id: A0A8M1RDR2 gene_symbol: gad1a product_type: PROTEIN status: COMPLETE taxon: id: NCBITaxon:7955 label: Danio rerio description: 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. existing_annotations: - term: id: GO:0004351 label: glutamate decarboxylase activity evidence_type: IBA original_reference_id: GO_REF:0000033 qualifier: enables supporting_entities: - FB:FBgn0004516 - MGI:MGI:95632 - PANTHER:PTN002903772 - RGD:2652 - RGD:2653 - UniProtKB:Q7PNL7 - UniProtKB:Q99259 review: summary: Glutamate decarboxylase activity propagated from the GAD node PTN002903772, seeded by fly Gad1, rodent Gad1/Gad2 and human GAD1. action: ACCEPT 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. supported_by: - reference_id: PMID:1549570 supporting_text: Both cDNAs direct the synthesis of enzymatically active GADs in bacterial expression systems. - reference_id: file:DANRE/gad1a/gad1a-bioinformatics/RESULTS.md supporting_text: Both copies keep the PLP lysine and the GABA-binding residues of human GAD1. - term: id: GO:0004351 label: glutamate decarboxylase activity evidence_type: IEA original_reference_id: GO_REF:0000003 qualifier: enables supporting_entities: - EC:4.1.1.15 review: summary: Glutamate decarboxylase activity from the EC 4.1.1.15 mapping of the UniProt (ARBA) name. action: ACCEPT reason: Same claim as the IBA row, and consistent with conservation of the catalytic residues. supported_by: - reference_id: file:DANRE/gad1a/gad1a-bioinformatics/RESULTS.md supporting_text: Both copies keep the PLP lysine and the GABA-binding residues of human GAD1. - term: id: GO:0005737 label: cytoplasm evidence_type: IBA original_reference_id: GO_REF:0000033 qualifier: is_active_in supporting_entities: - MGI:MGI:95632 - MGI:MGI:95634 - PANTHER:PTN000242648 - RGD:2653 - RGD:621030 - WB:WBGene00006762 review: summary: Cytoplasm propagated from the group II decarboxylase node PTN000242648. action: ACCEPT 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. supported_by: - reference_id: PMID:27461130 supporting_text: 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 - term: id: GO:0009449 label: GABA biosynthetic process evidence_type: IBA original_reference_id: GO_REF:0000033 qualifier: involved_in supporting_entities: - FB:FBgn0004516 - PANTHER:PTN002903772 - RGD:2652 - ZFIN:ZDB-GENE-030909-3 - ZFIN:ZDB-GENE-030909-9 review: summary: GABA biosynthetic process propagated from PTN002903772; the donors include zebrafish gad1b (ZDB-GENE-030909-3) and gad2 (ZDB-GENE-030909-9). action: ACCEPT 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. supported_by: - reference_id: PMID:17384644 supporting_text: GAD67 is constitutively active and is responsible for basal GABA production. - reference_id: file:DANRE/gad1a/gad1a-bioinformatics/RESULTS.md supporting_text: Both copies keep the PLP lysine and the GABA-binding residues of human GAD1. - term: id: GO:0016830 label: carbon-carbon lyase activity evidence_type: IEA original_reference_id: GO_REF:0000002 qualifier: enables supporting_entities: - InterPro:IPR002129 review: summary: Carbon-carbon lyase activity from the InterPro PLP-dependent decarboxylase domain (IPR002129). action: ACCEPT 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. supported_by: - reference_id: file:DANRE/gad1a/gad1a-bioinformatics/RESULTS.md supporting_text: Both copies keep the PLP lysine and the GABA-binding residues of human GAD1. - term: id: GO:0016831 label: carboxy-lyase activity evidence_type: IEA original_reference_id: GO_REF:0000002 qualifier: enables supporting_entities: - InterPro:IPR021115 review: summary: Carboxy-lyase activity from the InterPro pyridoxal-phosphate attachment site signature (IPR021115). action: ACCEPT reason: Correct parent of glutamate decarboxylase activity; the PLP attachment lysine is present in gad1a. supported_by: - reference_id: file:DANRE/gad1a/gad1a-bioinformatics/RESULTS.md supporting_text: Both copies keep the PLP lysine and the GABA-binding residues of human GAD1. - term: id: GO:0030170 label: pyridoxal phosphate binding evidence_type: IEA original_reference_id: GO_REF:0000002 qualifier: enables supporting_entities: - InterPro:IPR002129 review: summary: Pyridoxal phosphate binding from the InterPro PLP-dependent decarboxylase domain. action: ACCEPT reason: GAD enzymes bind PLP covalently through the active-site lysine, which gad1a keeps. PLP is the cofactor of the core activity. supported_by: - reference_id: PMID:17384644 supporting_text: Gamma-aminobutyric acid (GABA) is synthesized by two isoforms of the pyridoxal 5'-phosphate-dependent enzyme glutamic acid decarboxylase (GAD65 and GAD67). - reference_id: file:DANRE/gad1a/gad1a-bioinformatics/RESULTS.md supporting_text: Both copies keep the PLP lysine and the GABA-binding residues of human GAD1. - term: id: GO:0048786 label: presynaptic active zone evidence_type: IBA original_reference_id: GO_REF:0000033 qualifier: is_active_in supporting_entities: - MGI:MGI:95632 - PANTHER:PTN002903810 - RGD:2652 review: summary: Presynaptic active zone propagated from node PTN002903810, seeded by mouse and rat Gad1. action: KEEP_AS_NON_CORE 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. supported_by: - reference_id: PMID:27461130 supporting_text: 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 - reference_id: PMID:30200754 supporting_text: Nevetheless, this cannot be directly tested at this time, because an antibody specific to Gad1a has yet to be identified. core_functions: - description: Pyridoxal 5'-phosphate-dependent glutamate decarboxylase (GAD67-type) that, by homology, synthesizes GABA from L-glutamate in the cytoplasm. Catalytic residues are shared with gad1b; gad1a is the minor, low-expressed copy and has not been assayed or mutated. molecular_function: id: GO:0004351 label: glutamate decarboxylase activity directly_involved_in: - id: GO:0009449 label: GABA biosynthetic process locations: - id: GO:0005737 label: cytoplasm supported_by: - reference_id: file:DANRE/gad1a/gad1a-bioinformatics/RESULTS.md supporting_text: Both copies keep the PLP lysine and the GABA-binding residues of human GAD1. - reference_id: file:DANRE/gad1a/gad1a-bioinformatics/RESULTS.md supporting_text: gad1b is about 20-fold more abundant than gad1a in whole larvae (84 vs 4 TPM at day 5). - reference_id: PMID:17384644 supporting_text: GAD67 is constitutively active and is responsible for basal GABA production. references: - id: GO_REF:0000002 title: Gene Ontology annotation through association of InterPro records with GO terms findings: [] - id: GO_REF:0000003 title: Gene Ontology annotation based on Enzyme Commission mapping findings: [] - id: GO_REF:0000033 title: Annotation inferences using phylogenetic trees findings: [] - id: PMID:1549570 title: Two human glutamate decarboxylases, 65-kDa GAD and 67-kDa GAD, are each encoded by a single gene. findings: [] reference_review: relevance: MEDIUM correctness: VERIFIED review_notes: Abstract only; human GAD65/GAD67 cDNAs direct active enzymes in bacteria. Background for the activity. - id: PMID:17384644 title: GABA production by glutamic acid decarboxylase is regulated by a dynamic catalytic loop. findings: [] reference_review: relevance: MEDIUM correctness: VERIFIED review_notes: Abstract only; human GAD67/GAD65 structures; GAD67 constitutively active. - id: PMID:27461130 title: Three Distinct Glutamate Decarboxylase Genes in Vertebrates. findings: [] reference_review: relevance: MEDIUM correctness: VERIFIED review_notes: GAD family evolution (GAD1, GAD2, GAD3); background on GAD1 vs GAD2 roles; names teleost gad1a/gad1b but does not analyse them. - id: PMID:30200754 title: Bypassing Glutamic Acid Decarboxylase 1 (Gad1) Induced Craniofacial Defects with a Photoactivatable Translation Blocker Morpholino. findings: [] reference_review: relevance: HIGH correctness: VERIFIED review_notes: Full text; gad1b morphants and gad1b null mutants; states chromosome locations of both copies, MO mismatch with gad1a and lack of a Gad1a antibody. - id: PMID:34650032 title: Increased locomotor activity via regulation of GABAergic signalling in foxp2 mutant zebrafish-implications for neurodevelopmental disorders. findings: [] reference_review: relevance: MEDIUM correctness: DISPUTED review_notes: Full text; in situ comparison of gad1a and gad1b (reported as highly similar) and qPCR of both. The gad1a probe is described as the Martin et al. gad67a plasmid, and the sequenced Martin GAD67 cDNA is gad1b, so paralog identity of the in situ probe is uncertain; qPCR differences are more reliable. - id: PMID:35769333 title: Loss-of-Function Models of the Metabotropic Glutamate Receptor Genes Grm8a and Grm8b Display Distinct Behavioral Phenotypes in Zebrafish Larvae (Danio rerio). findings: [] reference_review: relevance: MEDIUM correctness: DISPUTED review_notes: Full text; gad1a used as in situ marker (same probe caveat as PMID:34650032); qPCR shows gad1a, not gad1b, reduced in grm8a mutants. - id: PMID:41950195 title: Single-cell analysis of inhibitory efferent neurons of the zebrafish lateral line. findings: [] reference_review: relevance: MEDIUM correctness: VERIFIED review_notes: Full text; single-cell RNA-seq; efferent neurons express gad1b and gad2 but not gad1a. - id: PMID:41097006 title: Ezh2 Loss-of-Function Alters Zebrafish Cerebellum Development. findings: [] reference_review: relevance: LOW correctness: VERIFIED review_notes: Passing statement that the two gad1 paralogs have similar expression; uses gad1b only. - id: PMID:42466317 title: Gene expression mapping of conserved GABAergic interneuron markers in developing zebrafish. findings: [] reference_review: relevance: LOW correctness: MISCITED review_notes: States that gad1a and gad1b overlap and cites Filippi et al. 2014 (PMID:24374659), which examined gad1b and gad2, not gad1a. - id: PMID:26896392 title: Evx1 and Evx2 specify excitatory neurotransmitter fates and suppress inhibitory fates through a Pax2-independent mechanism. findings: [] reference_review: relevance: LOW correctness: VERIFIED review_notes: Methods note that the old gad67a/gad67b probes target gad1b; used for the probe-identity caveat. - id: file:DANRE/gad1a/gad1a-bioinformatics/RESULTS.md title: gad1a / gad1b protein, expression and synteny comparison reference_review: relevance: HIGH correctness: VERIFIED review_notes: >- Local pair analysis directly supports GAD1-family active-site retention in both copies and resolves the classic AF017266 GAD67 probe as gad1b; the report also flags later probe-identity ambiguity where the sequence was not published. findings: [] suggested_questions: - question: Is gad1a translated into an active enzyme in any tissue, and where does the protein sit in neurons? - question: 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. - question: Are the liver and early-embryo RNA-seq signals of gad1a real (maternal transcript, hepatic GABA synthesis), and does gar GAD1 show the same? suggested_experiments: - hypothesis: gad1a retains glutamate decarboxylase activity comparable to gad1b. description: Express recombinant Gad1a and Gad1b and measure GABA formation from glutamate with PLP. experiment_type: biochemical assay - hypothesis: gad1a contributes a minor, partly redundant share of GABA synthesis that is revealed only without gad1b. description: 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. experiment_type: genetic interaction - hypothesis: gad1a and gad1b have partly different cellular expression domains. description: Paralog-specific HCR in situ with probes verified by sequence, plus single-cell RNA-seq mining, at embryonic, larval and adult stages. experiment_type: expression analysis