PHYLOGENETIC ANALYSIS OF CARBAMOYLPHOSPHATE SYNTHETASE GENES - COMPLEX EVOLUTIONARY HISTORY INCLUDES AN INTERNAL DUPLICATION WITHIN A GENE WHICH CAN ROOT THE TREE OF LIFE

Carbamoylphosphate synthetase (CPS) catalyzes the first committed step in pyrimidine biosynthesis, arginine biosynthesis, or the urea cycle. Organisms may contain either one generalized or two specific CPS enzy mes, and these enzymes may be heterodimeric (encoded by linked or unli nked genes), monomeric, or part of a multifunctional protein. In order to help elucidate the evolution of CPS, we have performed a comprehen sive phylogenetic analysis using the 21 available complete CPS sequenc es, including a sequence from Sulfolobus solfataricus P2 which we repo rt in this paper. This is the first report of a complete CPS gene sequ ence from an archaeon, and sequence analysis suggests that it encodes an enzyme similar to heterodimeric CPSII. We confirm that internal sim ilarity within the synthetase domain of CPS is the result of an ancien t gene duplication that preceded the divergence of the Bacteria, Archa ea, and Eukarya, and use this internal duplication in phylogenetic tre e construction to root the tree of life. Our analysis indicates with h igh confidence that this archaeal sequence is more closely related to those of Eukarya than to those of Bacteria. In addition to this ancien t duplication which created the synthetase domain, our phylogenetic an alysis reveals a complex history of further gene duplications, fusions , and other events which have played an integral part in the evolution of CPS.