The Genome of the Obligate Intracellular Parasite Trachipleistophora hominis: New Insights into Microsporidian Genome Dynamics and Reductive Evolution

Abstract

The dynamics of reductive genome evolution for eukaryotes living inside other eukaryotic cells are poorly understood compared to well-studied model systems involving obligate intracellular bacteria. Here we present 8.5 Mb of sequence from the genome of the microsporidian Trachipleistophora hominis, isolated from an HIV/AIDS patient, which is an outgroup to the smaller compacted-genome species that primarily inform ideas of evolutionary mode for these enormously successful obligate intracellular parasites. Our data provide detailed information on the gene content, genome architecture and intergenic regions of a larger microsporidian genome, while comparative analyses allowed us to infer genomic features and metabolism of the common ancestor of the species investigated. Gene length reduction and massive loss of metabolic capacity in the common ancestor was accompanied by the evolution of novel microsporidian-specific protein families, whose conservation among microsporidians, against a background of reductive evolution, suggests they may have important functions in their parasitic lifestyle. The ancestor had already lost many metabolic pathways but retained glycolysis and the pentose phosphate pathway to provide cytosolic ATP and reduced coenzymes, and it had a minimal mitochondrion (mitosome) making Fe-S clusters but not ATP. It possessed bacterial-like nucleotide transport proteins as a key innovation for stealing host-generated ATP, the machinery for RNAi, key elements of the early secretory pathway, canonical eukaryotic as well as microsporidian-specific regulatory elements, a diversity of repetitive and transposable elements, and relatively low average gene density. Microsporidian genome evolution thus appears to have proceeded in at least two major steps: an ancestral remodelling of the proteome upon transition to intracellular parasitism that involved reduction but also selective expansion, followed by a secondary compaction of genome architecture in some, but not all, lineages.

Evolution of a morphological novelty occurred before genome compaction in a lineage of extreme parasites

“…Despite showing a twofold difference in size, the M. daphniae genome is only slightly more compact than that of the water mold parasite R. allomycis (11.86 Mbp; 0.535 proteins/kbp). The number of predicted proteins in M. daphniae is roughly half that of R. allomycis and on par with the 3,266 ORFs predicted in 8.5+ Mbp genome of the microsporidian human pathogen Trachipleistophora hominis (20). The relative levels of similarity observed for the M. daphnia proteins suggest that it is closely related to both other microsporidian species and to R. allomycis (Table S1).…”

Nitrogen fixation in a chemoautotrophic lucinid symbiosis

“…MS spectra were searched against a target-decoy protein sequence database including all sequences from the C. orbicularis symbiont database (see 'Genome sequencing and genomic analysis' section) and common laboratory contaminants using the SEQUEST Sorcerer platform (Sage-N). Scaffold (version 4.2, Proteome Software) was used to validate MS/MS-based peptide and protein identifications using the XCorr-based filter settings described previously 61 . Proteins were considered identified if they passed the filter criteria in at least one of the three biological replicates.…”

Diversity and origins of anaerobic metabolism in mitochondria and related organelles

“…For example, Encephalitozoon cuniculi has a significantly reduced ATP generation machinery and must instead rely on ATP import from the host cell into the parasite cytoplasm, and eventually into the mitosomes, using bacteria-derived ADP/ATP translocators [64,65]. The mitosomes of Antonospora locustae and Trachypleistophora hominis encode an MRO-targeted alternative oxidase (AOX) and glycerol-3-phosphate dehydrogenase (G3PDH) indicating the likely presence of an electron-carrying quinone [64,66,67]; these may contribute to cytosolic NAD þ regeneration, rather than generating energy in the mitosomes. Two newly discovered deep-branching relatives of microsporidians, Rozella and Mitosporidium, have recently been shown to have more complex MROs compared with previously studied microsporidia (e.g.…”

“…mitosomes). In such lineages, ATP is either synthesized in the cytoplasm (by PFO, HYD and ACS in Giardia and Entamoeba) (figure 2) or imported from host cells (in Microsporidia) [64,65].…”