Phylogenetic characterization of the epithelial Na+ channel (ENaC) family

Sensory functions for degenerin/epithelial sodium channels (DEG/ENaC)

All animals use a sophisticated array of receptor proteins to sense their external and internal environments. Major advances have been made in recent years in understanding the molecular and genetic bases for sensory transduction in diverse modalities, indicating that both metabotropic and ionotropic pathways are important in sensory functions. Here, I review the historical background and recent advances in understanding the roles of a relatively newly discovered family of receptors, the degenerin/epithelial sodium channels (DEG/ENaC). These animal-specific cation channels show a remarkable sequence and functional diversity in different species and seem to exert their functions in diverse sensory modalities. Functions for DEG/ENaC channels have been implicated in mechanosensation as well as chemosensory transduction pathways. In spite of overall sequence diversity, all family members share a unique protein topology that includes just two transmembrane domains and an unusually large and highly structured extracellular domain, that seem to be essential for both their mechanical and chemical sensory functions. This review will discuss many of the recent discoveries and controversies associated with sensory function of DEG/ENaC channels in both vertebrate and invertebrate model systems, covering the role of family members in taste, mechanosensation, and pain.

Cytochrome P450-dependent metabolism of eicosapentaenoic acid in the nematode Caenorhabditis elegans

The genome of Caenorhabditis elegans contains 75 full length cytochrome P450 (CYP) genes whose individual functions are largely unknown yet. We tested the hypothesis that some of them may be involved in the metabolism of eicosapentaenoic acid (EPA), the predominant polyunsaturated fatty acid of this nematode. Microsomes isolated from adult worms contained spectrally active CYP proteins and showed NADPH-CYP reductase (CPR) activities. They metabolized EPA and with lower activity also arachidonic acid (AA) to specific sets of regioisomeric epoxy- and omega-/(omega-1)-hydroxy-derivatives. 17(R),18(S)-epoxyeicosatetraenoic acid was produced as the main EPA metabolite with an enantiomeric purity of 72%. The epoxygenase and hydroxylase reactions were NADPH-dependent, required the functional expression of the CPR-encoding emb-8 gene, and were inhibited by 17-ODYA and PPOH, two compounds known to inactivate mammalian AA-metabolizing CYP isoforms. Multiple followed by single RNAi gene silencing experiments identified CYP-29A3 and CYP-33E2 as the major isoforms contributing to EPA metabolism in C. elegans. Liquid chromatography/mass spectrometry revealed that regioisomeric epoxy- and hydroxy-derivatives of EPA and AA are endogenous constituents of C. elegans. The endogenous EPA metabolite levels were increased by treating the worms with fenofibrate, which also induced the microsomal epoxygenase and hydroxylase activities. These results demonstrate for the first time that C. elegans shares with mammals the capacity to produce CYP-dependent eicosanoids and may thus facilitate future studies on the mechanisms of action of this important class of signaling molecules.

Molecular phylogeny as a basis for the classification of transport proteins from bacteria, archaea and eukarya

Although enzymes catalyzing chemical reactions have long been classified according to the system developed by the Enzyme Commission (EC), no comparable system has been developed or proposed for transport proteins catalyzing transmembrane vectorial reactions. We here propose a comprehensive system, designated the Transport Commission (TC) system, based both on function and phylogeny. The TC system initially categorizes permeases according to mode of transport and energy coupling mechanism, and each category is assigned a one-component TC number (W). The secondary level of classification corresponds to the phylogenetic family (or superfamily) to which a particular permease is assigned, and each family is assigned a two-component TC number (W.X). The third level of classification refers to the phylogenetic cluster within a family (or the family within a superfamily) to which the permease belongs, and each cluster receives a three-component TC number (W.X.Y). Finally, the last level of categorization is based on substrate specificity and polarity of transport, and each entry is assigned a four component TC number (W.X.Y.Z). This system is based on the observation that mode of transport and energy coupling mechanism are fundamental properties of transport systems that very seldom transcend familial lines, but substrate specificity, being readily alterable by point mutations, is a superficial characteristic that often transcends familial lines. The proposed system has the potential to include all known permeases for which sequence data are available and has the flexibility to accommodate the multitude of permeases likely to be revealed by future genome sequencing and biochemical analysis. Major conclusions resulting from our classification efforts are described. The classification system, which will be continuously updated, is available on our World Wide Web site (http:/(/)www-biology.ucsd.edu/ approximately msaier/transport/titlepage.html).

Eukaryotic transmembrane solute transport systems

A comprehensive classification system for transmembrane molecular transporters has been proposed. This system is based on (i) mode of transport and energy-coupling mechanism, (ii) protein phylogenetic family, (iii) phylogenetic cluster, and (iv) substrate specificity. The proposed "Transport Commission" (TC) system is superficially similar to that implemented decades ago by the Enzyme Commission for enzymes, but it differs from the latter system in that it uses phylogenetic and functional data for classification purposes. Very few families of transporters include members that do not function exclusively in transport. Analyses reported reveal that channels, primary carriers, secondary carriers (uni-, sym-, and antiporters), and group translocators comprise distinct categories of transporters, and that transport mode and energy coupling are relatively immutable characteristics. By contrast, substrate specificity and polarity of transport are often readily mutable. Thus, with very few exceptions, a unified family of transporters includes members that function by a single transport mode and energy-coupling mechanism although a variety of substrates may be transported with either inwardly or outwardly directed polarity. The TC system allows cross-referencing according to substrates transported and protein sequence database accession numbers. Thus, familial assignments of newly sequenced transport proteins are facilitated. In this article I examine families of transporters that are eukaryotic specific. These families include (i) channel proteins, mostly from animals; (ii) facilitators and secondary active transport carriers; (iii) a few ATP-dependent primary active transporters; and (iv) transporters of unknown mode of action or energy-coupling mechanism. None of the several ATP-independent primary active transport energy-coupling mechanisms found in prokaryotes is represented within the eukaryotic-specific families. The analyses reported provide insight into transporter families that may have arisen in eukaryotes after the separation of eukaryotes from archaea and bacteria. On the basis of the reported analyses, it is suggested that the horizontal transfer of genes encoding transport proteins between eukaryotes and members of the other two domains of life occurred very infrequently during evolutionary history.

Microbial genome analyses: global comparisons of transport capabilities based on phylogenies, bioenergetics and substrate specificities

We have conducted genome sequence analyses of seven prokaryotic microorganisms for which completely sequenced genomes are available (Escherichia coli, Haemophilus influenzae, Helicobacter pylori, Bacillus subtilis, Mycoplasma genitalium, Synechocystis PCC6803 and Methanococcus jannaschii). We report the distribution of encoded known and putative polytopic cytoplasmic membrane transport proteins within these genomes. Transport systems for each organism were classified according to (1) putative membrane topology, (2) protein family, (3) bioenergetics, and (4) substrate specificities. The overall transport capabilities of each organism were thereby estimated. Probable function was assigned to greater than 90% of the putative transport proteins identified. The results show the following: (1) Numbers of transport systems in eubacteria are approximately proportional to genome size and correspond to 9.7 to 10.8% of the total encoded genes except for H. pylori (5.4%), Synechocystis (4.7%) and M. jannaschii (3.5%) which exhibit substantially lower proportions. (2) The distribution of topological types is similar in all seven organisms. (3) Transport systems belonging to 67 families were identified within the genomes of these organisms, and about half of these families are also found in eukaryotes. (4) 12% of these families are found exclusively in Gram-negative bacteria, but none is found exclusively in Gram-positive bacteria, cyanobacteria or archaea. (5) Two superfamilies, the ATP-binding cassette (ABC) and major facilitator (MF) superfamilies account for nearly 50% of all transporters in each organism, but the relative representation of these two transporter types varies over a tenfold range, depending on the organism. (6) Secondary, pmf-dependent carriers are 1.5 to threefold more prevalent than primary ATP-dependent carriers in E. coli, H. influenzae, H. pylori and B. subtilis while primary carriers are about twofold more prevalent in M. genitalium and Synechocystis. M. jannaschii exhibits a slight preference for secondary carriers. (7) Bioenergetics of transport generally correlate with the primary forms of energy generated via available metabolic pathways but ecological niche and substrate availability may also be determining factors. (8) All organisms display a similar range of transport specificities with quantitative differences presumably reflective of disparate ecological niches. (9) M. jannaschii and Synechocystis have a two to threefold increased proportion of transporters for inorganic ions with a concomitant decrease in transporters for organic compounds. (10) 6 to 18% of all transporters in these bacteria probably function as drug export systems showing that these systems are prevalent in non-pathogenic as well as pathogenic organisms. (11) All seven prokaryotes examined encode proteins homologous to known channel proteins, but none of the channel types identified occurs in all of these organisms. (12) The phosphoenolpyruvate:sugar phosphotransferase system is prevalent in the large genome organisms, E. coli and B. subtilis, and is present in the small genome organisms, H. influenzae and M. genitalium, but is totally lacking in H. pylori, Synechocystis and M. jannaschii. Details of the information summarized in this article are available on our web sites, and this information will be periodically updated and corrected as new sequence and biochemical data become available.

The alpha subunit of the epithelial sodium channel in the mouse: developmental regulation of its expression

Sodium reabsorption by the amiloride-sensitive sodium channel of epithelial cells plays a crucial role in the management of ionic composition and fluid volume in the body. In the respiratory system, sodium transport is involved in the clearance of pulmonary edema and of liquid secreted during fetal life at birth. We have cloned a partial cDNA of the alpha subunit of the mouse amiloride-sensitive sodium channel (alpha mENaC). In the region of comparison, the mouse alpha subunit shows 92% identity at the DNA level and 95% identity at the amino acid level with the rat sequence. The kidneys, lungs, and distal colon are major sites of expression of a 3.5-kb alpha mENaC mRNA. During mouse development, alpha mENaC transcripts appear late during gestation (d 17.5) and are expressed continuously thereafter. In the distal colon, a short 1.2-kb mRNA deleted of the 5' part of the transcript is detected during gestation and is replaced gradually by the mature 3.5-kb transcript after birth. Alpha mENaC and alpha1 Na+-K+-ATPase mRNAs have an expression profile that is modulated similarly during development for a given tissue. The expression of alpha mENaC transcripts increases transiently in the lungs at birth (2.5-fold), as for alpha1 Na+-K+-ATPase mRNAs (1.5-fold), suggesting that the expression of several components of the sodium transport system is modulated in the lungs at that time. In the kidney, there is no significant increase of alpha mENaC and alpha1 Na+-K+-ATPase mRNAs in newborns.