Microbial genome analyses: Comparative transport capabilities in eighteen prokaryotes

Here, we present a comprehensive analysis of solute transport systems encod ed within the completely sequenced genomes of 18 prokaryotic organisms. The se organisms include four Gram-positive bacteria, seven Gram-negative bacte ria, two spirochetes, one cyanobacterium and four archaea. Membrane protein s are analyzed in terms of putative membrane topology, and the recognized t ransport systems are classified into 76 families, including four families o f channel proteins, four families of primary carriers, 54 families of secon dary carriers, six families of group translocators, and eight unclassified families. These families are analyzed in terms of the paralogous and orthol ogous relationships of their protein members, the substrate specificities o f their constituent transporters and their distributions in each of the 18 organisms studied. The families vary from large superfamilies with hundreds of represented members, to small families with only one ora few members. T he mode of transport generally correlates with the primary mechanism of ene rgy generation, and the numbers of secondary transporters relative to prima ry transporters are roughly proportional to the total numbers of primary H and Na+ pumps in the cell. The phosphotransferase system is less prevalent in the analyzed bacteria than previously thought (only six of 14 bacteria transport sugars via this system) and is completely lacking in archaea and eukaryotes. Escherichia coli is shown to be exceptionally broad in its tran sport capabilities and therefore, at a membrane transport level, does not a ppear representative of the bacteria thus far sequenced. Archaea and spiroc hetes exhibit fewer proteins with multiple transmembrane segments and fewer net transporters than most bacteria. These results provide insight into th e relevance of transport to the overall physiology of prokaryotes. (C) 2000 Academic Press.