Phylogenetic characterization of novel transport protein families revealedby genome analyses

As a result of recent genome sequencing projects as well as detailed bioche mical, molecular genetic and physiological experimentation on representativ e transport proteins, we have come to realize that all organisms possess an extensive but limited array of transport protein types that allow the upta ke of nutrients and excretion of toxic substances. These proteins fall into phylogenetic families that presumably reflect their evolutionary histories . Some of these families are restricted to a single phylogenetic group of o rganisms and may have arisen recently in evolutionary time while others are found ubiquitously and may be ancient. In this study we conduct systematic phylogenetic analyses of 26 families of transport systems that either had not been characterized previously or were in need of updating. Among the fa milies analyzed are some that are bacterial-specific, others that are eukar yotic-specific, and others that are ubiquitous. They can function by either a channel-type or a carrier-type mechanism, and in the latter case, they a re frequently energized by coupling solute transport to the flux of an ion down its electrochemical gradient. We tabulate the currently sequenced memb ers of the 26 families analyzed, describe the properties of these families, and present partial multiple alignments, signature sequences and phylogene tic trees for them all. (C) 1999 Elsevier Science B.V. All rights reserved.