Proteomic profiling of kars knockout zebrafish larvae

Abstract

Background

KARS encodes both mitochondrial and cytoplasmic lysyl-tRNA synthetase, which is one of the aminoacyl-tRNA synthetases (ARSs) necessary for protein translation. Pathogenic variants in KARS have been reported to be involved in hearing loss, visual disorders, neuropathology, and diseases combined with multisystem phenotypes. In vitro studies have shown that KARS mutations cause a decrease in aminoacylation. However, the pathogenetic mechanisms underlying the complex neurological phenotypes remain largely unknown.

Methods

We developed kars knockout zebrafish and proteomic analyses on larvae with different genotypes at five days post-fertilization were performed using isobaric tags for relative and absolute quantitation (iTRAQ). Then the differentially abundant proteins (DAPs) analyzed by iTRAQ were validated by parallel reaction monitoring (PRM).

Results

420 differentially abundant proteins were identified between the knockout and wildtype groups, of which, 138 were up-regulated and 282 down-regulated. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways analyses showed the greatest DAP cluster enrichment in ribosome (P = 2.1 × 10^-6, 28 genes), aminoacyl-tRNA biosynthesis (P = 7.34 × 10^-6, 13 genes), and hypertrophic cardiomyopathy (P = 7.45 × 10^-6, 28 genes). A further PRM-based analysis identified changes in nars, mybphb, atp2a1l, col6a1 and rps3a that were specially linked to kars-deficency.

Conclusions

This work provides new valuable in vivo data for understanding the molecular mechanism of KARS deficiency-associated diseases, and will give us comprehensive insights into ARS-related disorders.