Selfish genetic elements have evolved manifold ways to persist in genomes and populations without offering any apparent benefit to the host. In a particularly radical example, toxin-antidote elements (TAs) secure their position in host populations by selectively removing progeny that do not inherit a copy of the respective underlying gene pair. Numerous TAs have been identified and mechanistically dissected in bacteria. However, only few examples have been reported in eukaryotes. Importantly, the underlying molecular mechanisms of eukaryotic TAs remain completely unresolved to date, hindering our understanding of this ongoing arms-race between the host genome and parasitic elements. Initially discovered in C. elegans, we recently greatly expanded the repertoire of known animal TAs with the discovery of multiple TAs in a cross between two isolates of the nematode Caenorhabditis tropicalis (Ben-David, Pliota et al., 2021). Here, we focus on a single TA from this cross, aiming to uncover its mechanism of action (for genetic and in vivo characterization see poster by Tikanova et al.). We identified and validated the novel toxin and antidote genes, which we named
klmt-1 (Killer of L1 and embryos Maternal Toxin) and
kss-1 (Klmt-rescue by zygotically-expreSSed antidote), respectively. We found that KLMT-1 shares 52% sequence identity with the beta subunit of the phenylalanyl-tRNA-synthetase (PheRS) and both N and C-terminal ends are predicted to be intrinsically disordered. We hypothesized that KLMT-1 kills worms by competing with the beta subunit in the heterotetrameric PheRS complex, thereby interfering with amino acid charging. In line with this hypothesis, we found that KLMT-1 is capable of binding the alpha subunit (FARS-1) of the PheRS in pulldown experiments and that FARS-1/KLMT-1 form an oligomeric complex in vitro. Furthermore, using a metabolic labelling approach, we quantified the activity of the C. tropicalis PheRS in bacteria and found that the presence of KLMT-1 strongly reduces the ability of the enzyme complex to charge its tRNA. Intriguingly, removal of the disordered termini of KLMT-1 further increased its inhibitory effect, indicating potential ways of spatial or temporal regulation of TA activity. Our findings serve as the basis to formulate a model for KLMT-1 toxicity, thereby for the first time providing mechanistic insight into a TA from animals and will be further substantiated by structural investigations of the FARS-1/KLMT-1 complex.