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.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0005886 plasma membrane | IBA GO_REF:0000033 | ACCEPT | 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. 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. Supporting Evidence: PMID:39746985 RasGEFU localized almost uniformly to the membrane and did not exhibit traveling waves |
| GO:0007265 Ras protein signal transduction | IBA GO_REF:0000033 | ACCEPT | 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. 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. Supporting Evidence: PMID:16769729 Here we demonstrate that GbpD activates Rap1 both in vivo and in vitro but not any of the five other characterized Ras proteins |
| GO:0005085 guanyl-nucleotide exchange factor activity | IBA GO_REF:0000033 | ACCEPT | 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. Reason: Phylogenetic inference of GEF activity is fully consistent with the RasGEF domain architecture and with direct biochemical demonstration that GbpD activates Rap1. Supporting Evidence: PMID:16769729 Here we demonstrate that GbpD activates Rap1 both in vivo and in vitro but not any of the five other characterized Ras proteins |
| GO:0005085 guanyl-nucleotide exchange factor activity | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro2GO inference from the RasGEF catalytic domain signatures (IPR001895, IPR008937, IPR036964). This correctly captures the core GEF activity. Reason: The RasGEF catalytic domain is present in GbpD and the GEF activity is experimentally validated on Rap1, so this electronic annotation is correct. Supporting Evidence: PMID:16769729 Here we demonstrate that GbpD activates Rap1 both in vivo and in vitro but not any of the five other characterized Ras proteins |
| GO:0007264 small GTPase-mediated signal transduction | IEA GO_REF:0000002 | ACCEPT | 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. Reason: Consistent with GbpD's demonstrated role as a Rap1 GEF driving downstream adhesion/polarity signaling. Supporting Evidence: PMID:16769729 Here we demonstrate that GbpD activates Rap1 both in vivo and in vitro but not any of the five other characterized Ras proteins |
| GO:0010810 regulation of cell-substrate adhesion | IMP PMID:39746985 Excitable Ras dynamics-based screens reveal RasGEFX is requi... | ACCEPT | 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. Reason: Directly supported by mutant/overexpression phenotypes in which RasGEFU enhances cell-substrate adhesion. Supporting Evidence: PMID:39746985 RasGEFU-GFP-expressing cells showed increased adhesion to the substrates and thus less motility as their expression increased PMID:39746985 RasGEFU enhanced cell adhesion to substrates, consistent with previous reports of cGMP-binding protein D (GbpD), which is the same as RasGEFU |
| GO:0031272 regulation of pseudopodium assembly | IMP PMID:39746985 Excitable Ras dynamics-based screens reveal RasGEFX is requi... | ACCEPT | 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. Reason: Supported by the overexpression phenotype affecting pseudopod size and formation, a well-established GbpD effect on protrusion dynamics. Supporting Evidence: PMID:39746985 RasGEFU overexpression in these cells led to a large pseudopod and also less motility PMID:16769729 Cells overexpressing GbpD are flat, exhibit strongly increased cell-substrate attachment, and extend many bifurcated and lateral pseudopodia |
| GO:0005886 plasma membrane | IDA PMID:39746985 Excitable Ras dynamics-based screens reveal RasGEFX is requi... | ACCEPT | 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. Reason: Direct experimental localization (GFP fusion) places GbpD at the plasma membrane. Supporting Evidence: PMID:39746985 RasGEFU localized almost uniformly to the membrane and did not exhibit traveling waves |
| GO:2000145 regulation of cell motility | IGI PMID:39746985 Excitable Ras dynamics-based screens reveal RasGEFX is requi... | KEEP AS NON CORE | 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. 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. Supporting Evidence: PMID:39746985 RasGEFX, RasGEFB, RasGEFU and RasGEFM are important for efficient spontaneous motility PMID:39746985 RasGEFU-GFP-expressing cells showed increased adhesion to the substrates and thus less motility as their expression increased |
| GO:0031271 lateral pseudopodium assembly | IMP PMID:15827084 RasGEF-containing proteins GbpC and GbpD have differential e... | ACCEPT | 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. Reason: Loss- and gain-of-function phenotypes directly implicate GbpD in lateral pseudopod assembly. Supporting Evidence: PMID:15827084 gbpD-null mutants exhibit the opposite phenotype: cells display improved chemotaxis and appear hyperpolar, because cells make very few lateral pseudopodia PMID:16769729 Cells overexpressing GbpD are flat, exhibit strongly increased cell-substrate attachment, and extend many bifurcated and lateral pseudopodia |
| GO:0032060 bleb assembly | IGI PMID:26317626 Microtubule-Mediated Inositol Lipid Signaling Plays Critical... | KEEP AS NON CORE | 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. 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. Supporting Evidence: PMID:26317626 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 |
| GO:0005085 guanyl-nucleotide exchange factor activity | IDA PMID:16769729 Characterization of the GbpD-activated Rap1 pathway regulati... | ACCEPT | 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. 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. Supporting Evidence: PMID:16769729 Here we demonstrate that GbpD activates Rap1 both in vivo and in vitro but not any of the five other characterized Ras proteins |
| GO:0007163 establishment or maintenance of cell polarity | IMP PMID:15827084 RasGEF-containing proteins GbpC and GbpD have differential e... | ACCEPT | 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. Reason: Reciprocal loss- and gain-of-function phenotypes directly implicate GbpD in the control of cell polarity. Supporting Evidence: PMID:15827084 GbpD induces the formation of substrate-attached pseudopodia, resulting in increased attachment and suppression of polarity PMID:15827084 gbpD-null mutants exhibit the opposite phenotype: cells display improved chemotaxis and appear hyperpolar, because cells make very few lateral pseudopodia |
| GO:0031589 cell-substrate adhesion | IMP PMID:15827084 RasGEF-containing proteins GbpC and GbpD have differential e... | ACCEPT | 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. Reason: Directly supported by the overexpression phenotype of increased substrate attachment; mechanism traced to the GbpD-Rap1-Phg2 axis. Supporting Evidence: PMID:15827084 cells are flat and adhesive owing to an increased number of substrate-attached pseudopodia PMID:16769729 identified Phg2 as Rap1 effector necessary for adhesion, but not cell polarity |
| GO:0050920 regulation of chemotaxis | IMP PMID:15827084 RasGEF-containing proteins GbpC and GbpD have differential e... | KEEP AS NON CORE | 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. 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. Supporting Evidence: PMID:15827084 Overexpression of GbpD protein results in severely reduced chemotaxis PMID:15827084 gbpD-null mutants exhibit the opposite phenotype: cells display improved chemotaxis and appear hyperpolar, because cells make very few lateral pseudopodia |
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