ActA is the first gene product of the five-gene act operon (actA-actE, MXAN_3213-MXAN_3217) of the fruiting-body-forming soil bacterium Myxococcus xanthus. It is a cytoplasmic response regulator: a CheY-like receiver domain (residues 41-157, with a phospho-accepting aspartate at position 90) fused to a C-terminal GGDEF-type output domain that lacks the canonical GG(D/E)EF catalytic motif and is therefore unlikely to act as a diguanylate cyclase. ActA works together with ActB, the sigma-54 activator encoded immediately downstream, in a signal transduction pathway that receives the C-signal, the cell-surface morphogen encoded by csgA that coordinates aggregation, rippling and myxospore differentiation during starvation-induced development. The pathway both responds to C-signal and raises csgA expression, forming a positive feedback loop, and ActA together with ActB sets the maximum level of C-signal reached: in an actA null mutant CsgA protein never exceeds a quarter of the wild-type peak, cells still aggregate and ripple (rippling is prolonged) but fail to sporulate. ActA is also required for the rapid, C-signal dependent second phase of transcription of its own operon, so it feeds back on act expression as well. The histidine kinase that phosphorylates ActA, the receptor that detects C-signal, and any ligand of the degenerate GGDEF domain are all unknown, and no biochemical activity has been measured for the protein.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0000160 phosphorelay signal transduction system | IEA GO_REF:0000002 | ACCEPT | Summary: Correct and informative: the InterPro receiver-domain signature matches residues 41-157 with the phospho-accepting Asp90 intact, and three independent publications describe ActA as a response regulator operating in a signal transduction pathway that receives the C-signal. This is the mechanistic core of the gene. Reason: IPR001789 is the response-regulator receiver (REC/CheY-like) domain, matched by PROSITE PS50110 over residues 41-157 of Q93P59, with a predicted 4-aspartylphosphate at Asp90. The inference is not left standing on the signature alone. The defining genetic study assigns the same identity ("By sequence homology, act A encodes a response regulator") and places ActA and ActB in one pathway that "responds to C-signal"; the promoter study restates it ("actA encodes a response regulator that works with actB") and gives the pathway logic explicitly, with C-signal signalling to ActA, which activates ActB; and the independent two-component-systems review of this organism agrees. The term is a process-level statement about participation in a phosphorelay, which is exactly what the evidence supports, so the granularity is right and no sub-term is needed. One caveat is recorded as a knowledge gap rather than as a reason to weaken the action: no histidine kinase has been shown to phosphorylate ActA, the C-signal receptor is unidentified, and phosphotransfer onto Asp90 has never been measured, so the phosphorelay is inferred from domain architecture plus genetics rather than demonstrated biochemically. Supporting Evidence: file:MYXXA/actA/actA-uniprot.txt Sig_transdc_resp-reg_receiver file:MYXXA/actA/actA-uniprot.txt Response regulatory file:MYXXA/actA/actA-uniprot.txt 4-aspartylphosphate PMID:11359579 By sequence homology, act A encodes a response regulator, and act B encodes a sigma-54 activator protein of the NTRC class. PMID:17189369 ActA and ActB appear to be part of a signal transduction pathway that receives input from C signal on the transmitting cell. PMID:26369581 ActA is a putative response regulator that is predicted to have a GGDEF-type effector domain, which is found in diguanylate cyclase enzymes. |
| 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, and the paper does assay actA itself: a dedicated actA null mutant caps CsgA (C-signal) at a quarter of the wild-type maximum. The claim is right, but the direction of the effect is established, so the sign-specific child GO:0009967 positive regulation of signal transduction is the supported term. Reason: What the paper shows for this gene, CACAO assessment. Gronewold and Kaiser constructed null mutants of each act gene separately and report the actA result by name in the abstract: in an actA (or actB) null the C-signal "never rises above one-quarter of the maximum wild-type level of CsgA protein". This is not an operon-wide phenotype attributed to one gene; the paper's whole point is that the four genes divide the job, with actA and actB setting the maximum level and actC and actD setting the timing. The pathway in which ActA sits both receives C-signal and raises CsgA production, "thus creating a positive feedback loop", so ActA modulates the extent of C-signal transduction and the term's essence is correct and sits at the right place in the ontology: a regulation-of-signalling term, not a developmental-process term that ActA would have to execute. Because the sign is determined (loss of actA reduces signalling; ActA is required for full C-signalling), the review replaces the unsigned parent with GO:0009967, an is_a child, under the rule that a correct but less specific term should be refined to the specific supported term. Granularity note, since the readout is csgA expression rather than signalling per se: a gene-expression regulation term is deliberately not proposed. ActA has no DNA-binding domain, the model is that it signals to the sigma-54 activator ActB, the DNA-binding member of the operon (and the member that carries GO:0006355 in UniProt), and a later independent analysis argues that even ActB does not bind the csgA promoter directly, so the csgA effect runs through at least one unidentified intermediate. The signalling terms say what ActA does; a transcription term would say what something downstream of ActA does. GONUTS, which would have carried the student's own evidence note, was re-checked on 2026-11-01 and now returns HTTP 410 with a permanent retirement notice, with no Wayback snapshot of the actA or Q93P59 pages, so the recorded student rationale is unrecoverable; the abstract states the gene-specific mutant result explicitly enough that no UNDECIDED is needed. Proposed replacements: positive regulation of signal transduction Supporting Evidence: PMID:11359579 The act A and act B genes regulate the maximum level of the C-signal, which never rises above one-quarter of the maximum wild-type level of CsgA protein in null mutants of either gene. PMID:11359579 the two gene products are part of the same signal transduction pathway. That pathway responds to C-signal and also regulates the production of CsgA protein, thus creating a positive feedback loop. PMID:17189369 The final level of csgA expression is set by actA and actB PMID:26369581 it seems unlikely that ActB directly regulates developmental expression of csgA |
| GO:0043937 regulation of sporulation | IMP PMID:11359579 The act operon controls the level and time of C-signal produ... | MODIFY | Summary: CACAO row with a gene-specific mutant phenotype behind it: the actA null aggregates and ripples but makes no spores, and the gene's contribution is to set the level of the morphogen that triggers sporulation. The shape of the term is right; only the spore type can be made specific, so this is refined to GO:0042173. Reason: What the paper shows for this gene, CACAO assessment. The abstract reports the actA null phenotype by name: "both aggregate, neither sporulates, both prolong rippling". The students did not read a developmental phenotype as a developmental process; they chose a regulation term, which is the correct shape for a protein whose output is the level of C-signal rather than any step of spore morphogenesis, and the asymmetry of the phenotype (aggregation intact, sporulation abolished) is exactly what a regulation-of-sporulation term expresses. The judgement is independently endorsed by a later review of this organism's two-component systems: "actA and actB are required for sporulation inside nascent fruiting bodies but not for the formation of aggregates of cells". The companion paper strengthens the specificity of the defect, since the act mutations leave the early C-signal-independent program untouched and only depress the reporters expressed from 6 h onward. What can be improved is granularity of spore type. Myxococcus myxospores are cellular spores, and other Myxococcus xanthus gene products are annotated in the GO:0030435 branch of sporulation resulting in formation of a cellular spore, so GO:0042173, the direct is_a child of GO:0043937 restricted to cellular-spore formation, is the specific supported term; GO:0043937 would otherwise also cover spore types this organism does not make. Kept as core, since the sporulation defect is the principal consequence of losing actA. GONUTS returned HTTP 410 (permanently retired) when re-checked on 2026-11-01, so the student's recorded evidence text could not be consulted; the gene-specific result is in the abstract. The redundant-entry defect recorded on the GO:0009966 row of this review applies equally to this row. Proposed replacements: regulation of sporulation resulting in formation of a cellular spore Supporting Evidence: PMID:11359579 The act A and act B mutants have the same developmental phenotype: both aggregate, neither sporulates, both prolong rippling. PMID:26369581 Mutational analyses indicate that actA and actB are required for sporulation inside nascent fruiting bodies but not for the formation of aggregates of cells PMID:11807078 The actA and actB null mutations substantially decreased the expression of all these reporters. PMID:11359579 The C-signal is a morphogen that controls the assembly of fruiting bodies and the differentiation of myxospores. |
Loading supporting content…
Download this section (compressed HTML)Q: Should ActA carry a regulation-of-gene-expression term for its effect on csgA? The directly measured readout in the defining paper is csgA expression and CsgA protein level, and ActA is also required for transcription of its own operon, but ActA has no DNA-binding domain, the model routes its effect through the sigma-54 activator ActB, and ActB itself apparently does not bind the csgA promoter. This review therefore annotates signalling only. A curator with access to the full text of PMID:11359579 could settle whether the csgA measurement was transcriptional and whether GO's conventions place such a term on a non-DNA-binding response regulator.
Q: Should UniProt merge the redundant act-operon entries? Q93P59 (AF350253, species taxon 34) and Q1D7F9 (CP000113, actA MXAN_3213, DK1622 taxon 246197) are the same 342-residue protein of the same strain, but only Q93P59 carries the experimental annotations, so they are invisible from the DK1622 reference proteome. The same split, in the opposite direction, affects actB (Q93P58 versus Q1D7F8) and actC (Q93P57 versus Q1D7F7).
Q: Is the prolonged rippling of an actA mutant a separate consequence of ActA signalling, or simply what a cell population does when C-signal stalls below the sporulation threshold? Rippling, aggregation and sporulation are triggered at successively higher C-signal levels, and the actA null stops at the rippling step.
Q: Is actE, the fifth gene of the operon recognised only in 2007, functional, and does it contribute to the phenotype attributed to the four-gene operon in the 2001 study? No actE mutant has been made and no homolog suggests a function.
Suggested experts: Anthony G. Garza, Lee Kroos
Experiment: Build a chromosomal allele series at the actA receiver domain (D90A non-phosphorylatable, D90E phosphomimetic, plus a receiver-domain deletion) in DK1622 and score each for fruiting body morphology, spore titre, CsgA immunoblot level, and the act and csgA transcriptional lacZ reporters used in PMID:17189369. In parallel, purify ActA and test phosphorylation by acetyl phosphate and by each of the orphan histidine kinases implicated in late development, following phosphotransfer to ActB.
Hypothesis: ActA is phosphorylated on Asp90 by a histidine kinase activated by C-signal, and this phosphorylation is required for ActB activation, csgA expression and sporulation.
Type: bacterial genetics with in vitro phosphotransfer assays
Experiment: Assay purified full-length ActA and its isolated GGDEF domain for diguanylate cyclase activity and for c-di-GMP binding (by HPLC product detection and by isothermal titration or differential radial capillary action of ligand assay), then test ActA-ActB interaction by bacterial two-hybrid and by pull-down from developing cells, comparing wild-type ActA with a GGDEF-domain deletion and with a restored GGDEF A-site motif. A dead domain that still binds ActB, while the deletion loses binding and phenocopies the null, would establish the module's role.
Hypothesis: The GGDEF domain of ActA is catalytically dead and functions as a protein-interaction module that engages ActB.
Type: enzymology plus protein interaction analysis
Experiment: Define the csgA promoter by scanning mutagenesis of a csgA-lacZ fusion in DK1622, identify proteins that bind it by DNA-affinity capture and mass spectrometry from cells at 18-24 h of development, and test each candidate by ChIP-seq in wild-type and delta actA backgrounds. Comparing the ActB ChIP-seq signal at the csgA promoter with that at the act promoter and MXAN4899 would resolve the contradiction between PMID:17189369 and PMID:26369581.
Hypothesis: ActA acts on csgA transcription through an intermediate transcription factor rather than through direct ActB binding at the csgA promoter.
Type: promoter mapping with ChIP-seq and affinity proteomics
Experiment: Place actA under an inducible promoter in an actA null background and titrate its expression, measuring CsgA level, rippling duration, aggregate morphology and spore titre at each induction level. If ActA acts purely on the maximum level of C-signal, spore titre should be a threshold function of actA dosage while the timing of csgA induction, which actC and actD control, should be unchanged.
Hypothesis: The level versus timing division of labour within the act operon is quantitative, so graded expression of actA alone can reconstruct intermediate developmental outcomes.
Type: inducible expression dose-response with developmental phenotyping
What is not known — curated, literature-grounded statements of the open unknowns (the inverse of core functions).
Gap: The GGDEF output domain of ActA has no known ligand, product or partner, and it is not known whether c-di-GMP signalling is involved in the act pathway at all.
BIOLOGY
What is known: Established: residues 207-342 match the GGDEF profile (PROSITE PS50887, Pfam PF00990, NCBIfam TIGR00254) and the domain is described in the literature as a predicted GGDEF-type effector. Observed here from the Q93P59 sequence: the canonical GG(D/E)EF A-site motif is absent, the nearest sequence at that position being GDCQF, which is the signature of a degenerate, probably non-catalytic GGDEF domain. Missing: any measurement of c-di-GMP synthesis, nucleotide binding or protein binding by this domain.
Significance: A catalytically dead GGDEF domain is usually a protein-protein interaction or c-di-GMP-binding module, so the identity of its partner would say how ActA transmits the C-signal to ActB, and whether the second messenger that governs the best-studied developmental decision in Myxococcus is c-di-GMP or something else.
What would resolve it: Purify ActA and its isolated GGDEF domain, assay diguanylate cyclase activity and c-di-GMP binding directly, and search for interaction partners of the domain by pull-down or bacterial two-hybrid in developing cells.
Provenance (the field's own admissions):
Gap: Which transcription factor actually drives csgA is unknown, so the mechanism by which ActA raises C-signal production is unresolved.
BIOLOGY
What is known: Established: csgA expression and CsgA protein level depend on actA and actB, and the act pathway and csgA form a positive feedback loop. Missing: the direct regulator of the csgA promoter. ActB, the operon's sigma-54 activator and the obvious candidate, has no detectable binding site or sigma-54 consensus upstream of csgA, and its only identified direct targets are the act operon itself and MXAN4899.
Significance: The number of steps between ActA and csgA transcription decides what ActA can legitimately be annotated to: with a direct link, a regulation-of-transcription term would be defensible; with an unidentified intermediate, the signalling terms used in this review are as far as the evidence reaches.
What would resolve it: Map the csgA promoter by deletion and point mutagenesis, identify proteins binding it by DNA-affinity capture from developing cells, and test candidate regulators by ChIP-seq in a wild-type and an actA background.
Provenance (the field's own admissions):
Loading supporting content…
Download this section (compressed HTML)Loading supporting content…
Download this section (compressed HTML)