Bioinformatic analyses of the bacterial L-ascorbate phosphotransferase system permease family

The tripartite L-ascorbate permease of Escherichia coli is the first functionally characterized member of a large family of enzyme II complexes (SgaTBA, encoding enzymes IIC, IIB and IIA) of the bacterial phosphotransferase system (PTS). We here report bioinformatic analyses of these proteins. Forty-five homologous systems from a wide variety of bacteria were identified, but no homologues were found in archaea or eukaryotes. These systems fell into five structural types: (1) IIC, IIB and IIA are encoded by distinct genes; (2) IIC and IIB are encoded by distinct genes, but the IIA-encoding gene is absent; (3) IIC and IIB are encoded by a fused gene, but IIA is a distinct gene product; (4) IIA and IIB are fused, but IIC is encoded by a distinct gene, and (5) IIC and IIB are encoded by distinct genes, but IIA is fused to a transcriptional regulator. Phylogenetic analyses revealed that gene fusion/splicing events have occurred repeatedly during the evolutionary divergence of family members, although no evidence for shuffling of constituents between systems was obtained. The SgaTBA family proved to be distantly related to the GatCBA family of PTS permeases, and this family was also analyzed. In contrast to the SgaTBA family, no gene splicing/fusion has occurred during the evolutionary divergence of GatCBA family members as each domain is always encoded by a distinct gene. However, GatC homologues were identified in organisms that lack other PTS proteins, suggesting a transport mechanism not coupled to substrate phosphorylation. Topological analyses suggest that in contrast to all other PTS permeases, IIC proteins of the Sga and Gat families exhibit 12 transmembrane alpha-helical segments and are distantly related to secondary carriers. Like many secondary carriers, GatC (IIC) homologues could be shown to have arisen by an ancient intragenic duplication event. These results suggest that the Sga and Gat families of PTS permeases comprise a small superfamily in which the transmembrane IIC domains evolved independently of all other known PTS permeases.