The aminoacyl-tRNA synthetases of Drosophila melanogaster

Abstract

Aminoacyl-tRNA synthetases (aaRSs) ligate amino acids to their cognate tRNAs, allowing them to decode the triplet code during translation. Through different mechanisms aaRSs also perform several non-canonical functions in transcription, translation, apoptosis, angiogenesis and inflammation. Drosophila has become a preferred system to model human diseases caused by mutations in aaRS genes, to dissect effects of reduced translation or non-canonical activities, and to study aminoacylation and translational fidelity. However, the lack of a systematic annotation of this gene family has hampered such studies. Here, we report the identification of the entire set of aaRS genes in the fly genome and we predict their roles based on experimental evidence and/or orthology. Further, we propose a new, systematic and logical nomenclature for aaRSs. We also review the research conducted on Drosophila aaRSs to date. Together, our work provides the foundation for further research in the fly aaRS field.

Keywords: Charcot-Marie-Tooth neuropathy; Drosophila gene family; aminoacyl-tRNA synthetase; multifunctional protein, translation.

Figure 1.

Aminoacyl-tRNA synthetase catalyzes a 2-step aminoacylation reaction. In the first step, the aaRS activates the substrate amino acid. By consuming an ATP it forms an aa-AMP intermediate. In the second step, the aa-AMP is transferred to the acceptor end of the cognate tRNA, generating an aa-tRNA that can be delivered to ribosomes for protein synthesis. aa, amino acid; aaRS, aminoacyl-tRNA synthetase; PPi, pyrophosphate.

Figure 2.

Dual-localized aaRSs in D. melanogaster. (A) GlyRS is shown as an example of dual-localized aaRS. It encodes 2 polypeptides, PA and PB. PB contains an extra N-terminal mitochondrial targeting sequence (MTS; in red) that can be used for its import into mitochondria. (B) The four dual-localized aaRSs with their predicted MTS and probabilities of mitochondrial localization. The analysis was performed by Mitoprot. E.C., experimentally confirmed.

Figure 3.

Phylogenetic analysis of 4 dual-localized aaRSs. Protein sequences of common eukaryotes, archaea, and bacteria were obtained from different databases (UniProt, Ensembl, HGNC, FlyBase, Xenbase, WormBase), and also by searching with BLAST. The sequences were aligned using Pagan, followed by TrimAl analysis, discarding the poorly aligned columns with the threshold of 60%. The treated multiple sequence alignments were used to generate the 4 gene trees using PhyML; for topology searches we chose the best out of the NNI and PhyML-Subtree-Pruning-Regrafting (SPR) methods. All parameters were optimized, i.e., tree topology, branch length and the substitution rate. The number of bootstrap replicates was set to 5. Eukaryotes are shown in yellow, archaea in blue, and bacteria in red. The scale bar stands for the number of substitutions per site.