Identification of the structural proteins of an ATP-driven potassium transport system in Escherichia coli

Mixotrophy broadens the ecological niche range of the iron oxidizer Sideroxydans sp. CL21 isolated from an iron-rich peatland

Sideroxydans sp. CL21 is a microaerobic, acid-tolerant Fe(II)-oxidizer, isolated from the Schlöppnerbrunnen fen. Since the genome size of Sideroxydans sp. CL21 is 21% larger than that of the neutrophilic Sideroxydans lithotrophicus ES-1, we hypothesized that strain CL21 contains additional metabolic traits to thrive in the fen. The common genomic content of both strains contains homologs of the putative Fe(II) oxidation genes, mtoAB and cyc2. A large part of the accessory genome in strain CL21 contains genes linked to utilization of alternative electron donors, including NiFe uptake hydrogenases, and genes encoding lactate uptake and utilization proteins, motility and biofilm formation, transposable elements, and pH homeostasis mechanisms. Next, we incubated the strain in different combinations of electron donors and characterized the fen microbial communities. Sideroxydans spp. comprised 3.33% and 3.94% of the total relative abundance in the peatland soil and peatland water, respectively. Incubation results indicate Sideroxydans sp. CL21 uses H2 and thiosulfate, while lactate only enhances growth when combined with Fe, H2, or thiosulfate. Rates of H2 utilization were highest in combination with other substrates. Thus, Sideroxydans sp. CL21 is a mixotroph, growing best by simultaneously using substrate combinations, which helps to thrive in dynamic and complex habitats.

The KdpFABC complex - K+ transport against all odds

In bacteria, K⁺ is used to maintain cell volume and osmotic potential. Homeostasis normally involves a network of constitutively expressed transport systems, but in K⁺ deficient environments, the KdpFABC complex uses ATP to pump K⁺ into the cell. This complex appears to be a hybrid of two types of transporters, with KdpA descending from the superfamily of K⁺ transporters and KdpB belonging to the superfamily of P-type ATPases. Studies of enzymatic activity documented a catalytic cycle with hallmarks of classical P-type ATPases and studies of ion transport indicated that K⁺ import into the cytosol occurred in the second half of this cycle in conjunction with hydrolysis of an aspartyl phosphate intermediate. Atomic structures of the KdpFABC complex from X-ray crystallography and cryo-EM have recently revealed conformations before and after formation of this aspartyl phosphate that appear to contradict the functional studies. Specifically, structural comparisons with the archetypal P-type ATPase, SERCA, suggest that K⁺ transport occurs in the first half of the cycle, accompanying formation of the aspartyl phosphate. Further controversy has arisen regarding the path by which K⁺ crosses the membrane. The X-ray structure supports the conventional view that KdpA provides the conduit, whereas cryo-EM structures suggest that K⁺ moves from KdpA through a long, intramembrane tunnel to reach canonical ion binding sites in KdpB from which they are released to the cytosol. This review discusses evidence supporting these contradictory models and identifies key experiments needed to resolve discrepancies and produce a unified model for this fascinating mechanistic hybrid.

A Novel Regulatory Pathway for K+ Uptake in the Legume Symbiont Azorhizobium caulinodans in Which TrkJ Represses the kdpFABC Operon at High Extracellular K+ Concentrations

Bacteria have multiple K⁺ uptake systems. Escherichia coli, for example, has three types of K⁺ uptake systems, which include the low-K⁺-inducible KdpFABC system and two constitutive systems, Trk (TrkAG and TrkAH) and Kup. Azorhizobium caulinodans ORS571, a rhizobium that forms nitrogen-fixing nodules on the stems and roots of Sesbania rostrata, also has three types of K⁺ uptake systems. Through phylogenetic analysis, we found that A. caulinodans has two genes homologous to trkG and trkH, designated trkI and trkJ We also found that trkI is adjacent to trkA in the genome and these two genes are transcribed as an operon; however, trkJ is present at a distinct locus. Our results demonstrated that trkAI, trkJ, and kup were expressed in the wild-type stem nodules, whereas kdpFABC was not. Interestingly, Δkup and Δkup ΔkdpA mutants formed Fix^- nodules, while the Δkup ΔtrkA ΔtrkI ΔtrkJ mutant formed Fix⁺ nodules, suggesting that with the additional deletion of Trk system genes in the Δkup mutant, Fix⁺ nodule phenotypes were recovered. kdpFABC of the Δkup ΔtrkJ mutant was expressed in stem nodules, but not in the free-living state, under high-K⁺ conditions. However, kdpFABC of the Δkup ΔtrkA ΔtrkI ΔtrkJ mutant was highly expressed even under high-K⁺ conditions. The cytoplasmic K⁺ levels in the Δkup ΔtrkA ΔtrkI mutant, which did not express kdpFABC under high-K⁺ conditions, were markedly lower than those in the Δkup ΔtrkA ΔtrkI ΔtrkJ mutant. Taking all these results into consideration, we propose that TrkJ is involved in the repression of kdpFABC in response to high external K⁺ concentrations and that the TrkAI system is unable to function in stem nodules.IMPORTANCE K⁺ is a major cytoplasmic cation in prokaryotic and eukaryotic cells. Bacteria have multiple K⁺ uptake systems to control the cytoplasmic K⁺ levels. In many bacteria, the K⁺ uptake system KdpFABC is expressed under low-K⁺ conditions. For years, many researchers have argued over how bacteria sense K⁺ concentrations. Although KdpD of Escherichia coli is known to sense both cytoplasmic and extracellular K⁺ concentrations, the detailed mechanism of K⁺ sensing is still unclear. In this study, we propose that the transmembrane TrkJ protein of Azorhizobium caulinodans acts as a sensor for the extracellular K⁺ concentration and that high extracellular K⁺ concentrations repress the expression of KdpFABC via TrkJ.

Reconstruction of the Metabolic Potential of Acidophilic Sideroxydans Strains from the Metagenome of an Microaerophilic Enrichment Culture of Acidophilic Iron-Oxidizing Bacteria from a Pilot Plant for the Treatment of Acid Mine Drainage Reveals Metabolic Versatility and Adaptation to Life at Low pH

Bacterial community analyses of samples from a pilot plant for the treatment of acid mine drainage (AMD) from the lignite-mining district in Lusatia (East Germany) had previously demonstrated the dominance of two groups of acidophilic iron oxidizers: the novel candidate genus "Ferrovum" and a group comprising Gallionella-like strains. Since pure culture had proven difficult, previous studies have used genome analyses of co-cultures consisting of "Ferrovum" and a strain of the heterotrophic acidophile Acidiphilium in order to obtain insight into the life style of these novel bacteria. Here we report on attempts to undertake a similar study on Gallionella-like acidophiles from AMD. Isolates belonging to the family Gallionellaceae are still restricted to the microaerophilic and neutrophilic iron oxidizers Sideroxydans and Gallionella. Availability of genomic or metagenomic sequence data of acidophilic strains of these genera should, therefore, be relevant for defining adaptive strategies in pH homeostasis. This is particularly the case since complete genome sequences of the neutrophilic strains G. capsiferriformans ES-2 and S. lithotrophicus ES-1 permit the direct comparison of the metabolic capacity of neutrophilic and acidophilic members of the same genus and, thus, the detection of biochemical features that are specific to acidophilic strains to support life under acidic conditions. Isolation attempts undertaken in this study resulted in the microaerophilic enrichment culture ADE-12-1 which, based on 16S rRNA gene sequence analysis, consisted of at least three to four distinct Gallionellaceae strains that appear to be closely related to the neutrophilic iron oxidizer S. lithotrophicus ES-1. Key hypotheses inferred from the metabolic reconstruction of the metagenomic sequence data of these acidophilic Sideroxydans strains include the putative role of urea hydrolysis, formate oxidation and cyanophycin decarboxylation in pH homeostasis.

The Basics of Bacteriuria: Strategies of Microbes for Persistence in Urine

Bacteriuria, the presence of bacteria in urine, is associated with asymptomatic, as well as symptomatic, urinary tract infection (UTI). Bacteriuria underpins some of the dynamics of microbial colonization of the urinary tract, and probably impacts the progression and persistence of infection in some individuals. Recent molecular discoveries in vitro have elucidated how some key bacterial traits can enable organisms to survive and grow in human urine as a means of microbial fitness adaptation for UTI. Several microbial characteristics that confer bacteruric potential have been identified including de novo synthesis of guanine, relative resistance to D-serine, and catabolism of malic acid. Microbial characteristics such as these are increasingly being defined through the use of synthetic human urine (SHU) in vitro as a model to mimic the in vivo environment that bacteria encounter in the bladder. There is considerable variation in the SHU model systems that have been used to study bacteriuria to date, and this influences the utility of these models. In this review, we discuss recent advances in our understanding of bacteruric potential with a focus on the specific mechanisms underlying traits that promote the growth of bacteria in urine. We also review the application of SHU in research studies modeling UTI and discuss the chemical makeup, and benefits and limitations that are encountered in utilizing SHU to study bacterial growth in urine in vitro.

Signature-tagged mutagenesis and co-infection studies demonstrate the importance of P fimbriae in a murine model of urinary tract infection

Escherichia coli is the leading cause of urinary tract infections (UTIs), one of the most common infections in humans. P fimbria was arguably the first proposed virulence factor for uropathogenic E. coli, based on the capacity of E. coli isolated from UTIs to adhere to exfoliated epithelial cells in higher numbers than fecal strains of E. coli. Overwhelming epidemiologic evidence has been presented for involvement of P fimbriae in colonization. It has been difficult, however, to demonstrate this requirement for uropathogenic strains in animal models of infections or in humans. In this study, a signature-tagged mutagenesis screen identified a P-fimbrial gene (papC) and 18 other genes as being among those required for full fitness of cystitis isolate E. coli F11. A P-fimbrial mutant was outcompeted by the wild-type strain in cochallenge in the murine model of ascending UTI, and this colonization defect could be complemented with the cloned pap operon. To our knowledge, this study is the first to fulfill molecular Koch's postulates in which a pathogenic strain was attenuated by mutation of pap genes and then complemented to restore fitness, confirming P fimbria as a virulence factor in a pathogenic clinical isolate.

KdpFABC reconstituted in Escherichia coli lipid vesicles: substrate dependence of the transport rate

KdpFABC complexes were reconstituted in Escherichia coli lipid vesicles, and ion pumping was activated by addition of ATP to the external medium which corresponds to the cytoplasm under physiological conditions. ATP-driven potassium extrusion was studied in the presence of various substrates potentially influencing transport rate. The pump current was detected as a decrease of the membrane potential by the voltage-sensitive dye DiSC3(5). The results indicate that high cytoplasmic K(+) concentrations have an inhibitory effect on the KdpFABC complex. The pump current decreased to ∼25% of the maximal value at 140 mM K(+) and minimal Mg(2+)concentrations. This effect could be counteracted with increased Mg(2+) concentrations on the cytoplasmic side. This observation may be explained by the Gouy-Chapman effect of two Mg(2+) ions probably bound with a K1/2 of 0.8 mM close to the entrance of the access channel to the binding sites. This factor ensures that under physiological conditions the rate-limiting effect of K(+) release is significantly reduced. Also both ADP and inorganic phosphate are able to reduce the turnover rate of the pump by reversing the phosphorylation step (Ki of 151 μM) and the dephosphorylation step (Ki of 268 μM), respectively. In the case of the DDM-solubilized KdpFABC complex, activation energy under turnover conditions was previously found to be 55 kJ/mol, and the o-vanadate inhibition constant is shown here to be ∼1 μM, which is in agreement with values reported for other P-type ATPases. In the case of the reconstituted enzyme, however, significant differences were observed that have to be assigned to effects of the lipid bilayer environment. The activation energy was increased by a factor of 2, whereas the inhibition by o-vanadate became reduced in a way that only ∼66% of the enzyme could be inhibited and the inhibition constant was increased to a value of ∼60 μM.

Mechanistic analysis of the pump cycle of the KdpFABC P-type ATPase

The high-affinity potassium uptake system KdpFABC is a unique type Ia P-type ATPase, because it separates the sites of ATP hydrolysis and ion transport on two different subunits. KdpFABC was expressed in Escherichia coli. It was then isolated and purified to homogeneity to obtain a detergent-solubilized enzyme complex that allowed the analysis of ion binding properties. The electrogenicity and binding affinities of the ion pump for K(+) and H(+) were determined in detergent-solubilized complexes by means of the electrochromic styryl dye RH421. Half-saturating K(+) concentrations and pK values for H(+) binding could be obtained in both the unphosphorylated and phosphorylated conformations of KdpFABC. The interaction of both ions with KdpFABC was studied in detail, and the presence of independent binding sites was ascertained. It is proposed that KdpFABC reconstituted in vesicles translocates protons at a low efficiency opposite from the well-established import of K(+) into the bacteria. On the basis of our results, various mechanistic pump cycle models were derived from the general Post-Albers scheme of P-type ATPases and discussed in the framework of the experimental evidence to propose a possible molecular pump cycle for KdpFABC.

Integrated stress response of Escherichia coli to methylglyoxal: transcriptional readthrough from the nemRA operon enhances protection through increased expression of glyoxalase I

Methylglyoxal (MG) elicits activation of K⁺ efflux systems to protect cells against the toxicity of the electrophile. ChIP-chip targeting RNA polymerase, supported by a range of other biochemical measurements and mutant creation, was used to identify genes transcribed in response to MG and which complement this rapid response. The SOS DNA repair regulon is induced at cytotoxic levels of MG, even when exposure to MG is transient. Glyoxalase I alone among the core MG protective systems is induced in response to MG exposure. Increased expression is an indirect consequence of induction of the upstream nemRA operon, encoding an enzyme system that itself does not contribute to MG detoxification. Moreover, this induction, via nemRA only occurs when cells are exposed to growth inhibitory concentrations of MG. We show that the kdpFABCDE genes are induced and that this expression occurs as a result of depletion of cytoplasmic K⁺ consequent upon activation of the KefGB K⁺ efflux system. Finally, our analysis suggests that the transcriptional changes in response to MG are a culmination of the damage to DNA and proteins, but that some integrate specific functions, such as DNA repair, to augment the allosteric activation of the main protective system, KefGB.

Lipid bilayers: an essential environment for the understanding of membrane proteins

Membrane protein structure and function is critically dependent on the surrounding environment. Consequently, utilizing a membrane mimetic that adequately models the native membrane environment is essential. A range of membrane mimetics are available but none generates a better model of native aqueous, interfacial, and hydrocarbon core environments than synthetic lipid bilayers. Transmembrane α-helices are very stable in lipid bilayers because of the low water content and low dielectric environment within the bilayer hydrocarbon core that strengthens intrahelical hydrogen bonds and hinders structural rearrangements within the transmembrane helices. Recent evidence from solid-state NMR spectroscopy illustrates that transmembrane α-helices, both in peptides and full-length proteins, appear to be highly uniform based on the observation of resonance patterns in PISEMA spectra. Here, we quantitate for the first time through simulations what we mean by highly uniform structures. Indeed, helices in transmembrane peptides appear to have backbone torsion angles that are uniform within ± 4°. While individual helices can be structurally stable due to intrahelical hydrogen bonds, interhelical interactions within helical bundles can be weak and nonspecific, resulting in multiple packing arrangements. Some helical bundles have the capacity through their amino acid composition for hydrogen bonding and electrostatic interactions to stabilize the interhelical conformations and solid-state NMR data is shown here for both of these situations. Solid-state NMR spectroscopy is unique among the techniques capable of determining three-dimensional structures of proteins in that it provides the ability to characterize structurally the membrane proteins at very high resolution in liquid crystalline lipid bilayers.

A common dimerization interface in bacterial response regulators KdpE and TorR

Bacterial response regulators are key regulatory proteins that function as the final elements of so-called two-component signaling systems. The activities of response regulators in vivo are modulated by phosphorylation that results from interactions between the response regulator and its cognate histidine protein kinase. The level of response regulator phosphorylation, which is regulated by intra-or extracellular signals sensed by the histidine protein kinase, ultimately determines the output response that is initiated or carried out by the response regulator. We have recently hypothesized that in the OmpR/PhoB subfamily of response regulator transcription factors, this activation involves a common mechanism of dimerization using a set of highly conserved residues in the alpha4-beta5-alpha5 face. Here we report the X-ray crystal structures of the regulatory domains of response regulators TorR (1.8 A), Ca(2+)-bound KdpE (2.0 A), and Mg(2+)/BeF(3)(-)-bound KdpE (2.2 A), both members of the OmpR/ PhoB subfamily from Escherichia coli. Both regulatory domains form symmetric dimers in the asymmetric unit that involve the alpha4-beta5-alpha5 face. As observed previously in other OmpR/PhoB response regulators, the dimer interfaces are mediated by highly conserved residues within this subfamily. These results provide further evidence that most all response regulators of the OmpR/ PhoB subfamily share a common mechanism of activation by dimerization.

Hydrogen peroxide mediates plant root cell response to nutrient deprivation

Potassium (K(+)) is an essential nutrient required by plants in large quantities, but changes in soil concentrations may limit K(+) acquisition by roots. It is not known how plant root cells sense or signal the changes that occur after the onset of K(+) deficiency. Changes in the kinetics of Rb(+) uptake in Arabidopsis roots occur within 6 h after K(+) deprivation. Reactive oxygen species (ROS) and ethylene increased when the plants were deprived of K(+). ROS accumulated in a discrete region of roots that has been shown to be active in K(+) uptake and translocation. Suppression of an NADPH oxidase in Arabidopsis (rhd2), which is involved in ROS production, prevented the up-regulation of genes that are normally induced by K(+) deficiency, but the induction of high-affinity K(+) transport activity was unchanged. Application of H(2)O(2) restored the expression of genes induced by K(+) deficiency in rhd2 and was also sufficient to induce high-affinity K(+) transport activity in roots grown under K(+)-sufficient conditions. ROS production is an early root response to K(+) deficiency that modulates gene expression and physiological changes in the kinetics of K(+) uptake.

Regulation of potassium-dependent Kdp-ATPase expression in the nitrogen-fixing cyanobacterium Anabaena torulosa

The KdpB polypeptides in the cyanobacterium Anabaena torulosa were shown to be two membrane-bound proteins of about 78 kDa, expressed strictly under K(+) deficiency and repressed or degraded upon readdition of K(+). In both Anabaena and Escherichia coli strain MC4100, osmotic and ionic stresses caused no significant induction of steady-state KdpB levels during extreme potassium starvation.

The KdpF subunit is part of the K(+)-translocating Kdp complex of Escherichia coli and is responsible for stabilization of the complex in vitro

The kdpABC operon codes for the high affinity K(+)-translocating Kdp complex (P-type ATPase) of Escherichia coli. Upon expression of this operon in minicells, a so far unrecognized small hydrophobic polypeptide, KdpF, could be identified on high resolution SDS-polyacrylamide gels in addition to the subunits KdpA, KdpB, and KdpC. Furthermore, it could be demonstrated that KdpF remains associated with the purified complex. As determined by mass spectrometry, this peptide is present in its formylated form and has a molecular mass of 3100 Da. KdpF is not essential for growth on low K(+) (0.1 mM) medium, as shown by deletion analysis of kdpF, but proved to be indispensable for a functional enzyme complex in vitro. In the absence of KdpF, the ATPase activity of the membrane-bound Kdp complex was almost indistinguishable from that of the wild type. In contrast, the purified detergent-solubilized enzyme complex showed a dramatic decrease in enzymatic activity. However, addition of purified KdpF to the KdpABC complex restored the activity up to wild type level. It is interesting to note that the addition of high amounts of E. coli lipids had a similar effect. Although KdpF is not essential for the function of the Kdp complex in vivo, it is part of the complex and functions as a stabilizing element in vitro. The corresponding operon should now be referred to as kdpFABC.

Assembly of the Kdp complex, the multi-subunit K+-transport ATPase of Escherichia coli

Kdp, the high affinity ATP-driven K+-transport system of Escherichia coli, is a complex of the membrane-bound subunits KdpA, KdpB, KdpC and the small peptide KdpF. The assembly of this complex was studied by the analysis of mutants that expressed two of the three large subunits and inserted them into the cytoplasmic membrane. In the strains that do not express KdpC or KdpA the other two subunits did not copurify on dye-ligand affinity columns after solubilization with non-ionic detergent. In the mutant lacking KdpB the other two subunits copurified under the same conditions. It is concluded that KdpC forms strong interactions with the KdpA subunit, serving to assemble and stabilise the Kdp complex. A structure in which KdpC could be one of the connecting links between the energy-delivering subunit KdpB and the K+-transporting subunit KdpA is suggested by these data.

Properties of the P-type ATPases encoded by the copAP operons of Helicobacter pylori and Helicobacter felis

The cop operons of Helicobacter pylori and Helicobacter felis were cloned by gene library screening. Both operons contain open reading frames for a P-type ion pump (CopA) with homology to Cd2+ and Cu2+ ATPases and a putative ion binding protein (CopP), the latter representing a CopZ homolog of the copYZAB operon of Enterococcus hirae. The predicted CopA ATPases contained an N-terminal GMXCXXC ion binding motif and a membrane-associated CPC sequence. A synthetic N-terminal peptide of the H. pylori CopA ATPase bound to Cu2+ specifically, and gene disruption mutagenesis of CopA resulted in an enhanced growth sensitivity of H. pylori to Cu2+ but not to other divalent cations. As determined experimentally, H. pylori CopA contains four pairs of transmembrane segments (H1 to H8), with the ATP binding and phosphorylation domains lying between H6 and H7, as found for another putative transition metal pump of H. pylori (K. Melchers, T. Weitzenegger, A. Buhmann, W. Steinhilber, G. Sachs, and K. P. Schäfer, J. Biol. Chem. 271:446-457, 1996). The corresponding transmembrane segments of the H. felis CopA pump were identified by hydrophobicity analysis and via sequence similarity. To define functional domains, similarly oriented regions of the two enzymes were examined for sequence identity. Regions with high degrees of identity included the N-terminal Cu2+ binding domain, the regions of ATP binding and phosphorylation in the energy transduction domain, and a transport domain consisting of the last six transmembrane segments with conserved cysteines in H4, H6, and H7. The data suggest that H. pylori and H. felis employ conserved mechanisms of ATPase-dependent copper resistance.

Purification, reconstitution, and characterization of KdpD, the turgor sensor of Escherichia coli

In response to K+ availability or medium osmolality, the sensor kinase KdpD and the response regulator KdpE control the expression of the kdpFABC operon, coding for the high affinity K+-translocating Kdp ATPase of Escherichia coli. The stimulus for KdpD to undergo autophosphorylation is believed to be a change in turgor or some effect thereof, reflecting the role of K+ as an important cytoplasmic osmotic solute. The membrane-bound sensor kinase KdpD was overproduced as a fusion protein containing six contiguous histidine residues two amino acids before the C terminus. This KdpD-His6 protein was functional in vitro and in vivo. KdpD-His6 was purified from everted membrane vesicles by solubilization with the zwitterionic detergent lauryldimethylamine oxide followed by nickel chelate chromatography and ion exchange chromatography to >99% homogeneity. The solubilized protein was not active with respect to autophosphorylation, but retained the ability to bind 2-azido-ATP. KdpD-His6 was reconstituted into proteoliposomes in a unidirectional inside-out orientation as revealed by ATP accessibility and protease susceptibility. Purified and reconstituted KdpD-His6 exhibited autokinase activity, and the phosphoryl group could be transferred to KdpE. Furthermore, KdpD-His6 was found to be the only protein that mediates dephosphorylation of KdpE approximately P.

Characterization of truncated forms of the KdpD protein, the sensor kinase of the K+-translocating Kdp system of Escherichia coli

The expression of the kdpFABC operon, coding for the K+-translocating Kdp system, is controlled by the two regulatory proteins, KdpD and KdpE, which belong to the group of sensor kinase/response regulator systems. This study describes the construction and analysis of KdpD sensor kinases, in which different deletions in the N-terminal part of the protein were introduced. Truncated KdpD proteins, in which the membrane-spanning segments were deleted, had lost their phosphorylation capacity. Truncated KdpD proteins, in which the four membrane-spanning helices were untouched, were still phosphorylated, and the phosphoryl group could be transferred to the response regulator KdpE in vitro. Furthermore, these truncated KdpD proteins cause dephosphorylation of KdpE(P), which is comparable with that of the wild-type protein. To investigate the effect of the deletions on signal transduction in vivo the corresponding kdp genes were transferred to the chromosome. Growth studies with the mutant strains are in accord with the data obtained from the in vitro studies. Furthermore, kdp expression was investigated using a KdpA-LacZ fusion. The data obtained support the notion that the extent of kdp expression is modulated by the N-terminal part of KdpD.

Low-affinity potassium uptake system in the archaeon Methanobacterium thermoautotrophicum: overproduction of a 31-kilodalton membrane protein during growth on low-potassium medium

During growth on low-K+ medium (1 mM K+), Methanobacterium thermoautotrophicum accumulated K+ up to concentration gradients ([K+]intracellular/[K+]extracellular) of 25,000- to 50,000-fold. At these gradients ([K+]extracellular of < 20 microM), growth ceased but could be reinitiated by the addition of K+ or Rb+. During K+ starvation, the levels of a protein with an apparent molecular weight of 31,000 increased about sixfold. The protein was associated with the membrane and could be extracted by detergents. Cell suspensions of M. thermoautotrophicum obtained after K+-limited growth catalyzed the transport of both K+ and Rb+ with apparent Km and Vmax values of 0.13 mM and 140 nmol/min/mg, respectively, for K+ and 3.4 mM and 140 nmol/min/mg, respectively, for Rb+. Rb+ competitively inhibited K+ uptake with an inhibitor constant of about 10 mM. Membranes of K+-starved cells did not exhibit K+-stimulated ATPase activity. Immunoblotting with antisera against Escherichia coli Kdp-ATPase did not reveal any specific cross-reactivity against membrane proteins of K+-starved cells. Cells of M. thermoautotrophicum grown at a high potassium concentration (50 mM) catalyzed K+ and Rb+ transport at similar apparent Km values (0.13 mM for K+ and 3.3 mM for Rb+) but at significantly lower apparent Vmax values (about 60 nmol/min/mg for both K+ and Rb+) compared with K+-starved cells. From these data, it is concluded that the archaeon M. thermoautotrophicum contains a low-affinity K+ uptake system which is overproduced during growth on low-K+ medium.

Membrane topology analysis of the sensor kinase KdpD of Escherichia coli

The expression of the kdpFABC operon, coding for the K(+)-translocating Kdp-ATPase, is under the control of the two regulatory proteins KdpD and KdpE, which belong to the group of sensor kinase/response regulator systems. The topology of the KdpD protein in the cytoplasmic membrane was investigated using LacZ and PhoA fusions at different sites within the polypeptide chain and by treating spheroplasts in the presence or absence of Triton X-100 with the protease kallikrein. The results revealed that KdpD has four membrane-spanning segments in the middle of the polypeptide chain, whereas N and C terminus are both cytoplasmic.

Genetic evidence for two sequentially occupied K+ binding sites in the Kdp transport ATPase

Substrate binding sites in Kdp, a P-type ATPase of Escherichia coli, were identified by the isolation and characterization of mutants with reduced affinity for K+, its cation substrate. Most of the mutants have an altered KdpA subunit, a hydrophobic subunit not found in other P-type ATPases. Topological analysis of KdpA and the locations of the residues changed in the mutants suggest that KdpA has 10 membrane-spanning segments and forms two separate and distinct sites where K+ is bound. One site is formed by three periplasmic loops of the protein and is inferred to be the site of initial binding. The other site is cytoplasmic. We believe K+ moves from the periplasmic site through the membrane to the cytoplasmic site where it becomes "occluded," i.e. inexchangeable with K+ outside the membrane. Membrane-spanning parts of KdpA probably form the path for transmembrane movement of K+. The kinetics of cation transport in the mutants indicate that each of the two binding sites contributes to the observed Km for cations as well as to the marked discrimination between K+ and Rb+ characteristic of wild-type Kdp. Energy coupling in Kdp, mediated by the KdpB subunit, is performed by a different subunit from the one that mediates transport.

Characterization of the KdpD protein, the sensor kinase of the K(+)-translocating Kdp system of Escherichia coli

KdpD and KdpE, proteins that control expression of the kdpFABC operon, are members of the class of sensor kinase/response regulator proteins. Using polyclonal antibodies raised against the KdpD protein, we have been able to identify and to localize the chromosome-encoded KdpD protein in the cytoplasmic membrane of Escherichia coli. Furthermore, it has been possible to detect differences in the expression of the KdpD protein according to the K+ concentration in the growth medium. The phosphorylation capacity of the plasmid-encoded KdpD protein and the phospho-transfer to KdpE was investigated. We found that both reactions were strictly dependent on the ionic conditions of the assay medium. Based on optimized conditions, we were able to detect phosphorylation of the chromosome-encoded KdpD protein. Furthermore, replacement of the conserved histidine (His673), the predicted phosphorylation site in KdpD, by glutamine revealed that phosphorylation of KdpD was no longer possible.

The products of the kdpDE operon are required for expression of the Kdp ATPase of Escherichia coli

The expression of the Kdp system for K+ uptake in Escherichia coli requires the products of two genes, kdpD and kdpE. These genes constitute an operon adjacent to the kdpABC operon that encodes the three membrane protein subunits of Kdp. Both operons are transcribed in the same direction and overlap; the kdpDE promoter is in kdpC, the last gene of the kdpABC operon. Transcription of the kdpDE operon is at a low level when Kdp is not expressed; transcription increases about 10-fold when kdpABC is turned on, indicating significant read-through of the kdpDE operon by transcripts beginning at the promoter of kdpABC operon. The proximal region of the kdpD gene is the site of most mutations that lead to constitutive expression of the kdpABC operon.

TRK2 is required for low affinity K+ transport in Saccharomyces cerevisiae

TRK1, the gene encoding the high affinity K+ transporter in Saccharomyces cerevisiae, is nonessential due to the existence of a functionally independent low affinity transporter. To identify the gene(s) encoding the low affinity K+ transporter, we screened trk1 delta cells for mutants (Kla-) that require higher concentrations of K+ in the medium to support growth. trk1 delta trk2 mutants require up to tenfold higher concentrations of K+ to exhibit normal growth compared to trk1 delta TRK2 cells. K+ and 86Rb+ transport assays demonstrate that the mutant phenotype is due to defective K+ transport (uptake). Each of 38 independent mutants contains a mutation in the same gene, TRK2. Cells deficient for both high and low affinity K+ transport (trk1 delta trk2) exhibit hypersensitivity to low extracellular pH that can be suppressed by high concentrations of K+ but not Na+. TRK1 completely suppresses both the K+ transport defect and low pH hypersensitivity of trk2 cells, suggesting that TRK1 and TRK2 are functionally independent.

Transmembrane segments of the P-type cation-transporting ATPases. A comparative study

The transmembrane segments predicted for the Neurospora H-ATPase are laid out diagrammatically in Figure 10. Although the eight segments have arbitrarily been compressed into rectangles of the same size, they range in length from 20 residues (II) to 30 residues (IV and VI), so the corresponding helices must vary in length as well. Notable features of the model include the charged residues located just outside the plane of the membrane, with a clear excess of negative charges (5-, 1+) at the extracellular surface and a slight excess of positive charges (4+, 3-) at the cytoplasmic surface. There are also a conspicuous number of bulky residues (tryptophan, phenylalanine, and tyrosine) just inside the plane of the membrane. Within the bilayer, most of the helices are noticeably amphipathic, consistent with the expectation that at least some of them stack together to form a channel-like structure with a hydrophobic surface and a hydrophilic core. The charged residues predicted to lie within the membrane are listed in Table 2, which is a summary of data from eight of the P-type ATPases; the S. cerevisiae and S. pombe enzymes have not been included because they are nearly identical in this respect to the Neurospora enzyme. Interestingly, all of the ATPases have more membrane-embedded negative charges (5 to 8) than positive ones (0 to 4), a pattern that may be connected with their role as cation transporters. Certainly, other unrelated transport proteins have a rather different pattern of positive and negative charges: for example, the mammalian glucose transporter (1+, 2-), Na-glucose transporter (3+, 3-), and the E. coli lac permease (11+, 7-). The actual positioning of the negative charges in the P-type ATPases does not make it easy to single out the functionally important ones, however. The glutamyl residue in segment I is present in the fungal, plant, and Leishmania H-ATPases but not in the gastric H,K-ATPase. The same is true for the aspartate in segment II, except that it also appears in the muscle and brain Ca-ATPases. A glutamate is found at one end of segment III in the E. coli and fungal enzymes and at the other end in Arabidopsis; in segment IV, another glutamate appears in a well-conserved region in the Leishmania and mammalian enzymes but not in the bacterial, fungal, or plant ones.(ABSTRACT TRUNCATED AT 400 WORDS)

The high-affinity K+-translocating ATPase complex from Bacillus acidocaldarius consists of three subunits

Cells of the thermoacidophilic bacterium Bacillus acidocaldarius express a high-affinity K+-uptake system when grown at low external K+. A vanadate-sensitive, K+- and Mg2+-stimulated ATPase was partially purified from membranes of these cells by solubilization with a non-ionic detergent followed by ion-exchange chromatography of the extract. Combinations of non-denaturing and denaturing electrophoretic separation methods revealed that the ATPase complex consisted of three subunits with molecular weights almost identical to those of the KdpA, B and C proteins, which together form the Kdp high-affinity, K+-translocating ATPase complex of Escherichia coli. The affinity of the partially purified ATPase from B. acidocaldarius for its substrates K+ (Km 2-3 microM) and ATP (Km 80 microM), its stimulation by various divalent cations, and its inhibition by vanadate (Ki 1-2 microM), bafilomycin A1 (Ki 20 microM), DCCD (Ki 200 microM) or Ca2+ were also similar to those of the E. coli enzyme, indicating that the two K+-translocating ATPases have almost identical properties.

Rhizobium meliloti fixGHI sequence predicts involvement of a specific cation pump in symbiotic nitrogen fixation

We present genetic and structural analyses of a fix operon conserved among rhizobia, fixGHI from Rhizobium meliloti. The nucleotide sequence of the operon suggests it may contain a fourth gene, fixS. Adjacent open reading frames of this operon showed an overlap between TGA stop codons and ATG start codons in the form of an ATGA motif suggestive of translational coupling. All four predicted gene products contained probable transmembrane sequences. FixG contained two cysteine clusters typical of iron-sulfur centers and is predicted to be involved in a redox process. FixI was found to be homologous with P-type ATPases, particularly with K+ pumps from Escherichia coli and Streptococcus faecalis but also with eucaryotic Ca2+, Na+/K+, H+/K+, and H+ pumps, which implies that FixI is a pump of a specific cation involved in symbiotic nitrogen fixation. Since prototrophic growth of fixI mutants appeared to be unimpaired, the predicted FixI cation pump probably has a specifically symbiotic function. We suggest that the four proteins FixG, FixH, FixI, and FixS may participate in a membrane-bound complex coupling the FixI cation pump with a redox process catalyzed by FixG.

The K+-translocating Kdp-ATPase from Escherichia coli. Purification, enzymatic properties and production of complex- and subunit-specific antisera

The Kdp system from Escherichia coli is a derepressible high-affinity K+-uptake ATPase. Its membrane-bound ATPase activity was approximately 50 mumol g-1 min-1. The Kdp-ATPase complex was purified from everted vesicles by solubilization with the nonionic detergent Aminoxid WS 35 followed by DEAE-Sepharose CL-6B chromatography at pH 7.5 and pH 6.4 and gel filtration on Fractogel TSK HW-65. The overall yield of activity was 6.5% and the purity at least 90%. The isolated KdpABC complex had a high affinity for its substrates K+ (Km app. = 10 microM) and Mg2+-ATP (Km = 80 microM) and a narrow substrate specificity. The ATPase activity was inhibited by vanadate (Ki = 1.5 microM), fluorescein isothiocyanate (Ki = 3.5 microM), N,N'-dicyclohexylcarbodiimide (Ki = 60 microM) and N-ethylmaleimide (Ki = 0.1 mM). The purification protocol was likewise applicable to the isolation of a KdpA mutant ATPase which in contrast to the wild-type enzyme exhibited an increased Km value for K+ of 6 mM and a 10-fold lowered sensitivity for vanadate. Starting from the purified Kdp complex the single subunits were obtained by gel filtration on Bio-Gel P-100 in the presence of SDS. Both the native Kdp-ATPase and the SDS-denatured polypeptides were used to raise polyclonal antibodies. The specificity of the antisera was established by immunoblot analysis. In functional inhibition studies the anti-KdpABC and anti-KdpB sera impaired ATPase activity in the membrane-bound as well as in the purified state of the enzyme. In contrast, the anti-KdpC serum did not inhibit enzyme activity.

Dimethylthetin can substitute for glycine betaine as an osmoprotectant molecule for Escherichia coli

Glycine betaine is believed to be the most active naturally occurring osmoprotectant molecule for Escherichia coli and other bacteria. It is a dipolar ion possessing a quaternary ammonimum group and a carboxylic acid group. To examine the molecular requirements for osmoprotective activity, dimethylthetin was compared with glycine betaine. Dimethylthetin is identical to glycine betaine except for substitution of dimethyl sulfonium for the quaternary nitrogen group. Dimethylthetin was found to be about equally as effective as glycine betaine in permitting E. coli to grow in hypertonic NaCl, and both compounds were recovered almost completely from bacterial cells grown in the presence of hypertonic NaCl. 3-Dimethylsulfonioproprionate, an analog of dimethylthetin observed in marine algae, and 3-Dimethylsulfonio-2-methylproprionate were found to be less active. Dimethylthetin may prove useful as a molecular probe to study betaine metabolism and as a model for the development of antibacterial agents.

Dimethylthetin can substitute for glycine betaine as an osmoprotectant molecule for Escherichia coli

Glycine betaine is believed to be the most active naturally occurring osmoprotectant molecule for Escherichia coli and other bacteria. It is a dipolar ion possessing a quaternary ammonimum group and a carboxylic acid group. To examine the molecular requirements for osmoprotective activity, dimethylthetin was compared with glycine betaine. Dimethylthetin is identical to glycine betaine except for substitution of dimethyl sulfonium for the quaternary nitrogen group. Dimethylthetin was found to be about equally as effective as glycine betaine in permitting E. coli to grow in hypertonic NaCl, and both compounds were recovered almost completely from bacterial cells grown in the presence of hypertonic NaCl. 3-Dimethylsulfonioproprionate, an analog of dimethylthetin observed in marine algae, and 3-Dimethylsulfonio-2-methylproprionate were found to be less active. Dimethylthetin may prove useful as a molecular probe to study betaine metabolism and as a model for the development of antibacterial agents.

Isolation of glycine betaine and proline betaine from human urine. Assessment of their role as osmoprotective agents for bacteria and the kidney

Human urine is osmoprotective for enteric bacteria, permitting E. coli to grow with high concentrations of NaCl and other salts and even higher concentrations of sucrose and mannitol but not urea. The active material in urine is soluble in methanol and is precipitated by ammonium reineckate at acid pH. Using gel filtration and high-pressure liquid chromatography, we have identified two major osmoprotective compounds in urine. One is glycine betaine; the other is proline betaine as demonstrated by nuclear magnetic resonance, mass spectrum scanning, and chemical synthesis. Proline betaine has not been described previously to our knowledge in vertebrate tissues. It is known to be a cell volume-regulating agent for marine red algae and the euryhaline mollusk Elysia chloritica. We suggest that the presence of glycine and proline betaines in human urine may reflect an osmoprotective role for the kidney and that they protect bacteria in the urine only fortuitously.

Sequence homology between two membrane transport ATPases, the Kdp-ATPase of Escherichia coli and the Ca2+-ATPase of sarcoplasmic reticulum

We have determined the DNA sequences of the genes encoding the three structural proteins of the Kdp-ATPase, an ATP-driven potassium transport system of Escherichia coli. Regions of the predicted amino acid sequence of KdpB, the phosphorylated protein of the system, are homologous to regions of the Ca2+-ATPase of rabbit sarcoplasmic reticulum. The phosphorylated aspartate residue of the latter is within a region of homology.

Energy coupling to ATP synthesis by the proton-translocating ATPase

This review summarizes recent work on energy coupling to ATP synthesis by the reversible, proton-translocating ATPase to mitochondria, chloroplasts, and bacteria. In the first sections, this enzyme is distinguished from other ATP-linked ion transport systems, and progress in the biochemical analysis is discussed. There is at present a reasonably consistent idea of the overall structure of the enzyme, and one can begin to assign specific functional roles to individual subunits of the complex. The latter half of the review deals with mechanisms of energy coupling, about which there is clear divergence of opinion. An "indirect coupling" model would allow for the possibility that H+ translocation transmits energy for ATP synthesis by driving the enzyme through a sequence of conformational states, so that H+ translocated need not take part in the chemistry of ATP synthesis. By contrast, a "direct coupling" mechanism would specify that H+ translocated must participate in the chemical reaction by combining with oxygen must participate in the chemical reaction by combining with oxygen from phosphate during the synthetic step. Such discussion is preceded by an outlined of the "proton well," since this idea forms the basis of one direct coupling model. In addition, it is suggested that the idea of a proton (ion) well may be of more general significance to the analysis of ion-coupled transport, because it includes the postulate that mechanistically significant ion binding can occur within the profile of the electric field. A proton (ion) well can be derived from both kinetic and equilibrium treatments, and from mechanistic considerations in fields as distinct as biochemistry and neurophysiology. As a result, it illustrates how further advances in formulating mechanisms of energy coupling might profit by a merger of technique and perspective from areas that have as a common goal an understanding of how large proteins catalyze movements of small molecules across a membrane.

Energetics of plasmid-mediated arsenate resistance in Escherichia coli

Plasmid R773, which codes for resistances to arsenate, arsenite, and antimony, was introduced into Escherichia coli strain AN120, a mutant deficient in the H+-translocating ATPase of oxidative phosphorylation. Cultures depleted of endogenous energy reserves were loaded with 74AsO3-4, and arsenate efflux was measured after dilution into medium containing various energy sources and inhibitors. Rapid extrusion of arsenate occurred when glucose was added. Arsenate was extruded both against and down a concentration gradient. In this strain glucose allows formation of both ATP via substrate-level phosphorylation and an electrochemical proton gradient (or protonmotive force) via oxidation of the products of glycolysis. When oxidation was inhibited by cyanide, glucose metabolism still produced arsenate efflux. Energy sources such as succinate, which supplies a protonmotive force but not ATP, did not result in efflux. Measurement of intracellular ATP concentration under each set of conditions demonstrated a direct correlation between the rate of efflux and ATP levels. Osmotically shocked cells lost the ability to extrude arsenate; however, no arsenate-binding activity was detected in osmotic shock fluid from induced cells. These results suggest that the arsenate efflux system is coupled to cellular ATP rather than an electrochemical proton gradient, possibly by an arsenate-translocating ATPase.

The use of gene fusions of study bacterial transport proteins

The transport of solutes by bacteria has been studied for about thirty years. Early experiments on amino acid entry and galactoside accumulation provided concrete evidence that bacteria possessed specific transport systems and that these were subject to regulation. Since than a large number of transport systems have been discovered and studied extensively. Many of these use entirely different strategies for capturing or accumulating substrates. This diversity reflects variation in the availability of nutrients an ions in the different environments tolerated and inhabited by microorganisms. Examination of a few bacterial transport systems provides an opportunity to gain insight into a wide range of topics in the area of membrane transport. These include: the identification of carrier proteins and their arrangement in the membrane, the regulation of transport protein synthesis by environmental factors, and the localization of transport proteins to their extracytoplasmic destinations. It has been possible to construct a number of bacterial strains in which the gene (lacZ) which codes for the cytoplasmic enzyme beta-galactosidase is fused to genes which code for transport proteins. The following article is intended to illustrate how these gene fusions have been used to study the regulation and structure of transport proteins in Escherichia coli.