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The Shaping of the Proteomes of the Pathogenic Protists

The availability of numerous complete genome sequences will allow phylogenetic studies having a whole-genome basis, thus improving our understanding of the radiation of the protozoans and their relative relationships to the metazoans. The protozoans as a group might be envisioned as deeply branched lineages of free-living protozoans, from which parasitic members have independently evolved along multiple branches (Fig. 19.1). The branching of the protozoan lineages, as well as their divergence from the crown group of multicellular eukaryotes, is at

Fig. 19.1 Phylogenetic tree showing the relative positions of the important pathogenic protozoans, their notable free-living relatives (indicated by a star), and the crown group composed of plants, fungi, slime molds, and animals. The dashed line at the base of the tree indicates a proposed genome fusion event creating the protozoan lineage ([145], reviewed in Ref. [146]). Question marks refer to unresolved nodes (after Refs.[19, 39]), and the overall tree is drawn in part from Refs. [17, 20].

Fig. 19.1 Phylogenetic tree showing the relative positions of the important pathogenic protozoans, their notable free-living relatives (indicated by a star), and the crown group composed of plants, fungi, slime molds, and animals. The dashed line at the base of the tree indicates a proposed genome fusion event creating the protozoan lineage ([145], reviewed in Ref. [146]). Question marks refer to unresolved nodes (after Refs.[19, 39]), and the overall tree is drawn in part from Refs. [17, 20].

19.3 Role of Lateral Gene Transfer in Protozoan Genome Plasticity | 421

present poorly defined, and models have at their extremes an explosive "big bang" radiation from a primordial eukaryote (with a generally unresolvable phylogeny and no clear outgroup) versus an orderly succession of deeply branching lineages [14-19]. An intuitive grouping places the plants and metazoans together as a crown group distinct from protozoans, and this is supported with respect to the apicomplexans plus Giardia using pooled amino acid sequence concatamers afforded by whole genome sequence data [20]. It is hoped that the imminently available kinetoplastid genome sequence information, as well as information from other free-living and parasitic protists, will further refine our understanding of the phylogeny of the protozoans.

All parasitic protozoans had free-living ancestors; for example, an ancestor common to Leishmania and Euglena, or common to Tetrahymena and Plasmodium. Whereas the parasitic protozoans encounter an elaborate interplay in evading the innate and adaptive host immune response (see Ref. [21] for a superb recent discussion), the free-living protozoans are driven by environmental pressures or evolutionary selection stemming from predation and prey. In fact, it has been proposed that the origin of multicellularity was an invention conferring advantage against predation [22, 23], and in turn the increasing complexity of the metazoans opened the opportunity for the numerous independent inventions of parasitism. There might be more than mere irony in these observations, because cellular mechanisms underpinning avoidance of predation, mediating search for prey, or sensing other environmental changes might have created cellular mechanisms that later facilitated the avoidance of an immune response. A foremost example for study in this regard is the possible relationship between antigenic variation in the free-living ciliates and the related alveolates, the pathogenic apicomplexans (Fig. 19.2). It is therefore of keen interest to compare the proteomes, particularly the protein-trafficking machineries and repertoires of surface proteins, encoded by the soon to be completed genome sequence of the ciliate Tetrahymena with the available complete genome sequences of the phylogenetically related apicomplex-ans Plasmodium and Cryptosporidium, as well as to initiate new genome sequencing projects for free-living protozoans.

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