InterB multigenic family, a gene repertoire associated with subterminal chromosome regions of Encephalitozoon cuniculi and conserved in several human-infecting microsporidian species

Abstract

Microsporidia are fungi-related obligate intracellular parasites that infect numerous animals, including man. Encephalitozoon cuniculi harbours a very small genome (2.9 Mbp) with about 2,000 coding sequences (CDSs). Most repeated CDSs are of unknown function and are distributed in subterminal regions that mark the transitions between subtelomeric rDNA units and chromosome cores. A potential multigenic family (interB) encoding proteins within a size range of 579-641 aa was investigated by PCR and RT-PCR. Thirty members were finally assigned to the E. cuniculi interB family and a predominant interB transcript was found to originate from a newly identified gene on chromosome III. Microsporidian species from eight different genera infecting insects, fishes or mammals, were tested for a possible intra-phylum conservation of interB genes. Only representatives of the Encephalitozoon, Vittaforma and Brachiola genera, differing in host range but all able to invade humans, were positive. Molecular karyotyping of Brachiola algerae showed a complex set of chromosome bands, providing a haploid genome size estimate of 15-20 Mbp. In spite of this large difference in genome complexity, B. algerae and E. cuniculi shared some similar interB gene copies and a common location of interB genes in near-rDNA subterminal regions.

The complete sequence of the smallest known nuclear genome from the microsporidian Encephalitozoon intestinalis

“…The contrast between these similarities and the chromosome ends is stark, but is in line with previous findings based on pulsed field gel electrophoresis and other methodologies202425. First, genes encoded near the ends of chromosomes are known to be evolving under different pressures than are other genes2627, and in Encephalitozoon , this is reflected by an even more elevated amino-acid sequence divergence compared with any other region of the genome.…”

“…3). These regions harbour a mixture of unique genes of known function in other organisms, hypothetical ORFs, and several members of a highly divergent Encephalitozoon -specific gene family (for example, DUF1609, DUF2463 or DUF1686) that seems to be actively transcribed2021. In none of these cases is there any evidence that the coding regions represent pseudogenes, and there is similarly no indication that these regions contain any transposable elements that have been completely eradicated from both genomes.…”

“…In either cases, the high dispensability and rapid evolution of the hypothetical genes and gene families located in those regions raise the possibility that some of these genes in extant genomes may not be functionally significant. Although there is no direct evidence that any of these genes are non-functional (and many are known to be expressed20), it is possible that some of them either represent pseudogenes in the process of eroding or even spurious ORFs in the case of hypothetical ORFs. For the genes that do encode functional proteins, if the clustering of dispensable genes at chromosome ends is favoured because of the unusual conditions faced by the genes encoded there, then, paradoxically, the outright loss of these regions as in E. intestinalis would expose what were formerly 'core' genes to those conditions.…”

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

“…Such expanded gene families are characteristic of other fungal pathogens such as Batrachochytrium dendrobatidis and Blumeria graminis , have also been reported in the microsporidia T. hominis , E. cuniculi , Anncaliia algerae and Vittaforma corneae [8], [64]–[66], and are also considered of importance in host-parasite interactions more generally [67]. Whilst the S. lophii members of this family have predicted N-terminal secretion signals, there is no evidence of an obvious conserved peptide motif involved in directing protein secretion into the host such as the oomycete crinkler motifs or the conserved tripeptide motif found in B. graminis which could help to define the microsporidian secretome [65], [68].…”

“…RAxML 8 protein phylogeny of microsporidia showing the phylogenetic context of S. lophii . Published expanded gene families were mapped onto this phylogeny, including InterB proteins [66], leucine rich-repeat proteins (LRR) [8], and other expanded gene families (EGF) as published [22], [23]. Stars indicate the detection of a single homolog of the protein in the genome.…”