Investigating the Origins of Membrane Phospholipid Biosynthesis Genes Using Outgroup-Free Rooting

Abstract

One of the key differences between Bacteria and Archaea is their canonical membrane phospholipids, which are synthesized by distinct biosynthetic pathwayswith nonhomologous enzymes. This lipid divide has important implications for the early evolution of cells andthe type ofmembranephospholipidspresent inthe last universal commonancestor.Oneof themain challenges instudies of membrane evolution is that the key biosynthetic genes are ancient and their evolutionary histories are poorly resolved. This poses major challenges for traditional rooting methods because the only available outgroups are distantly related. Here, we address this issue by using the best available substitution models for single-gene trees, by expanding our analyses to the diversity of uncultivated prokaryotes recently revealed by environmental genomics, and by using two complementary approaches to rooting that do not depend on outgroups. Consistent with some previous analyses, our rooted gene trees support extensive interdomain horizontal transfer of membrane phospholipid biosynthetic genes, primarily from Archaea to Bacteria. They also suggest that the capacity to make archaeal-type membrane phospholipids was already present in last universal common ancestor.