gad1a (glutamate decarboxylase 1a) is one of two zebrafish co-orthologs of vertebrate GAD1 (GAD67), retained from the teleost-specific genome duplication; its paralog is gad1b. It encodes a pyridoxal 5'-phosphate-dependent group II decarboxylase that, by homology, converts L-glutamate to the inhibitory neurotransmitter GABA in the cytoplasm. The protein is 86% identical to Gad1b and keeps the PLP-binding lysine, the GABA-binding residues and the C-terminus of human GAD1; its N-terminal region is the least conserved part. gad1a is expressed at a much lower level than gad1b in embryos and larvae, with RNA-seq signal in brain, liver and early embryos, and it is absent from lateral-line efferent neurons that express gad1b. No enzyme assay, antibody, mutant or morphant exists for gad1a, and some published in situ data labelled gad1a may come from a gad1b-derived probe.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0004351 glutamate decarboxylase activity | IBA GO_REF:0000033 | ACCEPT | Summary: Glutamate decarboxylase activity propagated from the GAD node PTN002903772, seeded by fly Gad1, rodent Gad1/Gad2 and human GAD1. Reason: Glutamate decarboxylation is the ancestral activity of the vertebrate GAD1/GAD2 clade, and gad1a sits inside it as a GAD1 co-ortholog. Gad1a has not been assayed, but it keeps every catalytic feature checked (PLP-binding lysine at the position of human K405, GABA-binding residues, catalytic-loop sequence) and is 86% identical to Gad1b and 80% to human GAD1, with no sign of accelerated evolution relative to gad1b. Nothing suggests loss of activity. Supporting Evidence: PMID:1549570 Both cDNAs direct the synthesis of enzymatically active GADs in bacterial expression systems. file:DANRE/gad1a/gad1a-bioinformatics/RESULTS.md Both copies keep the PLP lysine and the GABA-binding residues of human GAD1. |
| GO:0004351 glutamate decarboxylase activity | IEA GO_REF:0000003 | ACCEPT | Summary: Glutamate decarboxylase activity from the EC 4.1.1.15 mapping of the UniProt (ARBA) name. Reason: Same claim as the IBA row, and consistent with conservation of the catalytic residues. Supporting Evidence: file:DANRE/gad1a/gad1a-bioinformatics/RESULTS.md Both copies keep the PLP lysine and the GABA-binding residues of human GAD1. |
| GO:0005737 cytoplasm | IBA GO_REF:0000033 | ACCEPT | Summary: Cytoplasm propagated from the group II decarboxylase node PTN000242648. Reason: GAD1 is a soluble enzyme that makes cytoplasmic GABA; gad1a has no signal peptide or transmembrane segment. No Gad1a localization data exist, but the location follows from the enzyme class. Supporting Evidence: PMID:27461130 While both GADs synthesize GABA and are co-expressed in most vertebrate GABAergic neurons, GAD1 synthesizes cytoplasmic GABA that is used for extrasynaptic and metabolic purposes and GAD2 regulates the vesicular pool for release |
| GO:0009449 GABA biosynthetic process | IBA GO_REF:0000033 | ACCEPT | Summary: GABA biosynthetic process propagated from PTN002903772; the donors include zebrafish gad1b (ZDB-GENE-030909-3) and gad2 (ZDB-GENE-030909-9). Reason: The enzyme catalyses the step that makes GABA, so the process follows directly from the activity. The zebrafish donors are gad1b and gad2, whose GABA-synthesizing role rests on co-localisation of GAD mRNA with GABA immunoreactivity. Whether gad1a contributes much GABA in vivo is unknown, since it is expressed at low levels, but the annotation describes what the protein does, not how much. Supporting Evidence: PMID:17384644 GAD67 is constitutively active and is responsible for basal GABA production. file:DANRE/gad1a/gad1a-bioinformatics/RESULTS.md Both copies keep the PLP lysine and the GABA-binding residues of human GAD1. |
| GO:0016830 carbon-carbon lyase activity | IEA GO_REF:0000002 | ACCEPT | Summary: Carbon-carbon lyase activity from the InterPro PLP-dependent decarboxylase domain (IPR002129). Reason: Correct but very general; glutamate decarboxylase activity (GO:0004351), which the gene also carries, is the informative term. Kept as a correct domain-level inference. Supporting Evidence: file:DANRE/gad1a/gad1a-bioinformatics/RESULTS.md Both copies keep the PLP lysine and the GABA-binding residues of human GAD1. |
| GO:0016831 carboxy-lyase activity | IEA GO_REF:0000002 | ACCEPT | Summary: Carboxy-lyase activity from the InterPro pyridoxal-phosphate attachment site signature (IPR021115). Reason: Correct parent of glutamate decarboxylase activity; the PLP attachment lysine is present in gad1a. Supporting Evidence: file:DANRE/gad1a/gad1a-bioinformatics/RESULTS.md Both copies keep the PLP lysine and the GABA-binding residues of human GAD1. |
| GO:0030170 pyridoxal phosphate binding | IEA GO_REF:0000002 | ACCEPT | Summary: Pyridoxal phosphate binding from the InterPro PLP-dependent decarboxylase domain. Reason: GAD enzymes bind PLP covalently through the active-site lysine, which gad1a keeps. PLP is the cofactor of the core activity. Supporting Evidence: PMID:17384644 Gamma-aminobutyric acid (GABA) is synthesized by two isoforms of the pyridoxal 5'-phosphate-dependent enzyme glutamic acid decarboxylase (GAD65 and GAD67). file:DANRE/gad1a/gad1a-bioinformatics/RESULTS.md Both copies keep the PLP lysine and the GABA-binding residues of human GAD1. |
| GO:0048786 presynaptic active zone | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: Presynaptic active zone propagated from node PTN002903810, seeded by mouse and rat Gad1. Reason: The node is inside the GAD1 clade, so gad1a inherits it formally, and the annotation is not contradicted. However GAD1 is mainly a cytoplasmic enzyme (terminal association is more characteristic of GAD2), and nothing is known about where Gad1a protein sits in neurons, or even in which neurons it is made at a meaningful level. Kept as a plausible but non-core location. Supporting Evidence: PMID:27461130 While both GADs synthesize GABA and are co-expressed in most vertebrate GABAergic neurons, GAD1 synthesizes cytoplasmic GABA that is used for extrasynaptic and metabolic purposes and GAD2 regulates the vesicular pool for release PMID:30200754 Nevetheless, this cannot be directly tested at this time, because an antibody specific to Gad1a has yet to be identified. |
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Download this section (compressed HTML)Q: Is gad1a translated into an active enzyme in any tissue, and where does the protein sit in neurons?
Q: Which published zebrafish "gad1a" in situ probes are really gad1a? The probe described as the Martin et al. gad67a plasmid needs to be sequenced, because the sequenced Martin GAD67 cDNA is gad1b.
Q: Are the liver and early-embryo RNA-seq signals of gad1a real (maternal transcript, hepatic GABA synthesis), and does gar GAD1 show the same?
Experiment: Express recombinant Gad1a and Gad1b and measure GABA formation from glutamate with PLP.
Hypothesis: gad1a retains glutamate decarboxylase activity comparable to gad1b.
Type: biochemical assay
Experiment: Generate a gad1a null (ideally a promoter or whole-gene deletion to avoid transcriptional adaptation) and a gad1a;gad1b double mutant; measure brain GABA, seizure-like activity and craniofacial development.
Hypothesis: gad1a contributes a minor, partly redundant share of GABA synthesis that is revealed only without gad1b.
Type: genetic interaction
Experiment: Paralog-specific HCR in situ with probes verified by sequence, plus single-cell RNA-seq mining, at embryonic, larval and adult stages.
Hypothesis: gad1a and gad1b have partly different cellular expression domains.
Type: expression analysis
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