gbpD

id: Q54S40
gene_symbol: gbpD
product_type: PROTEIN
status: COMPLETE
taxon:
  id: NCBITaxon:44689
  label: Dictyostelium discoideum
description: GbpD (also known as GefU/RasGEFU) is a RasGEF-family guanine
  nucleotide exchange factor in Dictyostelium discoideum that specifically
  activates the small GTPase Rap1. The protein is a large multidomain molecule
  containing an N-terminal RasGEF domain pair (RasGEF_N and catalytic RasGEF), a
  GRAM domain, and cyclic-nucleotide-binding (cNMP/GAF-like) domains that give it
  cGMP-binding capacity. Acting at the plasma membrane, GbpD activates Rap1 both
  in vivo and in vitro but not the other characterized Ras proteins, and this
  Rap1 signal drives the formation of substrate-attached pseudopodia, increasing
  cell-substrate adhesion while suppressing cell polarity and thereby slowing
  chemotaxis. Downstream, Rap1 engages the effector kinase Phg2 for adhesion.
  Although GbpD binds cGMP, its adhesion/polarity phenotype is independent of
  intracellular cGMP or cAMP levels. Its expression rises during the aggregation
  phase of starvation-induced development, consistent with a role in regulating
  motility, spreading and pseudopod dynamics.
existing_annotations:
- term:
    id: GO:0005886
    label: plasma membrane
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: is_active_in
  review:
    summary: GbpD acts at the plasma membrane, where it encounters and activates
      membrane-associated Rap1. This phylogenetic inference is corroborated by
      direct localization data for the same protein.
    action: ACCEPT
    reason: Membrane localization is directly confirmed for GbpD/RasGEFU, which
      localizes almost uniformly to the plasma membrane. This is where a Rap1 GEF
      would be expected to function.
    supported_by:
    - reference_id: PMID:39746985
      supporting_text: RasGEFU localized almost uniformly to the membrane and did
        not exhibit traveling waves
- term:
    id: GO:0007265
    label: Ras protein signal transduction
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: involved_in
  review:
    summary: GbpD activates the Ras-superfamily small GTPase Rap1, functioning
      within a Ras/Rap signal transduction pathway. Rap1 is a member of the Ras
      family, so the general term is accurate, though the more precise process is
      Rap1-mediated signaling.
    action: ACCEPT
    reason: GbpD is a bona fide activator of Rap1 (a Ras-family GTPase), placing
      it within Ras protein signal transduction. Directly supported by biochemical
      and genetic evidence.
    supported_by:
    - reference_id: PMID:16769729
      supporting_text: Here we demonstrate that GbpD activates Rap1 both in vivo
        and in vitro but not any of the five other characterized Ras proteins
- term:
    id: GO:0005085
    label: guanyl-nucleotide exchange factor activity
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: enables
  review:
    summary: GbpD is a RasGEF-family guanine nucleotide exchange factor. This
      molecular function is the protein's defining activity and is directly
      demonstrated for its target Rap1.
    action: ACCEPT
    reason: Phylogenetic inference of GEF activity is fully consistent with the
      RasGEF domain architecture and with direct biochemical demonstration that
      GbpD activates Rap1.
    supported_by:
    - reference_id: PMID:16769729
      supporting_text: Here we demonstrate that GbpD activates Rap1 both in vivo
        and in vitro but not any of the five other characterized Ras proteins
- term:
    id: GO:0005085
    label: guanyl-nucleotide exchange factor activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  qualifier: enables
  review:
    summary: InterPro2GO inference from the RasGEF catalytic domain signatures
      (IPR001895, IPR008937, IPR036964). This correctly captures the core GEF
      activity.
    action: ACCEPT
    reason: The RasGEF catalytic domain is present in GbpD and the GEF activity is
      experimentally validated on Rap1, so this electronic annotation is correct.
    supported_by:
    - reference_id: PMID:16769729
      supporting_text: Here we demonstrate that GbpD activates Rap1 both in vivo
        and in vitro but not any of the five other characterized Ras proteins
- term:
    id: GO:0007264
    label: small GTPase-mediated signal transduction
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  qualifier: involved_in
  review:
    summary: GbpD acts as an upstream activator of the small GTPase Rap1, so it
      participates in small GTPase-mediated signal transduction. This is a correct
      but general process term.
    action: ACCEPT
    reason: Consistent with GbpD's demonstrated role as a Rap1 GEF driving
      downstream adhesion/polarity signaling.
    supported_by:
    - reference_id: PMID:16769729
      supporting_text: Here we demonstrate that GbpD activates Rap1 both in vivo
        and in vitro but not any of the five other characterized Ras proteins
- term:
    id: GO:0010810
    label: regulation of cell-substrate adhesion
  evidence_type: IMP
  original_reference_id: PMID:39746985
  qualifier: involved_in
  review:
    summary: GbpD/RasGEFU regulates cell-substrate adhesion. Overexpression
      increases adhesion to the substrate (with a corresponding decrease in
      motility), consistent with earlier GbpD studies. This is a core biological
      role of the protein.
    action: ACCEPT
    reason: Directly supported by mutant/overexpression phenotypes in which
      RasGEFU enhances cell-substrate adhesion.
    supported_by:
    - reference_id: PMID:39746985
      supporting_text: RasGEFU-GFP-expressing cells showed increased adhesion to
        the substrates and thus less motility as their expression increased
    - reference_id: PMID:39746985
      supporting_text: RasGEFU enhanced cell adhesion to substrates, consistent
        with previous reports of cGMP-binding protein D (GbpD), which is the same
        as RasGEFU
- term:
    id: GO:0031272
    label: regulation of pseudopodium assembly
  evidence_type: IMP
  original_reference_id: PMID:39746985
  qualifier: involved_in
  review:
    summary: GbpD regulates pseudopod formation; RasGEFU overexpression leads to
      enlarged pseudopods (and reduced motility), consistent with earlier reports
      that GbpD overexpression induces many bifurcated/lateral pseudopodia.
    action: ACCEPT
    reason: Supported by the overexpression phenotype affecting pseudopod size and
      formation, a well-established GbpD effect on protrusion dynamics.
    supported_by:
    - reference_id: PMID:39746985
      supporting_text: RasGEFU overexpression in these cells led to a large
        pseudopod and also less motility
    - reference_id: PMID:16769729
      supporting_text: Cells overexpressing GbpD are flat, exhibit strongly
        increased cell-substrate attachment, and extend many bifurcated and
        lateral pseudopodia
- term:
    id: GO:0005886
    label: plasma membrane
  evidence_type: IDA
  original_reference_id: PMID:39746985
  qualifier: located_in
  review:
    summary: Direct imaging shows GbpD/RasGEFU-GFP localizing almost uniformly to
      the plasma membrane, the site where it activates Rap1. This is a core
      localization for the protein.
    action: ACCEPT
    reason: Direct experimental localization (GFP fusion) places GbpD at the
      plasma membrane.
    supported_by:
    - reference_id: PMID:39746985
      supporting_text: RasGEFU localized almost uniformly to the membrane and did
        not exhibit traveling waves
- term:
    id: GO:2000145
    label: regulation of cell motility
  evidence_type: IGI
  original_reference_id: PMID:39746985
  qualifier: involved_in
  review:
    summary: GbpD/RasGEFU contributes to efficient spontaneous cell motility,
      shown genetically alongside other RasGEFs (including RasGEFM). Because GbpD
      acts on motility largely by modulating adhesion and pseudopod dynamics, this
      is a downstream/secondary consequence of its GEF activity rather than its
      core molecular role.
    action: KEEP_AS_NON_CORE
    reason: Motility regulation is a genuine phenotype but is an emergent
      consequence of GbpD-driven adhesion and pseudopod changes. Retained as a
      valid but non-core process annotation.
    supported_by:
    - reference_id: PMID:39746985
      supporting_text: RasGEFX, RasGEFB, RasGEFU and RasGEFM are important for
        efficient spontaneous motility
    - reference_id: PMID:39746985
      supporting_text: RasGEFU-GFP-expressing cells showed increased adhesion to
        the substrates and thus less motility as their expression increased
- term:
    id: GO:0031271
    label: lateral pseudopodium assembly
  evidence_type: IMP
  original_reference_id: PMID:15827084
  qualifier: acts_upstream_of_or_within
  review:
    summary: GbpD controls lateral pseudopod formation. gbpD-null cells make very
      few lateral pseudopodia (and are hyperpolar), whereas GbpD overexpression
      produces many lateral/bifurcated pseudopodia. This is a well-supported core
      process for GbpD.
    action: ACCEPT
    reason: Loss- and gain-of-function phenotypes directly implicate GbpD in
      lateral pseudopod assembly.
    supported_by:
    - reference_id: PMID:15827084
      supporting_text: 'gbpD-null mutants exhibit the opposite phenotype: cells
        display improved chemotaxis and appear hyperpolar, because cells make very
        few lateral pseudopodia'
    - reference_id: PMID:16769729
      supporting_text: Cells overexpressing GbpD are flat, exhibit strongly
        increased cell-substrate attachment, and extend many bifurcated and
        lateral pseudopodia
- term:
    id: GO:0032060
    label: bleb assembly
  evidence_type: IGI
  original_reference_id: PMID:26317626
  qualifier: acts_upstream_of_or_within
  review:
    summary: In a microsurgery-based blebbing screen, cells deficient in gbpC/gbpD
      extended blebs more frequently than wild-type, implicating this cGMP-pathway
      branch in the suppression/regulation of bleb formation. The evidence is
      genetic and comes from a double-mutant context (with gbpC), so the effect on
      bleb assembly is indirect and not a core GbpD function.
    action: KEEP_AS_NON_CORE
    reason: The blebbing phenotype is derived from a gbpC/gbpD-deficient background
      and reflects a modulatory role of the cGMP signaling branch rather than a
      direct, core molecular function of GbpD. Retained as a valid non-core
      regulatory annotation. Note the paper informally labels gbpC/gbpD as
      guanylate cyclases, whereas gbpD is a RasGEF.
    supported_by:
    - reference_id: PMID:26317626
      supporting_text: cells deficient in gbpC-/gbpD (guanylate cyclases), pkgB
        (serine/threonine-protein kinase), iplA (Ca2+ channel), or pi3k
        (phosphatidylinositol 3-kinase) extended blebs more frequently than wild
        type cells
- term:
    id: GO:0005085
    label: guanyl-nucleotide exchange factor activity
  evidence_type: IDA
  original_reference_id: PMID:16769729
  qualifier: enables
  review:
    summary: Direct biochemical evidence shows GbpD activates Rap1 (and
      specifically not the other five characterized Ras proteins) both in vivo and
      in vitro. The guanyl-nucleotide exchange factor activity is accepted as
      annotated; the Rap1 specificity is recorded in the reason and core function.
    action: ACCEPT
    reason: The direct assay establishes that GbpD is a Rap1-specific GEF. The
      annotated GEF term (GO:0005085) is accurate; the more specific Rap-GEF child
      term (GO:0017034) is obsolete/absent from the ontology used for validation,
      so the generic GEF term is retained with the Rap1 specificity noted here.
    supported_by:
    - reference_id: PMID:16769729
      supporting_text: Here we demonstrate that GbpD activates Rap1 both in vivo
        and in vitro but not any of the five other characterized Ras proteins
- term:
    id: GO:0007163
    label: establishment or maintenance of cell polarity
  evidence_type: IMP
  original_reference_id: PMID:15827084
  qualifier: acts_upstream_of_or_within
  review:
    summary: GbpD is a negative regulator of cell polarity. Its overexpression
      induces substrate-attached pseudopodia that suppress polarity, whereas
      gbpD-null cells are hyperpolar. GbpD thus acts within the establishment/
      maintenance of cell polarity, driving it toward a less polarized,
      more-adhesive state.
    action: ACCEPT
    reason: Reciprocal loss- and gain-of-function phenotypes directly implicate
      GbpD in the control of cell polarity.
    supported_by:
    - reference_id: PMID:15827084
      supporting_text: GbpD induces the formation of substrate-attached
        pseudopodia, resulting in increased attachment and suppression of polarity
    - reference_id: PMID:15827084
      supporting_text: 'gbpD-null mutants exhibit the opposite phenotype: cells
        display improved chemotaxis and appear hyperpolar, because cells make very
        few lateral pseudopodia'
- term:
    id: GO:0031589
    label: cell-substrate adhesion
  evidence_type: IMP
  original_reference_id: PMID:15827084
  qualifier: acts_upstream_of_or_within
  review:
    summary: GbpD promotes cell-substrate adhesion. Overexpressing cells become
      flat and adhesive due to an increased number of substrate-attached
      pseudopodia, mediated via Rap1 and its effector Phg2. This is a core
      biological role.
    action: ACCEPT
    reason: Directly supported by the overexpression phenotype of increased
      substrate attachment; mechanism traced to the GbpD-Rap1-Phg2 axis.
    supported_by:
    - reference_id: PMID:15827084
      supporting_text: cells are flat and adhesive owing to an increased number of
        substrate-attached pseudopodia
    - reference_id: PMID:16769729
      supporting_text: identified Phg2 as Rap1 effector necessary for adhesion,
        but not cell polarity
- term:
    id: GO:0050920
    label: regulation of chemotaxis
  evidence_type: IMP
  original_reference_id: PMID:15827084
  qualifier: acts_upstream_of_or_within
  review:
    summary: GbpD modulates chemotaxis; overexpression severely reduces chemotaxis
      (through excess adhesion and disorganized protrusions), whereas gbpD-null
      cells chemotax better and are hyperpolar. This chemotaxis effect is a
      downstream consequence of GbpD's control of adhesion and pseudopod dynamics
      rather than a direct core function.
    action: KEEP_AS_NON_CORE
    reason: Chemotaxis regulation is a real and reproducible phenotype but emerges
      from GbpD's primary effects on adhesion and polarity; retained as a valid
      non-core process annotation.
    supported_by:
    - reference_id: PMID:15827084
      supporting_text: Overexpression of GbpD protein results in severely reduced
        chemotaxis
    - reference_id: PMID:15827084
      supporting_text: 'gbpD-null mutants exhibit the opposite phenotype: cells
        display improved chemotaxis and appear hyperpolar, because cells make very
        few lateral pseudopodia'
references:
- id: GO_REF:0000002
  title: Gene Ontology annotation through association of InterPro records with GO
    terms
  findings: []
- id: GO_REF:0000033
  title: Annotation inferences using phylogenetic trees
  findings: []
- id: PMID:15827084
  title: RasGEF-containing proteins GbpC and GbpD have differential effects on cell
    polarity and chemotaxis in Dictyostelium.
  findings:
  - statement: GbpD induces substrate-attached pseudopodia that increase adhesion
      and suppress cell polarity.
    supporting_text: GbpD induces the formation of substrate-attached pseudopodia,
      resulting in increased attachment and suppression of polarity
  - statement: gbpD-null cells are hyperpolar, chemotax better, and make few
      lateral pseudopodia; the phenotype is opposite to overexpression.
    supporting_text: 'gbpD-null mutants exhibit the opposite phenotype: cells
      display improved chemotaxis and appear hyperpolar, because cells make very
      few lateral pseudopodia'
  - statement: The GbpD adhesion/polarity phenotype is independent of intracellular
      cGMP or cAMP.
    supporting_text: This GbpD phenotype is not dependent on intracellular cGMP or
      cAMP
  reference_review:
    relevance: HIGH
    correctness: VERIFIED
    review_notes: Abstract-only cache; abstract directly establishes GbpD's
      loss-/gain-of-function effects on adhesion, lateral pseudopodia, polarity and
      chemotaxis. Assigned by dictyBase for multiple IMP annotations.
- id: PMID:16769729
  title: Characterization of the GbpD-activated Rap1 pathway regulating adhesion and
    cell polarity in Dictyostelium discoideum.
  findings:
  - statement: GbpD activates Rap1 specifically (not the other five characterized
      Ras proteins) both in vivo and in vitro.
    supporting_text: Here we demonstrate that GbpD activates Rap1 both in vivo and
      in vitro but not any of the five other characterized Ras proteins
  - statement: GbpD overexpression yields flat, strongly adhesive cells with many
      bifurcated and lateral pseudopodia.
    supporting_text: Cells overexpressing GbpD are flat, exhibit strongly increased
      cell-substrate attachment, and extend many bifurcated and lateral pseudopodia
  - statement: Phg2 is the Rap1 effector required for adhesion downstream of GbpD.
    supporting_text: identified Phg2 as Rap1 effector necessary for adhesion, but
      not cell polarity
  reference_review:
    relevance: HIGH
    correctness: VERIFIED
    review_notes: Abstract-only cache; establishes the direct GEF-substrate
      relationship (GbpD to Rap1 to Phg2) that underpins the IDA GEF-activity
      annotation and the specificity supporting the MODIFY to Rap-GEF activity.
- id: PMID:26317626
  title: Microtubule-Mediated Inositol Lipid Signaling Plays Critical Roles in Regulation
    of Blebbing.
  findings:
  - statement: Cells deficient in gbpC/gbpD extended blebs more frequently than
      wild-type in a microsurgery blebbing screen.
    supporting_text: cells deficient in gbpC-/gbpD (guanylate cyclases), pkgB
      (serine/threonine-protein kinase), iplA (Ca2+ channel), or pi3k
      (phosphatidylinositol 3-kinase) extended blebs more frequently than wild
      type cells
  reference_review:
    relevance: MEDIUM
    correctness: VERIFIED
    review_notes: Full text available. gbpD contribution comes from a gbpC/gbpD
      double-deficient background and the paper informally labels these as
      guanylate cyclases; supports a modulatory (non-core) bleb-regulation role.
- id: PMID:39746985
  title: Excitable Ras dynamics-based screens reveal RasGEFX is required for macropinocytosis
    and random cell migration.
  findings:
  - statement: RasGEFU is the same protein as cGMP-binding protein D (GbpD) and its
      overexpression enhances cell-substrate adhesion.
    supporting_text: RasGEFU enhanced cell adhesion to substrates, consistent with
      previous reports of cGMP-binding protein D (GbpD), which is the same as
      RasGEFU
  - statement: RasGEFU/GbpD localizes almost uniformly to the plasma membrane
      without traveling waves.
    supporting_text: RasGEFU localized almost uniformly to the membrane and did not
      exhibit traveling waves
  - statement: RasGEFU overexpression increases adhesion and enlarges pseudopods
      while reducing motility.
    supporting_text: RasGEFU-GFP-expressing cells showed increased adhesion to the
      substrates and thus less motility as their expression increased
  reference_review:
    relevance: HIGH
    correctness: VERIFIED
    review_notes: Full text available. Explicitly equates RasGEFU with GbpD,
      confirms plasma-membrane localization and adhesion/pseudopod/motility
      phenotypes underpinning the dictyBase IMP/IDA/IGI annotations.
core_functions:
- description: GbpD is a Rap1-specific guanine nucleotide exchange factor that acts
    at the plasma membrane to convert Rap1-GDP to active Rap1-GTP. Through this
    activity it drives the formation of substrate-attached pseudopodia, promoting
    cell-substrate adhesion and suppressing cell polarity (with downstream effects
    on pseudopod dynamics and chemotactic motility). The Rap1 signal engages the
    effector kinase Phg2 for adhesion.
  molecular_function:
    id: GO:0005085
    label: guanyl-nucleotide exchange factor activity
  directly_involved_in:
  - id: GO:0010810
    label: regulation of cell-substrate adhesion
  - id: GO:0031272
    label: regulation of pseudopodium assembly
  - id: GO:0007163
    label: establishment or maintenance of cell polarity
  locations:
  - id: GO:0005886
    label: plasma membrane
  supported_by:
  - reference_id: PMID:16769729
    supporting_text: Here we demonstrate that GbpD activates Rap1 both in vivo and
      in vitro but not any of the five other characterized Ras proteins
  - reference_id: PMID:15827084
    supporting_text: GbpD induces the formation of substrate-attached pseudopodia,
      resulting in increased attachment and suppression of polarity
  - reference_id: PMID:39746985
    supporting_text: RasGEFU localized almost uniformly to the membrane and did not
      exhibit traveling waves