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

Structural insights into the signal transduction mechanism of the K+-sensing two-component system KdpDE

Two-component systems (TCSs), which consist of a histidine kinase (HK) sensor and a response regulator (RR), are important for bacteria to quickly sense and respond to various environmental signals. HKs and RRs typically function as a cognate pair, interacting only with one another to transduce signaling. Precise signal transduction in a TCS depends on the specific interactions between the receiver domain (RD) of the RR and the dimerization and histidine phosphorylation domain (DHp) of the HK. Here, we determined the complex structure of KdpDE, a TCS consisting of the HK KdpD and the RR KdpE, which is responsible for K⁺ homeostasis. Both the RD and the DNA binding domain (DBD) of KdpE interacted with KdpD. Although the RD of KdpE and the DHp of KdpD contributed to binding specificity, the DBD mediated a distinct interaction with the catalytic ATP-binding (CA) domain of KdpD that was indispensable for KdpDE-mediated signal transduction. Moreover, the DBD-CA interface largely overlapped with that of the DBD-DNA complex, leading to competition between KdpD and its target promoter in a KdpE phosphorylation-dependent manner. In addition, the extended C-terminal tail of the CA domain was critical for stabilizing the interaction with KdpDE and for signal transduction. Together, these data provide a molecular basis for specific KdpD and KdpE interactions that play key roles in efficient signal transduction and transcriptional regulation by this TCS.

Regulation of Inducible Potassium Transporter KdpFABC by the KdpD/KdpE Two-Component System in Mycobacterium smegmatis

Kdp-ATPase is an inducible high affinity potassium uptake system that is widely distributed in bacteria, and is generally regulated by the KdpD/KdpE two-component system (TCS). In this study, conducted on Mycobacterium smegmatis, the kdpFABC (encoding Kdp-ATPase) expression was found to be affected by low concentration of K⁺, high concentrations of Na⁺, and/or [Formula: see text] of the medium. The KdpE was found to be a transcriptional regulator that bound to a specific 22-bp sequence in the promoter region of kdpFABC operon to positively regulate kdpFABC expression. The KdpE binding motif was highly conserved in the promoters of kdpFABC among the mycobacterial species. 5'-RACE data indicated a transcriptional start site (TSS) of the kdpFABC operon within the coding sequence of MSMEG_5391, which comprised a 120-bp long 5'-UTR and an open reading frame of the 87-bp kdpF gene. The kdpE deletion resulted in altered growth rate under normal and low K⁺ conditions. Furthermore, under K⁺ limiting conditions, a single transcript (kdpFABCDE) spanning kdpFABC and kdpDE operons was observed. This study provided the first insight into the regulation of kdpFABC operon by the KdpD/KdpE TCS in M. smegmatis.

Towards the complete proteinaceous regulome of Acinetobacter baumannii

The emergence of Acinetobacter baumannii strains, with broad multidrug-resistance phenotypes and novel virulence factors unique to hypervirulent strains, presents a major threat to human health worldwide. Although a number of studies have described virulence-affecting entities for this organism, very few have identified regulatory elements controlling their expression. Previously, our group has documented the global identification and curation of regulatory RNAs in A. baumannii. As such, in the present study, we detail an extension of this work, the performance of an extensive bioinformatic analysis to identify regulatory proteins in the recently annotated genome of the highly virulent AB5075 strain. In so doing, 243 transcription factors, 14 two-component systems (TCSs), 2 orphan response regulators, 1 hybrid TCS and 5 σ factors were found. A comparison of these elements between AB5075 and other clinical isolates, as well as a laboratory strain, led to the identification of several conserved regulatory elements, whilst at the same time uncovering regulators unique to hypervirulent strains. Lastly, by comparing regulatory elements compiled in this study to genes shown to be essential for AB5075 infection, we were able to highlight elements with a specific importance for pathogenic behaviour. Collectively, our work offers a unique insight into the regulatory network of A. baumannii strains, and provides insight into the evolution of hypervirulent lineages.

An asymmetric heterodomain interface stabilizes a response regulator-DNA complex

Two-component signal transduction systems consist of pairs of histidine kinases and response regulators, which mediate adaptive responses to environmental cues. Most activated response regulators regulate transcription by binding tightly to promoter DNA via a phosphorylation-triggered inactive-to-active transition. The molecular basis for formation of stable response regulator-DNA complexes that precede the assembly of RNA polymerases is unclear. Here, we present structures of DNA complexed with the response regulator KdpE, a member of the OmpR/PhoB family. The distinctively asymmetric complex in an active-like conformation reveals a unique intramolecular interface between the receiver domain (RD) and the DNA-binding domain (DBD) of only one of the two response regulators in the complex. Structure-function studies show that this RD-DBD interface is necessary to form stable complexes that support gene expression. The conservation of sequence and structure suggests that these findings extend to a large group of response regulators that act as transcription factors.

DNA binding site analysis of Burkholderia thailandensis response regulators

Bacterial response regulators (RR) that function as transcription factors in two component signaling pathways are crucial for ensuring tight regulation and coordinated expression of the genome. Currently, consensus DNA binding sites in the promoter for very few bacterial RRs have been identified. A systematic method to characterize these DNA binding sites for RRs would enable prediction of specific gene expression patterns in response to extracellular stimuli. To identify RR DNA binding sites, we functionally activated RRs using beryllofluoride and applied them to a protein-binding microarray (PBM) to discover DNA binding motifs for RRs expressed in Burkholderia, a Gram-negative bacterial genus. We identified DNA binding motifs for conserved RRs in Burkholderia thailandensis, including KdpE, RisA, and NarL, as well as for a previously uncharacterized RR at locus BTH_II2335 and its ortholog in the human pathogen Burkholderia pseudomallei at locus BPSS2315. We further demonstrate RR binding of predicted genomic targets for the two orthologs using gel shift assays and reveal a pattern of RR regulation of expression of self and other two component systems. Our studies illustrate the use of PBMs to identify DNA binding specificities for bacterial RRs and enable prediction of gene regulatory networks in response to two component signaling.

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.

The complexity of the 'simple' two-component system KdpD/KdpE in Escherichia coli

The KdpD/KdpE two-component system of Escherichia coli activates the expression of the kdpFABC operon encoding the high-affinity K(+) uptake system KdpFABC in response to K(+) limitation or salt stress. Earlier, it was proposed that the histidine kinase KdpD is a turgor sensor; recent studies suggest that KdpD integrates three chemical stimuli from the cytoplasm. The histidine kinase KdpD contains several structural features and subdomains that are important for stimulus perception, modulation of the kinase to phosphatase ratio, and signaling. The response regulator KdpE receives the phosphoryl group from KdpD and induces kdpFABC transcription. The three-dimensional structure of the receiver domain was resolved, providing insights into the activation mechanism of this transcriptional regulator. Two accessory components, the universal stress protein UspC and the phosphotransferase system component IIA(Ntr), are known to interact with KdpD, allowing the modulation of kdpFABC expression under certain physiological conditions. Here, we will discuss the complexity of a 'simple' two-component system and its interconnectivity with metabolism and the general stress response.

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.

RESULTS

Full response to salt stress was only achieved with a chimera that contains UspC, probably due to unaffected scaffolding of the KdpD/KdpE signaling cascade by soluble UspC. Unexpectedly, chimeras containing either UspF or UspG not only prevented kdpFABC expression under salt stress but also under K+ limiting conditions, although these hybrid proteins exhibited kinase and phosphotransferase activities in vitro. These are the first KdpD derivatives that do not respond to K+ limitation due to alterations in the N-terminal domain. Analysis of the KdpD-Usp tertiary structure revealed that this domain has a net positively charged surface, while UspF and UspG are characterized by net negative surface charges.

CONCLUSION

The Usp domain within KdpD not only functions as a binding surface for the scaffold UspC, but it is also important for KdpD signaling. We propose that KdpD sensing/signaling involves alterations of electrostatic interactions between the large N- and C-terminal cytoplasmic domains.

An amphiphilic region in the cytoplasmic domain of KdpD is recognized by the signal recognition particle and targeted to the Escherichia coli membrane

The sensor protein KdpD of Escherichia coli is composed of a large N-terminal hydrophilic region (aa 1–400), four transmembrane regions (aa 401–498) and a large hydrophilic region (aa 499–894) at the C-terminus. KdpD requires the signal recognition particle (SRP) for its targeting to the membrane. Deletions within KdpD show that the first 50 residues are required for SRP-driven membrane insertion. A fusion protein of the green fluorescent protein (GFP) with KdpD is found localized at the membrane only when SRP is present. The membrane targeting of GFP was not observed when the first 50 KdpD residues were deleted. A truncated mutant of KdpD containing only the first 25 amino acids fused to GFP lost its ability to specifically interact with SRP, whereas a specific interaction between SRP and the first 48 amino acids of KdpD fused to GFP was confirmed by pull-down experiments. Conclusively, a small amphiphilic region of 27 residues within the amino-terminal domain of KdpD (aa 22–48) is recognized by SRP and targets the protein to the membrane. This shows that membrane proteins with a large N-terminal region in the cytoplasm can be membrane-targeted early on to allow co-translational membrane insertion of their distant transmembrane regions.

Characterization of a response regulator protein that binds to Anabaena sp. strain L-31 kdp-promoter region

The potassium dependent adenosine triphosphatase (Kdp-ATPase), encoded by the kdp operon, is a potassium uptake system found in several prokaryotes. The cyanobacterium Anabaena sp. strain L-31 shows the presence of two kdp operons (kdp1 and kdp2) of which the kdp2 is predominantly induced in response to potassium limitation or desiccation stress. Two ORFs, encoding a sensor kinase and a response regulator, respectively, were identified upstream of the kdp2 operon in Anabaena sp. strain L-31. The response regulator protein, tagged with 6 additional C-terminal histidine residues, was over-expressed in Escherichia coli and purified by affinity chromatography. Employing the protein-specific antiserum, the response regulator protein was detected in Anabaena L-31 cytosolic fractions. The response regulator protein bound to the kdp2 promoter region with higher affinity than kdp1 promoter region. Addition of acetyl phosphate increased the ability of the protein to bind to kdp2 promoter region by several fold, suggesting a phosphorylation-dependent binding of response regulator to the promoter. These data implicate the response regulator protein in regulation of kdp2 expression in Anabaena sp. strain L-31.

The Kdp-ATPase system and its regulation

K+, the dominant intracellular cation, is required for various physiological processes like turgor homeostasis, pH regulation etc. Bacterial cells have evolved many diverse K+ transporters to maintain the desired concentration of internal K+. In E.coli, the KdpATPase (comprising of the KdpFABC complex), encoded by the kdpFABC operon, is an inducible high-affinity K+ transporter that is synthesised under conditions of severe K+ limitation or osmotic upshift. The E.coli kdp expression is transcriptionally regulated by the KdpD and KdpE proteins, which together constitute a typical bacterial two-component signal transduction system. The Kdp system is widely dispersed among the different classes of bacteria including the cyanobacteria. The ordering of the kdpA, kdpB and kdpC is relatively fixed but the kdpD/E genes show different arrangements in distantly related bacteria. Our studies have shown that the cyanobacterium Anabaena sp. strain L-31 possesses two kdp operons, kdp1 and kdp2, of which, the later is expressed under K+ deficiency and desiccation. Among the regulatory genes,the kdpD ORF of Anabaena L-31 is truncated when compared to the kdpD of other bacteria, while a kdpE -like gene is absent. The extremely radio-resistant bacterium, Deinococcus radiodurans strain R1, also shows the presence of a naturally short kdpD ORF similar to Anabaena in its kdp operon. The review elaborates the expression of bacterial kdp operons in response to various environmental stress conditions, with special emphasis on Anabaena. The possible mechanism(s)of regulation of the unique kdp operons from Anabaena and Deinococcus are also discussed.

The cytoplasmic C-terminal domain of the Escherichia coli KdpD protein functions as a K+ sensor

The KdpD protein is a K(+) sensor kinase located in the cytoplasmic membrane of Escherichia coli. It contains four transmembrane stretches and two short periplasmic loops of 4 and 10 amino acid residues, respectively. To determine which part of KdpD functions as a K(+) sensor, genetic variants were constructed with truncations or altered arrangements of the transmembrane segments. All KdpD constructs were tested by complementation of an E. coli kdpD deletion strain for their ability to grow at a K(+) concentration of 0.1 mM in the medium. A soluble protein composed of the C-terminal cytoplasmic domain was able to complement the kdpD deletion strain. In addition, analysis of the beta-galactosidase activity of an E. coli strain which carries a transcriptional fusion of the upstream region of the kdpFABC operon and a promoterless lacZ gene revealed that this soluble KdpD mutant responds to changes in the K(+) concentration in the extracellular medium. The results suggest that the sensing and response functions are both located in the C-terminal domain and might be modulated by the N-terminal domain as well as by membrane anchoring.

Membrane fluidity and its roles in the perception of environmental signals

Poikilothermic organisms are exposed to frequent changes in environmental conditions and their survival depends on their ability to acclimate to such changes. Changes in ambient temperature and osmolarity cause fluctuations in the fluidity of cell membranes. Such fluctuations are considered to be critical to the initiation of the regulatory reactions that ultimately lead to acclimation. The mechanisms responsible for the perception of changes in membrane fluidity have not been fully characterized. However, the analysis of genome-wide gene expression using DNA microarrays has provided a powerful new approach to studies of the contribution of membrane fluidity to gene expression and to the identification of environmental sensors. In this review, we focus on the mechanisms that regulate membrane fluidity, on putative sensors that perceive changes in membrane fluidity, and on the subsequent expression of genes that ensures acclimation to a new set of environmental conditions.

Global gene expression in Staphylococcus aureus biofilms

We previously demonstrated that mutation of the staphylococcal accessory regulator (sarA) in a clinical isolate of Staphylococcus aureus (UAMS-1) results in an impaired capacity to form a biofilm in vitro (K. E. Beenken, J. S. Blevins, and M. S. Smeltzer, Infect. Immun. 71:4206-4211, 2003). In this report, we used a murine model of catheter-based biofilm formation to demonstrate that a UAMS-1 sarA mutant also has a reduced capacity to form a biofilm in vivo. Surprisingly, mutation of the UAMS-1 ica locus had little impact on biofilm formation in vitro or in vivo. In an effort to identify additional loci that might be relevant to biofilm formation and/or the adaptive response required for persistence of S. aureus within a biofilm, we isolated total cellular RNA from UAMS-1 harvested from a biofilm grown in a flow cell and compared the transcriptional profile of this RNA to RNA isolated from both exponential- and stationary-phase planktonic cultures. Comparisons were done using a custom-made Affymetrix GeneChip representing the genomic complement of six strains of S. aureus (COL, N315, Mu50, NCTC 8325, EMRSA-16 [strain 252], and MSSA-476). The results confirm that the sessile lifestyle associated with persistence within a biofilm is distinct by comparison to the lifestyles of both the exponential and postexponential phases of planktonic culture. Indeed, we identified 48 genes in which expression was induced at least twofold in biofilms over expression under both planktonic conditions. Similarly, we identified 84 genes in which expression was repressed by a factor of at least 2 compared to expression under both planktonic conditions. A primary theme that emerged from the analysis of these genes is that persistence within a biofilm requires an adaptive response that limits the deleterious effects of the reduced pH associated with anaerobic growth conditions.

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.

The transmembrane domains of the sensor kinase KdpD of Escherichia coli are not essential for sensing K+ limitation

The sensor kinase/response regulator system KdpD/KdpE of Escherichia coli regulates the expression of the kdpFABC operon, which encodes the high affinity K+ transport system KdpFABC. The membrane-bound sensor kinase KdpD consists of four transmembrane domains, a large cytoplasmic N-terminal domain and a cytoplasmic C-terminal transmitter domain. To elucidate the role of the four transmembrane domains, various deletions were introduced in kdpD and the activities of the resulting truncated derivatives of KdpD were determined. A KdpD protein lacking all four transmembrane domains was able to sense low K+ concentrations, whereas at higher K+ concentrations kdpFABC expression was constitutive. These and further results with various truncated KdpD proteins lacking distinct parts of the transmembrane domains or derivatives in which a linker peptide or two transmembrane domains of PutP, the Na+/proline transporter of Escherichia coli, replaced the missing part indicated that the transmembrane domains are not essential for sensing of K+ limitation, but may be important for the correct positioning of the large N- and C-terminal cytoplasmic domains to each other.

The roles and regulation of potassium in bacteria

Potassium is the major intracellular cation in bacteria as well as in eucaryotic cells. Bacteria accumulate K+ by a number of different transport systems that vary in kinetics, energy coupling, and regulation. The Trk and Kdp systems of enteric organisms have been well studied and are found in many distantly related species. The Ktr system, resembling Trk in many ways, is also found in many bacteria. In most species two or more independent saturable K(+)-transport systems are present. The KefB and KefC type of system that is activated by treatment of cells with toxic electrophiles is the only specific K(+)-efflux system that has been well characterized. Pressure-activated channels of at least three types are found in bacteria; these represent nonspecific paths of efflux when turgor pressure is dangerously high. A close homolog of eucaryotic K+ channels is found in many bacteria, but its role remains obscure. K+ transporters are regulated both by ion concentrations and turgor. A very general property is activation of K+ uptake by an increase in medium osmolarity. This response is modulated by both internal and external concentrations of K+. Kdp is the only K(+)-transport system whose expression is regulated by environmental conditions. Decrease in turgor pressure and/or reduction in external K+ rapidly increase expression of Kdp. The signal created by these changes, inferred to be reduced turgor, is transmitted by the KdpD sensor kinase to the KdpE-response regulator that in turn stimulates transcription of the kdp genes. K+ acts as a cytoplasmic-signaling molecule, activating and/or inducing enzymes and transport systems that allow the cell to adapt to elevated osmolarity. The signal could be ionic strength or specifically K+. This signaling response is probably mediated by a direct sensing of internal ionic strength by each particular system and not by a component or system that coordinates this response by different systems to elevated K+.

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.

trans-acting mutations in loci other than kdpDE that affect kdp operon regulation in Escherichia coli: effects of cytoplasmic thiol oxidation status and nucleoid protein H-NS on kdp expression

Transcription of the K(+) transport operon kdp in Escherichia coli is induced during K(+)-limited growth by the action of a dual-component phosphorelay regulatory system comprised of a sensor kinase (integral membrane protein), KdpD, and a DNA-binding response regulator (cytoplasmic protein), KdpE. In this study, we screened for new dke (named dke for decreased kdp expression) mutations (in loci other than kdpDE) that led to substantially decreased kdp expression. One dke mutation was shown to be in hns, encoding the nucleoid protein H-NS. Another dke mutation was mapped to trxB (encoding thioredoxin reductase), and an equivalent reduction in kdp expression was demonstrated also for trxA mutants that are deficient in thioredoxin 1. Exogenously provided dithiothreitol rescued the kdp expression defect in trxB but not trxA mutants. Neither trxB nor trxA affected gene regulation mediated by another dual-component system tested, EnvZ-OmpR. Mutations in genes dsbC and dsbD did not affect kdp expression, suggesting that the trx effects on kdp are not mediated by alterations in protein disulfide bond status in the periplasm. Reduced kdp expression was observed even in a trxB strain that harbored a variant KdpD polypeptide bearing no Cys residues. A trxB hns double mutant was even more severely affected for kdp expression than either single mutant. The dke mutations themselves had no effect on strength of the signal controlling kdp expression, and constitutive mutations in kdpDE were epistatic to hns and trxB. These results indicate that perturbations in cytoplasmic thiol oxidation status and in levels of the H-NS protein exert additive effects, direct or indirect, at a step(s) upstream of KdpD in the signal transduction pathway, which significantly influence the magnitude of KdpD kinase activity obtained for a given strength of the inducing signal for kdp transcription.

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.

Phosphorylation, dephosphorylation and DNA-binding of the Bradyrhizobium japonicum RegSR two-component regulatory proteins

Under low oxygen conditions, induction of many genes required for nitrogen fixation in Bradyrhizobium japonicum depends on the redox-responsive transcriptional activator NifA which is encoded in the fixR-nifA operon. Basal expression of this operon depends on the response regulator RegR and a DNA element located around position -68 in the fixR-nifA promoter region. To investigate the functional properties of RegR and the interaction with its putative cognate kinase, RegS, we overproduced and affinity-purified RegR and a truncated soluble variant of RegS (RegS(C)), both as N-terminally His(6)-tagged proteins. RegS(C) autophosphorylated when incubated with [gamma-(32)P]ATP, and it catalyzed the transfer of the phosphoryl label to RegR. The phosphorylated form of RegS(C) exhibited phosphatase activity on RegR-phosphate. Chemical stability tests and site-specific mutagenesis identified amino acids H219 and D63 of RegS and RegR, respectively, as the phosphorylated residues. Competition experiments with isolated domains demonstrated that the N-terminal but not the C-terminal domain of RegR interacts with RegS(C). Band-shift experiments revealed that phosphorylated RegR had at least eightfold enhanced DNA-binding activity compared with dephosphorylated RegR or the mutant protein RegR-D63N, which cannot be phosphorylated. In conclusion, the RegSR proteins of B. japonicum exhibit functional properties in vitro that are typical of two-component regulatory systems.

Osmosensing by bacteria: signals and membrane-based sensors

Bacteria can survive dramatic osmotic shifts. Osmoregulatory responses mitigate the passive adjustments in cell structure and the growth inhibition that may ensue. The levels of certain cytoplasmic solutes rise and fall in response to increases and decreases, respectively, in extracellular osmolality. Certain organic compounds are favored over ions as osmoregulatory solutes, although K+ fluxes are intrinsic to the osmoregulatory response for at least some organisms. Osmosensors must undergo transitions between "off" and "on" conformations in response to changes in extracellular water activity (direct osmosensing) or resulting changes in cell structure (indirect osmosensing). Those located in the cytoplasmic membranes and nucleoids of bacteria are positioned for indirect osmosensing. Cytoplasmic membrane-based osmosensors may detect changes in the periplasmic and/or cytoplasmic solvent by experiencing changes in preferential interactions with particular solvent constituents, cosolvent-induced hydration changes, and/or macromolecular crowding. Alternatively, the membrane may act as an antenna and osmosensors may detect changes in membrane structure. Cosolvents may modulate intrinsic biomembrane strain and/or topologically closed membrane systems may experience changes in mechanical strain in response to imposed osmotic shifts. The osmosensory mechanisms controlling membrane-based K+ transporters, transcriptional regulators, osmoprotectant transporters, and mechanosensitive channels intrinsic to the cytoplasmic membrane of Escherichia coli are under intensive investigation. The osmoprotectant transporter ProP and channel MscL act as osmosensors after purification and reconstitution in proteoliposomes. Evidence that sensor kinase KdpD receives multiple sensory inputs is consistent with the effects of K+ fluxes on nucleoid structure, cellular energetics, cytoplasmic ionic strength, and ion composition as well as on cytoplasmic osmolality. Thus, osmoregulatory responses accommodate and exploit the effects of individual cosolvents on cell structure and function as well as the collective contribution of cosolvents to intracellular osmolality.

Individual substitutions of clustered arginine residues of the sensor kinase KdpD of Escherichia coli modulate the ratio of kinase to phosphatase activity

Escherichia coli responds to K+ limitation or high osmolarity by induction of the kdpFABC operon coding for the high affinity K+-translocating Kdp-ATPase. KdpD, the sensor kinase of this system, is a bifunctional enzyme catalyzing the autophosphorylation by ATP and the dephosphorylation of the corresponding response regulator KdpE. Here we demonstrate that individual replacements of clustered arginine residues located close to transmembrane domain TM4 modulate the ratio of kinase to phosphatase activity. Thus KdpD-Arg511 --> Gln is characterized by an increase in the kinase activity and a loss of the phosphatase activity. However, when Arg at position 511 is replaced with Lys, activities of the corresponding protein are comparable with wild-type KdpD. In contrast, replacement of arginine residues at positions 503, 506, or 508 with glutamine or lysine causes a decrease of the kinase and an increase of the phosphatase activities. Changes of the activities of these KdpD proteins correspond with alterations in kdpFABC expression. Thus KdpD-Arg511 --> Gln causes constitutive expression of kdpFABC. KdpD proteins with Arg replacements at positions 503, 506, or 508 are unable to respond to osmolarity, whereas the sensing of K+ limitation is not influenced. Simultaneous replacement of arginine residues 508 and 511 or 506, 508, and 511 with glutamine leads to a decrease of the phosphatase activity. However, kdpFABC expression is dependent on K+ and osmolarity. Finally, when Arg513 is replaced with glutamine the amount of KdpD detected in the membrane is drastically reduced. These results imply that there is an equilibrium between the kinase and phosphatase activities of KdpD, which can be shifted by the replacement of one arginine residue. An electrostatic switch mechanism within the protein is proposed through which the ratio of kinase to phosphatase is regulated. Finally, these results lend support to the notion that KdpD can be activated by two distinct stimuli, K+ limitation and osmolarity.

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.

Linkage map of Escherichia coli K-12, edition 10: the traditional map

This map is an update of the edition 9 map by Berlyn et al. (M. K. B. Berlyn, K. B. Low, and K. E. Rudd, p. 1715-1902, in F. C. Neidhardt et al., ed., Escherichia coli and Salmonella: cellular and molecular biology, 2nd ed., vol. 2, 1996). It uses coordinates established by the completed sequence, expressed as 100 minutes for the entire circular map, and adds new genes discovered and established since 1996 and eliminates those shown to correspond to other known genes. The latter are included as synonyms. An alphabetical list of genes showing map location, synonyms, the protein or RNA product of the gene, phenotypes of mutants, and reference citations is provided. In addition to genes known to correspond to gene sequences, other genes, often older, that are described by phenotype and older mapping techniques and that have not been correlated with sequences are included.

Effect of cysteine replacements on the properties of the turgor sensor KdpD of Escherichia coli

Escherichia coli responds rapidly to K+-limitation or high osmolarity by induction of the kdpFABC operon coding for the high affinity K+-translocating Kdp-ATPase. This process is controlled by the membrane-bound histidine kinase KdpD and the response regulator KdpE. Here, it is demonstrated that replacements of the native Cys residues at positions 409, 852, and 874 influence distinct activities of KdpD, whereas replacements of Cys residues at positions 32, 256, and 402 have no effect. Replacements of Cys409 in KdpD reveal that transmembrane domain I is important for perception and/or propagation of the stimulus. When Cys409 is replaced with Ala, kdpFABC expression becomes constitutive regardless of the external stimuli. In contrast, when Cys409 is replaced with Val or Tyr, induction of kdpFABC expression in response to different stimuli is drastically reduced. KdpD with Ser at position 409 supports levels of kdpFABC expression comparable to those seen in wild-type. Since neither the kinase nor phosphatase activity of these proteins is affected, it is proposed that different amino acid side-chains at position 409 alter the switch between the inactive and active forms of the kinase. When Cys852 or Cys874 is replaced with Ala or Ser, kinase activity is reduced to 10% of the wild-type level. However, kinetic studies reveal that the apparent ATP binding affinity is not affected. Surprisingly, introduction of Cys852 and Cys874 into a KdpD protein devoid of Cys residues leads to full recovery of the kinase activity. Labeling studies support the idea that a disulfide bridge forms between these two residues.

Truncation of amino acids 12-128 causes deregulation of the phosphatase activity of the sensor kinase KdpD of Escherichia coli

The kdpFABC operon, which encodes the structural genes for the high affinity K+ transport complex KdpFABC, is regulated by the sensor kinase KdpD and the response regulator KdpE. KdpD is a bifunctional enzyme catalyzing the autophosphorylation by ATP and the dephosphorylation of the corresponding response regulator KdpE. Here, we demonstrate that the phosphatase activity of KdpD is dependent on ATP, whereas GTP, ITP, CTP, ADP, and GDP have no effect. The phosphatase activity requires only ATP binding, because nonhydrolyzable analogs (adenosine-5'-[gamma-thio]triphosphate and adenosine-5'-[beta,gamma-imido]triphosphate) work as well. However, KdpD proteins missing amino acids 12-128 are characterized by a phosphatase activity that is independent of ATP. These proteins are still able to respond to K+ starvation, but an increase in osmolarity is no longer sensed. Comparison of different KdpD sequences reveals a conserved motif in this amino acid region that is very similar to a classical ATP-binding site (Walker A motif). Replacement of the conserved Gly37, Lys38, and Thr39 residues in the consensus ATP-binding sequence results in a KdpD protein that causes a kdpFABC expression pattern comparable with that seen with KdpD proteins missing amino acids 12-128. However, in vitro phosphatase activity is comparable with that of wild-type KdpD. These results suggest that amino acids 12-128 of KdpD are important for its activity and that an additional ATP-binding site in the N-terminal region seems to be involved in modulation of the phosphatase activity.

Regulation of compatible solute accumulation in bacteria

In their natural habitats, microorganisms are often exposed to osmolality changes in the environment. The osmotic stress must be sensed and converted into an activity change of specific enzymes and transport proteins and/or it must trigger their synthesis such that the osmotic imbalance can be rapidly restored. On the basis of the available literature, we conclude that representative gram-negative and gram-positive bacteria use different strategies to respond to osmotic stress. The main focus of this paper is on the initial response of bacteria to hyper- and hypo-osmotic conditions, and in particular the osmosensing devices that allow the cell to rapidly activate and/or to synthesize the transport systems necessary for uptake and excretion of compatible solutes. The experimental data allow us to discriminate the transport systems by the physicochemical parameter that is sensed, which can be a change in external osmotic pressure, turgor pressure, membrane strain, internal osmolality and/or concentration of specific signal molecule. We also evaluate the molecular basis for osmosensing by reviewing the unique structural features of known osmoregulated transport systems.

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.

Protein patterns, osmolytes, and aldose reductase of L-929 cells exposed to hyperosmotic media

L-929 cells acclimated to media made hyperosmotic (600 mosmol/kgH2O) by addition of NaCl, sorbitol, or mannitol show, on SDS-polyacrylamide gels, a markedly enhanced protein band at 40 kDa, most likely corresponding to the enzyme aldose reductase. The effect was not observed in cells acclimated to a medium rendered hyperosmotic by addition of proline. The major organic osmolyte accumulated is sorbitol in cells acclimated to high-sorbitol or high-NaCl medium, proline in cells acclimated to high-proline medium. Cells acclimated to any of these hyperosmotic media display unaltered Na+ levels and similarly increased K+ levels and decreased Cl-levels. These results are interpreted in terms of the mechanisms involved in aldose reductase induction and in regulation of the enzyme activity in long-term acclimation to hyperosmotic media.

Salt tolerance in plants and microorganisms: toxicity targets and defense responses

Salt tolerance of crops could be improved by genetic engineering if basic questions on mechanisms of salt toxicity and defense responses could be solved at the molecular level. Mutant plants accumulating proline and transgenic plants engineered to accumulate mannitol or fructans exhibit improved salt tolerance. A target of salt toxicity has been identified in Saccharomyces cerevisiae: it is a sodium-sensitive nucleotidase involved in sulfate activation and encoded by the HAL2 gene. The major sodium-extrusion system of S. cerevisiae is a P-ATPase encoded by the ENA1 gene. The regulatory system of ENA1 expression includes the protein phosphatase calcineurin and the product of the HAL3 gene. In Escherichia coli, the Na(+)-H+ antiporter encoded by the nhaA gene is essential for salt tolerance. No sodium transport system has been identified at the molecular level in plants. Ion transport at the vacuole is of crucial importance for salt accumulation in this compartment, a conspicuous feature of halophytic plants. The primary sensors of osmotic stress have been identified only in E. coli. In S. cerevisiae, a protein kinase cascade (the HOG pathway) mediates the osmotic induction of many, but not all, stress-responsive genes. In plants, the hormone abscisic acid mediates many stress responses and both a protein phosphatase and a transcription factor (encoded by the ABI1 and ABI3 genes, respectively) participate in its action.

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.

Isolation and in vitro phosphorylation of sensory transduction components controlling anaerobic induction of light harvesting and reaction center gene expression in Rhodobacter capsulatus

Anaerobic induction of light harvesting and reaction center gene expression involves two transacting factors termed RegA and RegB. Sequence and mutational analysis has indicated that RegA and RegB constitute cognate components of a prokaryotic sensory transduction cascade with RegB comprising a membrane-spanning sensor kinase and RegA a cytosolic response regulator. In this study we have purified RegA, as well as a truncated portion of RegB (RegB') and undertaken an in vitro analysis of autophosphorylation and phosphotransfer activities. Incubation of RegB' with [gamma-32P]ATP and MgCl2 resulted in phosphorylation of RegB' (RegB' approximately P) over a 20-min incubation period. Incubation of RegB' approximately P with RegA resulted in rapid transfer of the phosphate from RegB' to RegA. In analogy to other characterized prokaryotic sensory transduction components, mutational and chemical stability studies also indicate that RegB' is autophosphorylated at a conserved histidine and that RegA accepts the phosphate from RegB at a conserved aspartate.

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.

Phosphorylation and dephosphorylation of the NarQ, NarX, and NarL proteins of the nitrate-dependent two-component regulatory system of Escherichia coli

The NarX, NarQ, and NarL proteins make up a nitrate-responsive regulatory system responsible for control of the anaerobic respiratory pathway genes in Escherichia coli, including nitrate reductase (narGHJI), dimethyl sulfoxide/trimethylamine-N-oxide reductase (dmsABC), and fumarate reductase (frdABCD) operons among others. The two membrane-bound proteins NarX and NarQ can independently sense the presence of nitrate and transfer this signal to the DNA-binding regulatory protein NarL, which controls gene expression by transcriptional activation or repression. To establish the role of protein phosphorylation in this process and to determine whether the NarX and NarQ proteins differ in their interaction with NarL, the cytoplasmic domains of NarX and NarQ were overproduced and purified. Both proteins were autophosphorylated in the presence of [gamma-32P]ATP and MgCl2 but not with [alpha-32P]ATP. Whereas these autophosphorylation reactions were unaffected by the presence of nitrate, molybdate, GTP, or AMP, ADP was an inhibitor. The phosphorylated forms of 'NarX and 'NarQ were stable for hours at room temperature. Each protein transferred its phosphoryl group to purified NarL protein, although 'NarQ-phosphate catalyzed the transfer reaction at an apparently much faster rate than did 'NarX-phosphate. In addition, NarL was autophosphorylated with acetyl phosphate but not with ATP as a substrate. NarL-phosphate remained phosphorylated for at least 3 h. However, addition of 'NarX resulted in rapid dephosphorylation of NarL-phosphate. In contrast, 'NarQ exhibited a much slower phosphatase activity with NarL-phosphate. These studies establish that the cytoplasmic domains of the two nitrate sensors 'NarX and 'NarQ differ in their ability to interact with NarL.

A copper-transporting P-type ATPase found in the thylakoid membrane of the cyanobacterium Synechococcus species PCC7942

P-type ATPases constitute a large family of cation pumps that play crucial physiological roles in many organisms, including bacteria, plants and mammals. They are postulated to play important roles in a variety of environmental adaptation systems. Recently, we cloned two distinct putative P-type ATPase genes (pacS and pacL) from a photosynthetic cyanobacterium, Synechococcus species PCC7942. In this study, one of the gene products (named PacS) was found to possess a putative metal-binding motif (Gly-Met-X-Cys-X-X-Cys) in its N-terminal portion. Thus we supposed that this ATPase may function as a metal pump. Indeed, the results of Northern blotting analysis showed that pacS-mRNA specifically increases upon addition of copper or silver to the growth medium. The results of Western blotting analysis confirmed the view that PacS accumulates in copper-treated Synechococcus cells. Thus we concluded that the expression of PacS ATPase is regulated in response to the change in concentration of external metals, namely copper and silver. Consistent with this, an insertional inactivation mutant of pacS exhibited hypersensitivity in terms of growth to these potentially toxic metals. It was also revealed that PacS was mainly located in the thylakoid membrane, in which the photosynthetic reactions take place. This P-type ATPase in the thylakoid membrane is implicated as a copper-transporting system that may be involved in copper-homeostasis crucial to the photosynthetic thylakoid function.

Adaptation of Escherichia coli to high osmolarity environments: osmoregulation of the high-affinity glycine betaine transport system proU

A sudden increase in the osmolarity of the environment is highly detrimental to the growth and survival of Escherichia coli and Salmonella typhimurium since it triggers a rapid efflux of water from the cell, resulting in a decreased turgor. Changes in the external osmolarity must therefore be sensed by the microorganisms and this information must be converted into an adaptation process that aims at the restoration of turgor. The physiological reaction of the cell to the changing environmental condition is a highly coordinated process. Loss of turgor triggers a rapid influx of K+ ions into the cell via specific transporters and the concomitant synthesis of counterions, such as glutamate. The increased intracellular concentration of K(+)-glutamate allows the adaptation of the cell to environments of moderately high osmolarities. At high osmolarity, K(+)-glutamate is insufficient to ensure cell growth, and the bacteria therefore replace the accumulated K+ ions with compounds that are less deleterious for the cell's physiology. These compatible solutes include polyoles such as trehalose, amino acids such as proline, and methyl-amines such as glycine betaine. One of the most important compatible solutes for bacteria is glycine betaine. This potent osmoprotectant is widespread in nature, and its intracellular accumulation is achieved through uptake from the environment or synthesis from its precursor choline. In this overview, we discuss the properties of the high-affinity glycine betaine transport system ProU and the osmotic regulation of its structural genes.

A mutation in the receiver domain of the Agrobacterium tumefaciens transcriptional regulator VirG increases its affinity for operator DNA

We fused the wild-type Agrobacterium tumefaciens virG gene and the constitutive virGN54D allele to the malE gene of Escherichia coli, and studied the binding of MBP-VirG fusions to the autoregulated virG promoter. MBP-VirGN54D protein bound this promoter with 10-fold higher affinity than MBP-VirG, and bound to vir box I with eightfold higher affinity than to vir box III. Disruption of vir box III did not alter the affinity for vir box I, suggesting a lack of cooperativity between these sites. We provide evidence that protein bound at a single vir box may have a higher oligomeric state than non-bound protein, and that a DNA distortion adjacent to vir box I may occur during activation.

The sphR product, a two-component system response regulator protein, regulates phosphate assimilation in Synechococcus sp. strain PCC 7942 by binding to two sites upstream from the phoA promoter

In the photosynthetic cyanobacterium Synechococcus sp. strain PCC 7942, the sphS and sphR genes were previously suggested to encode a typical pair of two-component signal transduction proteins. A deletion mutant strain lacking these genes failed to exhibit induction of alkaline phosphatase, the phoA gene product, in response to phosphate limitation in the medium. The SphR protein was overexpressed in Escherichia coli and then purified to near homogeneity. A truncated form of the SphS polypeptide (named SphS*) was also isolated. Here, we demonstrate that purified SphR is phosphorylated by phosphotransfer from SphS and binds to two distinct sites upstream from the phoA promoter. From these results, we conclude that the SphS and SphR proteins are directly involved in the regulation of phoA transcription in response to phosphate limitation in Synechococcus species.

Molecular characterization of the promoter of osmY, an rpoS-dependent gene

The osmY gene, which encodes a periplasmic protein with an apparent M(r) of 22,000, is induced by both osmotic and growth phase signals. We demonstrate here that osmY expression is regulated at the level of transcription and that transcription initiates 242 nucleotides upstream of the osmY open reading frame. Relative to the transcriptional start site, 5' deletions up to -36 did not inhibit osmY expression. 3' deletions that extended into the untranslated leader region affected the overall level of osmY::lacZ expression but did not affect inducibility. 5' and 3' deletions that extended past the transcriptional start region essentially abolished osmY expression, suggesting that there is a single promoter region. A putative promoter was identified, and its -10 region, TATATT, closely resembles the sigma 70 consensus -10 sequence, TATAAT. However, we show that osmY is not absolutely dependent on a functional sigma 70 for its expression. Since osmY expression does require rpoS (R. Hengge-Aronis, R. Lange, N. Henneberg, and D. Fischer, J. Bacteriol. 175:259-265, 1993), which encodes a stationary-phase sigma factor, sigma S (K. Tanaka, Y. Takayanagi, N. Fujita, A. Ishihama, and H. Takahashi, Proc. Natl. Acad. Sci. USA 90:3511-3515, 1993), E sigma S may be the form of RNA polymerase responsible for transcription of osmY.

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 cyanobacterium, Synechococcus sp. PCC7942, possesses two distinct genes encoding cation-transporting P-type ATPases

P-type (or E1 E2-type) ATPases comprise a large family of prokaryotic and eukaryotic proteins capable of transporting a variety of cations, and function in a wide variety of cellular processes. The present study was carried out to search for genes encoding P-type ATPases in the phototrophic cyanobacterium, Synechococcus sp. PCC7942. We succeeded in cloning two genes each encoding P-type ATPases from this bacterium. It was found that Synechococcus at least, two distinct P-type ATPases; one belongs to the family of typical prokaryotic P-type ATPases and the other markedly resembles eukaryotic P-type ATPases. An insertion mutant lacking either of these two ATPase-genes was constructed. The results showed that the growth of these mutants is hypersensitive to osmotic stress upon addition of NaCl or sorbitol to the medium.