Eukaryotic Transmembrane Solute Transport Systems

Milton H. Saier, Jr.1    Department of Biology, University of California at San Diego, La Jolla, California 92093-0116
1 Phone: 619-534-4084; fax: 619-534-7108 email address: msaier@ucsd.edu

I Introduction

Transport systems serve the cell in numerous capacities (Paulsen et al., 1998a,b; Saier, 1998, 1999). First, they allow entry of all essential nutrients into the cytoplasmic compartment and subsequently into organelles, allowing metabolism of exogenous sources of carbon, nitrogen, sulfur, and phosphorus. Second, they provide a means for the regulation of metabolite concentrations by catalyzing the excretion of end products of metabolic pathways from organelles and cells. Third, they mediate the active extrusion of drugs and other toxic substances from either the cytoplasm or the plasma membrane. Fourth, they mediate uptake and efflux of ionic species that must be maintained at concentrations that differ drastically from those in the external milieu. The maintenance of conditions conducive to life requires a membrane potential, requisite ion concentration gradients, and appropriate cytoplasmic concentrations of all essential trace minerals that participate as cofactors in metabolic processes. Such conditions are required for the generation of bioelectricity and for enzymatic activity. Fifth, transporters participate in the secretion of proteins, complex carbohydrates, and lipids into and beyond the cytoplasmic membrane, and these macromolecules serve a variety of biologically important roles in protection against environmental insult and predation, in communication with members of the same and different species, and in pathogenesis. Sixth, transport systems allow the transfer of nucleic acids across cell membranes, allowing for genetic exchange between organisms, thereby promoting species diversification. Seventh, transporters facilitate the uptake and release of pheromones, alarmones, hormones, neurotransmitters, and a variety of other signaling molecules that allow a cell to participate in the biological experience of multicellularity. Finally, transport proteins allow living organisms to conduct biological warfare, secreting, for example, antibiotics, antiviral agents, and antifungal agents that may confer upon the organism a selective advantage for survival purposes. Thus, from a functional standpoint, the importance of molecular transport to all facets of life cannot be overestimated.

The importance of transport processes to biological systems was recognized more than half a century ago (Gale and Taylor, 1947; Mitchell, 1949). Thanks largely to concerted efforts on the part of Jacques Monod and coworkers at the Pasteur Institute in Paris, who studied the mechanism of action of the Escherichia coli lactose permease, the involvement of specific carrier proteins in transport became established (Rickenberg et al., 1956; Cohen and Monod, 1957). Since these early studies, tremendous progress has been made in understanding the molecular bases of transport phenomena, and the E. coli lactose permease has frequently been at the forefront. Initially, transport processes were characterized from physiological standpoints using intact cells. Cell “ghosts” in which the cytoplasmic contents had been released by osmotic shock proved useful, particularly as applied to human red blood cells and later to bacteria. Work with such systems provided detailed kinetic descriptions of transport processes, and by analogy with chemical reactions catalyzed by enzymes, the proteinaceous nature of all types of permeases became firmly established. Subsequent biochemical experimentation provided extensive documentation of this suggestion (Kaback, 1974).

With the advent of gene sequencing technologies, the primary structures of permeases first became available. Hydrophobicity analyses of these sequences revealed the strikingly hydrophobic natures of various types of integral membrane transporters (Kyte and Doolittle, 1982; Büchel et al., 1980; Lee and Saier, 1983; Overath and Wright, 1983). Current multidisciplinary approaches are slowly yielding three-dimensional structural information about transport systems. However, since only a few such systems have yielded to X-ray crystallographic analyses (Deisenhofer and Michel, 1991; Unwin, 1995; Tsukihara et al., 1996), we still base our views of solute transport on molecular models that provide reasonable pictures of transport systems and the processes they catalyze without providing absolute assurance of accuracy (Goswitz and Brooker, 1995; Varela and Wilson, 1996; Kaback et al., 1997).

It is well recognized that any two proteins that can be shown to be homologous (i.e., that exhibit sufficient primary and/or secondary structural similarity to establish that they arose from a common evolutionary ancestor) will prove to exhibit strikingly similar three-dimensional structures (Doolittle, 1986). Furthermore, the degree of tertiary structural similarity correlates well with the degree of primary structural similarity. For this reason, phylogenetic analyses allow application of modeling techniques to a large number of related proteins and additionally allow reliable extrapolation from one protein member of a family of known structure to others of unknown structure. Thus, once three-dimensional structural data are available for any one family member, these data can be applied to all other members within limits dictated by their degrees of sequence similarity. The same cannot be assumed for members of two independently evolving families.

Similar arguments apply to mechanistic considerations. Thus, the mechanism of solute transport is likely to be similar for all members of a permease family, and variations upon a specific mechanistic theme will be greatest when the sequence divergence is greatest. By contrast, for members of any two independently evolving permease families, the transport mechanisms may be strikingly different. Knowledge of these considerations allows unified mechanistic deductive approaches to be correctly applied to the largest numbers of transport systems, even when evidence is obtained piecemeal from the study of different systems.

The capacity to deduce and extrapolate structural and mechanistic information illustrates the value of phylogenetic data. However, another benefit that may result from the study of molecular phytogeny is to allow an understanding of the mechanistic restrictions that were imposed on an evolving family due to architectural constraints. Specific architectural features may allow one family to diversify in function with respect to substrate specificity, substrate affinity, velocity of transport, polarity of transport, and even mechanism of energy coupling. By contrast, architectural constraints imposed on a second family may not allow functional diversification. Knowledge of the architectural constraints imposed on a permease...