eef1da (eukaryotic translation elongation factor 1 delta a) is one of two zebrafish co-orthologs of vertebrate EEF1D, retained from the teleost-specific genome duplication; its paralog is eef1db (chromosome 20; eef1da is on chromosome 2). It encodes the delta subunit of the eEF1B complex, the guanine-nucleotide exchange factor that regenerates GTP-bound eEF1A during translation elongation. The protein has an N-terminal region, a leucine zipper for complex assembly, an acidic region and a C-terminal GEF domain that is 78% identical to human EEF1D and 89% identical to eef1db. The gene makes short isoforms (about 245-291 aa) and predicted long isoforms (417-463 aa; the reviewed entry is a 463-aa model) with an N-terminal extension whose similarity to the mammalian eEF1BdeltaL extension is not distinguishable from background. eef1da mRNA is broadly expressed, with a higher maternal and early-embryo signal than eef1db. No gene-specific functional study exists in zebrafish.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0003746 translation elongation factor activity | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro2GO mapping from the EF1B beta/delta GEF and conserved-site signatures. Reason: The eef1da product keeps the conserved EF-1-delta core, including a complete GEF region 78-81% identical to human EEF1D and 89% identical between the two zebrafish paralogs (DANRE/eef1da/eef1da-bioinformatics/RESULTS.md). eEF1Bdelta is an elongation factor acting as the nucleotide-exchange subunit for eEF1A. No zebrafish biochemical data exist; the annotation rests on strong sequence conservation. Supporting Evidence: file:DANRE/eef1da/eef1da-bioinformatics/RESULTS.md No copy has lost any part of the GEF region PMID:36576126 the eEF1B complex acts as a guanine exchange factor (GEF) of GTP for GDP indirectly catalyzing the release of eEF1A from the ribosome. |
| GO:0005085 guanyl-nucleotide exchange factor activity | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT inference at the EF1B beta/delta node (seeded by yeast EFB1) that the family has guanyl-nucleotide exchange activity toward eEF1A. Reason: Core molecular function of the EF-1beta/delta family, which is placed deep in the eukaryotic tree. The catalytic GEF region is complete and highly conserved in both zebrafish paralogs; there is no sign of loss or divergence of the catalytic domain in either copy. Supporting Evidence: PMID:36576126 the eEF1B complex acts as a guanine exchange factor (GEF) of GTP for GDP indirectly catalyzing the release of eEF1A from the ribosome. file:DANRE/eef1da/eef1da-bioinformatics/RESULTS.md No copy has lost any part of the GEF region |
| GO:0005829 cytosol | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT inference that the family is active in the cytosol. Reason: eEF1B acts on cytosolic eEF1A during translation elongation; in mammals the short EEF1D isoforms also anchor the complex to the ER surface, which is still cytosolic-facing. Supporting Evidence: PMID:30787422 EEF1D encodes a ubiquitously expressed translational elongation factor functioning in the cytoplasm. |
| GO:0005853 eukaryotic translation elongation factor 1 complex | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro2GO mapping placing the protein in the eukaryotic translation elongation factor 1 complex. Reason: EF-1delta is a subunit of the eEF1B(alpha-beta-gamma-delta) complex; the leucine zipper that mediates assembly is present in both zebrafish copies. Supporting Evidence: PMID:36576126 The gene EEF1D encodes the eEF1BΞ΄ subunit of the eEF1B complex. |
| GO:0006414 translational elongation | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT inference at the EF1B beta/delta node. Reason: Core process: recycling eEF1A-GDP to eEF1A-GTP for each elongation cycle. The zebrafish protein keeps the conserved core. Supporting Evidence: PMID:25686034 canonical eEF1BΞ΄, is highly conserved from worm to human, especially the leucine-zipper motif and GEF domain. |
| GO:0006414 translational elongation | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro2GO mapping from the EF1B beta/delta signatures. Reason: Same process as the IBA row; correct. |
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Download this section (compressed HTML)Q: Are eef1da long isoforms (N-terminal extension) actually translated in zebrafish, and do they enter the nucleus like mammalian eEF1BdeltaL?
Q: Do eef1da and eef1db proteins both assemble into eEF1B, in what ratio, and does the ratio change between oocyte/early embryo (eef1da-biased) and later tissues?
Q: Is eef1da dispensable, and is eef1db upregulated in eef1da mutants?
Experiment: Generate eef1da and eef1db single and double mutants (including RNA-less alleles) and measure viability, growth and global translation (puromycin incorporation, polysome profiles).
Hypothesis: The paralogs are dosage-redundant eEF1B subunits.
Type: genetic interaction analysis
Experiment: Paralog-specific peptide quantification (targeted proteomics) of eEF1B immunoprecipitates from embryos and adult tissues.
Hypothesis: Both paralog proteins are incorporated into eEF1B.
Type: proteomics
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