cDNA sequence of zebrafish (Brachydanio rerio) translation elongation factor-1 alpha: molecular phylogeny of eukaryotes based on elongation factor-1 alpha protein sequences.

We have isolated and determined the nucleotide sequence of a cDNA clone containing the complete coding region for elongation factor-1 alpha (EF-1 alpha) from an embryonic zebrafish cDNA library. A secondary structure model based on all known EF-1 alpha and EF-Tu protein sequences is presented and the presence of conserved putative protein kinase C phosphorylation sites in loop regions of eukaryotic EF-1 alpha is demonstrated. Using distance matrix and maximum parsimony methods we constructed multi-kingdom phylogenetic trees containing 22 different eukaryotic sequences. Strikingly, both tree constructions show Fungi to be the closest relative of Animalia among eukaryotic kingdoms. A 12 amino acid stretch present in all animal and fungal sequences known to date was found to be absent from all plant, protist an archaebacterial EF-1 alpha sequences suggesting that this sequence was inserted following the separation of plants from the lineage leading to fungi and animals. In contrast to our results, molecular phylogenies based on small subunit ribosomal RNA sequences as well as other protein sequences have failed to yield consistent results regarding the branching order among the kingdoms Plantae, Fungi and Animalia. The slow evolutionary rate and universal occurrence of EF-1 alpha (EF-Tu in eubacteria) makes this protein a particularly interesting tool for probing distant evolutionary relationships.