Table lists and summarizes the properties of transport protein families found within the current MFS. We have classified current members of the MFS into 17 (possibly 18) distinct families. This number of MFS families represents more than a threefold expansion over that published previously (51
). The table provides the family number; the name of the family; the abbreviation of the family to be used in this study; the number of currently recognized sequenced members in each family; the range of organisms in which members of the family are found; the size range of the proteins (in numbers of amino acyl residues) for fully sequenced members; the number of putative TMSs in each protein (believed to be uniform for members of a given family); the energy-coupling mechanisms, if any, used by members of the family; the polarities of transport catalyzed by family members; the substrates known to be transported by various members of the family; and a representative and well-characterized member of the family.
The largest family (family 1) is the sugar porter (SP) family, with 133 identified members. These proteins are derived from all of the major groups of living organisms: bacteria, archaea, eukaryotic protists, fungi, mostly yeasts, animals, and plants. These proteins have 12 established or putative TMSs. They can function by uniport, solute:solute antiport, and/or solute:cation symport, depending on the system and/or conditions. Uniporters exhibit no polarity but can usually catalyze both uniport and antiport depending on whether a substrate is present on the trans side of the membrane. The polarity of solute:solute antiporters is indicated in Table by “both.” Symporters function with inwardly-direct polarity in the presence of a membrane potential (negative inside), but many of these proteins have also been shown to catalyze antiport when a substrate is present on the trans side of the membrane. Substrates transported by SP family members include hexoses, pentoses, disaccharides, quinate, inositols, and organic cations. Most but not all members of the SP family thus catalyze sugar transport.
Family 1 permeases exhibit a size range of 404 to 818 residues. The smaller permeases possess very short hydrophilic N and C termini and short loops connecting the 12 TMSs. As is true of many MFS families, the bacterial sugar porters are usually smaller than the eukaryotic proteins. The larger sizes of the eukaryotic proteins are due to large hydrophilic N and/or C termini or, less frequently, to increased sizes of specific inter-TMS loops. The hydrophilic regions of the eukaryotic proteins may play roles in regulation or in cytoskeletal attachment, and they are frequently subject to phosphorylation by ATP-dependent protein kinases. A representative well-characterized example of the SP family is the arabinose:H+
symport permease (AraE) of Escherichia coli
Families 2 and 3 consist of drug efflux systems which possess 14 and 12 TMSs, respectively (74
). Since these permeases uniformly catalyze drug:H+
antiport, they are referred to as the DHA14 and DHA12 families, respectively. A total of 30 and 46 sequenced members are currently recognized in these two families. Because these permeases have recently been the subject of an extensive review which presented multiple alignments and phylogenetic trees (60
), they will not be described or analyzed here. Members of both families are found in bacteria and eukaryotes, and DHA12 family members have also been identified in archaea.
Families 4, 5, and 6, the organophosphate:inorganic phosphate antiporters (OPA), the oligosaccharide:H+
symporters (OHS), and the metabolite:H+
symporters (MHS), respectively, were recognized to be families within the MFS in 1993 (30
). Since these permeases are restricted to bacteria, it is not surprising that they are all relatively small (400 to 500 residues). All three of these families have become substantially larger and more diverse in function since 1993, due to the sequencing and functional identification of new members.
All the remaining families listed in Table (families 7 to 18) were not recognized in 1993 and are therefore new MFS families. Family 7 (the fucose-galactose-glucose:H+ symporters [FGHS]) is a small family with four distantly related members. As with most members of the SP family, these proteins are specific for sugars. They all probably function by proton symport. They are relatively small (404 to 438 residues), as expected since they are derived exclusively from bacteria.
The nitrate-nitrite porter (NNP) family (family 8) has members in bacteria, yeasts, and plants. Not surprisingly, these proteins exhibit a larger size range (395 to 547 residues) than was observed for FGHS family members. These proteins catalyze either nitrate uptake or nitrite efflux. The energy-coupling mechanisms are not well defined.
Family 9, the phosphate:H+ symporter (PHS) family, has sequenced representatives only in yeast and plants. The 11 proteins of the PHS family are fairly uniform in size, but they are substantially larger than most bacterial MFS proteins (518 to 587 residues). The characterized members are uniform in function.
Family 10, the nucleoside:H+ symporter (NHS) family, has only two bacterial members, and they are of the same size (418 residues each). They are both from E. coli and differ in specificity.
Family 11, the oxalate/formate antiporter (OFA) family, is a small but diverse family. Only five members have been sequenced, but these proteins are found in the bacterial, archaeal, and eukaryotic kingdoms. Surprisingly, they are of fairly uniform size (373 to 470 residues). The very small size of one of these proteins (see below) raises the possibility that its sequence is incomplete.
Family 12, the sialate:H+ symporter (SHS) family, like the NHS family, is very small (with only three members), and, again like the NHS family, the members are all derived from gram-negative bacteria. Their sizes are consistent with those generally observed for bacterial MFS proteins (407 to 496 residues). These proteins differ from most MFS proteins in possessing 14 putative TMSs.
Family 13, with 13 members derived exclusively from yeasts and animals, is the monocarboxylate porter (MCP) family. These permeases transport pyruvate, lactate, and/or mevalonate with inwardly-directed polarity. They all presumably function by proton symport. Their reported sizes range from 450 to 808 residues.
Family 14, the anion:cation symporter (ACS) family, is a relatively large family with 40 sequenced members. The proteins are derived from bacteria, yeasts, and animals, and they exhibit an intermediate range of sizes (411 to 596 residues). They accumulate their substrates in symport with either Na+ or H+, depending on the system. They may transport either inorganic anions (e.g., phosphate) or organic anions (e.g., glucarate, hexuronate, tartrate, allantoate, or 4-hydroxylphenyl acetate). Of the functionally characterized porters, the inorganic anion porters of the ACS family cotransport Na+ while the organic anion porters cotransport H+.
Family 15, the aromatic acid:H+
symporter (AAHS) family, consists of seven sequenced proteins, all from bacteria. As expected, these porters show fairly uniform sizes (418 to 460 residues), all on the low end of the scale. They transport a variety of aromatic acids as well as cis
-muconate, as indicated in Table . Interestingly, one member of the family has been implicated in chemotaxis, allowing the bacteria to swim up concentration gradients of its substrates (34
). This is the only documented case where an MFS protein apparently serves as a chemoreceptor. One of the AAHS proteins (BenK Aca) transports benzoate (11
). Two additional (putative) benzoate:H+
symporters (BenE) have been sequenced. They are both derived from gram-negative bacteria. One is the functionally characterized BenE protein of Acinetobacter calcoaceticus
, and the other is a closely related protein from E. coli
). These two proteins both contain a single region that exhibits limited sequence similarity to family 15 porters, as might be expected on the basis of the specificity of the A. calcoaceticus
protein. However, they are very divergent in sequence from the latter proteins and cannot be shown to be homologous to any member of the MFS. They are therefore included in a separate family designated the benzoate:H+
symporter (BenE; TC #2.46) family (72a
Six members of a novel family, family 16, the unknown major facilitator (UMF) family, have recently been identified (26
). Although it has been proposed that these carriers are drug efflux pumps, no member of this family has been functionally characterized, and consequently the designation UMF has tentatively been assigned to this family. All six currently recognized members of the family are from Saccharomyces cerevisiae
, and no close homologs are found in other organisms. These proteins exhibit the less common putative 14-TMS topology observed for only two other MFS families. The proteins of the UMF family exhibit almost no size variation (range, 606 to 637 residues).
Family 17, the cyanate permease (CP) family, includes only three proteins, all from bacteria. They are small proteins (393 to 402 residues with 12 TMSs). The substrate of one of these proteins (CynX of E. coli) is believed to be cyanate (NCO−). The other two members, from E. coli and Bacillus subtilis, are strikingly divergent in sequence but not in size, as noted above.
The proton-dependent oligopeptide transporter (POT) family has been described previously (62
). We have observed sequence similarities of these proteins to members of the SP and DHA14 families (see below). Although this similarity is insufficient to establish homology, the similarities in sequence, mechanism, and topology between proteins of the POT family and those of several MFS families strongly suggest that the POT family is a distant constituent of the MFS.