Structural and phylogenetic analysis of the MotA and MotB families of bacterial flagellar motor proteins.

MotA and MotB are two well-characterized proteins in Escherichia coli which are believed to function as the proton channel and the anchor, respectively, of the motor component of the bacterial flagellum. We have identified and analysed all currently sequenced members of the MotA and MotB families. Members of these families include (1) these E. coli proteins, (2) their pmf-interacting motor homologues in other bacteria, (3) two ORFs which map downstream of the gene encoding the catabolite repression-mediating CepA protein in Bacillus species and (4) unidentified open reading frames. With one exception (the MotB protein of Rhodobactec sphaeroides), members of the MotB family exhibit a C-terminal domain that is homologous to peptidoglycan-interaction domains of numerous sequenced lipoproteins and outer membrane proteins. Multiple alignments, average hydropathy and similarity plots, and phylogenetic trees have allowed (1) identification of regions of relative conservation, (2) definition of signature sequences for these protein families and (3) determination of relative phylogenetic distances relating all members of each family. The phylogenies of these proteins do not follow those of the organisms from which they were isolated, suggesting the presence of divergent isoforms in many bacteria. Phylogenetic analyses of the peptidoglycan-interaction domains of MotB proteins indicated that, except for MotB of R. sphaeroides, these domains became associated with the MotB proteins early during evolutionary history, before members of the MotB family or members of the outer membrane protein family diverged from each other.