The evolutionary history of carbamoyltransferases: A complex set of paralogous genes was already present in the last universal common ancestor

Forty-four sequences of ornithine carbamoyltransferases (OTCases) and 33 se quences of aspartate carbamoyltransferases (ATCases) representing the three domains of life were multiply aligned and a phylogenetic tree was inferred from this multiple alignment. The global topology of the composite rooted tree (each enzyme family being used as an outgroup to root the other one) s uggests that present-day genes are derived from paralogous ancestral genes which were already of the same size and argues against a mechanism of fusio n of independent modules. A closer observation of the detailed topology sho ws that this tree could not be used to assess the actual order of organisma l descent. Indeed, this tree displays a complex topology for many prokaryot ic sequences, with polyphyly for Bacteria in both enzyme trees and for the Archaea in the OTCase tree. Moreover, representatives of the two prokaryoti c Domains are found to be interspersed in various combinations in both enzy me trees, This complexity may be explained by assuming the occurrence of tw o subfamilies in the OTCase tree (OTC alpha and OTC beta) and two other one s in the ATCase tree (ATC I and ATC Il). These subfamilies could have arise n from duplication and selective losses of some differentiated copies durin g the successive speciations. We suggest that Archaea and Eukaryotes share a common ancestor in which the ancestral copies giving the present-day ATC II/OTC beta combinations were present, whereas Bacteria comprise two classe s: one containing the ATC II/OTC alpha combination and the other harboring the ATC I/OTC beta combination. Moreover, multiple horizontal gene transfer s could have occurred rather recently amongst prokaryotes. Whichever the ac tual history of carbamoyltransferases, our data suggest that the last commo n ancestor to all extant life possessed differentiated copies of genes codi ng for both carbamoyltransferases, indicating it as a rather sophisticated organism.