early development untouched, including the time of first expression and the rate of increase of genes expressed up to 3 h. supporting_text: Neither the time of first expression nor the rate of expression increase was changed in actA, actB, actC, or actD mutant strains reference_section_type: ABSTRACT - statement: The actC null mutation causes premature expression of aggregation- and sporulation-related reporters, which still reach wild-type levels; actD delays them. supporting_text: 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 reference_section_type: ABSTRACT full_text_unavailable: true reference_review: relevance: HIGH correctness: VERIFIED review_notes: 'Verified against PubMed: Gronewold & Kaiser, J Bacteriol 184:1172-1179 (2002), PMC134796. Abstract-only in our cache (the PMC HTML and PDF fallbacks both returned no body on fetch). Not the reference cited by any GOA row; used here to establish that actC''s effect on aggregation and sporulation gene expression is a timing shift to unchanged final levels, which is what makes the sporulation row non-core.' - id: PMID:17189369 title: Mutations of the act promoter in Myxococcus xanthus. findings: - statement: The actC deletion phenotype reported in PMID:11359579 is premature formation of many small fruiting bodies, resembling a 10-fold overexpression of CsgA. supporting_text: deletion of the actC gene led to the premature formation of many small fruiting bodies reference_section_type: INTRODUCTION - statement: The authors conclude that ActC inhibits the rise of csgA expression, and propose that the ActD protease degrades ActC to release the inhibition on schedule. supporting_text: Since deletion of actC leads to precocious C-signal-dependent gene expression, actC protein appears to inhibit the rise of csgA expression reference_section_type: DISCUSSION - statement: The act operon has five genes, actA to actE, co-expressed as one transcription unit; actE was not part of the four-gene operon described in 2001. supporting_text: actE , are expressed together and constitute an operon, because an in-frame deletion of actB decreased expression of actA and actE to the same extent reference_section_type: RESULTS - statement: The AF350253 sequence submitted with the 2001 paper was verified against the DK1622 genome sequence CP000113, establishing that the species-level and DK1622-level records describe one organism. supporting_text: The entire sequence was verified in the complete sequence of the M. xanthus genome, GenBank accession number CP000113 reference_section_type: RESULTS reference_review: relevance: HIGH correctness: VERIFIED review_notes: 'Verified against PubMed and fetched as full text from PMC1855723: Gronewold & Kaiser, J Bacteriol 189:1836-1844 (2007). Not cited by any GOA row. Decisive for this review on three counts: it restates the actC fruiting-body phenotype while citing PMID:11359579, it states the direction of ActC''s effect on csgA expression, and it ties AF350253 to the DK1622 genome, which is what rules out the cross-isolate reading of the two taxon ids. The ActC-degraded-by-ActD mechanism in its discussion is explicitly a proposal, and is treated as such.' - id: file:MYXXA/actC/actC-uniprot.txt title: UniProt record for actC (Q93P57) findings: [] reference_review: relevance: MEDIUM correctness: VERIFIED review_notes: Unreviewed TrEMBL entry, PE 4 (Predicted), with no functional comments. Used for domain and family signatures (FT N-acetyltransferase domain 273-437, PROSITE PS51186, Pfam PF00583, Gene3D 3.40.50.720, SUPFAM SSF51735, PANTHER PTHR48079) and for the RC STRAIN=DK1622 line. Its DR GO lines and keywords restate the annotations under review and are not cited as support. - id: file:MYXXA/actC/actC-bioinformatics/RESULTS.md title: 'Bioinformatics: UniProtKB entry duplication across two taxon ids for the act operon, and the span of the PTN005180820 graft' findings: [] reference_review: relevance: HIGH correctness: VERIFIED review_notes: Own analysis, reproducible from check_act_entries.py in the same folder; it only compares public records and predicts nothing. Establishes that Q93P57 and Q1D7F7 are byte-identical and share a RefSeq accession, that only Q1D7F7 is in the reference proteome while only Q93P57 carries the experimental rows, and that PTN005180820 emits GO:0004029 and GO:0005737 to roughly 1,324 proteins. suggested_questions: - question: 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. experts: - Gronewold TM - Kaiser D - question: 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. experts: - Gronewold TM - Kaiser D - question: 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. experts: [] - question: 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. experts: [] suggested_experiments: - hypothesis: The GNAT domain of ActC is catalytically active and acetylates a protein of the C-signalling or act circuit. description: 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. experiment_type: in vitro enzyme assay with targeted mutagenesis - hypothesis: ActC is degraded during development by the ActD protease, and this is what releases csgA expression on schedule. description: 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. experiment_type: developmental time-course immunoblot and in vitro proteolysis - hypothesis: ActC lowers csgA expression by acting at or near the csgA promoter. description: 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. experiment_type: DNA-binding assays and ChIP-seq - hypothesis: actC regulates the timing of sporulation but not sporulation competence. description: 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. experiment_type: quantitative sporulation time course