Computer-based analyses of the protein constituents of transport systems catalysing export of complex carbohydrates in bacteria.

Bacteria synthesize and secrete an array of complex carbohydrates including exopolysaccharides (EPSs), capsular polysaccharides (CPSs), lipopolysaccharides (LPSs), lipo-oligosaccharides (LOSs) and teichoic acids (TCAs). We have analysed the families of homologous proteins that appear to mediate excretion of complex carbohydrates into or across the bacterial cell envelope. Two principal families of cytoplasmic-membrane transport systems appear to drive polysaccharide export: polysaccharide-specific transport (PST) systems and ATP-binding cassette-2 (ABC-2) systems. We present evidence that the secretion of CPSs and EPSs, but not of LPSs, LOSs or TCAs via a PST or ABC-2 system requires the presence of a cytoplasmic-membrane-periplasmic auxiliary protein (MPA1 or MPA2, respectively) in both Gram-negative and Gram-positive bacteria as well as an outer-membrane auxiliary (OMA) protein in Gram-negative bacteria. While all OMA proteins are included within a single family, MPA1 and MPA2 family proteins are not demonstrably homologous to each other, even though they share common topological features. Moreover, MPA1 family proteins (which function with PST systems), but not MPA2 family proteins (which function with ABC-2 systems), possess cytoplasmic ATP-binding domains that may either exist as separate polypeptide chains (for those from Gram-positive bacteria) or constitute the C-terminal domain of the MPA1 polypeptide chain (for those from Gram-negative bacteria). The sizes, substrate specificities and regions of relative conservation and hydrophobicity are defined allowing functional and structural predictions as well as delineation of family-specific sequence motifs. Each family is characterized phylogenetically.