Inventory, assembly and analysis of Bacillus subtilis ABC transport systems

We have undertaken the inventory and assembly of the ATP binding cassette ( ABC) transporter systems in the complete genome of Bacillus subtilis. We co mbined the identification of the three protein partners that compose an ABC transporter (nucleotide-binding domain, NBD; membrane spanning domain, MSD ; and solute-binding protein, SEP) with constraints on the genetic organiza tion This strategy allowed the identification of 86 NBDs in 78 proteins, 10 3 MSD proteins and 37 SBPs. The analysis of transcriptional units allows th e reconstruction of 59 ABC transporters, which include at least one NBD and one MSD. A particular class of five dimeric ATPases was not associated to MSD partners and is assumed to be involved either in macrolide resistance o r regulation of translation elongation. In addition, we have detected five genes encoding ATPases without any gene coding for MSD protein in their nei ghborhood and 11 operons that encode only the membrane and solute-binding p roteins. On the bases of similarities, three ATP-binding proteins are propo sed to energize ten incomplete systems, suggesting that one ATPase may be r ecruited by more than one transporter. Finally, we estimate that the B. sub tilis genome encodes for at least 78 ABC transporters that have been split in 38 importers and 40 extruders. The ABC systems have been further classif ied into 11 sub-families according to the tree obtained from the NBDs and t he clustering of the MSDs and the SBPs. Comparisons with Escherichia coli s how that the extruders are over-represented in B. subtilis, corresponding t o an expansion of the sub-families of antibiotic and drug resistance system s. (C) 1999 Academic Press.