Extreme genome diversity in the hyper-prevalent parasitic eukaryote Blastocystis

Abstract

Blastocystis is the most prevalent eukaryotic microbe colonizing the human gut, infecting approximately 1 billion individuals worldwide. Although Blastocystis has been linked to intestinal disorders, its pathogenicity remains controversial because most carriers are asymptomatic. Here, the genome sequence of Blastocystis subtype (ST) 1 is presented and compared to previously published sequences for ST4 and ST7. Despite a conserved core of genes, there is unexpected diversity between these STs in terms of their genome sizes, guanine-cytosine (GC) content, intron numbers, and gene content. ST1 has 6,544 protein-coding genes, which is several hundred more than reported for ST4 and ST7. The percentage of proteins unique to each ST ranges from 6.2% to 20.5%, greatly exceeding the differences observed within parasite genera. Orthologous proteins also display extreme divergence in amino acid sequence identity between STs (i.e., 59%–61% median identity), on par with observations of the most distantly related species pairs of parasite genera. The STs also display substantial variation in gene family distributions and sizes, especially for protein kinase and protease gene families, which could reflect differences in virulence. It remains to be seen to what extent these inter-ST differences persist at the intra-ST level. A full 26% of genes in ST1 have stop codons that are created on the mRNA level by a novel polyadenylation mechanism found only in Blastocystis. Reconstructions of pathways and organellar systems revealed that ST1 has a relatively complete membrane-trafficking system and a near-complete meiotic toolkit, possibly indicating a sexual cycle. Unlike some intestinal protistan parasites, Blastocystis ST1 has near-complete de novo pyrimidine, purine, and thiamine biosynthesis pathways and is unique amongst studied stramenopiles in being able to metabolize α-glucans rather than β-glucans. It lacks all genes encoding heme-containing cytochrome P450 proteins. Predictions of the mitochondrion-related organelle (MRO) proteome reveal an expanded repertoire of functions, including lipid, cofactor, and vitamin biosynthesis, as well as proteins that may be involved in regulating mitochondrial morphology and MRO/endoplasmic reticulum (ER) interactions. In sharp contrast, genes for peroxisome-associated functions are absent, suggesting Blastocystis STs lack this organelle. Overall, this study provides an important window into the biology of Blastocystis, showcasing significant differences between STs that can guide future experimental investigations into differences in their virulence and clarifying the roles of these organisms in gut health and disease.

Viability Screen of LOPAC 1280 Reveals Phosphorylation Inhibitor Auranofin as a Potent Inhibitor of Blastocystis Subtype 1, 4, and 7 Isolates

“…Genetic heterogeneity was also reported. In a study comparing the genome sequences of isolates from the three STs mentioned, the data showed differences in DNA base composition, genome size, number of genes, and number of introns (43). These differences then could contribute to the variations in drug susceptibilities (7,44), as well as effects on the host (2,45) and host immune responses (9,(46)(47)(48).…”

An ectosymbiosis-based mechanism of eukaryogenesis

“…However, Figure 5b panels 1-8 show that a series of archaeal proteins including DNA-biology enzymes and eukaryotic signature proteins 36 (ESPs) maintained fairly steady similarity bitscores toward both AMIs and MTEs ranging from Microsporidia to Hsa, which attested to the vertical transmission of these proteins between eukaryotes, and their significance as part of the core of eukaryotic proteomes. Bho and its subtypes Bs1, Bs4, and Bs3 (no reported proteome and therefore not included in Figure 4), which were in possession of both hydrogenosome components and partial mitochondria 37 , shared with the mitosome- and hydrogenosome-containing AMIs as well as the MTEs Bbo and Pfa the presence of Ssp-Tte-Hth proteins in their proteomes, thus pointing to a relationship between these firmicute species and the MRO-containing AMIs in keeping with the metabolic resemblance between hydrogenosome and Clostridium 38 . This was confirmed in Figure 5b panels 9-10, where the MRO-containing AMIs other than Microsporidia exhibited substantial bitscores toward the [Fe] hydrogenase and pyruvate:ferredoxin oxidoreductase (PFO) of clostridial Tte.…”

Mitochondrial targeting of glycolysis in a major lineage of eukaryotes

“…When analysing the genome of the intestinal parasite Blastocystis 8 , we discovered putative mitochondrial targeting signals on phosphoglycerate kinase (PGK) and on a fusion protein of triose phosphate isomerase (TPI) and glyceraldehyde phosphate dehydrogenase (GAPDH). The amino-terminal sequences conform to typical mitochondrial targeting signals 9 and are easily predicted by programmes such as MitoProt 10 .…”

“…The end-product of glycolysis, pyruvate, is transported into mitochondria via a specific mitochondrial transporter that has only recently been identified 22 and that is absent from the Blastocystis genome 8 . The translocation of the C3 part of glycolysis into mitochondria would necessitate a novel transporter (presumably for triose phosphates).…”

“…Both have serious consequences for aquaculture and the latter causes epizootic ulcerative syndrome, an OIE listed disease 23,24 . Our recent genome analysis of Blastocystis identified several putative candidate transporters lacking clear homology to non-stramenopile organisms 8 . Such a unique transporter would not be present in the host (including humans) and could be exploited to prevent, or control, disease outbreaks that currently affect food production while the world population continuous to increase 25 .…”