A tandem duplication of manganese superoxide dismutase in Nosema bombycis and its evolutionary origins

Evolutionary Genomics of Metchnikovella incurvata (Metchnikovellidae): An Early Branching Microsporidium

Metchnikovellids are highly specialized hyperparasites, which infect and reproduce inside gregarines (Apicomplexa) inhabiting marine invertebrates. Their phylogenetic affiliation was under constant discussion until recently, when analysis of the first near-complete metchnikovellid genome, that of Amphiamblys sp., placed it in a basal position with respect to most Microsporidia. Microsporidia are a highly diversified lineage of extremely reduced parasites related to Rozellida (Rozellosporidia = Rozellomycota = Cryptomycota) within the Holomycota clade of Opisthokonta. By sequencing DNA from a single-isolated infected gregarine cell we obtained an almost complete genome of a second metchnikovellid species, and the first one of a taxonomically described and well-documented species, Metchnikovella incurvata. Our phylogenomic analyses show that, despite being considerably divergent from each other, M. incurvata forms a monophyletic group with Amphiamplys sp., and confirm that metchnikovellids are one of the deep branches of Microsporidia. Comparative genomic analysis demonstrates that, like most Microsporidia, metchnikovellids lack mitochondrial genes involved in energy transduction and are thus incapable of synthesizing their own ATP via mitochondrial oxidative phosphorylation. They also lack the horizontally acquired ATP transporters widespread in most Microsporidia. We hypothesize that a family of mitochondrial carrier proteins evolved to transport ATP from the host into the metchnikovellid cell. We observe the progressive reduction of genes involved in DNA repair pathways along the evolutionary path of Microsporidia, which might explain, at least partly, the extremely high evolutionary rate of the most derived species. Our data also suggest that genome reduction and acquisition of novel genes co-occurred during the adaptation of Microsporidia to their hosts.

Genomic Survey of a Hyperparasitic Microsporidian Amphiamblys sp. (Metchnikovellidae)

Metchnikovellidae are a group of unusual microsporidians that lack some of the defining ultrastructural features characteristic of derived Microsporidia and are thought to be one of their earliest-branching lineages. The basal position of metchnikovellids was never confirmed by molecular phylogeny in published research, and thus far no genomic data for this group were available. In this work, we obtain a partial genome of metchnikovellid Amphiamblys sp. using multiple displacement amplification, next-generation sequencing, and metagenomic binning approaches. The partial genome, which we estimate to be close to 90% complete, displays genome compaction on par with gene-dense microsporidian genomes, but contains an unusual repertoire of unique repeat elements. Phylogenetic analyses of multigene datasets place Amphiamblys sp. as the first branch of the microsporidian lineage following the divergence of a mitochondriate microsporidian Mitosporidium. We find evidence for a mitochondrial remnant presumably functionally equivalent to a mitosome in Amphiamblys sp. and the common enzymatic complement for microsporidian anaerobic metabolism. Comparative genomic analyses identify the conservation of components for clathrin vesicle formation as one of the key features distinguishing the metchnikovellid from its highly derived relatives. The presented data confirm the notion of Metchnikovellidae as a less derived microsporidian group, and provide an additional stepping stone for reconstruction of an evolutionary transition from the early diverging parasitic fungi to derived Microsporidia.

Microsporidia: Eukaryotic Intracellular Parasites Shaped by Gene Loss and Horizontal Gene Transfers

Microsporidia are eukaryotic parasites of many animals that appear to have adapted to an obligate intracellular lifestyle by modifying the morphology and content of their cells. Living inside other cells, they have lost many, or all, metabolic functions, resulting in genomes that are always gene poor and often very small. The minute content of microsporidian genomes led many to assume that these parasites are biochemically static and uninteresting. However, recent studies have demonstrated that these organisms can be surprisingly complex and dynamic. In this review I detail the most significant recent advances in microsporidian genomics and discuss how these have affected our understanding of many biological aspects of these peculiar eukaryotic intracellular pathogens.

Microsporidia: Horizontal gene transfers in vicious parasites

Microsporidia are obligate intracellular parasites whose genomes have been shaped by an extreme lifestyle. Specifically, their obligate intracellular parasitism has resulted in the loss of many genes and biochemical pathways, but these reductive processes have been often offset by the acquisition of several genes by means of horizontal gene transfer (HGT). Until recently, these HGTs were all found to have derived from prokaryotic donors, but a recent study suggests that some species took advantage of this mechanism to acquire one gene from an animal, which they maintained in their genome for metabolic purposes. The gene encodes for a purine nucleoside phosphorylase, and shows a strong phylogenetic signal of arthropod origin. Here, we briefly review our current knowledge of HGTs discovered across microsporidian genomes and discuss the implications of the most recent findings in this research area for understanding the origin and evolution of this highly adapted group of intracellular parasites. A novel gene potentially transferred by means of HGT to one microsporidia is also reported.

Microsporidian genomes harbor a diverse array of transposable elements that demonstrate an ancestry of horizontal exchange with metazoans

Microsporidian genomes are the leading models to understand the streamlining in response to a pathogenic lifestyle; they are gene-poor and often possess small genomes. In this study, we show a feature of microsporidian genomes that contrasts this pattern of genome reduction. Specifically, genome investigations targeted at Anncaliia algerae, a human pathogen with a genome size of 23 Mb, revealed the presence of a hitherto undetected diversity in transposable elements (TEs). A total of 240 TE families per genome were identified, exceeding that found in many free-living fungi, and searches of microsporidian species revealed that these mobile elements represent a significant portion of their coding repertoire. Their phylogenetic analysis revealed that many cases of ancestry involve recent and bidirectional horizontal transfers with metazoans. The abundance and horizontal transfer origin of microsporidian TEs highlight a novel dimension of genome evolution in these intracellular pathogens, demonstrating that factors beyond reduction are at play in their diversification.

Searching for convergent evolution in manganese superoxidase dismutase using hydrophobic cluster analysis

There are numerous examples of convergent evolution in nature. Major ecological adaptations such as flight, loss of limbs in vertebrates, pesticide resistance, adaptation to a parasitic way of life, etc., have all evolved more than once, as seen by their analogous functions in separate taxa. But what about protein evolution? Does the environment have a strong enough influence on intracellular processes that enzymes and other functional proteins play, to evolve similar functional roles separately in different organisms? Manganese Superoxide Dismutase (MnSOD) is a manganesedependant metallo-enzyme which plays a crucial role in protecting cells from anti-oxidative stress by eliminating reactive (superoxide) oxygen species. It is a ubiquitous housekeeping enzyme found in nearly all organisms. In this study we compare phylogenies based on MnSOD protein sequences to those based on scores from Hydrophobic Cluster Analysis (HCA). We calculated HCA similarity values for each pair of taxa to obtain a pair-wise distance matrix. A UPGMA tree based on the HCA distance matrix and a common tree based on the primary protein sequence for MnSOD was constructed. Differences between these two trees within animals, enterobacteriaceae, planctomycetes and cyanobacteria are presented and cited as possible examples of convergence. We note that several residue changes result in changes in hydrophobicity at positions which apparently are under the effect of positive selection.

Identification and characterization of superoxide dismutase in Phytophthora cinnamomi

Superoxide dismutase (SOD) activities of the oomycete Phytophthora cinnamomi were examined. Five polypeptides with manganese superoxide dismutase (MnSOD) activity were found in mycelium growing in liquid culture with relative molecular weights ranging from approximately 25 to 100 kDa. Comparison with characterized avocado SODs showed no evidence for the presence of either iron or copper/zinc SODs in P. cinnamomi. The level of activity of the MnSOD polypeptides decreased in the presence of avocado root or cell wall components. Growth of P. cinnamomi, measured as dry weight, increased when the mycelium was grown in the presence of superoxide anion (O(2) (-)), which was added exogenously. Our results suggest that the metabolism of O(2) (-) has an important role in the development of P. cinnamomi.