Patterns of prokaryotic lateral gene transfers affecting parasitic microbial eukaryotes

Abstract

Background: The influence of lateral gene transfer on gene origins and biology in eukaryotes is poorly understood compared with those of 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: We used a phylogenomic approach to systematically investigate lateral gene transfer affecting the proteomes of thirteen, 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 the 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 is involved in such 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 show that ecology and lifestyle strongly influence gene origins and opportunities for gene transfer and reveal that, although the outlines of the 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.

Figure 1

Functional categories of identified lateral gene transfer (LGTs). (a) Distribution of functional annotation from the Kyoto Encyclopedia of Genes and Genomes (KEGG) database of LGTs supported by at least one node (357 entries; see Additional file 2; see Additional file 5). In total, 220 enzymes were identified, of which 165 (75%) could be mapped onto a KEGG pathway. The 'Other Metabolic Pathways' category includes the following KEGG pathways: 'Signal Transduction,' 'Metabolism of Secondary Metabolites,' and 'Metabolism of Terpenoids and Polyketides.' In total, 49 enzymes, labeled as 'Enzyme Reactions,' are not part of any metabolic pathway. Hypothetical proteins and poorly characterized entries are pooled in the category 'Hypothetical Proteins'. The number of entries in each functional category is based on the number of LGT events rather than genes, with an ancient LGT counted once. (b,c) Comparison of functional characterization of LGTs for (b) extracellular mucosal parasites (Trichomonas vaginalis, Entamoeba histolytica, Giardia lamblia) versus insect-transmitted blood parasites (Trypanosoma brucei, Trypanosoma cruzi, Plasmodium falciparum, Plasmodium vivax, Plasmodium yoelii yoelii) and (c) the parasitic amoebozoan E. histolytica versus the free-living amoebozoan Dictyostelium discoideum. Fisher's exact test was performed to test the null hypothesis that functional annotations of LGTs are distributed equally between the compared taxa. The P-values for the tests are indicated. The numbers of LGTs for each set of taxa are indicated between brackets.

Figure 2

Mapping of candidate lateral gene transfer (LGTs) onto the Kyoto Encyclopedia of Genes and Genomes (KEGG) central metabolic pathways. Candidate LGTs (thick edges) were mapped on the KEGG central metabolic pathways using the tool iPath (version 2.0 [78]) which provides an overview of metabolic and other pathways annotated in KEGG. Nodes correspond to substrates and edges to enzymatic reactions. The 11 major metabolic pathways are color-coded (for example, light orange for amino acid metabolism). The LGTs are broadly distributed across pathways: all 11 major KEGG metabolic pathway categories are affected by LGTs. Note that the individual enzymes acyl-CoA dehydrogenase (EC:1.3.8.7) and acetyl-CoA C-acyltransferase (EC:2.3.1.16) each occur several times in the fatty-acid metabolism and elongation pathways, respectively (teal-colored pathways). The mapping of candidate LGTs onto the 'Biosynthesis of secondary metabolites map' and the 'Regulatory pathways or functional modules' is also illustrated (see Additional file 15).

Figure 3

Trichomonas vaginalis lateral gene transfer (LGTs) that are potentially involved in glycan metabolism. (a) Schematic overview of the structures of a typical N-glycan and the enzymes (EC numbers in black delineated boxes) that can degrade them, according to the KEGG pathway ec00511. A typical O-glycan (extended core 1) [79] is also illustrated, along with selected enzymes shared with N-glycan degradation. O-glycans are the major glycans found in mucins, which are degraded by T. vaginalis. The characteristic components of glycans are shown. NeuNAc, N-acetylneuraminic acid; Gal, galactose; GlcNAc, N-acetylglucosamine; Man, Mannose; GalNac, N-acetylgalactosamine (O-glycan specific). The activities of six glycosidases originating form LGTs, out of a total of nine required to degrade N-glycans/gangliosides, are indicated by violet arrows, with their respective EC numbers in pink boxes. Two additional enzymes (EC numbers in orange boxes), N-acetylneuraminate lyase and acylglucosamine 2-epimerase, which also correspond to LGTs, could contribute to the further metabolism of the sugars liberated during glycan degradation. (b) Enzyme names and activities and evidence for LGT. Enzymes shared with the pathway for gangliosides metabolism are indicated. The final step of the degradation of gangliosides by a glucosylceramidase (EC:3.2.1.45) is also an LGT into T. vaginalis. The structure of gangliosides and the enzymes processing them are also illustrated (see Additional file 16).

Figure 4

Assessment of gains and losses of lateral gene transfer (LGTs) during parasite speciation. Maximum parsimony was used to map candidate LGTs on the species trees for taxa among (a) Trypanosomatidae and (b) Apicomplexa. Gains and losses are indicated as green and orange bars respectively. Characters were analyzed using Dollo parsimony, so each character is allowed to have only a single gain, but may have multiple losses. It is inferred that 45 LGTs occurred (over 75 genes affected by LGT) before the divergence of the three Trypanosomatidae lineages. Fewer (7/75) LGTs are specific to the individual Trypanosoma spp. lineages, whereas the branch to L. major is inferred to have experienced 22 gains after splitting from Trypanosoma. The reference phylogeny for the Apicomplexa used to map the LGTs is from Wasmuth et al. [80]. Four LGTs were inferred to been gained by the common ancestors of all sampled apicomplexans. Losses of two and four LGTs were inferred for Toxoplasma gondii and Plasmodium yoelii yoelii, respectively. Additional LGTs were inferred across the other branches, clearly indicating the dynamic nature of LGTs during the diversification of these parasites.

Figure 5

Taxonomy of donor lineages for candidate lateral gene transfer (LGTs). (a) Donor lineages for LGTs were defined as the adjacent (as defined by Wilkinson et al. [81]) prokaryote to our target eukaryote(s) in trees where the relevant eukaryote(s) were separated from other eukaryotes by at least one well-supported node. Complete lists of donor lineages and the corresponding phylogenies are presented (see Additional file 13; see Additional file 5). (b) Taxonomic diversity of donor lineages and their contributions to LGTs. The red bars represent the proportion (%) of protein sequences identified as LGTs per donor lineage compared with the blue bars that show the proportion (%) of sequences from that lineage in the reference dataset used as the search space for the analyses. The relative significance of over-representation or under-representation established by a hypergeometric test is indicated. (c) Comparison of the prokaryotic lineages inferred to be donating genes to the extracellular mucosal parasites Entamoeba histolytica, Trichomonas vaginalis, and Giardia lamblia compared with the inferred donor lineages for the insect-transmitted blood parasites Trypanosoma brucei, Trypanosoma cruzi, Plasmodium falciparum, Plasmodium vivax and Plasmodium yoelii yoelii. (d) Comparison of the prokaryotic lineages inferred to be donating genes to the parasite E. histolytica and its free-living amoebozoan relative Dictyostelium discoideum. (c, d) 'Other bacteria' comprise the Actinobacteria, Aquificae, Fusobacteria, Plantomycetes, Spirochaetes, or Tenericutes. Fisher's exact test was performed to test the null hypothesis that the taxonomy of the donors is distributed equally between the compared taxa. The P-values for the tests are indicated; they both reject the null hypothesis. The numbers of LGTs considered for each set of taxa are indicated between brackets. Complete diagrams showing all categories, including the unresolved 'Bacteria' donors and the different donors summarized as 'other bacteria,' are also presented (see Additional file 12).