Comparative genomics of parasites

Abstract

Comparative genomics is an emerging field in biology that started in 1995 when the first two genomes of self-replicating organisms had been sequenced. Since then, a plethora of genome sequences from parasites, hosts and vectors has been made available. The comparison of genomes may shed light on the genetic and evolutionary bases of convergent and divergent properties throughout the tree of life. Comparative genomics of parasites may be performed at different levels: (i) between parasites and free-living organisms, (ii) between parasite and host, (iii) within closely related species (family, genus), and (iv) within species. Studies on all four levels were performed in the framework of this PhD thesis. On the one hand I took advantage of the wealth of genomes available to gain new insights into the molecular nature of host-pathogen interactions, drug target discovery and evolution of parasites in general. On the other hand whole genome sequencing projects were carried out that directly addressed parasite chemotherapy. Three algorithms were invented to study important aspects of parasitology. Automated tools were developed that are widely applicable to parasites and they were included in the Dirofilaria immits genome project. First, whole parasite proteomes were screened for molecular mimicry candidates by comparing parasite sequences to host and control species. Linear epitopes were identified that were present in the host proteome as well as in the parasite but not in free-living control organisms. The designed pipeline returned several interesting hits, most notably a motif in several PfEMP1 variants identical to part of the heparin-binding domain in the cytoadhesive and immunosuppressive serum protein vitronectin. Moreover, a homolog of cytokine suppressor SOCS5 was found in several pathogenic nematodes. Second, a tool was built that discriminates DNA sequences to the level of species of origin based on palindrome frequency patterns. It relied on the highly specific palindrome occurrence among species for DNA typing. The power of the program was illustrated when the comparison of palindrome frequency patterns provided further evidence for horizontal gene transfer between D. immitis and its Wolbachia endosymbiont. Third, a drug target prediction pipeline was designed that is based on the assumption that proteins are likely to be essential if they are highly conserved among related species and if there are no similar proteins in the same proteome. By inclusion of other criteria such as matchlessness in the human proteome, expression in a relevant stage and prediction of druggability, candidates were identified that may serve as starting points for rational drug discovery. When applied to P. falciparum, a sizeable list of 40 proteins with proven and new targets was obtained. Further, whole genome sequencing was conducted of a drug-sensitive Trypanosoma brucei rhodesiense STIB900 line and two drug-resistant derivatives STIB900-M and STIB900-P. By comparative genomics, mutations and gene deletions were detected that may confer drug resistance to melarsoprol and pentamidine. Proof-of-principle was the detection of the loss of known determinants of drug susceptibility, the adenosine transporter TbAT1 and the aquaporin TbAQP2. Moreover, a coding mutation occurred in both resistance lines in the gene for the RNA-binding protein UBP1. In conclusion, comparative genomics is a powerful tool that offers new opportunities in biological research. Comparative genomics can be applied at different levels, from basic research to applied questions such as drug discovery and resistance.