Early-diverging fungi from the phylum Microsporidia are opportunistic pathogens of humans and other animals. A genome-wide search was conducted in four species of Microsporidia and one species of Cryptomycota for genes acquired by horizontal transfer from other organisms. Up to 2% of their genes had strong evidence for horizontal transfer. We showed that many transferred nucleic acid metabolism genes lie on the boundary of the host and pathogen metabolic networks. Finally, we functionally characterized the gene encoding thymidine kinase, whose multiple parallel transfers from three different sources strongly suggest an integral adaptive role in the lifestyles of these intracellular parasites. Microsporidian thymidine kinases activate a prodrug, suggesting a treatment route for microsporidian infections.

Abstract

Horizontal gene transfer (HGT) among bacteria, archaea, and viruses is widespread, but the extent of transfers from these lineages into eukaryotic organisms is contentious. Here we systematically identify hundreds of genes that were likely acquired horizontally from a variety of sources by the early-diverging fungal phyla Microsporidia and Cryptomycota. Interestingly, the Microsporidia have acquired via HGT several genes involved in nucleic acid synthesis and salvage, such as those encoding thymidine kinase (TK), cytidylate kinase, and purine nucleotide phosphorylase. We show that these HGT-derived nucleic acid synthesis genes tend to function at the interface between the metabolic networks of the host and pathogen. Thus, these genes likely play vital roles in diversifying the useable nucleic acid components available to the intracellular parasite, often through the direct capture of resources from the host. Using an in vivo viability assay, we also demonstrate that one of these genes, TK, encodes an enzyme that is capable of activating known prodrugs to their active form, which suggests a possible treatment route for microsporidiosis. We further argue that interfacial genes with well-understood activities, especially those horizontally transferred from bacteria or viruses, could provide medical treatments for microsporidian infections.