pufA

id: Q54WA7
gene_symbol: pufA
product_type: PROTEIN
status: COMPLETE
taxon:
  id: NCBITaxon:44689
  label: Dictyostelium discoideum
description: 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.
existing_annotations:
- term:
    id: GO:0010608
    label: post-transcriptional regulation of gene expression
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: involved_in
  review:
    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.
    action: ACCEPT
    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.
    supported_by:
    - reference_id: PMID:10375515
      supporting_text: PufA is a translational regulator that directly controls
        PKA-C synthesis
- term:
    id: GO:0005737
    label: cytoplasm
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: is_active_in
  review:
    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.
    action: ACCEPT
    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.
- term:
    id: GO:0003730
    label: mRNA 3'-UTR binding
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: enables
  review:
    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.
    action: ACCEPT
    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.
    supported_by:
    - reference_id: PMID:10375515
      supporting_text: 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
- term:
    id: GO:0003723
    label: RNA binding
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  qualifier: enables
  review:
    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.
    action: ACCEPT
    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.
- term:
    id: GO:0005737
    label: cytoplasm
  evidence_type: IEA
  original_reference_id: GO_REF:0000044
  qualifier: located_in
  review:
    summary: UniProt subcellular-location mapping places PufA in the cytoplasm,
      consistent with its role as a cytoplasmic translational repressor.
    action: ACCEPT
    reason: Cytoplasmic localization is appropriate for a PUF-family translational
      regulator and is consistent with the phylogenetic (IBA) cytoplasm annotation.
- term:
    id: GO:0003729
    label: mRNA binding
  evidence_type: IMP
  original_reference_id: PMID:10375515
  qualifier: enables
  review:
    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.
    action: ACCEPT
    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.
    supported_by:
    - reference_id: PMID:10375515
      supporting_text: 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
- term:
    id: GO:0005575
    label: cellular_component
  evidence_type: ND
  original_reference_id: GO_REF:0000015
  qualifier: is_active_in
  review:
    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.
    action: REMOVE
    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.
- term:
    id: GO:0017148
    label: negative regulation of translation
  evidence_type: IMP
  original_reference_id: PMID:10375515
  qualifier: acts_upstream_of_or_within
  review:
    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.
    action: ACCEPT
    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.
    supported_by:
    - reference_id: PMID:10375515
      supporting_text: Upon starvation, pufA- cells develop precociously and
        overexpress developmentally important proteins, including the catalytic
        subunit of cAMP-dependent protein kinase, PKA-C
- term:
    id: GO:0030587
    label: sorocarp development
  evidence_type: IMP
  original_reference_id: PMID:10375515
  qualifier: acts_upstream_of_or_within
  review:
    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.
    action: KEEP_AS_NON_CORE
    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.
    supported_by:
    - reference_id: PMID:10375515
      supporting_text: Upon starvation, pufA- cells develop precociously and
        overexpress developmentally important proteins, including the catalytic
        subunit of cAMP-dependent protein kinase, PKA-C
    - reference_id: PMID:10375515
      supporting_text: YakA regulates the initiation of development by inhibiting
        the expression of PufA
references:
- id: GO_REF:0000002
  title: Gene Ontology annotation through association of InterPro records with GO
    terms
  findings: []
- id: GO_REF:0000015
  title: Use of the ND evidence code for Gene Ontology (GO) terms
  findings: []
- id: GO_REF:0000033
  title: Annotation inferences using phylogenetic trees
  findings: []
- id: GO_REF:0000044
  title: Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location
    vocabulary mapping, accompanied by conservative changes to GO terms applied by
    UniProt
  findings: []
- id: PMID:10375515
  title: Starvation promotes Dictyostelium development by relieving PufA inhibition
    of PKA translation through the YakA kinase pathway.
  findings:
  - statement: pufA encodes a member of the PUF (Pumilio) family of translational
      regulators, identified as a suppressor of yakA.
    supporting_text: encodes a member of the Puf protein family of translational
      regulators
  - statement: PufA binds a recognition element in the PKA-C mRNA, forming a complex
      detectable in wild-type but not pufA-null extracts.
    supporting_text: 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
  - statement: PufA is a translational repressor that directly controls synthesis
      of the PKA catalytic subunit; loss of PufA causes PKA-C overexpression and
      precocious development.
    supporting_text: Upon starvation, pufA- cells develop precociously and
      overexpress developmentally important proteins, including the catalytic
      subunit of cAMP-dependent protein kinase, PKA-C
  - statement: PufA acts as a translational regulator directly controlling PKA-C
      synthesis, and YakA initiates development by inhibiting PufA expression.
    supporting_text: PufA is a translational regulator that directly controls
      PKA-C synthesis
  reference_review:
    relevance: HIGH
    correctness: VERIFIED
    review_notes: PubMed-verified primary paper (Souza, da Silva and Kuspa, Development
      1999) that defines PufA as a PUF-family translational repressor of PKA-C mRNA
      and establishes the YakA-PufA-PKA axis. Abstract-only cache; all supporting
      text quotes are verbatim from the abstract.
core_functions:
- description: PufA is a sequence-specific mRNA-binding protein that recognizes an
    element in the PKA-C (pkaC) mRNA via its Pumilio homology domain and represses
    its translation in the cytoplasm, keeping PKA catalytic subunit levels low
    during growth.
  molecular_function:
    id: GO:0003730
    label: mRNA 3'-UTR binding
  directly_involved_in:
  - id: GO:0017148
    label: negative regulation of translation
  locations:
  - id: GO:0005737
    label: cytoplasm
  supported_by:
  - reference_id: PMID:10375515
    supporting_text: 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
  - reference_id: PMID:10375515
    supporting_text: PufA is a translational regulator that directly controls
      PKA-C synthesis