Functional consequences of reductive protein evolution in a minimal eukaryotic genome

Abstract

Microsporidia are parasites with the smallest known eukaryotic genomes. The extent of protein loss in these organisms has been well documented, but much less is known about how compaction of microsporidia proteins affects their function. Taking a comparative genomic approach, we identified microsporidia orthologs of budding yeast proteins and show that these orthologs are enriched for essential yeast genes. We show that the median microsporidia protein is 21% shorter than its yeast counterpart and although extensive protein loss occurred after the divergence of microsporidia, reduced protein sizes were already present in microsporidian relatives. Microsporidia proteins are shorter through reduced domain lengths, diminished linker lengths, and domain loss, with 21% of microsporidia orthologs having lost domains present in yeast. On average, 34% of microsporidia orthologs have lost C-terminal residues essential for function in yeast, including 13 essential domains lost per genome. We also found that microsporidia display distinct phylogenetic patterns of domain loss, with losses occurring in a clade-specific manner. To investigate conservation of function, we used yeast complementation assays to test orthologs from several microsporidia species and their relative Rozella allomycis. These experiments reveal that most microsporidia proteins cannot complement their yeast orthologs, the ability to complement is about three-fold less than observed for R. allomycis orthologs, and proteins that do not complement are more reduced in length than their yeast orthologs. Altogether, our results demonstrate the drastic reduction of microsporidia proteins and show that these reductions have resulted in functional divergence from their fungal ancestors.