The sensor kinase KdpD of Escherichia coli senses external K+

The Kdp system of Escherichia coli is composed of the high‐affinity K⁺ transporter KdpFABC and the two regulatory proteins KdpD (sensor kinase) and KdpE (response regulator), which constitute a typical two‐component system. The kdpFABC operon is induced under K⁺‐limiting conditions and, to a lesser extent, under high osmolality in the medium. In search for the stimulus sensed by KdpD, we studied the inhibitory effect of extracellular K⁺ on the Kdp system at pH 6.0, which is masked by unspecific K⁺ transport at higher pH values. Based on KdpD derivatives carrying single aspartate replacements in the periplasmic loops which are part of the input domain, we concluded that the inhibition of the Kdp system at extracellular K⁺ concentrations above 5 mM is mediated via KdpD/KdpE and not due to inhibition of the K⁺‐transporting KdpFABC complex. Furthermore, time‐course analyses of kdpFABC expression revealed that a decline in the extracellular K⁺ concentration efficiently stimulates KdpD/KdpE‐mediated signal transduction. In this report we provide evidence that the extracellular K⁺ concentration serves as one of the stimuli sensed by KdpD.     

The Universal Stress Protein UspC Scaffolds the KdpD/KdpE Signaling Cascade of Escherichia coli under Salt Stress

The sensor kinase KdpD and the response regulator KdpE control induction of the kdpFABC operon encoding the high-affinity K⁺-transport system KdpFABC in response to K⁺ limitation or salt stress. Under K⁺ limiting conditions the Kdp system restores the intracellular K⁺ concentration, while in response to salt stress K⁺ is accumulated far above the normal content. The kinase activity of KdpD is inhibited at high concentrations of K⁺, so it has been puzzling how the sensor can be activated in response to salt stress. Here, we demonstrate that the universal stress protein UspC acts as a scaffolding protein of the KdpD/KdpE signaling cascade by interacting with a Usp domain in KdpD of the UspA subfamily under salt stress. Escherichia coli encodes three single domain proteins of this subfamily, UspA, UspC, and UspD, whose expression is up-regulated under various stress conditions. Among these proteins only UspC stimulated the in vitro reconstructed signaling cascade (KdpD→KdpE→DNA) resulting in phosphorylation of KdpE at a K⁺ concentration that would otherwise almost prevent phosphorylation. In agreement, in a ΔuspC mutant KdpFABC production was down-regulated significantly when cells were exposed to salt stress, but unchanged under K⁺ limitation. Biochemical studies revealed that UspC interacts specifically with the Usp domain in the stimulus perceiving N-terminal domain of KdpD. Furthermore, UspC stabilized the KdpD/KdpE∼P/DNA complex and is therefore believed to act as a scaffolding protein. This study describes the stimulation of a bacterial two-component system under distinct stress conditions by a scaffolding protein, and highlights a new role of the universal stress proteins.     

Domain swapping reveals that the N-terminal domain of the sensor kinase KdpD in Escherichia coli is important for signaling

Background  

The KdpD/KdpE two-component system of Escherichia coli regulates expression of the kdpFABC operon encoding the high affinity K⁺ transport system KdpFABC. The input domain of KdpD comprises a domain that belongs to the family of universal stress proteins (Usp). It has been previously demonstrated that UspC binds to this domain, resulting in KdpD/KdpE scaffolding under salt stress. However the mechanistic significance of this domain for signaling remains unclear. Here, we employed a "domain swapping" approach to replace the KdpD-Usp domain with four homologous domains or with the six soluble Usp proteins of E. coli.     

Negatively charged phospholipids influence the activity of the sensor kinase KdpD of Escherichia coli

Synthesis of the high-affinity K⁺-translocating Kdp-ATPase of Escherichia coli, encoded by the kdpFABC operon, is regulated by the membrane-bound sensor kinase KdpD and the soluble response regulator KdpE. K⁺ limitation or a sudden increase in osmolarity induces the expression of kdpFABC. Due to the importance of K⁺ to maintain turgor, it has been proposed that KdpD is a turgor sensor. Although the primary stimulus that KdpD senses is unknown, alterations in membrane strain or the interaction between KdpD and membrane components might be good candidates. Here, we report a study of the influence of the membrane phospholipid composition on the function of KdpD in vivo and in vitro using various E. coli mutants defective in phospholipid biosynthesis. Surprisingly, neither the lack of the major E. coli phospholipid phosphatidylethanolamine nor the drastic reduction of the phosphatidylglycerol/cardiolipin content influenced induction of kdpFABC expression significantly. However, in vitro reconstitution experiments with synthetic phospholipids clearly demonstrated that KdpD kinase activity is dependent on negatively charged phospholipids, whereas the structure of the phospholipids plays a minor role. These results indicate that electrostatic interactions are important for the activity of KdpD. Received: 29 March 1999 / Accepted: 26 July 1999     

Signal transduction between the two regulatory components involved in the regulation of the kdpABC operon in Escherichia coli: Phosphorylation-dependent functioning of the positive regulator, KdpE

The proteins KdpD and KdpE are crucial to the osmotic regulation of the kdpABC operon that is responsible for the high-affinity K⁺ ion transport system in Escherichia coli. We demonstrated previously that the response regulator, KdpE, is capable of undergoing Phosphorylation mediated by the sensory protein kinase, KdpD. In this study, we obtained biochemical evidence supporting the view that when KdpE is phosphorylated, it takes on an active form that exhibits relatively high affinity for the kdpABC promoter, which in turn results in activation of the kdpABC operon. It was also suggested that the central hydrophobic domain of KdpD, which is conceivably responsible for membrane anchoring of this protein, plays a role in the signalling mechanism underlying KdpE Phosphorylation in response to hyperosmotic stress.     

Expression of the Kdp ATPase Is Consistent with Regulation by Turgor Pressure

The kdpFABC operon of Escherichia coli encodes the four protein subunits of the Kdp K⁺ transport system. Kdp is expressed when growth is limited by the availability of K⁺. Expression of Kdp is dependent on the products of the adjacent kdpDE operon, which encodes a pair of two-component regulators. Studies with kdp-lac fusions led to the suggestion that change in turgor pressure acts as the signal to express Kdp (L. A. Laimins, D. B. Rhoads, and W. Epstein, Proc. Natl. Acad. Sci. USA 78:464–468, 1981). More recently, effects of compatible solutes, among others, have been interpreted as inconsistent with the turgor model (H. Asha and J. Gowrishankar, J. Bacteriol. 175:4528–4537, 1993). We re-examined the effects of compatible solutes and of medium pH on expression of Kdp in studies in which growth rate was also measured. In all cases, Kdp expression correlated with the K⁺ concentration when growth began to slow. Making the reasonable but currently untestable assumptions that the reduction in growth rate by K⁺ limitation is due to a reduction in turgor and that addition of betaine does not increase turgor, we concluded that all of the data on Kdp expression are consistent with control by turgor pressure.     

The KdpD/KdpE Two-Component System: Integrating K+ Homeostasis and Virulence

The two-component system (TCS) KdpD/KdpE, extensively studied for its regulatory role in potassium (K⁺) transport, has more recently been identified as an adaptive regulator involved in the virulence and intracellular survival of pathogenic bacteria, including Staphylococcus aureus, entero-haemorrhagic Escherichia coli, Salmonella typhimurium, Yersinia pestis, Francisella species, Photorhabdus asymbiotica, and mycobacteria. Key homeostasis requirements monitored by KdpD/KdpE and other TCSs such as PhoP/PhoQ are critical to survival in the stressful conditions encountered by pathogens during host interactions. It follows these TCSs may therefore acquire adaptive roles in response to selective pressures associated with adopting a pathogenic lifestyle. Given the central role of K⁺ in virulence, we propose that KdpD/KdpE, as a regulator of a high-affinity K⁺ pump, has evolved virulence-related regulatory functions. In support of this hypothesis, we review the role of KdpD/KdpE in bacterial infection and summarize evidence that (i) KdpD/KdpE production is correlated with enhanced virulence and survival, (ii) KdpE regulates a range of virulence loci through direct promoter binding, and (iii) KdpD/KdpE regulation responds to virulence-related conditions including phagocytosis, exposure to microbicides, quorum sensing signals, and host hormones. Furthermore, antimicrobial stress, osmotic stress, and oxidative stress are associated with KdpD/KdpE activity, and the system''s accessory components (which allow TCS fine-tuning or crosstalk) provide links to stress response pathways. KdpD/KdpE therefore appears to be an important adaptive TCS employed during host infection, promoting bacterial virulence and survival through mechanisms both related to and distinct from its conserved role in K⁺ regulation.     

Towards an understanding of the molecular mechanisms of stimulus perception and signal transduction by the KdpD/KdpE system of Escherichia coli

The membrane-bound histidine kinase KdpD is a putative turgor sensor that regulates, together with the response regulator KdpE, expression of the kdpFABC operon. This operon encodes the high affinity K+-uptake system KdpFABC of Escherichia coli. Expression of kdpFABC is induced under K+ limiting growth conditions and in response to an osmotic upshift. Various structural features of KdpD and KdpE, which are important for stimulus perception and/or signal transduction were identified and are described here. Furthermore, various studies undertaken to elucidate the nature of the stimulus for KdpD result in a new model for KdpD stimulus perception. According to this, autophosphorylation activity of KdpD is not a result of changes in turgor per se. Instead, various--mainly intracellular parameters--that are related to changes of environmental conditions influence the activities of KdpD.     

Three-dimensional structure of the KdpFABC complex of Escherichia coli by electron tomography of two-dimensional crystals

The KdpFABC complex (Kdp) functions as a K⁺ pump in Escherichia coli and is a member of the family of P-type ATPases. Unlike other family members, Kdp has a unique oligomeric composition and is notable for segregating K⁺ transport and ATP hydrolysis onto separate subunits (KdpA and KdpB, respectively). We have produced two-dimensional crystals of the KdpFABC complex within reconstituted lipid bilayers and determined its three-dimensional structure from negatively stained samples using a combination of electron tomography and real-space averaging. The resulting map is at a resolution of 2.4 nm and reveals a dimer of Kdp molecules as the asymmetric unit; however, only the cytoplasmic domains are visible due to the lack of stain penetration within the lipid bilayer. The sizes of these cytoplasmic domains are consistent with Kdp and, using a pseudo-atomic model, we have described the subunit interactions that stabilize the Kdp dimer within the larger crystallographic array. These results illustrate the utility of electron tomography in structure determination of ordered assemblies, especially when disorder is severe enough to hamper conventional crystallographic analysis.     

The N-terminal input domain of the sensor kinase KdpD of Escherichia coli stabilizes the interaction between the cognate response regulator KdpE and the corresponding DNA-binding site

The sensor kinase/response regulator system KdpD/KdpE of Escherichia coli regulates expression of the kdpFABC operon, which encodes the high affinity K+ transport system KdpFABC. The membrane-bound sensor kinase KdpD consists of an N-terminal input domain (comprising a large cytoplasmic domain and four transmembrane domains) and a cytoplasmic C-terminal transmitter domain. Here we show that the cytoplasmic N-terminal domain of KdpD (KdpD/1-395) alone supports semi-constitutive kdpFABC expression, which becomes dependent on the extracellular K+ concentration under K+-limiting growth conditions. However, it should be noted that the non-phosphorylatable derivative KdpD/H673Q or the absence of KdpD abolishes kdpFABC expression completely. KdpD/1-395 mediated kdpFABC expression requires the corresponding response regulator KdpE with an intact phosphorylation site. Experiments with an Escherichia coli mutant unable to synthesize acetyl phosphate as well as transposon mutagenesis suggest that KdpE is phosphorylated in vivo by low molecular weight phosphodonors in the absence of the full-length sensor kinase. Various biochemical approaches provide first evidence that kdpFABC expression mediated by KdpD/1-395 is due to a stabilizing effect of this domain on the binding of KdpE approximately P to its corresponding DNA-binding site. Such a stabilizing effect of a sensor kinase domain on the DNA-protein interaction of the cognate response regulator has never been observed before for any other sensor kinase. It describes a new mechanism in bacterial two-component signal transduction.     

Structure-function studies of DNA binding domain of response regulator KdpE reveals equal affinity interactions at DNA half-sites

Expression of KdpFABC, a K⁺ pump that restores osmotic balance, is controlled by binding of the response regulator KdpE to a specific DNA sequence (kdpFABC_BS) via the winged helix-turn-helix type DNA binding domain (KdpE_DBD). Exploration of E. coli KdpE_DBD and kdpFABC_BS interaction resulted in the identification of two conserved, AT-rich 6 bp direct repeats that form half-sites. Despite binding to these half-sites, KdpE_DBD was incapable of promoting gene expression in vivo. Structure-function studies guided by our 2.5 Å X-ray structure of KdpE_DBD revealed the importance of residues R193 and R200 in the α-8 DNA recognition helix and T215 in the wing region for DNA binding. Mutation of these residues renders KdpE incapable of inducing expression of the kdpFABC operon. Detailed biophysical analysis of interactions using analytical ultracentrifugation revealed a 2∶1 stoichiometry of protein to DNA with dissociation constants of 200±100 and 350±100 nM at half-sites. Inactivation of one half-site does not influence binding at the other, indicating that KdpE_DBD binds independently to the half-sites with approximately equal affinity and no discernable cooperativity. To our knowledge, these data are the first to describe in quantitative terms the binding at half-sites under equilibrium conditions for a member of the ubiquitous OmpR/PhoB family of proteins.     

Analysis of two-component signal transduction by mathematical modeling using the KdpD/KdpE system of Escherichia coli

A mathematical model for the KdpD/KdpE two-component system is presented and its dynamical behavior is analyzed. KdpD and KdpE regulate expression of the kdpFABC operon encoding the high affinity K+ uptake system KdpFABC of Escherichia coli. The model is validated in a two step procedure: (i) the elements of the signal transduction part are reconstructed in vitro. Experiments with the purified sensor kinase and response regulator in presence or absence of DNA fragments comprising the response regulator binding-site are performed. (ii) The mRNA and molecule number of KdpFABC are determined in vivo at various extracellular K+ concentrations. Based on the identified parameters for the in vitro system it is shown, that different time hierarchies appear which are used for model reduction. Then the model is transformed in such a way that a singular perturbation problem is formulated. The analysis of the in vivo system shows that the model can be separated into two parts (submodels which are called functional units) that are connected only in a unidirectional way. Hereby one submodel represents signal transduction while the second submodel describes the gene expression.     

KdpD and KdpE, proteins that control expression of the kdpABC operon, are members of the two-component sensor-effector class of regulators.

The Kdp system of Escherichia coli, a transport ATPase with high affinity for potassium, is expressed when turgor pressure is low. Expression requires KdpD, a 99-kDa membrane protein, and KdpE, a 25-kDa soluble cytoplasmic protein. The sequences of KdpD and KdpE show they are members of the sensor-effector class of regulatory proteins: the C-terminal half of KdpD is homologous to sensors such as EnvZ and PhoR, and KdpE is homologous to effectors such as OmpR and PhoB. The predicted structure of KdpD suggests that it is anchored to the membrane by four membrane-spanning segments near its middle, with both C- and N-terminal portions in the cytoplasm. Subcellular fractionation confirms the expected location of the protein in the inner membrane. The N-terminal region has no homology to known proteins and is the site of mutations that make Kdp expression partially constitutive; this portion may serve to sense turgor pressure. Since several other sensor-effectors have been shown to mediate control through phosphorylation, this mechanism is proposed to control expression of Kdp.     

Modulation of KdpD phosphatase implicated in the physiological expression of the kdp ATPase of Escherichia coli

The KdpD sensor kinase and the KdpE response regulator control the expression of the kdpFABC operon, encoding the KdpFABC high-affinity K+ transport system of Escherichia coli. Low turgor pressure has been postulated to be the environmental stimulus to express KdpFABC. KdpD has autokinase, phosphotransferase and, like many sensor kinases, response regulator (phospho-KdpE) specific phosphatase activity. To determine which of these activities are altered in response to the environmental stimulus, we isolated and analysed six kdpD mutants that cause constitutive expression of KdpFABC. In three of the mutants, phosphatase activity was undetectable and, in two, phosphatase was reduced. Kinase activity was unaffected in four of the mutants, but elevated in one. In one mutant, a pseudorevertant of a kdpD null mutation, kinase and phosphatase were both reduced to 20% of the wild-type level. These findings suggest that initiation of signal transduction by KdpD is mediated by the inhibition of the phospho-KdpE-specific phosphatase activity of KdpD, leading to an accumulation of phospho-KdpE, which in turn activates the expression of the KdpFABC system. The data also suggest that levels of activity in vitro may differ from what occurs in vivo, because in vitro conditions cannot replicate those in vivo.     

Signal-sensing mechanisms of the putative osmosensor KdpD in Escherichia coli

The KdpD protein is a membrane-located sensory kinase (or signal transducer) critically involved in the regulation of the kdpABC operon that is responsible for a high-affinity transport system in Escherichia coli. In this study, a set of KdpD mutants, each resulting in a single amino acid substitution around the membrane-spanning regions of KdpD, was isolated. Amino acid substitutions in these KdpD mutants were located non-randomly, particularly within the C-terminal half of the membrane-spanning regions. This set of KdpD mutants exhibited altered transmembrane-signalling properties in response to external K⁺ and other stimuli. In particular, these mutants were found to be insensitive, if not completely, to the K⁺ signal. However, they were able to respond to other stimuli such as high-salt stress, as in the wild type. Therefore, in contrast to the wild type, the cells carrying these mutations exhibited high levels of the steady-state expression of kdp, regardless of external K⁺, provided that high concentrations of ionic solutes were supplemented to the cultures. More interestingly, the set of KdpD mutants could also respond to high concentrations of external non-ionic solutes such as sucrose and D-arabinose, thereby increasing substantially the steady-state expression of kdp in response to the medium osmolarity. Furthermore, it was found that certain chemicals, ethanol, chlorpromazine and procaine, could function as effectors for the KdpD mutants at relatively low concentrations in the media. Based on these findings, we have examined the primary signal(s) that regulates the function of KdpD. We propose here that KdpD can be considered to be an environmental sensor that exhibits sensing mechanisms in response to both the level of K⁺ and the physico-chemical state of the cytoplasmic membrane.     

Amino acid replacements in transmembrane domain 1 influence osmosensing but not K<Superscript>+</Superscript> sensing by the sensor kinase KdpD of <Emphasis Type="Italic">Escherichia coli</Emphasis>

Expression of the kdpFABC operon coding for the high affinity K+ -translocating KdpFABC complex of Escherichia coli is induced by K+ limitation or high osmolality. This process is controlled by the sensor kinase/response regulator system KdpD/KdpE. To study the importance of the transmembrane domains of KdpD for stimulus perception, each amino acid residue of the transmembrane domain 1 and Asp-424 of the adjacent periplasmic loop were replaced with Cys in a KdpD derivative devoid of native Cys residues. In vivo analysis of KdpD proteins with a single Cys residue revealed that 14 out of 18 amino acid replacements caused an altered response towards an osmotic upshift imposed by NaCl, whereby only four replacements also altered the response towards changes in the K+ concentration. The in vitro activities of most of the KdpD derivatives were in the range of KdpD devoid of native Cys residues. The results reveal that the osmosensing and K+ -sensing properties of KdpD can be dissected. Furthermore, the data support the hypothesis that osmosensing involves amino acid residues of the transmembrane domains.