PufA is a Pumilio/FBF (PUF) family sequence-specific RNA-binding protein of Dictyostelium discoideum that acts as a translational repressor. Its C-terminal Pumilio homology domain (PUM-HD), built from eight tandem Pumilio repeats, binds a recognition element in the mRNA encoding the catalytic subunit of cAMP-dependent protein kinase (PKA-C, pkaC) and represses its translation in the cytoplasm. During vegetative growth PufA keeps PKA-C levels low; upon nutrient depletion the YakA kinase pathway drives the decline of PufA protein and mRNA, relieving repression so that PKA-C accumulates and triggers the growth-to-development transition, aggregation, and progression toward fruiting body (sorocarp) formation. PufA thereby couples nutritional status to the developmental program through post-transcriptional control of PKA-C synthesis.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0010608 post-transcriptional regulation of gene expression | IBA GO_REF:0000033 | ACCEPT | Summary: PufA is a PUF-family translational regulator that represses PKA-C mRNA translation, a canonical form of post-transcriptional regulation of gene expression. The phylogenetic inference is consistent with direct experimental evidence for this gene. Reason: This term accurately captures PufA's role as a sequence-specific mRNA binding translational repressor, supported both by the PUF family assignment and by direct experimental evidence that PufA controls PKA-C synthesis. The more specific child term negative regulation of translation is also annotated. Supporting Evidence: PMID:10375515 PufA is a translational regulator that directly controls PKA-C synthesis |
| GO:0005737 cytoplasm | IBA GO_REF:0000033 | ACCEPT | Summary: PUF-family translational repressors act in the cytoplasm, where translation occurs. This localization is consistent with PufA's function as a cytoplasmic translational regulator of PKA-C mRNA and with the UniProt subcellular location assignment. Reason: Cytoplasmic activity is expected for a translational repressor and is consistent both with phylogenetic inference from the PUF family and the UniProt subcellular-location mapping. This represents the compartment in which the core molecular function is exercised. |
| GO:0003730 mRNA 3'-UTR binding | IBA GO_REF:0000033 | ACCEPT | Summary: PUF proteins characteristically recognize sequence elements in the 3'-UTR of target mRNAs through their Pumilio homology domain. PufA binds a recognition element in the PKA-C mRNA, and this term is the most informative molecular-function descriptor of that sequence-specific binding activity. Reason: The PUM-HD domain of PufA (eight Pumilio repeats) mediates sequence-specific mRNA recognition, the defining molecular function of the family. Direct experimental evidence shows PufA forms a complex with a segment of PKA-C mRNA, and 3'-UTR recognition is the canonical PUF binding mode, making this the preferred informative MF term. Supporting Evidence: PMID:10375515 Gel mobility-shift assays using a 200-base segment of PKA-C's mRNA as a probe reveals a complex with wild-type cell extracts, but not with pufA- cell extracts |
| GO:0003723 RNA binding | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro2GO annotation from the Pumilio/PUF RNA-binding domain signatures. This is correct but general; the more specific terms mRNA binding and mRNA 3'-UTR binding better describe PufA's actual sequence-specific activity. Reason: The RNA-binding assignment is correct and consistent with the PUM-HD domain architecture, but it is a broad parent term. It is retained as an accurate general annotation subsumed by the more specific mRNA-binding terms. |
| GO:0005737 cytoplasm | IEA GO_REF:0000044 | ACCEPT | Summary: UniProt subcellular-location mapping places PufA in the cytoplasm, consistent with its role as a cytoplasmic translational repressor. Reason: Cytoplasmic localization is appropriate for a PUF-family translational regulator and is consistent with the phylogenetic (IBA) cytoplasm annotation. |
| GO:0003729 mRNA binding | IMP PMID:10375515 Starvation promotes Dictyostelium development by relieving P... | ACCEPT | Summary: Direct experimental evidence (gel mobility-shift) shows that PufA forms a complex with a segment of PKA-C mRNA, present in wild-type but not pufA-null extracts. This is a well-supported core molecular function. Reason: Gel mobility-shift assays demonstrate sequence-specific binding of PufA to PKA-C mRNA, and this activity is lost in pufA-null cells, providing direct genetic and biochemical support for the mRNA-binding function. Supporting Evidence: PMID:10375515 Gel mobility-shift assays using a 200-base segment of PKA-C's mRNA as a probe reveals a complex with wild-type cell extracts, but not with pufA- cell extracts |
| GO:0005575 cellular_component | ND GO_REF:0000015 | REMOVE | Summary: Root-level cellular_component annotation with the ND (no biological data) evidence code. This is an uninformative placeholder that predates the cytoplasm annotations now available for this gene. Reason: This is a root-term ND placeholder indicating that no specific cellular component was assignable at the time of curation. It is now superseded by the cytoplasm annotations (IBA and IEA) and carries no biological information. |
| GO:0017148 negative regulation of translation | IMP PMID:10375515 Starvation promotes Dictyostelium development by relieving P... | ACCEPT | Summary: PufA represses translation of the PKA-C mRNA; loss of PufA leads to PKA-C overexpression. This is a core biological process directly demonstrated by mutant analysis. Reason: PufA acts as a translational inhibitor of PKA-C, and pufA-null cells overexpress PKA-C, providing direct experimental support for negative regulation of translation as a core function. Supporting Evidence: PMID:10375515 Upon starvation, pufA- cells develop precociously and overexpress developmentally important proteins, including the catalytic subunit of cAMP-dependent protein kinase, PKA-C |
| GO:0030587 sorocarp development | IMP PMID:10375515 Starvation promotes Dictyostelium development by relieving P... | KEEP AS NON CORE | Summary: PufA regulates the timing of the developmental program, and its downregulation by the YakA pathway de-represses PKA-C and triggers aggregation and fruiting body (sorocarp) development. pufA-null cells develop precociously. This is an upstream regulatory role rather than the core molecular function. Reason: PufA influences sorocarp development indirectly by controlling PKA-C translation at the growth-to-development transition. The acts_upstream_of_or_within qualifier is appropriate, but developmental progression is a downstream consequence of PufA's translational repressor activity, so this is best retained as a non-core process annotation. Supporting Evidence: PMID:10375515 Upon starvation, pufA- cells develop precociously and overexpress developmentally important proteins, including the catalytic subunit of cAMP-dependent protein kinase, PKA-C PMID:10375515 YakA regulates the initiation of development by inhibiting the expression of PufA |
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