Zebrafish gmppb encodes GDP-mannose pyrophosphorylase B, the catalytic subunit of the GMPPA-GMPPB complex. It condenses alpha-D-mannose 1-phosphate with GTP to give GDP-alpha-D-mannose and diphosphate (EC 2.7.7.13), the activated sugar donor from which mannosyltransferases build N-glycans, GPI anchors, C- and O-mannosyl glycans and dolichol-phosphate-mannose. In the complex the catalytically inactive GMPPA subunit binds GDP-mannose with high affinity and allosterically inhibits GMPPB, making the pair a feedback sensor for cellular mannose supply (PMID:33986552). The reaction takes place in the cytosol; the zebrafish protein is about 81% identical to human GMPPB and is expressed ubiquitously from the one-cell stage, rising to a peak around 48 hours post fertilization (PMID:35006422). Knockdown lowers alpha-dystroglycan glycosylation and produces sparse, disordered muscle fibres, shortened CaP motor axons, reduced pan-neuronal HuC signal and impaired movement; wild-type but not catalytically weakened GMPPB mRNA rescues these defects (PMID:23768512, PMID:35006422). In humans, GMPPB mutations cause a spectrum of dystroglycanopathies from congenital muscular dystrophy to limb-girdle forms (PMID:23768512).
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0009101 glycoprotein biosynthetic process | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: IBA from the same node for glycoprotein biosynthesis. GDP-mannose made by gmppb is the donor substrate for mannosyltransferases, including the dolichol-phosphate-mannose route that builds N-glycans and the O-mannose glycans of alpha-dystroglycan. Reason: gmppb supplies the activated sugar but transfers no sugar onto a protein itself; the mannosyltransferases do that work. The link to glycoprotein synthesis is real and is why loss of gmppb causes hypoglycosylation of alpha-dystroglycan (PMID:23768512), but under the participation test this is an upstream metabolic contribution, so it is graded non-core rather than accepted as a core process. Supporting Evidence: file:DANRE/gmppb/gmppb-uniprot.txt Catalyzes the formation of GDP-mannose, an essential precursor of glycan moieties of glycoproteins and glycolipids (PubMed:33986552). PMID:23768512 reduced glycosylation of Ξ±-DG |
| GO:0009298 GDP-mannose biosynthetic process | IBA GO_REF:0000033 | ACCEPT | Summary: IBA from the GDP-mannose pyrophosphorylase node (PTN000500861) with yeast, Candida, mouse and human donors. The process is the single reaction gmppb catalyses: condensation of alpha-D-mannose 1-phosphate with GTP to give GDP-mannose and diphosphate. Reason: Participation is as direct as it gets - gmppb performs the reaction that defines the process, as the catalytic subunit of the GMPPA-GMPPB complex (PMID:33986552). All three rows for this term (IBA, IEA, ISS) make the same claim and are accepted alike; this is the core process. Supporting Evidence: file:DANRE/gmppb/gmppb-uniprot.txt PATHWAY: Nucleotide-sugar biosynthesis; GDP-alpha-D-mannose file:DANRE/gmppb/gmppb-uniprot.txt Catalytic subunit of the GMPPA-GMPPB mannose-1-phosphate PMID:33986552 GDP-mannose (GDP-Man) is a key metabolite essential for protein glycosylation |
| GO:0004475 mannose-1-phosphate guanylyltransferase (GTP) activity | IEA GO_REF:0000120 | ACCEPT | Summary: Automated annotation from InterPro IPR045233 (GMPPB family), RHEA:15229 and EC 2.7.7.13 for the same guanylyltransferase activity. Reason: The InterPro entry is the GMPPB family rather than a generic nucleotidyltransferase fold, and the Rhea reaction is the one curated on this entry from PMID:33986552. Consistent with the EXP and IBA rows. Supporting Evidence: file:DANRE/gmppb/gmppb-uniprot.txt Reaction=alpha-D-mannose 1-phosphate + GTP file:DANRE/gmppb/gmppb-uniprot.txt Catalytic subunit of the GMPPA-GMPPB mannose-1-phosphate |
| GO:0005525 GTP binding | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: InterPro2GO mapping of IPR045233 to GTP binding. GTP is a substrate of the guanylyltransferase reaction and was resolved bound in the cryo-EM structures of the complex (PMID:33986552). Reason: Substrate binding is real but is a component of the catalytic activity already annotated as GO:0004475, not a separate function; the protein is not a GTPase or a GTP-regulated switch. Kept as non-core. Supporting Evidence: file:DANRE/gmppb/gmppb-uniprot.txt Reaction=alpha-D-mannose 1-phosphate + GTP PMID:33986552 GDP-mannose (GDP-Man) is a key metabolite essential for protein glycosylation |
| GO:0009298 GDP-mannose biosynthetic process | IEA GO_REF:0000120 | ACCEPT | Summary: Automated annotation from InterPro IPR045233 and UniPathway UPA00126. The process is the single reaction gmppb catalyses: condensation of alpha-D-mannose 1-phosphate with GTP to give GDP-mannose and diphosphate. Reason: Participation is as direct as it gets - gmppb performs the reaction that defines the process, as the catalytic subunit of the GMPPA-GMPPB complex (PMID:33986552). All three rows for this term (IBA, IEA, ISS) make the same claim and are accepted alike; this is the core process. Supporting Evidence: file:DANRE/gmppb/gmppb-uniprot.txt PATHWAY: Nucleotide-sugar biosynthesis; GDP-alpha-D-mannose file:DANRE/gmppb/gmppb-uniprot.txt Catalytic subunit of the GMPPA-GMPPB mannose-1-phosphate PMID:33986552 GDP-mannose (GDP-Man) is a key metabolite essential for protein glycosylation |
| GO:0016740 transferase activity | IEA GO_REF:0000002 | MODIFY | Summary: InterPro2GO mapping of IPR018357 (nucleotidyltransferase hexapeptide/transferase signature) to the top-level transferase activity term. Reason: The root transferase term says nothing a reader can use when the exact reaction is known and experimentally supported for this family (alpha-D-mannose 1-phosphate + GTP to GDP-mannose; UniProt CATALYTIC ACTIVITY, PMID:33986552). Replace with the specific child already annotated. Proposed replacements: mannose-1-phosphate guanylyltransferase (GTP) activity Supporting Evidence: file:DANRE/gmppb/gmppb-uniprot.txt Reaction=alpha-D-mannose 1-phosphate + GTP |
| GO:0004475 mannose-1-phosphate guanylyltransferase (GTP) activity | EXP PMID:33986552 Cryo-EM structures of human GMPPA-GMPPB complex reveal how c... | ACCEPT | Summary: UniProt EXP row from the cryo-EM study of the GMPPA-GMPPB complex (PMID:33986552), which solved the human complex with GDP-mannose or GTP bound, showed GMPPB is the catalytic subunit allosterically inhibited by GMPPA, and tested the same interactions in zebrafish, where disruption caused brain and muscle abnormalities. Deep research adds the assay dependence on Mg2+ and mannose-1-phosphate, matching the UniProt cofactor requirement. Reason: This is the reaction UniProt records for the zebrafish entry (RHEA:15229, EC 2.7.7.13) with this paper as the ECO:0000269 source. The enzymology was done on the human complex while the in vivo test in the same paper was in zebrafish; the zebrafish protein is 81% identical to human GMPPB, so the assignment is sound. Core molecular function. Supporting Evidence: PMID:33986552 GDP-mannose (GDP-Man) is a key metabolite essential for protein glycosylation PMID:33986552 disruption of the interactions between GMPPA and GMPPB or the binding of GDP-Man to GMPPA in zebrafish leads to abnormal brain development and muscle abnormality, analogous to phenotypes observed in individuals carrying GMPPA or GMPPB mutations. file:DANRE/gmppb/gmppb-uniprot.txt Catalytic subunit of the GMPPA-GMPPB mannose-1-phosphate file:DANRE/gmppb/gmppb-uniprot.txt Reaction=alpha-D-mannose 1-phosphate + GTP file:DANRE/gmppb/gmppb-deep-research-falcon.md activity requires **MgΒ²βΊ** and the sugar-phosphate substrate **mannose-1-phosphate**; omitting MgΒ²βΊ or mannose-1-P yields **no detectable GDP-mannose formation** |
| GO:0007519 skeletal muscle tissue development | IMP PMID:35006422 GMPPB-congenital disorders of glycosylation associate with d... | KEEP AS NON CORE | Summary: ZFIN IMP from gmppb morpholino knockdown (PMID:35006422): morphants show sparse, disordered muscle fibres and markedly reduced movement, and the defect is rescued by wild-type GMPPB mRNA but not by the low-activity V111G variant. Reason: The rescue-by-catalytic-competence experiment is strong evidence that the muscle phenotype flows from the enzyme activity, and it is exactly what makes the annotation non-core: the enzyme acts by supplying GDP-mannose, while muscle tissue development is carried out by the myofibres whose glycoproteins depend on it. Downstream phenotype, kept as non-core. Supporting Evidence: PMID:35006422 Consistent with the previous study [13], we also observed sparse and disordered muscle fibers in gmppb-MO-injected embryos (Fig. PMID:35006422 GMPPB V111G mutant with decreased activity fails to rescue axonal phenotype in gmppb MO-injected zebrafish. PMID:35006422 Thus, enzymatic activity of GMPPB might be a critical determinant for phenotypes of zebrafish. |
| GO:0048666 neuron development | IMP PMID:35006422 GMPPB-congenital disorders of glycosylation associate with d... | KEEP AS NON CORE | Summary: ZFIN IMP from PMID:35006422: gmppb morphants have shortened, abnormal CaP motor axons at 24 and 48 hpf and reduced pan-neuronal HuC/elavl3 signal, both rescued by wild-type but not low-activity GMPPB mRNA. Reason: A specific, rescued neuronal phenotype, but neuron development is executed by the neurons; gmppb contributes the mannose donor their glycoproteins require. Kept as non-core, consistently with the muscle rows. Supporting Evidence: PMID:35006422 Furthermore, immunofluorescence assay revealed that the level of HuC (elavl3), an early marker of pan-neuronal cells, was remarkably decreased in the MO embryos. PMID:35006422 GMPPB V111G mutant with decreased activity fails to rescue axonal phenotype in gmppb MO-injected zebrafish. |
| GO:0009298 GDP-mannose biosynthetic process | ISS GO_REF:0000024 | ACCEPT | Summary: Manual ISS transfer from human GMPPB (UniProtKB:Q9Y5P6), with which the zebrafish protein shares about 81% identity. The process is the single reaction gmppb catalyses: condensation of alpha-D-mannose 1-phosphate with GTP to give GDP-mannose and diphosphate. Reason: Participation is as direct as it gets - gmppb performs the reaction that defines the process, as the catalytic subunit of the GMPPA-GMPPB complex (PMID:33986552). All three rows for this term (IBA, IEA, ISS) make the same claim and are accepted alike; this is the core process. Supporting Evidence: file:DANRE/gmppb/gmppb-uniprot.txt PATHWAY: Nucleotide-sugar biosynthesis; GDP-alpha-D-mannose file:DANRE/gmppb/gmppb-uniprot.txt Catalytic subunit of the GMPPA-GMPPB mannose-1-phosphate PMID:33986552 GDP-mannose (GDP-Man) is a key metabolite essential for protein glycosylation |
| GO:0009101 glycoprotein biosynthetic process | IMP PMID:23768512 Mutations in GDP-mannose pyrophosphorylase B cause congenita... | KEEP AS NON CORE | Summary: ZFIN IMP from morpholino knockdown (PMID:23768512), the paper that identified GMPPB mutations in congenital and limb-girdle muscular dystrophy; zebrafish morphants show reduced glycosylation of alpha-dystroglycan, and UniProt records defective DAG1 glycosylation. Reason: Changed from ACCEPT for consistency with the IBA row for the same term and for the same reason: hypoglycosylation on knockdown shows the enzyme is required for glycoprotein synthesis, which is what supplying a donor substrate means, not that gmppb performs a glycosylation step. Kept as a well-evidenced non-core process. Supporting Evidence: PMID:23768512 reduced glycosylation of Ξ±-DG file:DANRE/gmppb/gmppb-uniprot.txt Immunostaining shows defective glycosylation of DAG1 file:DANRE/gmppb/gmppb-uniprot.txt Catalyzes the formation of GDP-mannose, an essential precursor of glycan moieties of glycoproteins and glycolipids (PubMed:33986552). |
| GO:0055001 muscle cell development | IMP PMID:23768512 Mutations in GDP-mannose pyrophosphorylase B cause congenita... | KEEP AS NON CORE | Summary: ZFIN IMP from the earlier morpholino study (PMID:23768512), which reported structural muscle defects in zebrafish gmppb morphants alongside the human muscular dystrophy mutations. Reason: Same phenotype and same argument as the skeletal muscle tissue development row, graded identically: the metabolic enzyme supplies a substrate, the muscle cells do the developing. Abstract-only cache, so the curator reading of the full text is deferred to. Supporting Evidence: PMID:23768512 knockdown of the GMPPB ortholog in zebrafish caused structural muscle defects PMID:23768512 reduced glycosylation of Ξ±-DG |
| GO:0004475 mannose-1-phosphate guanylyltransferase (GTP) activity | IBA GO_REF:0000033 | ACCEPT | Summary: IBA from the GDP-mannose pyrophosphorylase node (PTN000500861), seeded by yeast PSA1, Candida, Arabidopsis, human GMPPB (Q9Y5P6) and the zebrafish gene itself. The activity is ancestral and essentially universal in eukaryotes. Reason: A single-activity family with donors spanning plants, fungi and vertebrates makes the node placement secure, and the target carries its own EXP row for the same term (PMID:33986552) - its presence in the WITH/FROM list marks that grounding rather than circularity. Same action as the EXP and Rhea IEA rows. Supporting Evidence: file:DANRE/gmppb/gmppb-uniprot.txt Catalytic subunit of the GMPPA-GMPPB mannose-1-phosphate PMID:33986552 GDP-mannose (GDP-Man) is a key metabolite essential for protein glycosylation |
| GO:0005575 cellular_component | ND GO_REF:0000015 | ACCEPT | Summary: ZFIN ND placeholder recording that no experimental cellular-component data exist for zebrafish gmppb; the cytoplasm assignment comes from phylogenetic inference only. Reason: Factually accurate: no localization experiment has been published for the zebrafish protein. It is not in conflict with the cytoplasm IBA row, which is an inference rather than an observation. Kept until direct data appear. Supporting Evidence: file:DANRE/gmppb/gmppb-uniprot.txt Catalytic subunit of the GMPPA-GMPPB mannose-1-phosphate |
| GO:0005737 cytoplasm | IBA GO_REF:0000033 | ACCEPT | Summary: IBA from a node (PTN000500804) spanning yeast PSA1, Arabidopsis, mouse and human GMPPA/GMPPB donors, placing the activity in the cytoplasm. GDP-mannose synthesis is a cytosolic step: the product is then used by cytosolic mannosyltransferases and delivered into the ER as dolichol-phosphate-mannose. Reason: The enzyme has no signal peptide or membrane anchor in UniProt and its substrates (mannose-1-phosphate, GTP) and the complex partner GMPPA are cytosolic, so the node assignment fits the biochemistry. Accepted as the location of the core activity; there is no zebrafish localization experiment, which is why the ZFIN ND row for cellular component also stands. Supporting Evidence: file:DANRE/gmppb/gmppb-uniprot.txt Catalytic subunit of the GMPPA-GMPPB mannose-1-phosphate file:DANRE/gmppb/gmppb-uniprot.txt Catalyzes the formation of GDP-mannose, an essential precursor of glycan moieties of glycoproteins and glycolipids (PubMed:33986552). |
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Download this section (compressed HTML)Q: Does zebrafish have a gmppa ortholog that inhibits Gmppb as in the human complex, and is the feedback sensing by GDP-mannose conserved?
Q: Which glycan classes are most sensitive to partial loss of gmppb in zebrafish - alpha-dystroglycan O-mannosyl glycans, N-glycans, or GPI anchors - and does that explain the muscle and motor-neuron selectivity of the phenotype?
Experiment: Co-express zebrafish Gmppa and Gmppb, measure guanylyltransferase activity with and without added GDP-mannose, and test whether disrupting the interaction in embryos reproduces the brain and muscle phenotypes reported for the human complex (PMID:33986552).
Hypothesis: Zebrafish Gmppb acts in a complex with Gmppa that is feedback-inhibited by GDP-mannose.
Type: biochemistry and genetics
Experiment: Make a stable gmppb mutant line, quantify GDP-mannose and glycan profiles by mass spectrometry, and test whether mannose supplementation or expression of a catalytically dead protein separates metabolic from non-metabolic contributions.
Hypothesis: The muscle and neuronal phenotypes of gmppb loss are caused by depletion of GDP-mannose rather than by a moonlighting function of the protein.
Type: metabolomics and genetic rescue
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