Horizontal gene transfer of an entire metabolic pathway between a eukaryotic alga and its DNA virus

Abstract

Interactions between viruses and phytoplankton, the main primary producers in the oceans, affect global biogeochemical cycles and climate. Recent studies are increasingly revealing possible cases of gene transfers between cyanobacteria and phages, which might have played significant roles in the evolution of cyanobacteria/phage systems. However, little has been documented about the occurrence of horizontal gene transfer in eukaryotic phytoplankton/virus systems. Here we report phylogenetic evidence for the transfer of seven genes involved in the sphingolipid biosynthesis pathway between the cosmopolitan eukaryotic microalga Emiliania huxleyi and its large DNA virus EhV. PCR assays indicate that these genes are prevalent in E. huxleyi and EhV strains isolated from different geographic locations. Patterns of protein and gene sequence conservation support that these genes are functional in both E. huxleyi and EhV. This is the first clear case of horizontal gene transfer of multiple functionally linked enzymes in a eukaryotic phytoplankton-virus system. We examine arguments for the possible direction of the gene transfer. The virus-to-host direction suggests the existence of ancient viruses that controlled the complex metabolic pathway in order to infect primitive eukaryotic cells. In contrast, the host-to-virus direction suggests that the serial acquisition of genes involved in the same metabolic pathway might have been a strategy for the ancestor of EhVs to stay ahead of their closest relatives in the great evolutionary race for survival.

Figure 1.

A model of de novo sphingolipid/ceramide biosynthesis pathway. The enzymes found in both EhV-86 and E. huxleyi are indicated in red. The enzyme present only in E. huxleyi is indicated in green.

Figure 2.

Domain architectures of serine palmitoyltransferases from E. huxleyi, EhV-86, O. tauri, and Entamoeba spp. LCB2-like domains correspond to red ovals; LCB1-like domain, pink ovals; and PAP2 domains, green rectangles. Background gray scales correspond to the level of sequence similarity from the E. huxleyi SPT sequence (darker gray for higher BLAST scores).

Figure 3.

Maximum likelihood phylogenetic trees based on the amino acid sequences of the four central enzymes in the sphingolipid biosynthesis pathway. (A) Serine palmitoyltransferase LCB1 and LCB2 domain sequences and their homologs. (B) Dihydroceramide synthases (LAG1). (C) Dsd1-like fatty acid desaturases. (D) Lipid phosphate phosphatase (LPP), the PAP2-domain sequence from the E. huxleyi SPT, and their homologs. These trees are unrooted per se, although we have arbitrarily chosen a root (mostly by mid-point rooting) for each tree only for visualization purpose. The number of substitutions per site is indicated under the scale bar. In D, (#) sequences best hitting to sphingosine 1-phosphate phosphatases (cd03388) after NCBI/CDD searches; (*) sequences best hitting to phosphatidic acid phosphatases (cd03390); (§) sequences best hitting to the wunen subfamily sequences (a family of membrane associated phosphatidic acid phosphatases; cd03384).

Figure 4.

Synonymous (K_s) and nonsynonymous (K_a) substitution rates for the orthologous sequences between EhV-86 and EhV-163. Of the seven EhV-86 sphingolipid enzyme genes, EhV-163 orthologs were found for four genes (SPT, LAG1, Dsd1-like FAD, LPP), which are indicated as diamonds.