Functional prokaryotic-like dCTP deaminases and thymidylate synthase in eukaryotic social amoebae: vertical, endosymbiotic or horizontal gene transfer?

Abstract

The de novo synthesis of dTTP uses several pathways: gram-negative bacteria use dCTP deaminase (Dcd) to convert dCTP into dUTP, whereas eukaryotes and gram-positive bacteria instead use dCMP deaminase to transform dCMP to dUMP. It is then unusual that in addition to dCMP deaminases, the eukaryote Dictyostelium discoideum has two dCTP deaminases (Dcd1Dicty and Dcd2Dicty). Expression of either DcdDicty can fully rescue the slow growth of an E. coli dcd knockout. Both DcdDicty mitigate the hydroxyurea sensitivity of a Schizosaccharomyces pombe dCMP deaminase knockout. Phylogenies show that Dcd1Dicty homologs may have entered the common ancestor of the eukaryotic groups of Amoebozoa, Obazoa, Metamonada, and Discoba through an ancient horizontal gene transfer (HGT) from a prokaryote, or an ancient endosymbiotic gene transfer (EGT) from a mitochondrion, followed by HGT from Amoebozoa to several other unrelated groups of eukaryotes. In contrast, the Dcd2Dicty homologs were a separate HGT from a prokaryote, or a virus into either Amoebozoa or Rhizaria, followed by an HGT between them. ThyXDicty, the D. discoideum thymidylate synthase (TS), another enzyme of the dTTP biosynthesis pathway, was suggested previously to be acquired from the ancestral mitochondria or by HGT from alpha-proteobacteria. ThyXDicty can fully rescue the E. coli TS knockout, and we establish that it was obtained by the common ancestor of social amoebae not from mitochondria but from a bacterium. We propose HGT and EGT contributed to the enzyme diversity of the dTTP synthesis pathway in most social amoebae, many Amoebozoa, and other eukaryotes.