Patterns of prokaryotic lateral gene transfers affecting parasitic microbial eukaryotes

BACKGROUND:The impact of lateral gene transfer on eukaryotic gene origins and biology is poorly understood compared to prokaryotes. A number of independent investigations focusing on specific genes, individual genomes or specific functional categories from various eukaryotes have indicated that lateral gene transfer does indeed affect eukaryotic genomes. However the lack of common methodology and criteria in these studies makes it difficult to assess the general importance and influence of lateral gene transfer on eukaryotic genome evolution.RESULTS:Here we used a phylogenomic approach to systematically investigate lateral gene transfers affecting the proteomes of 13, mainly parasitic, microbial eukaryotes, representing four of the six eukaryotic super-groups. All of the genomes investigated have been significantly affected by prokaryote to eukaryote lateral gene transfers, dramatically affecting enzymes of core pathways, particularly amino acid and sugar metabolism, but also providing new genes of potential adaptive significance in the life of parasites. A broad range of prokaryotic donors are involved in transfers, but there is clear and significant enrichment for bacterial groups that share the same habitats, including the human microbiota, as the parasites investigated.CONCLUSIONS:Our data demonstrate that ecology and lifestyle strongly influence gene origins and opportunities for gene transfer and reveal that, while the outlines of core eukaryotic metabolism are conserved among lineages, the genes making up those pathways can have very different origins in different eukaryotes. Thus, from the perspective of the effects of lateral gene transfer on individual gene ancestries in different lineages, eukaryotic metabolism appears to be chimeric.