The Genome of Spraguea lophii and the Basis of Host-Microsporidian Interactions

Abstract

Microsporidia are obligate intracellular parasites with the smallest known eukaryotic genomes. Although they are increasingly recognized as economically and medically important parasites, the molecular basis of microsporidian pathogenicity is almost completely unknown and no genetic manipulation system is currently available. The fish-infecting microsporidian Spraguea lophii shows one of the most striking host cell manipulations known for these parasites, converting host nervous tissue into swollen spore factories known as xenomas. In order to investigate the basis of these interactions between microsporidian and host, we sequenced and analyzed the S. lophii genome. Although, like other microsporidia, S. lophii has lost many of the protein families typical of model eukaryotes, we identified a number of gene family expansions including a family of leucine-rich repeat proteins that may represent pathogenicity factors. Building on our comparative genomic analyses, we exploited the large numbers of spores that can be obtained from xenomas to identify potential effector proteins experimentally. We used complex-mix proteomics to identify proteins released by the parasite upon germination, resulting in the first experimental isolation of putative secreted effector proteins in a microsporidian. Many of these proteins are not related to characterized pathogenicity factors or indeed any other sequences from outside the Microsporidia. However, two of the secreted proteins are members of a family of RICIN B-lectin-like proteins broadly conserved across the phylum. These proteins form syntenic clusters arising from tandem duplications in several microsporidian genomes and may represent a novel family of conserved effector proteins. These computational and experimental analyses establish S. lophii as an attractive model system for understanding the evolution of host-parasite interactions in microsporidia and suggest an important role for lineage-specific innovations and fast evolving proteins in the evolution of the parasitic microsporidian lifecycle.

Transcriptome sequencing and characterization of ungerminated and germinated spores of <italic>Nosema bombycis</italic>

“…Two ricin B lectin-like secreted proteins were also identified in the supernatant of germinated Spraguea lophii spores [9]. Some research showed that lectins play diverse roles in parasites such as mediating parasite adhesion to host cell during infection, mediating immune evasion, and triggering different developmental pathways in the parasite [56,57].…”

“…Thus, spore germination may play a major role in host invasion, and the elucidation of spore germination will provide some valuable information for understanding the whole invasion process. Some genomes of important microsporidia have been reported and analyzed [7][8][9]. Based on the understanding of the microsporidia genome, transcriptome studies have been widely carried out [9][10][11], which generated information on the changes of total mRNA during a particular period.…”

“…Some genomes of important microsporidia have been reported and analyzed [7][8][9]. Based on the understanding of the microsporidia genome, transcriptome studies have been widely carried out [9][10][11], which generated information on the changes of total mRNA during a particular period. The genome of N. bombycis was published in 2013, and studies have shown that the genome of N. bombycis is expanded, rather than compact as some other parasitic microsporidian genomes are through several common molecular mechanisms [12].…”

Horizontally acquired genes in early-diverging pathogenic fungi enable the use of host nucleosides and nucleotides

“…In particular, HGT into fungi was thought to be rare, but several examples from bacteria into fungi or between fungi have recently been described (5,8,9). For example, one phylum of early-diverging fungi, the Microsporidia, has had a handful of HGT events documented (5,(10)(11)(12), but these fungi are thought to have acquired relatively few genes through HGT (13).…”

“…Known HGT events into Microsporidia include the following: (i) the ADP/ATP translocase gene family, originating from an HGT event that transferred the founding gene from a member of the bacterial phylum Chlamydia (10), which are known to steal energy-bearing molecules from their host; (ii) a sixgene folate synthesis pathway transferred into Encephalitozoon hellem from multiple donors, a transfer hypothesized to reduce host metabolic stress (11); and (iii) the acquisition of a glutamateammonia ligase from an unknown prokaryotic source by Spraguea lophii, which is thought to provide spores a mechanism for defense against the ammonia generated by the decomposing flesh in which they are embedded (12). These case studies, the first of which is shared with the Cryptomycota (19), suggest a role for HGT in the evolution of their unusual pathogenic metabolisms and indicate the need for a thorough, systematic analysis of HGT events in these early-diverging fungi.…”