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Sequence relationships between integral inner membrane proteins of binding protein‐dependent transport systems: Evolution by recurrent gene duplications

Periplasmic binding protein‐dependent transport systems are composed of a periplasmic substrate‐binding protein, a set of 2 (sometimes 1) very hydrophobic integral membrane proteins, and 1 (sometimes 2) hydrophilic peripheral membrane protein that binds and hydrolyzes ATP. These systems are members of the superfamily of ABC transporters. We performed a molecular phylogenetic analysis of the sequences of 70 hydrophobic membrane proteins of these transport systems in order to investigate their evolutionary history. Proteins were grouped into 8 clusters. Within each cluster, protein sequences displayed significant similarities, suggesting that they derive from a common ancestor. Most clusters contained proteins from systems transporting analogous substrates such as monosaccharides, oligopeptides, or hydrophobic amino acids, but this was not a general rule. Proteins from diverse bacteria are found within each cluster, suggesting that the ancestors of current clusters were present before the divergence of bacterial groups. The phylogenetic trees computed for hydrophobic membrane proteins of these per‐meases are similar to those described for the periplasmic substrate‐binding proteins. This result suggests that the genetic regions encoding binding protein‐dependent permeases evolved as whole units. Based on the results of the classification of the proteins and on the reconstructed phylogenetic trees, we propose an evolutionary scheme for periplasmic permeases. According to this model, it is probable that these transport systems derive from an ancestral system having only 1 hydrophobic membrane protein. None of the proteins considered in this study display detectable sequence similarity to hydrophobic membrane proteins or domains from other ABC transporters such as bacterial polysaccharide export systems, bacterial toxin proteins exporters, and eukaryotic ABC proteins. It is likely that they constitute a specific subfamily within the superfamily of ABC transporters.