Nephromyces Encodes a Urate Metabolism Pathway and Predicted Peroxisomes, Demonstrating That These Are Not Ancient Losses of Apicomplexans

Abstract

The phylum Apicomplexa is a quintessentially parasitic lineage, whose members infect a broad range of animals. One exception to this may be the apicomplexan genus Nephromyces, which has been described as having a mutualistic relationship with its host. Here we analyze transcriptome data from Nephromyces and its parasitic sister taxon, Cardiosporidium, revealing an ancestral purine degradation pathway thought to have been lost early in apicomplexan evolution. The predicted localization of many of the purine degradation enzymes to peroxisomes, and the in silico identification of a full set of peroxisome proteins, indicates that loss of both features in other apicomplexans occurred multiple times. The degradation of purines is thought to play a key role in the unusual relationship between Nephromyces and its host. Transcriptome data confirm previous biochemical results of a functional pathway for the utilization of uric acid as a primary nitrogen source for this unusual apicomplexan.

Fig. 1.

—Maximum-likelihood protein trees of (A) xanthine dehydrogenase, (B) urate oxidase, (C) allantoicase, and (D) MLS. Genes (A–C) are involved in purine degradation and their position supports an ancestral apicomplexan purine degradation pathway in Nephromyces/Cardiosporidium. MLS (D) acts on glyoxylate and acetyl-CoA to produce malate to complete the pathway. Stramenopiles are paraphyletic in the MLS phylogeny, possibly indicating a deep gene duplication. Although the support for deeper nodes is variable among all four genes, there is consistent support for a monophyletic origin of Nephromyces/Cardiosporidium genes with Chromerids (red box). Major lineages have been collapsed for presentation. Support values are percentage bootstrap support above 50%.

Fig. 2.

—Predicted purine degradation pathway in Nephromyces, within the peroxisome and cytosol. Dark blue arrows represent enzymes identified in the Nephromyces transcriptome. The light blue arrow represents the highly expressed amidohydrolase (red box) predicted to convert ureidoglycolate into glyoxylate. Enzymes on the left side are localized to peroxisomes, the right side to the cytosol, with the green vertical line representing the peroxisomal membrane. The predicted pathway is able to convert uric acid into glyoxylate, and subsequent conversion by AGXT or MLS, creates glycine and pyruvate or malate, respectively. The * by AGXT indicates ambiguous predicted localization, to either peroxisomes or mitochondria.