Horizontal transfer of ATPase genes — the tree of life becomes a net of life

An ancient gene duplication gave rise to the catalytic and non-catalytic subunits of each of the three types of proton pumping ATPases: vacuolar, archaebacterial and eubacterial. Previously, this gene duplication has been used to root the universal tree of life. However, recent findings of archaebacterial type ATPases in eubacteria and of eubacterial type in an archaebacterium suggested that both types of ATPases may have been already present in the last common ancestor. Here we show that a phylogenetic analysis of these ATPase subunits indicates that this conclusion is premature. We suggest that horizontal gene transfer can explain the data. In addition, we show that the analysis of glutamate dehydrogenases data neither affirm nor contradict any particular placement of the last common ancestor in the universal tree of life. The prevalence and the mode of horizontal gene transfer is discussed.