A major superfamily of transmembrane facilitators that catalyse uniport, symport and antiport

Contrasting patterns of evolutionary divergence within the Acinetobacter calcoaceticus pca operon

The six enzymes required for catabolism of protocatechuate to succinate and acetylCoA are encoded by the pca genes in the Gram-bacterium, Acinetobacter calcoaceticus. The clustered A. calcoaceticus cat genes encode an analogous set of enzymes associated with the metabolic dissimilation of catechol. The nucleotide (nt) sequences of pcaIJFB and pcaK, reported here, complete evidence showing that all of the pca structural genes are tightly grouped in the order pcaIJFBDKCHG within a single operon. The pcaIJF region is nearly identical in nt sequence to the A. calcoaceticus catIDJF region which exhibits a G+C content and a codon usage pattern exceptional for A. calcoaceticus. In contrast, pcaD, pcaC, pcaH and pcaG have diverged substantially from their evolutionary counterparts in the cat region; all of these divergent genes exhibit G+C contents and codon usage patterns that are typical for A. calcoaceticus. The pcaIJF and catIJF regions are known to exchange DNA sequence information, and this property may have contributed to their nt sequence conservation. The pcaK gene has no counterpart among known cat genes. The deduced amino-acid sequence of PcaK indicates that it may be a transmembrane protein associated with transport.

Construction and in vivo analysis of new split lactose permeases

The capacity of incomplete segments of Escherichia coli lactose permease to form transport-competent complexes in vivo was further tested. Two series of mutant lacY genes were constructed. One encoded N-terminal lactose permease segments of different length. The proteins specified by the other group contained deletions of different length and location within the N-terminal region. Several pairs of such mutant proteins reconstituted active lactose transport. For certain combinations duplications of protein segments were compatible with the formation of an active carrier. Duplication of helices could also be tolerated, when part of a single polypeptide chain.

The Saccharomyces cerevisiae SGE1 gene product: a novel drug-resistance protein within the major facilitator superfamily

Several pleiotropic drug sensitivities have been described in yeast. Some involve the loss of putative drug efflux pumps analogous to mammalian P-glycoproteins, others are caused by defects in sterol synthesis resulting in higher plasma membrane permeability. We have constructed a Saccharomyces cerevisiae strain that exhibits a strong crystal violet-sensitive phenotype. By selecting cells of the supersensitive strain for normal sensitivity after transformation with a wild-type yeast genomic library, a complementing 10-kb DNA fragment was isolated, a 3.4-kb subfragment of which was sufficient for complementation. DNA sequence analysis revealed that the complementing fragment comprised the recently sequenced SGE1 gene, a partial multicopy suppressor of gal11 mutations. The supersensitive strain was found to be a sge1 null mutant. Overexpression of SGE1 on a high-copy-number plasmid increased the resistance of the supersensitive strain. Disruption of SGE1 in a wild-type strain increased the sensitivity of the strain. These features of the SGE1 phenotype, as well as sequence homologies of SGE1 at the amino acid level, confirm that the Sge1 protein is a member of the drug-resistance protein family within the major facilitator superfamily (MFS).

Bacterial transporters

Recent experiments in bacterial systems have established an extended database of sequences broadly relevant to all membrane transporters, allowing serious study of evolutionary relationships. The database will be especially useful in integrating conclusions derived from work with proteins in the major facilitator superfamily, because this kinship includes both eukaryotic and prokaryotic model systems. Even among carriers not linked by evolution, clear hints of functional homology have been note. Advances are also evident in the structural analysis of membrane carriers. Site-directed mutagenesis in a bacterial antiporter has shown how the translocation pathway might be identified; this should complement recent progress in preparing two-dimensional crystals of the eukaryotic anion-exchange protein, band 3. Together, these studies could soon verify or reject the idea that the transport pathway lies at the interface between the amino-terminal and carboxy-terminal helical bundles found in the hydrophobic core of most carrier proteins. If verified, the argument might allow construction of informed three-dimensional models in the absence of crystallographic evidence.

A family of extracytoplasmic proteins that allow transport of large molecules across the outer membranes of gram-negative bacteria

Seventeen fully sequenced and two partially sequenced extracytoplasmic proteins of purple, gram-negative bacteria constitute a homologous family termed the putative membrane fusion protein (MFP) family. Each such protein apparently functions in conjunction with a cytoplasmic membrane transporter of the ATP-binding cassette family, major facilitator superfamily, or heavy metal resistance/nodulation/cell division family to facilitate transport of proteins, peptides, drugs, or carbohydrates across the two membranes of the gram-negative bacterial cell envelope. Evidence suggests that at least some of these transport systems also function in conjunction with a distinct outer membrane protein. We report here that the phylogenies of these proteins correlate with the types of transport systems with which they function as well as with the natures of the substrates transported. Characterization of the MFPs with respect to secondary structure, average hydropathy, and average similarity provides circumstantial evidence as to how they may allow localized fusion of the two gram-negative bacterial cell membranes. The membrane fusion protein of simian virus 5 is shown to exhibit significant sequence similarity to representative bacterial MFPs.

A functional superfamily of sodium/solute symporters

Eleven families of sodium/solute symporters are defined based on their degrees of sequence similarities, and the protein members of these families are characterized in terms of their solute and cation specificities, their sizes, their topological features, their evolutionary relationships, and their relative degrees and regions of sequence conservation. In some cases, particularly where site-specific mutagenesis analyses have provided functional information about specific proteins, multiple alignments of members of the relevant families are presented, and the degrees of conservation of the mutated residues are evaluated. Signature sequences for several of the eleven families are presented to facilitate identification of new members of these families as they become sequenced. Phylogenetic tree construction reveals the evolutionary relationships between members of each family. One of these families is shown to belong to the previously defined major facilitator superfamily. The other ten families do not show sufficient sequence similarity with each other or with other identified transport protein families to establish homology between them. This study serves to clarify structural, functional and evolutionary relationships among eleven distinct families of functionally related transport proteins.

Properties of permease dimer, a fusion protein containing two lactose permease molecules from Escherichia coli

An engineered fusion protein containing two tandem lactose permease molecules (permease dimer) exhibits high transport activity and is used to test the phenomenon of negative dominance. Introduction of the mutation Glu-325-->Cys into either the first or the second half of the dimer results in a 50% decrease in activity, whereas introduction of the mutation into both halves of the dimer abolishes transport. Lactose transport by permease dimer is completely inactivated by N-ethylmaleimide; however, 40-45% activity is retained after N-ethylmaleimide treatment when either the first or the second half of the dimer is replaced with a mutant devoid of cysteine residues. The observations demonstrate that both halves of the fusion protein are equally active and suggest that each half may function independently. To test the possibility that oligomerization between dimers might account for the findings, a permease dimer was constructed that contains two different deletion mutants that complement functionally when expressed as untethered molecules. Because this construct does not catalyze lactose transport to any extent whatsoever, it is unlikely that the two halves of the dimer interact or that there is an oligomeric interaction between dimers. The approach is consistent with the contention that the functional unit of lactose permease is a monomer.

Molecular cloning of a maltose transport gene from Bacillus stearothermophilus and its expression in Escherichia coli K-12

Genes responsible for maltose utilization from Bacillus stearothermophilus ATCC7953 were cloned in the plasmid vector pBR325 and functionally expressed in Escherichia coli. The 4.2 kb Bacillus DNA insert in clone pAM1750 suppressed the growth defects on maltose caused by mutations in E. coli maltose transport genes (malE, malK or complete malB deletion) but not mutations in genes affecting intracellular maltose metabolism (malA region). Transport studies in E. coli and B. stearothermophilus suggested that pAM1750 codes for a high affinity transport system, probably one of two maltose uptake systems found in B. stearothermophilus ATCC7953. Nucleotide sequence analysis of a 3.6 kb fragment of pAM1750 revealed three open reading frames (ORFs). One of the ORFs, malA, encoded a putative hydrophobic protein with 12 potential transmembrane segments. MalA showed amino acid sequence similarity to proteins in the superfamily containing LacY lactose permease and also some similarity to MalG protein, a member of a binding protein-dependent transport system in E. coli. The products of two other ORFs were not hydrophobic, did not show similarity to other known sequences and were found not to be essential for maltose utilization in transport-defective E. coli mutants. Hence MalA protein was the only protein necessary for maltose transport, but despite giving a detectable but low level of transport function in E. coli, the protein was very poorly expressed and could not be identified.

Prevention of drug access to bacterial targets: permeability barriers and active efflux

Some species of bacteria have low-permeability membrane barriers and are thereby "intrinsically" resistant to many antibiotics; they are selected out in the multitude of antibiotics present in the hospital environment and thus cause many hospital-acquired infections. Some strains of originally antibiotic-susceptible species may also acquire resistance through decreases in the permeability of membrane barriers. Another mechanism for preventing access of drugs to targets is the membrane-associated energy-driven efflux, which plays a major role in drug resistance, especially in combination with the permeation barrier. Recent results indicate the existence of bacterial efflux systems of extremely broad substrate specificity, in many ways reminiscent of the multidrug resistance pump of mammalian cells. One such system seems to play a major role in the intrinsic resistance of Pseudomonas aeruginosa, a common opportunistic pathogen. As the pharmaceutical industry succeeds in producing agents that can overcome specific mechanisms of bacterial resistance, less specific resistance mechanisms such as permeability barriers and multidrug active efflux may become increasingly significant in the clinical setting.

Multiple drug resistance in the pathogenic protozoa

Evidence for the phenomenon of multiple drug resistance (MDR) in the well studied pathogenic protozoa has been examined. This has been placed in the more familiar context of the MDR efflux transporters and the cloned mdr genes of mammalian cells. Homologues of the mdr gene family in protozoa and their possible role in drug efflux have been compared with their mammalian counterparts. Possible mechanisms and models for drug efflux have been considered. The unusual and extensive range of substrates transported by the ATP-binding cassette (ABC) family of transporters which includes the MDRs has been raised. The impact of kinetics, structure and bioenergetics of the MDR family members on mechanisms of transport has been accentuated to argue that MDR efflux considered in isolation appears bizarre but may be better understood in a broader context.

Multidrug resistance pumps in bacteria: variations on a theme

Multidrug resistance pumps (MDRs) arise from three different gene families and are widespread in bacteria. For example, in Escherichia coli alone, there seem to be seven distinct MDRs. The most common belong to the major facilitator family of membrane translocases; this type of MDR is closely related to specific antibiotic extrusion pumps such as the tetracycline/H+ antiporter. This similarity in design, and the high incidence of apparently independent evolution of MDRs, suggests that the property of multidrug resistance might have resulted from a loss of specificity in a specific hydrophobic-drug efflux pump.

Two novel families of bacterial membrane proteins concerned with nodulation, cell division and transport

Homology has been established for members of two families of functionally related bacterial membrane proteins. The first family (the resistance/nodulation/cell division (RND) family) includes (i) two metal-resistance efflux pumps in Alcaligenes eutrophus (CzcA and CnrA), (ii) three proteins which function together in nodulation of alfalfa roots by Rhizobium meliloti (NoIGHI), and (iii) a cell division protein in Escherichia coli (EnvD). The second family (the putative membrane fusion protein (MFP) family) includes a nodulation protein (NoIF), a cell division protein (EnvC), and a multidrug resistance transport protein (EmrA). We propose that an MFP functions co-operatively with an RND protein to transport large or hydrophobic molecules across the two membranes of the Gram-negative bacterial cell envelope.

Computer-aided analyses of transport protein sequences: gleaning evidence concerning function, structure, biogenesis, and evolution

Three-dimensional structures have been elucidated for very few integral membrane proteins. Computer methods can be used as guides for estimation of solute transport protein structure, function, biogenesis, and evolution. In this paper the application of currently available computer programs to over a dozen distinct families of transport proteins is reviewed. The reliability of sequence-based topological and localization analyses and the importance of sequence and residue conservation to structure and function are evaluated. Evidence concerning the nature and frequency of occurrence of domain shuffling, splicing, fusion, deletion, and duplication during evolution of specific transport protein families is also evaluated. Channel proteins are proposed to be functionally related to carriers. It is argued that energy coupling to transport was a late occurrence, superimposed on preexisting mechanisms of solute facilitation. It is shown that several transport protein families have evolved independently of each other, employing different routes, at different times in evolutionary history, to give topologically similar transmembrane protein complexes. The possible significance of this apparent topological convergence is discussed.

Facilitative glucose transporters

Facilitative glucose transport is mediated by members of the Glut protein family that belong to a much larger superfamily of 12 transmembrane segment transporters. Six members of the Glut family have been described thus far. These proteins are expressed in a tissue- and cell-specific manner and exhibit distinct kinetic and regulatory properties that reflect their specific functional roles. Glut1 is a widely expressed isoform that provides many cells with their basal glucose requirement. It also plays a special role in transporting glucose across epithelial and endothelial barrier tissues. Glut2 is a high-Km isoform expressed in hepatocytes, pancreatic beta cells, and the basolateral membranes of intestinal and renal epithelial cells. It acts as a high-capacity transport system to allow the uninhibited (non-rate-limiting) flux of glucose into or out of these cell types. Glut3 is a low-Km isoform responsible for glucose uptake into neurons. Glut4 is expressed exclusively in the insulin-sensitive tissues, fat and muscle. It is responsible for increased glucose disposal in these tissues in the postprandial state and is important in whole-body glucose homeostasis. Glut5 is a fructose transporter that is abundant in spermatozoa and the apical membrane of intestinal cells. Glut7 is the transporter present in the endoplasmic reticulum membrane that allows the flux of free glucose out of the lumen of this organelle after the action of glucose-6-phosphatase on glucose 6-phosphate. This review summarizes recent advances concerning the structure, function, and regulation of the Glut proteins.

The mannitol repressor (MtlR) of Escherichia coli

The mannitol operon of Escherichia coli, encoding the mannitol-specific enzyme II of the phosphotransferase system (Mt1A) and mannitol phosphate dehydrogenase (Mt1D), is here shown to contain a single additional downstream open reading frame which encodes the mannitol repressor (Mt1R). Mt1R contains 195 amino acids and has a calculated molecular weight of 21,990 and a calculated pI of 4.5. It is homologous to the product of an open reading frame (URF2D) upstream of the E. coli gapB gene but represents a novel type of transcriptional regulatory protein.

Role of glutamate-269 in the lactose permease of Escherichia coli

Glu-269, which is located on the hydrophilic face of putative helix VIII in the lactose permease of Escherichia coli, has been replaced with Asp, Gln or Cys by oligonucleotide-directed, site specific mutagenesis. Cells expressing Asp-269 permease exhibit no lactose accumulation or lactose-induced H+ translocation, but retain some ability to mediate lactose influx down a concentration gradient at high substrate concentrations. Furthermore, right-side-out membrane vesicles containing Asp-269 permease do not catalyse active lactose transport, facilitated lactose efflux or equilibrium exchange. Remarkably, however, Asp-269 permease accumulates beta, D-galactopyranosyl 1-thio-beta,D-galactopyranoside in a partially uncoupled fashion, whereas no transport of methyl-beta,D-thiogalactopyranoside, sucrose or maltose is detectable. Mutant permeases containing neutral replacements (Gln or Cys) or Glu-269 are completely devoid of activity, although the proteins are present in the membrane at concentrations comparable with wild-type or Asp-269 permease. The observations demonstrate that a carboxylate at position 269 is essential for transport activity, and Glu-269 is important for substrate binding and/or recognition.

Convergence and divergence in the evolution of transport proteins

Different families of transport proteins catalyze transmembrane solute translocation, employing different mechanisms and energy sources. Several of these functionally dissimilar proteins nevertheless exhibit similar structural units, consisting of six tightly packed alpha-helices which may comprise all or part of a transmembrane channel. It is now recognized that some of these families arose independently of each other by convergence, while others arose from common precursors by divergence. The former families apparently arose at different times in evolutionary history, in different groups of organisms, employing different routes.

Regulation of the raffinose permease of Escherichia coli by the glucose-specific enzyme IIA of the phosphoenolpyruvate:sugar phosphotransferase system

In enteric bacteria, chromosomally encoded permeases specific for lactose, maltose, and melibiose are allosterically regulated by the glucose-specific enzyme IIA of the phosphotransferase system. We here demonstrate that the plasmid-encoded raffinose permease of enteric bacteria is similarly subject to this type of inhibition.

The pur8 gene from the pur cluster of Streptomyces alboniger encodes a highly hydrophobic polypeptide which confers resistance to puromycin

A novel puromycin-resistance determinant (pur8) was isolated from one end of the pur cluster that encodes the puromycin biosynthetic pathway from Streptomyces alboniger and expressed in Streptomyces lividans. The gene pur8 induced antibiotic resistance that was highly specific for puromycin. The nucleotide sequence of pur8 contains an open reading frame of 1512 bp whose deduced amino acid sequence encodes a polypeptide (Pur8) with 14 possible transmembrane-spanning segments. It shows significant similarities to other known or putative transmembrane proteins, including a number which confer drug resistance in a variety of antibiotic-producing Streptomyces, Gram-positive and Gram-negative bacteria, and some solute transporters of prokaryotic and eukaryotic origin. As is probably the case for most of these proteins, Pur8 may be involved in active puromycin efflux energized by a proton-dependent electrochemical gradient. In addition, it could be implicated in secreting N-acetylpuromycin, the last intermediate of the biosynthesis pathway, to the environment.

What's new with lactose permease

The lactose permease of Escherichia coli is a paradigm for polytopic membrane transport proteins that transduce free energy stored in an electrochemical ion gradient into work in the form of a concentration gradient. Although the permease consists of 12 hydrophobic transmembrane domains in probable alpha-helical conformation that traverse the membrane in zigzag fashion connected by hydrophilic "loops", little information is available regarding the folded tertiary structure of the molecule. In a recent approach site-directed fluorescence labeling is being used to study proximity relationships in lactose permease. The experiments are based upon site-directed pyrene labeling of combinations of paired Cys replacements in a mutant devoid of Cys residues. Since pyrene exhibits excimer fluorescence if two molecules are within about 3.5A, the proximity between paired labeled residues can be determined. The results demonstrate that putative helices VIII and IX are close to helix X. Taken together with other findings indicating that helix VII is close to helices X and XI, the data lead to a model that describes the packing of helices VII to XI.

Identification of the gene encoding an N-acetylpuromycin N-acetylhydrolase in the puromycin biosynthetic gene cluster from Streptomyces alboniger

The biologically inactive compound N-acetylpuromycin is the last intermediate of the puromycin antibiotic biosynthetic pathway in Streptomyces alboniger. Culture filtrates from either this organism or Streptomyces lividans transformants harboring the puromycin biosynthetic gene cluster cloned in low-copy-number cosmids contained an enzymic activity which hydrolyzes N-acetylpuromycin to produce the active antibiotic. A gene encoding the deacetylase enzyme was located at one end of this cluster, subcloned in a 2.5-kb DNA fragment, and expressed from a high-copy-number plasmid in S. lividans.

Nucleotide sequence and 3'-end deletion studies indicate that the K(+)-uptake protein kup from Escherichia coli is composed of a hydrophobic core linked to a large and partially essential hydrophilic C terminus

The kup (formerly trkD) gene from Escherichia coli encodes a minor K(+)-uptake system. The gene is located just upstream of the rbsDACBK operon at 84.5 min on the chromosome and is transcribed clockwise. kup codes for a 69-kDa protein, which may be composed of two domains. The first 440 amino acid residues appear to form an integral membrane protein that might traverse the cell membrane 12 times. The C-terminal 182 amino acid residues are predicted to form a hydrophilic domain located at the cytoplasmic side of the membrane. Deletion studies from the 3' end of kup showed that removal of almost the complete hydrophilic domain of the protein reduced, but did not abolish, K(+)-uptake activity.

Structural and evolutionary relationships between two families of bacterial extracytoplasmic chaperone proteins which function cooperatively in fimbrial assembly

Gram-negative purple bacteria possess pairs of extracytoplasmic, ATP-independent, fimbrium-specific chaperone proteins which cooperatively function in the assembly of this extracellular organelle. The two non-homologous families of these proteins have been termed "Fimbrial chaperone family no. 1" (FCF1) and "Fimbrial chaperone family no. 2" (FCF2). The eleven sequenced or partially sequenced members of each of these two protein families were analysed. Their sequences were multiply aligned, and average similarity and hydropathy plots were generated. Statistical analyses of the sequences revealed that the short FCF1 proteins (of about 240 residues) have been better conserved through evolutionary time than have the much larger FCF2 proteins (of about 830 residues). Moreover, the N-terminal thirds of the FCF2 proteins are better conserved than the central or C-terminal thirds of these proteins. Phylogenetic tree construction revealed that, in general, the two proteins which cooperate in the assembly of a particular fimbrial type have similar positions on their respective phylogenetic trees, suggesting that the two proteins evolved in parallel as a functional unit. Two exceptions were noted, however. In one case, a hybrid protein appears to have arisen, possibly by genetic recombination. In another case, the two proteins of a particular pair may have evolved separately and come together late in the evolutionary process to provide their cooperative function.

The 12-transmembrane helix transporters

From the hydropathic profiles of their amino acid sequences many transport proteins are conceived to comprise 12-transmembrane alpha-helices. In only a few examples, however, is there genetical and/or biochemical evidence to support the 12-helix structure or illuminate the molecular mechanism of the transport process. A number of these transport proteins occur in evolutionarily related families, and sometimes superfamilies, indicating divergent evolution of the 12-helix structure. Other individual members or families of transport proteins are sufficiently different in amino acid sequence for their evolution to have taken place by convergence from independent ancestral origins.

Sequence of a class E tetracycline resistance gene from Escherichia coli and comparison of related tetracycline efflux proteins

We determined the nucleotide sequence of the class E tetA gene on plasmid pSL1456 from Escherichia coli SLH1456A. The deduced amino acid sequence of the class E TetA protein shows 50 to 56% identity with the sequences of five related TetA proteins (classes A through D and G). Hydrophobicity profiles identify 12 putative transmembrane segments with similar boundaries in all six TetA sequences. The N-terminal alpha domain of the six sequences is more highly conserved than the C-terminal beta domain; the central hydrophilic loop connecting the alpha and beta domains is the least conserved region. Amino acid residues that have been shown to be important for class B (Tn10) TetA function are conserved in all six TetA sequences. Unlike the class B tetA gene, the class D and E tetA genes do not exhibit a negative gene dosage effect when present on multicopy plasmids derived from pACYC177.

Structural, functional, and evolutionary relationships among extracellular solute-binding receptors of bacteria

Extracellular solute-binding proteins of bacteria serve as chemoreceptors, recognition constituents of transport systems, and initiators of signal transduction pathways. Over 50 sequenced periplasmic solute-binding proteins of gram-negative bacteria and homologous extracytoplasmic lipoproteins of gram-positive bacteria have been analyzed for sequence 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 B12-binding protein of Escherichia coli, which is homologous to human glutathione peroxidase, they are not demonstrably homologous to any of the several thousand sequenced eukaryotic proteins. Most of these proteins fall into eight distinct clusters as follows. Cluster 1 solute-binding proteins are specific for malto-oligosaccharides, multiple oligosaccharides, glycerol 3-phosphate, and iron. Cluster 2 proteins are specific for galactose, ribose, arabinose, and multiple monosaccharides, and they are homologous to a number of transcriptional regulatory proteins including the lactose, galactose, and fructose repressors of E. coli. Cluster 3 proteins are specific for histidine, lysine-arginine-ornithine, glutamine, octopine, nopaline, and basic amino acids. Cluster 4 proteins are specific for leucine and leucine-isoleucine-valine, and they are homologous to the aliphatic amidase transcriptional repressor, AmiC, of Pseudomonas aeruginosa. Cluster 5 proteins are specific for dipeptides and oligopeptides as well as nickel. Cluster 6 proteins are specific for sulfate, thiosulfate, and possibly phosphate. Cluster 7 proteins are specific for dicarboxylates and tricarboxylates, but these two proteins exhibit insufficient sequence similarity to establish homology. Finally, cluster 8 proteins are specific for iron complexes and possibly vitamin B12. Members of each cluster of binding proteins exhibit greater sequence conservation in their N-terminal domains than in their C-terminal domains. Signature sequences for 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 proteins specific for different solutes from the same organism, although exceptions exist. They also suggest that a requirement for high-affinity solute binding imposes severe structural constraints on a protein. The occurrence of two distinct classes of bacterial cytoplasmic repressor proteins which are homologous to two different clusters of periplasmic binding proteins suggests that the gene-splicing events which allowed functional conversion of these proteins with retention of domain structure have occurred repeatedly during evolutionary history.(ABSTRACT TRUNCATED AT 400 WORDS)

Nucleotide and deduced protein sequences of the class D tetracycline resistance determinant: relationship to other antimicrobial transport proteins

The nucleotide sequence of the plasmid pRA1 gene encoding the TetA(D) tetracycline/H+ antiporter was determined. The deduced amino acid sequence was compared with those of other antimicrobial and antiseptic transporters. The deduced product of tetA(D) is a 41.1-kDa protein consisting of 394 amino acids comprising 12 membrane-spanning domains. Three classes of amino acid motifs found in TetA(D) are highly conserved in other transporters, implying that they participate in structures necessary for substrate recognition, binding, or translocation. A common mechanism of transport is suggested, with subtle sequence variations accounting for varied substrate specificities, modes of transport, and directions of transport.

Alamethicin and related peptaibols--model ion channels

Peptaibols are considered as models of those ion channels which consist of a bundle of transbilayer helices surrounding a central pore. X-Ray diffraction and NMR studies have yielded high resolution structures for several peptaibols. In conjunction with other spectroscopic investigations and molecular dynamics simulations, these studies suggest that peptaibols form proline-kinked alpha-helices, and that there may be "hinge-bending" movement of the helix in the region of the central proline residue. The amphipathicity of peptaibol helices is analyzed in relation to their channel-forming properties. Studies of the interactions of peptaibols with lipid bilayers suggest that they are helical when in a membrane-like environment, and that the helix orientation relative to the bilayer is sensitive to the peptaibol:lipid ratio, and to the degree of hydration of the bilayer. Electrical studies reveal that many peptaibols form multiple-conductance level channels in a voltage-dependent fashion. Analysis of conductance levels provides support for the "barrel stave" model of channel formation, whereby different conductance levels correspond to different numbers of monomers in a helix bundle. Alternative models for voltage-activation are discussed, and the roles of molecular dipoles and of hinge-bending in this process are considered. Two molecular models for an N = 6 bundle of alamethicin helices are presented and their electrostatic properties analyzed. The relevance of studies of peptaibols to channel and transport proteins in general is considered.

Transport proteins in bacteria: common themes in their design

Bacterial transport proteins mediate passive and active transport of small solutes across membranes. Comparison of amino acid sequences shows strong conservation not only among bacterial transporters, but also between them and many transporters of animal cells; thus the study of bacterial transporters is expected to contribute to our understanding of transporters in more complex cells. During the last few years, structures of three bacterial outer membrane transporters were solved by x-ray crystallography. Much progress has also occurred in the biochemical and molecular genetic studies of transporters in the cytoplasmic membranes of bacteria, and a unifying design among membrane transporters is gradually emerging. Common structural motives and evolutionary origins among transporters with diverse energy-coupling mechanisms suggest that many transporters contain a central module forming a transmembrane channel through which the solute may pass. Energy-coupling mechanisms can be viewed as secondary features added on to these fundamental translocation units.