STRUCTURAL, FUNCTIONAL, AND EVOLUTIONARY RELATIONSHIPS AMONG EXTRACELLULAR SOLUTE-BINDING RECEPTORS OF BACTERIA

Extracellular solute-binding proteins of bacteria serve as chemorecept ors, recognition constituents of transport systems, and initiators of signal transduction pathways. Over 50 sequenced periplasmic solute-bin ding proteins of gram-negative bacteria and homologous extracytoplasmi c lipoproteins of gram-positive bacteria have been analyzed for sequen ce similarities, and their degrees of relatedness have been determined . Some of these proteins are homologous to cytoplasmic transcriptional regulatory proteins of bacteria; however, with the sole exception of the vitamin B-12-binding protein of Escherichia coli, which is homolog ous to human glutathione peroxidase, they are not demonstrably homolog ous to any of the several thousand sequenced eukaryotic proteins. Most of these proteins fall into eight distinct clusters as follows. Clust er 1 solute-binding proteins are specific for malto-oligosaccharides, multiple oligosaccharides, glycerol 3-phosphate, and iron. Cluster 2 p roteins are specific for galactose, ribose, arabinose, and multiple mo nosaccharides, and they are homologous to a number of transcriptional regulatory proteins including the lactose, galactose, and fructose rep ressors of E. coli. Cluster 3 proteins are specific for histidine, lys ine-arginine-ornithine, glutamine, octopine, nopaline, and basic amino acids. Cluster 4 proteins are specific for leucine and leucine-isoleu cine-valine, and they are homologous to the aliphatic amidase transcri ptional repressor, AmiC, of Pseudomonas aeruginosa. Cluster 5 proteins are specific for dipeptides and oligopeptides as well as nickel. Clus ter 6 proteins are specific for sulfate, thiosulfate, and possibly pho sphate. Cluster 7 proteins are specific for dicarboxylates and tricarb oxylates, but these two proteins exhibit insufficient sequence similar ity to establish homology. Finally, cluster 8 proteins are specific fo r iron complexes and possibly vitamin B-12. Members of each cluster of binding proteins exhibit greater sequence conservation in their N-ter minal domains than in their C-terminal domains. Signature sequences fo r these eight protein families are presented. The results reveal that binding proteins specific for the same solute from different bacteria are generally more closely related to each other than are binding prot eins specific for different solutes from the same organism, although e xceptions exist. They also suggest that a requirement for high-affinit y solute binding imposes severe structural constraints on a protein. T he occurrence of two distinct classes of bacterial cytoplasmic repress or proteins which are homologous to two different clusters of periplas mic binding proteins suggest that the gene-splicing events which allow ed functional conversion of these proteins with retention of domain st ructure have occurred repeatedly during evolutionary history. On the b asis of results reported, as well as previously published sequence and three-dimensional analyses, it is tentatively proposed that many of t he periplasmic solute-binding proteins, together with the homologous c ytoplasmic DNA-binding proteins, make up a single superfamily. The div ergence of cytoplasmic repressor proteins from periplasmic receptor pr oteins must have occurred after the proposed duplication and divergenc e events which gave rise to the eight major families of external recep tors characterized in this report.