The Species-Specific Acquisition and Diversification of a K1-like Family of Killer Toxins in Budding Yeasts of the Saccharomycotina

Abstract

Killer toxins are extracellular antifungal proteins that are produced by a wide variety of fungi, including Saccharomyces yeasts. Although many Saccharomyces killer toxins have been previously identified, their evolutionary origins remain uncertain given that many of these genes have been mobilized by double-stranded RNA (dsRNA) viruses. A survey of yeasts from the Saccharomyces genus has identified a novel killer toxin with a unique spectrum of activity produced by Saccharomyces paradoxus. The expression of this killer toxin is associated with the presence of a dsRNA totivirus and a satellite dsRNA. Genetic sequencing of the satellite dsRNA confirmed that it encodes a killer toxin with homology to the canonical ionophoric K1 toxin from Saccharomyces cerevisiae and has been named K1-like (K1L). Genomic homologs of K1L were identified in six non-Saccharomyces yeast species of the Saccharomycotina subphylum, predominantly in subtelomeric regions of the genome. When ectopically expressed in S. cerevisiae from cloned cDNAs, both K1L and its homologs can inhibit the growth of competing yeast species, confirming the discovery of a family of biologically active K1-like killer toxins. The sporadic distribution of these genes supports their acquisition by horizontal gene transfer followed by diversification. The phylogenetic relationship between K1L and its genomic homologs suggests a common ancestry and gene flow via dsRNAs and DNAs across taxonomic divisions. This appears to enable the acquisition of a diverse arsenal of killer toxins by different yeast species for potential use in niche competition. Antifungal killer toxins produced by Saccharomyces yeasts can be found mostly encoded by cytoplasmic double-stranded RNAs (dsRNAs) rather than the DNA genome. A survey of Saccharomyces yeasts has identified a new dsRNA-encoded killer toxin that has a unique antifungal activity and is related in structure and function to the canonical K1 killer toxin. This “K1-like” (K1L) killer toxin was identified to be part of a larger family of DNA-encoded “K1 killer toxin-like” (KKT) genes in more distantly related yeasts. KKT genes encode active killer toxins and appear to have been acquired sporadically during the evolution of each yeast species, with evidence of ongoing gene duplication. The common ancestry of K1L and homologous killer toxins suggests the transfer of these genes via dsRNAs and DNAs between different yeast species that inhabit similar natural and artificial environments. The potential evolutionary advantage of acquiring killer toxins for niche competition rationalizes the ongoing acquisition and diversification of these genes in yeasts.