Structure-function relationships of integral membrane proteins: membrane transporters vs channels

Escherichia coli lactose permease, a paradigm for membrane transport proteins, and Streptomyces lividans KcsA, a paradigm for K+ channels, are compared on the level of structure, dynamics, and function. The homotetrameric channel, which allows the downhill movement of K+ with an electrochemical gradient, is relatively rigid and inflexible, as observed by Fourier transform infrared spectroscopy. Lactose permease catalyzes transduction of free energy stored in an electrochemical H+ gradient into work in the form of a concentration gradient. In marked contrast to KcsA, the permease exhibits a high degree of H/D exchange, in addition to enhanced sensitivity to lateral lipid packing pressure, thereby indicating that this symport protein is extremely flexible and conformationally active. Finally, the differences between lactose permease and KcsA are discussed in the context of their specific functions with particular emphasis on differences between coupling in symport proteins and gating in channels.     

Proteomics of Synechocystis sp. PCC 6803. Identification of novel integral plasma membrane proteins

The cyanobacterial plasma membrane is an essential cell barrier with functions such as the control of taxis, nutrient uptake and secretion. These functions are carried out by integral membrane proteins, which are difficult to identify using standard proteomic methods. In this study, integral proteins were enriched from purified plasma membranes of Synechocystis sp. PCC 6803 using urea wash followed by protein resolution in 1D SDS/PAGE. In total, 51 proteins were identified by peptide mass fingerprinting using MALDI-TOF MS. More than half of the proteins were predicted to be integral with 1-12 transmembrane helices. The majority of the proteins had not been identified previously, and include members of metalloproteases, chemotaxis proteins, secretion proteins, as well as type 2 NAD(P)H dehydrogenase and glycosyltransferase. The obtained results serve as a useful reference for further investigations of the address codes for targeting of integral membrane proteins in cyanobacteria.     

Evolution of the MIP family of integral membrane transport proteins

Six integral membrane proteins of bacterial, animal, and plant origin, which are believed to function in solute transport, share sequence identity and are grouped together as members of the MIP family. These include the Escherichia coli glycerol facilitator, the major intrinsic protein from bovine lens fibre junction membranes, a plant tonoplast membrane protein, a soybean protein from the peribacteroid membrane, and a Drosophila neurogenic protein. These proteins, each of which appears to consist of six transmembrane helical segments per subunit, apparently arose by internal duplication of a three-transmembrane segment. Phylogenetic‘trees’interrelating these proteins and segments are presented.     

A novel ubiquitous family of putative efflux transporters

We describe a novel family of putative efflux transporters (PET) found in bacteria, yeast and plants. None of the members of the PET family has been functionally characterized. The bacterial and yeast proteins display a duplicated internal repeat element consisting of an N-terminal hydrophobic sequence of about 170 residues, exhibiting six putative transmembrane alpha-helical spanners (TMSs), followed by a large (230 residue), C-terminal, hydrophilic, cytoplasmic domain. The plant proteins exhibit only one such unit, but they have a larger C-terminal cytoplasmic domain. Arabidopsis thaliana encodes at least seven paralogues of the PET family. The gram-negative bacterial proteins are sometimes encoded by genes that are found in operons that also contain genes that encode membrane fusion proteins. This fact strongly suggests that PET family proteins are efflux pumps. The sequence, topological and phylogenetic characteristics of these proteins as well as the operonic structures of their encoded genes when relevant are described.     

A novel approach for the identification of protein-protein interaction with integral membrane proteins

Protein-protein interaction plays a major role in all biological processes. The currently available genetic methods such as the two-hybrid system and the protein recruitment system are relatively limited in their ability to identify interactions with integral membrane proteins. Here we describe the development of a reverse Ras recruitment system (reverse RRS), in which the bait used encodes a membrane protein. The bait is expressed in its natural environment, the membrane, whereas the protein partner (the prey) is fused to a cytoplasmic Ras mutant. Protein-protein interaction between the proteins encoded by the prey and the bait results in Ras membrane translocation and activation of a viability pathway in yeast. We devised the expression of the bait and prey proteins under the control of dual distinct inducible promoters, thus enabling a rapid selection of transformants in which growth is attributed solely to specific protein-protein interaction. The reverse RRS approach greatly extends the usefulness of the protein recruitment systems and the use of integral membrane proteins as baits. The system serves as an attractive approach to explore novel protein-protein interactions with high specificity and selectivity, where other methods fail.     

ARAMEMNON,a novel database for Arabidopsis integral membrane proteins

A specialized database (DB) for Arabidopsis membrane proteins, ARAMEMNON, was designed that facilitates the interpretation of gene and protein sequence data by integrating features that are presently only available from individual sources. Using several publicly available prediction programs, putative integral membrane proteins were identified among the approximately 25,500 proteins in the Arabidopsis genome DBs. By averaging the predictions from seven programs, approximately 6,500 proteins were classified as transmembrane (TM) candidate proteins. Some 1,800 of these contain at least four TM spans and are possibly linked to transport functions. The ARAMEMNON DB enables direct comparison of the predictions of seven different TM span computation programs and the predictions of subcellular localization by eight signal peptide recognition programs. A special function displays the proteins related to the query and dynamically generates a protein family structure. As a first set of proteins from other organisms, all of the approximately 700 putative membrane proteins were extracted from the genome of the cyanobacterium Synechocystis sp. and incorporated in the ARAMEMNON DB. The ARAMEMNON DB is accessible at the URL http://aramemnon.botanik.uni-koeln.de.     

A novel family of cys-rich membrane proteins mediates cadmium resistance in Arabidopsis

Cadmium (Cd) is a widespread pollutant that is toxic to plant growth. However, only a few genes that contribute to Cd resistance in plants have been identified. To identify additional Cd(II) resistance genes, we screened an Arabidopsis cDNA library using a yeast (Saccharomyces cerevisiae) expression system employing the Cd(II)-sensitive yeast mutant ycf1. This screening process yielded a small Cys-rich membrane protein (Arabidopsis plant cadmium resistance, AtPcrs). Database searches revealed that there are nine close homologs in Arabidopsis. Homologs were also found in other plants. Four of the five homologs that were tested also increased resistance to Cd(II) when expressed in ycf1. AtPcr1 localizes at the plasma membrane in both yeast and Arabidopsis. Arabidopsis plants overexpressing AtPcr1 exhibited increased Cd(II) resistance, whereas antisense plants that showed reduced AtPcr1 expression were more sensitive to Cd(II). AtPcr1 overexpression reduced Cd uptake by yeast cells and also reduced the Cd contents of both yeast and Arabidopsis protoplasts treated with Cd. Thus, it appears that the Pcr family members may play an important role in the Cd resistance of plants.     

A new family of integral membrane proteins involved in transport of aromatic amino acids in Escherichia coli.

The nucleotide sequence of tnaB of the tryptophanase operon of Escherichia coli is presented. TnaB is a tryptophan-specific permease that is homologous to Mtr, a second tryptophan-specific permease, and to TyrP, a tyrosine-specific permease. Each member of this family appears to contain 11 membrane-spanning domains.     

A collection of well characterised integral membrane proteins

SUMMARY: A collection of transmembrane proteins with annotated transmembrane regions, for which good experimental evidence exist, was created as a test or training set for algorithms to predict transmembrane regions in proteins.     

Purification of integral plasma membrane proteins by reverse-phase high performance liquid chromatography

Following dissolution in anhydrous trifluoroacetic acid, plasma membrane isolated from two eukaryotic species was directly injected onto a reverse-phase high performance liquid chromatograph column. Upon development with a 60 to 100% (v/v) linear gradient of ethanol containing 0.1% trifluoroacetic acid, most of the polypeptides eluted without retention. Only the lipids and very hydrophobic proteins were retained and resolved. Most noticeable among retained proteins was the Mr 100,000 catalytic polypeptide of each species' primary plasma membrane cation pump, the Na+,K+-ATPase of pig kidney and the H+-ATPase of Neurospora crassa hyphae. This simple 60-min procedure yielded nearly pure ATPase starting from crude membranes and in a completely volatile solvent, without detergent. When fungal plasma membranes were phosphorylated in vitro with [gamma-32P]ATP prior to injection, protein kinase activity was observed and this resulted in the phosphorylation of the H+-ATPase as well as of several other less-abundant hydrophobic membrane proteins. This procedure is useful as an alternative method for the rapid characterization of those membrane-associated polypeptides that contain several hydrophobic, transmembrane sequences.     

A murine T lymphocyte antigen belongs to a supergene family of type II integral membrane proteins

A murine cell surface, disulfide-linked 85kDa dimer, defined with murine mAb A1, is expressed at high levels on EL-4 cells, but at low levels on normal C57BL/6 T cells. A similar structure is recognized by the rat mAbs YE1/32 and YE1/48. We isolated a cDNA clone encoding the antigen recognized by mAb A1 by immunoselection of a cDNA library in the eukaryotic expression vector CDM8. COS 7.2 cells transfected with this cDNA clone expressed an mAb A1-reactive 85 kDa disulfide-linked dimer with 44 kDa subunits, which was also reactive with the mAbs YE1/32 and YE1/48. The A1 gene displayed extensive strain polymorphism, underwent no rearrangement in EL-4, and hybridized with multiple restriction fragments, suggesting that it is a member of a multi-gene family. The deduced polypeptide contained 262 residues with an m.w. of 30,648, multiple cysteines, and three potential N-linked glycosylation sites, consistent with previous observations. In contrast to most integral membrane proteins, the putative A1 protein had features of a type II integral membrane protein structure, with its carboxyl terminus exposed extracellularly and an intracytoplasmic amino terminus. There was significant homology with several type II integral membrane proteins, including the human and chicken asialoglycoprotein receptors, and especially the human low affinity Fc epsilon receptor, in the putative extracellular domains of these proteins. This analysis suggested that the A1 gene belongs to a novel supergene family of type II integral membrane proteins and suggested that the A1 protein itself may be involved in binding a soluble ligand such as carbohydrates or immunoglobulin.     

Neurotransmitter transporters: target for endocrine regulation.

Aminergic signaling in the CNS is terminated by clearance from the synapse via high-affinity transporter molecules in the presynaptic membrane. Relatively recent sequence identification of these molecules has now permitted the initiation of studies of regulation of transporter function at the cellular and systems levels. In vitro studies provide evidence that the transporters for dopamine, serotonin, and gamma-aminobutyric acid are substrates for regulation by protein kinase C signaling. In vivo studies provide evidence that insulin and adrenal and gonadal steroid hormones may regulate the synthesis and activity of the transporters. Future directions should permit evaluation of the role of endocrine regulation in neurotransmitter clearance, and thus in the maintenance of normal CNS aminergic signaling.     

Junctophilins: a novel family of junctional membrane complex proteins

Junctional complexes between the plasma membrane (PM) and endoplasmic/sarcoplasmic reticulum (ER/ SR) are a common feature of all excitable cell types and mediate cross-talk between cell surface and intracellular ion channels. We have identified the junctophilins (JPs), a novel conserved family of proteins that are components of the junctional complexes. JPs are composed of a carboxy-terminal hydrophobic segment spanning the ER/SR membrane and a remaining cytoplasmic domain that shows specific affinity for the PM. In mouse, there are at least three JP subtypes: JP-1, -2, and -3. JP-2 is abundantly expressed in the heart, and mutant mice lacking JP-2 exhibited embryonic lethality. Cardiac myocytes from the mutant mice showed deficiency of the junctional membrane complexes and abnormal Ca2+ transients. Our results suggest that JPs are important components of junctional membrane complexes.     

Sequence of human syndecan indicates a novel gene family of integral membrane proteoglycans

The structure of human syndecan, an integral membrane proteoglycan, has been determined by cloning its full-length cDNA, which codes for the entire 310-amino acid-long core protein, including the NH2-terminal signal peptide. Similar to mouse syndecan (Saunders, S., Jalkanen, M., O'Farrell, S., and Bernfield, M. (1989) J. Cell Biol. 108, 1547-1556), the core protein of human syndecan can be divided into three domains: a matrix-interacting ectodomain containing putative glycosaminoglycan attachment sites, a 25-residue hydrophobic membrane-spanning domain, and a 34-residue cytoplasmic domain. Several interesting conserved structures were revealed by comparing the human syndecan sequence to the murine one. (i) Although the ectodomains are only 70% identical, all putative glycosaminoglycan attachment sites are identical (two of them belong to the consensus sequence SGXG and three others to (E/D)GSG(E/D), as are also (ii) the single putative N-glycosylation site and (iii) the proteinase-sensitive dibasic RK site adjacent to the extracellular face of the transmembrane domain. Furthermore, (iv) the transmembrane domain is 96% identical, as the only change in human syndecan was an alteration of an alanine residue to glycine; and finally, (v) the cytoplasmic domain is 100% identical, including 3 identically located tyrosine residues. Comparison of transmembrane and cytoplasmic domains to a third cell-surface proteoglycan, 48K5 from human lung fibroblasts (Marynen, P., Zhang, J., Cassiman, J., Vanden Berghe, H., and David, C. (1989) J. Biol. Chem. 264, 7017-7024), indicates that the transmembrane and cytoplasmic domains are similar also in this molecule regardless of the presence of a totally nonhomologous ectodomain. Thus, the transmembrane and cytoplasmic domains are unique for these cell-surface proteoglycans, which we propose to be members of a novel gene family of syndecans.     

A novel family of yeast chaperons involved in the distribution of V-ATPase and other membrane proteins.

Null mutations in genes encoding V-ATPase subunits in Saccharomyces cerevisiae result in a phenotype that is unable to grow at high pH and is sensitive to high and low metal-ion concentrations. Treatment of these null mutants with ethylmethanesulfonate causes mutations that suppress the V-ATPase null phenotype, and the mutant cells are able to grow at pH 7.5. The suppressor mutants were denoted as svf (suppressor of V-ATPase function). The frequency of svf is relatively high, suggesting a large target containing several genes for the ethylmethanesulfonate mutagenesis. The suppressors' frequency is dependent on the individual genes that were inactivated to manifest the V-ATPase null mutation. The svf mutations are recessive, because crossing the svf mutants with their corresponding V-ATPase null mutants resulted in diploid strains that are unable to grow at pH 7.5. A novel gene family in which null mutations cause pleiotropic effects on metal-ion resistance or sensitivity and distribution of membrane proteins in different targets was discovered. The family was defined as VTC (Vacuolar Transporter Chaperon) and it contains four genes in the S. cerevisiae genome. Inactivation of one of them, VTC1, in the background of V-ATPase null mutations resulted in svf phenotype manifested by growth at pH 7.5. Deletion of the VTC1 gene (DeltaVTC1) results in a reduced amount of V-ATPase in the vacuolar membrane. These mutant cells fail to accumulate quinacrine into their vacuoles, but they are able to grow at pH 7.5. The VTC1 null mutant also results in a reduced amount of the plasma membrane H(+)-ATPase (Pma1p) in membrane preparations and possibly mis-targeting. This observation may provide an explanation for the svf phenotype in the double disruptant mutants of DeltaVTC1 and DeltaVMA subunits.     

Immunoblotting of hydrophobic integral membrane proteins

For diagnosis and research purposes it is frequently desirable to measure by immunoblotting small amounts of proteins in complex mixtures such as tissue biopsy homogenates. Standard immunoblot procedures that give excellent results for soluble proteins unexpectedly gave low and irreproducible signals with some hydrophobic membrane proteins. We found that this was due to inefficient electrophoretic transfer to nitrocellulose, which could be corrected by modification of the transblot buffer. Hydrophobic integral membrane proteins of peroxisomes as well as other rat and human liver proteins were subjected to sodium dodecyl sulfate-polyacrylamide gel electrophoresis and transferred to nitrocellulose filters. The nitrocellulose-bound proteins were detected both by staining and by immunoblotting with an antiserum against the 22-kDa integral membrane protein of peroxisomes plus 125I-labeled protein A. A modified transblot buffer with 0.7 M glycine and 25 mM Tris (pH 7.7) but no methanol allowed use of a much shorter transfer time and strikingly improved the electrophoretic transfer of membrane proteins such that a peroxisomal integral membrane protein could be easily detected in human liver biopsy homogenates.     

Characterization of two antigenically related integral membrane proteins of the guinea pig sperm periacrosomal plasma membrane

The periacrosomal plasma membrane of mammalian spermatozoa functions both in recognition and in binding of the egg's zona pellucida and in the acrosome reaction. This study characterizes two antigenically related proteins with molecular weights of 35 kD (PM35) and 52 kD (PM52) of the guinea pig sperm periacrosomal plasma membrane. Polyclonal antisera were prepared against electrophoretically purified PM35 or PM52. Each antiserum recognized both the 35-kD and 52-kD polypeptides on Western blots, indicating that they are structurally related. This conclusion was supported by peptide mapping experiments demonstrating comparably sized fragments of both PM35 and PM52. Both PM35 and PM52 behave as integral membrane proteins during phase-separation analysis with Triton X-114. Electron microscopic immunocytochemistry and differential fractionation of sperm membranes established that both PM35 and PM52 are exclusively localized to the periacrosomal plasma membrane. Three different antisera were used for ultrastructural studies, and each specifically bound the cytoplasmic but not the extracellular membrane surface. The electrophoretic mobilities of the PM35 and PM52 polypeptides were unchanged during sperm maturation and during the ionophore-induced acrosome reaction. The localization of PM35 and PM52 suggests a potential role for these integral plasma membrane proteins in signal transduction or membrane fusion events of the acrosome reaction. © 1994 Wiley-Liss, Inc.