Inverted repeats in ion-coupled transporters have evolved independently in many unrelated families. It has been suggested that this inverted symmetry is an essential element of the mechanism that allows for the conformational transitions in transporters. We show here that small multidrug transporters offer a model for the evolution of such repeats. This family includes both homodimers and closely related heterodimers. In the former, the topology determinants, evidently identical in each protomer, are weak, and we show that for EmrE, an homodimer from Escherichia coli, the insertion into the membrane is random, and dimers are functional whether they insert into the cytoplasmic membrane with the N-and C-terminal domains facing the inside or the outside of the cell. Also, mutants designed to insert with biased topology are functional regardless of the topology. In the case of EbrAB, a heterodimer homologue supposed to interact antiparallel, we show that one of the subunits, EbrB, can also function as a homodimer, most likely in a parallel mode. In addition, the EmrE homodimer can be forced to an antiparallel topology by fusion of an additional transmembrane segment. The simplicity of the mechanism of coupling ion and substrate transport and the few requirements for substrate recognition provide the robustness necessary to tolerate such a unique and unprecedented ambiguity in the interaction of the subunits and in the dimer topology relative to the membrane. The results suggest that the small multidrug transporters are at an evolutionary junction and provide a model for the evolution of structure of transport proteins.Evolution of large transporter genes is thought to have started from a small single one that duplicated, evolved independently, and then fused to the original one to generate a new gene coding for the large polytopic protein (1). Inverted repeats in ion-coupled transporters have now been observed in transporters from many different families (2, 3). It has been suggested that this inverted symmetry is an essential element of the mechanism that allows for the conformational transitions in transporters (3).A possible mode for evolution of these inverted repeats has been suggested based on the supposedly inverted topology of EmrE, a small multidrug transporter from Escherichia coli. A claim for an antiparallel topology of the monomers in the EmrE homodimer was made, but this is still a controversial issue and, in our view, is still inconsistent with the biochemical data. The reasoning that the topology of the monomers in the EmrE dimer is parallel and N in -C in was supported by data from our laboratory that demonstrated the same topology for all protomers in the intact cell and in membrane vesicles (4), by biochemical studies that established the equivalence of the residues in the protomers (reviewed in Ref. 5 and 6), and by extensive cross-linking studies that suggested the proximity of equivalent residues in the two monomers (7). Moreover, dimers cross-linked at positions not compatible with antiparalle...

EmrE is a small H þ -coupled multidrug transporter in Escherichia coli. Claims have been made for an antiparallel topology of this homodimeric protein. However, our own biochemical studies performed with detergent-solubilized purified protein support a parallel topology of the protomers. We developed an alternative approach to constrain the relative topology of the protomers within the dimer so that their activity can be assayed also in vivo before biochemical handling. Tandem EmrE was built with two identical monomers genetically fused tail to head (C-terminus of the first to N-terminus of the second monomer) with hydrophilic linkers of varying length. All the constructs conferred resistance to ethidium by actively removing it from the cytoplasm. The purified proteins bound substrate and transported methyl viologen into proteoliposomes by a proton-dependent mechanism. A tandem where one of the essential glutamates was replaced with glutamine transported only monovalent substrates and displayed a modified stoichiometry. The results support a parallel topology of the protomers in the functional dimer. The implications regarding insertion and evolution of membrane proteins are discussed.

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