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E P Bakker

Publications and source records attributed to E P Bakker.

At least 19 recordsLinked to original sources
PubMed2001

Evidence in support of a four transmembrane-pore-transmembrane topology model for the Arabidopsis thaliana Na+/K+ translocating AtHKT1 protein, a member of the superfamily of K+ transporters.

The Arabidopsis thaliana AtHKT1 protein, a Na(+)/K(+) transporter, is capable of mediating inward Na(+) currents in Xenopus laevis oocytes and K(+) uptake in Escherichia coli. HKT1 proteins are members of a superfamily of K(+) transporters. These proteins have been proposed to contain eight transmembrane segments and four pore-forming regions arranged in a mode similar to that of a K(+) channel tetramer. However, computer analysis of the AtHKT1 sequence identified eleven potential transmembrane segments. We have investigated the membrane topology of AtHKT1 with three different techniques. First, a gene fusion alkaline phosphatase study in E. coli clearly defined the topology of the N-terminal and middle region of AtHKT1, but the model for membrane folding of the C-terminal region had to be refined. Second, with a reticulocyte-lysate supplemented with dog-pancreas microsomes, we demonstrated that N-glycosylation occurs at position 429 of AtHKT1. An engineered unglycosylated protein variant, N429Q, mediated Na(+) currents in X. laevis oocytes with the same characteristics as the wild-type protein, indicating that N-glycosylation is not essential for the functional expression and membrane targeting of AtHKT1. Five potential glycosylation sites were introduced into the N429Q. Their pattern of glycosylation supported the model based on the E. coli-alkaline phosphatase data. Third, immunocytochemical experiments with FLAG-tagged AtHKT1 in HEK293 cells revealed that the N and C termini of AtHKT1, and the regions containing residues 135-142 and 377-384, face the cytosol, whereas the region of residues 55-62 is exposed to the outside. Taken together, our results show that AtHKT1 contains eight transmembrane-spanning segments.

Alkaline Phosphatase↗
PubMed2001

Identification of the ABC protein SapD as the subunit that confers ATP dependence to the K+-uptake systems Trk(H) and Trk(G) from Escherichia coli K-12.

The activity of the two almost identical K+-uptake systems, Trk(H) and Trk(G), from Escherichia coli K-12 depends completely and partially on the presence of the trkE gene, respectively. trkE maps inside the sapABCDF operon, which encodes an ATP-binding cassette (ABC) transporter of unknown function from the subgroup of peptide-uptake systems. This study was carried out to clarify the role of sapABCDF gene products in the ATP dependence of the E. coli Trk systems. For this purpose DeltasapABCDF DeltatrkG and DeltasapABCDF DeltatrkH strains of E. coli containing plasmids with sap genes from either E. coli or Vibrio alginolyticus were used. All five plasmid-encoded E. coli Sap proteins were made in E. coli mini-cells. The presence of the ATP-binding SapD protein from either E. coli or V. alginolyticus alone was sufficient for stimulating the K+ transport activity of the Trk(H) and Trk(G) systems. K+-uptake experiments with Escherichia coli cells containing SapD variants with changes in the Walker A box Lys-46 residue, the Walker B box Asp-183 residue and the signature motif residues Gly-162 or Gln-165 suggested that adenine nucleotide binding to SapD rather than ATP hydrolysis by this subunit is required for the activity of the E. coli Trk(H) system. K+ transport via two plasmid-encoded Trk systems in a DeltasapABCDF E. coli strain remained dependent on both a high membrane potential and a high cytoplasmic ATP concentration, indicating that in E. coli ATP dependence of Trk activity can be independent of Sap proteins. These data are interpreted to mean that Trk systems can interact with an ABC protein other than SapD.

ATP-Binding Cassette Transporters↗
PubMed2000

Gene cloning, nucleotide sequence and biochemical properties of a cytoplasmic cyclomaltodextrinase (neopullulanase) from Alicyclobacillus acidocaldarius, reclassification of a group of enzymes.

A gene encoding a cyclomaltodextrinase (neopullulanase) was cloned from the thermoacidophilic bacterium Alicyclobacillus acidocaldarius ATCC27009 and its nucleotide sequence was determined. The encoded CdaA protein lacked an N-terminal signal sequence and aligned well with a family of bacterial proteins described as maltogenic alpha-amylases, neopullulanases or cyclomaltodextrinases. Escherichia coli cells harboring the cloned cdaA gene produced a 66-kDa protein that degraded pullulan in a sodium dodecyl sulfate-polyacrylamide gel. A. acidocaldarius cells grown on maltose, soluble starch or pullulan synthesized the same protein. Neopullulanase activity of the protein was cytoplasmic and its pH optimum of 5.5 was close to the pH value of the cytoplasm. CdaA degraded cyclomaltodextrins rapidly and pullulan (to panose) more slowly. It is proposed that CdaA functions as a cytoplasmic cyclomaltodextrinase (EC 3.2.1.54).

Amino Acid Sequence↗
PubMed2000

Does the KdpA subunit from the high affinity K(+)-translocating P-type KDP-ATPase have a structure similar to that of K(+) channels?

Evidence is presented that the transmembrane KdpA subunit of the high affinity K(+)-translocating P-type Kdp-ATPase is evolutionarily derived from the superfamily of 2TM-type K(+) channels in bacteria. This extends a previous study relating the K(+) channels to the KtrAB, Trk, Trk1,2, and HKT1 K(+) symporter superfamily of both prokaryotes and eukaryotes. Although the channels are formed by four single-MPM motif subunits, the transmembrane KdpA subunit and the transmembrane subunit of the symporter proteins are postulated to have four corresponding MPM motifs within a single sequence. Analysis of 17 KdpA sequences reveals a pattern of residue conservation similar to that of the symporters and channels, and consistent with the crystal structure of the KcsA K(+) channel. In addition, the most highly conserved residues between the families, specifically the central glycines of the P2 segments, are those previously identified as crucial for the property of K(+)-selectivity that is common to each protein. This hypothesis is consistent with an experimental study of mutations that alter K(+) binding affinity of the Kdp transporter. Although most of the results of a previous study of the transmembrane topology of KdpA are consistent with the 4-MPM model, the one deviation can be explained by a plausible change in the structure due to the experimental method.

Adenosine Triphosphatases↗
PubMed2000

The Arabidopsis HKT1 gene homolog mediates inward Na(+) currents in xenopus laevis oocytes and Na(+) uptake in Saccharomyces cerevisiae.

The Na(+)-K(+) co-transporter HKT1, first isolated from wheat, mediates high-affinity K(+) uptake. The function of HKT1 in plants, however, remains to be elucidated, and the isolation of HKT1 homologs from Arabidopsis would further studies of the roles of HKT1 genes in plants. We report here the isolation of a cDNA homologous to HKT1 from Arabidopsis (AtHKT1) and the characterization of its mode of ion transport in heterologous systems. The deduced amino acid sequence of AtHKT1 is 41% identical to that of HKT1, and the hydropathy profiles are very similar. AtHKT1 is expressed in roots and, to a lesser extent, in other tissues. Interestingly, we found that the ion transport properties of AtHKT1 are significantly different from the wheat counterpart. As detected by electrophysiological measurements, AtHKT1 functioned as a selective Na(+) uptake transporter in Xenopus laevis oocytes, and the presence of external K(+) did not affect the AtHKT1-mediated ion conductance (unlike that of HKT1). When expressed in Saccharomyces cerevisiae, AtHKT1 inhibited growth of the yeast in a medium containing high levels of Na(+), which correlates to the large inward Na(+) currents found in the oocytes. Furthermore, in contrast to HKT1, AtHKT1 did not complement the growth of yeast cells deficient in K(+) uptake when cultured in K(+)-limiting medium. However, expression of AtHKT1 did rescue Escherichia coli mutants carrying deletions in K(+) transporters. The rescue was associated with a less than 2-fold stimulation of K(+) uptake into K(+)-depleted cells. These data demonstrate that AtHKT1 differs in its transport properties from the wheat HKT1, and that AtHKT1 can mediate Na(+) and, to a small degree, K(+) transport in heterologous expression systems.

Amino Acid Sequence↗
PubMed1999

Change to alanine of one out of four selectivity filter glycines in KtrB causes a two orders of magnitude decrease in the affinities for both K+ and Na+ of the Na+ dependent K+ uptake system KtrAB from Vibrio alginolyticus.

KtrAB from Vibrio alginolyticus is a recently described new type of high affinity bacterial K+ uptake system. Its activity assayed in an Escherichia coli K+ uptake negative mutant depended on Na+ ions (Km of 40 microM). Subunit KtrB contains four putative P-loops. The selectivity filter from each P-loop contains a conserved glycine residue. Residue Gly-290 from the third P-loop selectivity filter in KtrB was exchanged for Ala, Ser or Asp. KtrB variants Ser-290 and Asp-290 were without activity. In contrast, KtrB variant Ala-290 was still active. This variant transported K+ with a two orders of magnitude decrease in apparent affinity for both K+ and Na+ with little effect on Vmax.

Alanine↗
PubMed1999

Evolutionary relationship between K(+) channels and symporters.

The hypothesis is presented that at least four families of putative K(+) symporter proteins, Trk and KtrAB from prokaryotes, Trk1,2 from fungi, and HKT1 from wheat, evolved from bacterial K(+) channel proteins. Details of this hypothesis are organized around the recently determined crystal structure of a bacterial K(+) channel: i. e., KcsA from Streptomyces lividans. Each of the four identical subunits of this channel has two fully transmembrane helices (designated M1 and M2), plus an intervening hairpin segment that determines the ion selectivity (designated P). The symporter sequences appear to contain four sequential M1-P-M2 motifs (MPM), which are likely to have arisen from gene duplication and fusion of the single MPM motif of a bacterial K(+) channel subunit. The homology of MPM motifs is supported by a statistical comparison of the numerical profiles derived from multiple sequence alignments formed for each protein family. Furthermore, these quantitative results indicate that the KtrAB family of symporters has remained closest to the single-MPM ancestor protein. Strong sequence evidence is also found for homology between the cytoplasmic C-terminus of numerous bacterial K(+) channels and the cytoplasm-resident TrkA and KtrA subunits of the Trk and KtrAB symporters, which in turn are homologous to known dinucleotide-binding domains of other proteins. The case for homology between bacterial K(+) channels and the four families of K(+) symporters is further supported by the accompanying manuscript, in which the patterns of residue conservation are demonstrated to be similar to each other and consistent with the known 3D structure of the KcsA K(+) channel.

Amino Acid Sequence↗
PubMed1998

KtrAB, a new type of bacterial K(+)-uptake system from Vibrio alginolyticus.

Vibrio alginolyticus contained two adjacent genes, ktrA and ktrB, which encode a new type of bacterial K(+)-uptake system. KtrA and KtrB are peripheral and integral membrane proteins, respectively. Six of the nine sequenced bacterial genomes contain homologs to both ktrA and ktrB, suggesting that KtrAB is widespread.

Chromosome Mapping↗
PubMed1998

Identification of OmpT as the protease that hydrolyzes the antimicrobial peptide protamine before it enters growing cells of Escherichia coli.

The influence of extracytoplasmic proteases on the resistance of Escherichia coli to the antimicrobial peptide protamine was investigated by testing strains with deletions in the protease genes degP, ptr, and ompT. Only DeltaompT strains were hypersusceptible to protamine. This effect was abolished by plasmids carrying ompT. Both at low and at high Mg2+ concentrations, ompT+ strains cleared protamine from the medium within a few minutes. By contrast, at high Mg2+ concentrations, protamine remained present for at least 1 h in the medium of an ompT strain. These data indicate that OmpT is the protease that degrades protamine and that it exerts this function at the external face of the outer membrane.

Escherichia coli↗
PubMed1997

Acidostable and acidophilic proteins: the example of the alpha-amylase from Alicyclobacillus acidocaldarius.

Acidophilic microorganisms grow optimally at pH values between 1-4. They have adapted to the acid condition by maintaining their cytoplasmic pH at a value close to neutrality. Hence, only those (macro)-molecules, which face the acid medium, have had to adapt to this extreme condition. Literature data show that several exoproteins from thermoacidophilic prokaryotes are characterized by a low charge density. It is proposed that this property contributes to the stability of these proteins both below and above the pKa-values of their glutamate and aspartate residues. As an example of an acidophilic protein, the alpha-amylase from the Gram-positive Alicyclobacillus acidocaldarius ATCC27009 was studied. The enzyme is thermoacidophilic, with optima of temperature and pH of 75 degrees C and pH 3, respectively. The nucleotide sequence of the cloned gene (8) indicates that the alpha-amylase belongs to a large family of starch-degrading enzymes with a characteristic catalytic (beta alpha)8-domain. Three essential and probably catalytic acidic residues have been conserved, suggesting that the acidophilic alpha-amylase degrades starch with essentially the same mechanism as do its neutrophilic relatives. Still, the acidophilic protein contains three exchanges in residues uniformally or almost uniformally conserved among all members of the enzyme family. In order to test whether these exchanges contribute to the acidic pH optimum, the alpha-amylase gene was expressed in Escherichia coli. Sonication of the enzyme-producing cells released alpha-amylase activity associated with a 140 kDa protein. The optima of temperature and pH for the protein produced in E. coli were similar to those of the native enzyme. Experiments are underway in which it is tested which residues contribute to the acid pH optimum of the alpha-amylase.

Amino Acid Sequence↗
PubMed1995

TrkH and its homolog, TrkG, determine the specificity and kinetics of cation transport by the Trk system of Escherichia coli.

The corrected sequence of the trkH gene of Escherichia coli predicts that the TrkH protein is a hydrophobic membrane protein of 483 amino acid residues, of which 41% are identical to those of the homologous and functionally analogous TrkG protein. These two proteins form the transmembrane component of the Trk system for the uptake of K+. Each protein alone is sufficient for high-level Trk activity. When Trk is assembled with the TrkG protein, Rb+ and K+ are transported with a Km near or below 1 mM; however, the Vmax for Rb+ is only about 7% of that for K+. When Trk is formed with TrkH, the affinities for both for K+ and Rb+ are somewhat lower, and the Vmax for Rb+ is only 1% of that for K+ transport. The kinetics of transport in strains with wild-type alleles at trkG and at trkH suggest that both products participate in transport.

Amino Acid Sequence↗
PubMed1994

Purification, properties and structural aspects of a thermoacidophilic alpha-amylase from Alicyclobacillus acidocaldarius atcc 27009. Insight into acidostability of proteins.

The alpha-amylase from the thermoacidophilic eubacterium Alicyclobacillus (Bacillus) acidocaldarius strain ATCC 27009 was studied as an example of an acidophilic protein. The enzyme was purified from the culture fluid. On an SDS/polyacrylamide gel, the protein an apparent molecular mass of 160 kDa, which is approximately 15% higher than that predicted from the nucleotide sequence. The difference is due to the enzyme being a glycoprotein. Deglycosylation or synthesis of the enzyme in Escherichia coli gave a product with the mass expected for the mature protein. The amylase hydrolyzed starch at random and from the inside, and its main hydrolysis products were maltotriose and maltose. It also formed glucose from starch (by hydrolysing the intermediate product maltotetraose to glucose and maltotriose) and exhibited some pullulanase activity. the pH and temperature optima were pH3 and 75 degrees C, respectively, characterizing the enzyme as being thermoacidophilic. Alignment of the sequence of the enzyme with that of its closest neutrophilic relatives and with that of alpha-1,4 or alpha-1,6 glycosidic-bond hydrolyzing enzymes of known three-dimensional structure showed that the acidophilic alpha-amylase contains approximately 30% less charged residues than do its closest relatives, that these residues are replaced by neutral polar residues, and that hot spots for these exchanges are likely to be located at the surface of the protein. Literature data show that similar effects are observed in three other acidophilic proteins. It is proposed that these proteins have adapted to the acidic environment by reducing the density of both positive and negative charges at their surface, that this effect circumvents electrostatic repulsion of charged groups at low pH, and thereby contributes to the acidostability of these proteins.

Amino Acid Sequence↗
PubMed1993

Transient, specific and extremely rapid release of osmolytes from growing cells of Escherichia coli K-12 exposed to hypoosmotic shock.

The influence of hypoosmotic shock on the solute content of growing Escherichia coli K-12 cells was investigated at 37 degrees C. Within 20 s after the shock the cells had released most of their osmolytes K+, glutamate and trehalose. This release was specific and not due to rupture of the cell membrane, since under these conditions i) the cells neither lost protein nor ATP, ii) [14C]-labeled sucrose did not enter the cytoplasm from the periplasm, and iii) except for their glutamate and aspartate level, which decreased, the amino acid pool of alanine, lysine and arginine of the cells remained approximately constant. Within a minute after the shock the cells started to reaccumulate parts of their previously released glutamate, aspartate and K+, but not trehalose and resumed growth within 10 min after the shock. Experiments with K(+)-transport mutants showed that none of the genetically-identified K+ transport systems is involved in the K(+)-release process. Reaccumulation of K+ took place via the uptake systems TrkG and TrkH. The possibility is discussed that the exit of solutes after hypoosmotic shock occurs via several stretch-activated channels, which each allow the release of a specific osmolyte.

Adaptation, Physiological↗
PubMed1993

NAD+ binding to the Escherichia coli K(+)-uptake protein TrkA and sequence similarity between TrkA and domains of a family of dehydrogenases suggest a role for NAD+ in bacterial transport.

The nucleotide sequence of trkA, a gene encoding a surface component of the constitutive K(+)-uptake systems TrkG and TrkH from Escherichia coli, was determined. The structure of the TrkA protein deduced from the nucleotide sequence accords with the view that TrkA is peripherally bound to the inner side of the cytoplasmic membrane. Analysis by a dot matrix revealed that TrkA is composed of similar halves. The N-terminal part of each TrkA half (residues 1-130 and 234-355, respectively) is similar to the complete NAD(+)-binding domain of NAD(+)-dependent dehydrogenases. The C-terminal part of each TrkA half (residues 131-233 and 357-458, respectively) aligns with the first 100 residues of the catalytic domain of glyceraldehyde-3-phosphate dehydrogenase. Strong u.v. illumination at 252 nm led to cross-linking of NAD+ or NADH, but not of ATP to the isolated TrkA protein.

ATP-Binding Cassette Transporters↗
PubMed1993

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.

Amino Acid Sequence↗
PubMed1992

The bactericidal action of streptomycin: membrane permeabilization caused by the insertion of mistranslated proteins into the cytoplasmic membrane of Escherichia coli and subsequent caging of the antibiotic inside the cells due to degradation of these proteins.

The mechanism by which the aminoglycoside antibiotic streptomycin permeabilizes the cytoplasmic membrane of Escherichia coli cells was reinvestigated. For this purpose, the extent of streptomycin-induced K+ loss from cells growing at low external K+ concentrations was taken as a measure of membrane permeabilization. Experiments with different K(+)-uptake mutants showed that the antibiotic specifically increased the passive permeability of the cell membrane to K+ and other ions. These permeability changes were small and the membrane potential of the treated cells remained high. The membrane permeabilization was not due to a direct interaction of the antibiotic with the cell membrane, since cells that carry an rpsL mutation and synthesize proteins in a streptomycin-insensitive way did not lose K+ after the addition of the antibiotic. Due to misreading and premature termination of translation the cells synthesized aberrant proteins under the conditions where membrane permeabilization occurred. Two conditions are described under which the cells both degraded these mistranslated proteins rapidly and reaccumulated K+, lending support to the hypothesis that membrane permeabilization is due to the presence of the mistranslated proteins in the cell membrane. Evidence is presented that the irreversibility of (dihydro)streptomycin uptake by cells washed free from the antibiotic might also be due to rapid degradation of the mistranslated proteins, leading to 'caging' of the antibiotic inside the cells.

Biological Transport↗
PubMed1992

Aminoglycoside and aminocyclitol antibiotics: hygromycin B is an atypical bactericidal compound that exerts effects on cells of Escherichia coli characteristics for bacteriostatic aminocyclitols.

The effects of aminoglycoside and aminocyclitol antibiotics on intact cells of Escherichia coli were compared. The aminoglycosides streptomycin, gentamicin, kanamycin and neomycin had similar, but not identical, effects. They all caused misreading during protein synthesis, permeabilization of the cell membrane, inhibition of the initiation of DNA replication, and loss of cell viability. Cells treated with these antibiotics continued to synthesize two proteins (apparent molecular masses 72 and 60 kDa) that were not made by cells treated with the aminocyclitol hygromycin B, which did not cause misreading. Cells treated with the aminoglycosides regained their membrane tightness after residual protein synthesis in these cells had been inhibited by chloramphenicol, suggesting that under these conditions the mistranslated membrane proteins were rapidly degraded. The bacteriostatic aminocyclitols spectinomycin and kasugamycin did not cause membrane permeabilization, suggesting that these compounds do not cause misreading. Hygromycin B resembled these aminocyclitols in that it inhibited protein synthesis without causing misreading, membrane permeabilization or inhibition of initiation of DNA synthesis. However, hygromycin B also decreased cell viability. In minimal medium this lethal effect began late in comparison to the process of inhibition of protein synthesis. It is concluded that hygromycin B is an atypical bactericidal antibiotic that strongly resembles the bacteriostatic aminocyclitols spectinomycin and kasugamycin in its action.

Anti-Bacterial Agents↗