Reduction of turgor is not the stimulus for the sensor kinase KdpD of Escherichia coli

Water Stress-Driven Changes in Bacterial Cell Surface Properties

Increased drought intensity and frequency exposes soil bacteria to prolonged water stress. While numerous studies reported on behavioral and physiological mechanisms of bacterial adaptation to water stress, changes in bacterial cell surface properties during adaptation are not well researched. We studied adaptive changes in cell surface hydrophobicity (CSH) after exposure to osmotic (NaCl) and matric stress (polyethylene glycol 8000 [PEG 8000]) for six typical soil bacteria (Bacillus subtilis, Arthrobacter chlorophenolicus, Pseudomonas fluorescens, Novosphingobium aromaticivorans, Rhodococcus erythropolis, and Mycobacterium pallens) covering a wide range of cell surface properties. Additional physicochemical parameters (surface chemical composition, surface charge, cell size and stiffness) of B. subtilis and P. fluorescens were analyzed to understand their possible contribution to CSH development. Changes in CSH caused by osmotic and matric stress depend on strain and stress type. CSH of B. subtilis and P. fluorescens increased with stress intensity, R. erythropolis and M. pallens exhibited a generally high but constant contact angle, while the response of A. chlorophenolicus and N. aromaticivorans depended on growth conditions and stress type. Osmotically driven changes in CSH of B. subtilis and P. fluorescens are accompanied by increasing surface N/C ratio, suggesting an increase in protein concentration within the cell wall. Cell envelope proteins thus presumably control bacterial CSH in two ways: (i) by increases in the relative density of surface proteins due to efflux of cytoplasmic water and subsequent cell shrinkage, and (ii) by destabilization of cell wall proteins, resulting in conformational changes which render the surface more hydrophobic. IMPORTANCE Changes in precipitation frequency, intensity, and temporal distribution are projected to result in increased frequency and intensity of droughts and heavy rainfall events. Prolonged droughts can promote the development of soil water repellency (SWR); this impacts the infiltration and distribution of water in the soil profile, exposing soil microorganisms to water stress. Exposure to water stress has recently been reported to result in increased cell surface hydrophobicity. However, the mechanism of this development is poorly understood. This study investigates the changes in the physicochemical properties of bacterial cell surfaces under water stress as a possible mechanism of increased surface hydrophobicity. Our results improve understanding of the microbial response to water stress in terms of surface properties, the variations in stress response depending on cell wall composition, and its contribution to the development of SWR.

Bacterial transmembrane signalling systems and their engineering for biosensing

Every living cell possesses numerous transmembrane signalling systems that receive chemical and physical stimuli from the environment and transduce this information into an intracellular signal that triggers some form of cellular response. As unicellular organisms, bacteria require these systems for survival in rapidly changing environments. The receptors themselves act as ‘sensory organs’, while subsequent signalling circuits can be regarded as forming a ‘neural network’ that is involved in decision making, adaptation and ultimately in ensuring survival. Bacteria serve as useful biosensors in industry and clinical diagnostics, in addition to producing drugs for therapeutic purposes. Therefore, there is a great demand for engineered bacterial strains that contain transmembrane signalling systems with high molecular specificity, sensitivity and dose dependency. In this review, we address the complexity of transmembrane signalling systems and discuss principles to rewire receptors and their signalling outputs.

Coping with low water activities and osmotic stress in Acinetobacter baumannii: significance, current status and perspectives

Multidrug resistant (MDR) pathogens are one of the most pressing challenges of contemporary health care. Acinetobacter baumannii takes a predominant position, emphasized in 2017 by the World Health Organization. The increasing emergence of MDR strains strengthens the demand for new antimicrobials. Possible targets for such compounds might be proteins involved in resistance against low water activity environments, since A. baumannii is known for its pronounced resistance against desiccation stress. Despite the importance of desiccation resistance for persistence of this pathogen in hospitals, comparable studies and precise data on this topic are rare and the mechanisms involved are largely unknown. This review aims to give an overview of the studies performed so far and the current knowledge on genes and proteins important for desiccation survival. 'Osmotic stress' is not identical to 'desiccation stress', but the two share the response of bacteria to low water activities. Osmotic stress resistance is in general studied much better, and in recent years it turned out that accumulation of compatible solutes in A. baumannii comprises some special features such as the bifunctional enzyme MtlD synthesizing the unusual solute mannitol. Furthermore, the regulatory pathways, as understood today, will be discussed.

Regulation of potassium dependent ATPase (kdp) operon of Deinococcus radiodurans

The genome of D. radiodurans harbors genes for structural and regulatory proteins of Kdp ATPase, in an operon pattern, on Mega plasmid 1. Organization of its two-component regulatory genes is unique. Here we demonstrate that both, the structural as well as regulatory components of the kdp operon of D. radiodurans are expressed quickly as the cells experience potassium limitation but are not expressed upon increase in osmolarity. The cognate DNA binding response regulator (RR) effects the expression of kdp operon during potassium deficiency through specific interaction with the kdp promoter. Deletion of the gene encoding RR protein renders the mutant D. radiodurans (ΔRR) unable to express kdp operon under potassium limitation. The ΔRR D. radiodurans displays no growth defect when grown on rich media or when exposed to oxidative or heat stress but shows reduced growth following gamma irradiation. The study elucidates the functional and regulatory aspects of the novel kdp operon of this extremophile, for the first time.

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.

Revisiting regulation of potassium homeostasis in Escherichia coli: the connection to phosphate limitation

Two-component signal transduction constitutes the predominant strategy used by bacteria to adapt to fluctuating environments. The KdpD/KdpE system is one of the most widespread, and is crucial for K⁺ homeostasis. In Escherichia coli, the histidine kinase KdpD senses K⁺ availability, whereas the response regulator KdpE activates synthesis of the high-affinity K⁺ uptake system KdpFABC. Here we show that, in the absence of KdpD, kdpFABC expression can be activated via phosphorylation of KdpE by the histidine kinase PhoR. PhoR and its cognate response regulator PhoB comprise a phosphate-responsive two-component system, which senses phosphate limitation indirectly through the phosphate transporter PstCAB and its accessory protein PhoU. In vivo two-hybrid interaction studies based on the bacterial adenylate cyclase reveal pairwise interactions between KdpD, PhoR, and PhoU. Finally, we demonstrate that cross-regulation between the kdpFABC and pstSCAB operons occurs in both directions under simultaneous K⁺ and phosphate limitation, both in vitro and in vivo. This study for the first time demonstrates direct coupling between intracellular K⁺ and phosphate homeostasis and provides a mechanism for fine-tuning of the balance between positively and negatively charged ions in the bacterial cell.

Osmotic Stress

Escherichia coli and Salmonella encounter osmotic pressure variations in natural environments that include host tissues, food, soil, and water. Osmotic stress causes water to flow into or out of cells, changing their structure, physics, and chemistry in ways that perturb cell functions. E. coli and Salmonella limit osmotically induced water fluxes by accumulating and releasing electrolytes and small organic solutes, some denoted compatible solutes because they accumulate to high levels without disturbing cell functions. Osmotic upshifts inhibit membrane-based energy transduction and macromolecule synthesis while activating existing osmoregulatory systems and specifically inducing osmoregulatory genes. The osmoregulatory response depends on the availability of osmoprotectants (exogenous organic compounds that can be taken up to become compatible solutes). Without osmoprotectants, K+ accumulates with counterion glutamate, and compatible solute trehalose is synthesized. Available osmoprotectants are taken up via transporters ProP, ProU, BetT, and BetU. The resulting compatible solute accumulation attenuates the K+ glutamate response and more effectively restores cell hydration and growth. Osmotic downshifts abruptly increase turgor pressure and strain the cytoplasmic membrane. Mechanosensitive channels like MscS and MscL open to allow nonspecific solute efflux and forestall cell lysis. Research frontiers include (i) the osmoadaptive remodeling of cell structure, (ii) the mechanisms by which osmotic stress alters gene expression, (iii) the mechanisms by which transporters and channels detect and respond to osmotic pressure changes, (iv) the coordination of osmoregulatory programs and selection of available osmoprotectants, and (v) the roles played by osmoregulatory mechanisms as E. coli and Salmonella survive or thrive in their natural environments.

The KdpD Sensor Kinase of Escherichia coli Responds to Several Distinct Signals To Turn on Expression of the Kdp Transport System

Kdp, one of three saturable K(+) uptake systems in Escherichia coli, is the system with the highest affinity for K(+) and the only one whose expression is strongly controlled by medium K(+) concentration. Expression is controlled by a two-component system of KdpD, the sensor kinase, and KdpE, the response regulator. There is general agreement that expression occurs when the growth rate of cells begins to become limited by K(+) availability. How K(+) limitation results in expression has been controversial. Studying the roles of the major components of the growth medium shows that KdpD senses at least two distinct signals inside the cell, those of Na(+) and NH4 (+), and it probably senses other monovalent cations in the cell. KdpD does not sense turgor.

IMPORTANCE

The expression of the Kdp K(+) transport system of E. coli occurs when cells become limited in their growth rate by the availability of K(+). Cells sense limited K(+) and try to compensate by taking up other monovalent cations, particularly Na(+) and NH4 (+). These cations are sensed in the cytoplasm by the KdpD response regulator, presumably to stimulate its kinase activity. It is shown that KdpD does not sense turgor, as was suggested earlier.

Metabolic Regulation and Coordination of the Metabolism in Bacteria in Response to a Variety of Growth Conditions

Living organisms have sophisticated but well-organized regulation system. It is important to understand the metabolic regulation mechanisms in relation to growth environment for the efficient design of cell factories for biofuels and biochemicals production. Here, an overview is given for carbon catabolite regulation, nitrogen regulation, ion, sulfur, and phosphate regulations, stringent response under nutrient starvation as well as oxidative stress regulation, redox state regulation, acid-shock, heat- and cold-shock regulations, solvent stress regulation, osmoregulation, and biofilm formation, and quorum sensing focusing on Escherichia coli metabolism and others. The coordinated regulation mechanisms are of particular interest in getting insight into the principle which governs the cell metabolism. The metabolism is controlled by both enzyme-level regulation and transcriptional regulation via transcription factors such as cAMP-Crp, Cra, Csr, Fis, P(II)(GlnB), NtrBC, CysB, PhoR/B, SoxR/S, Fur, MarR, ArcA/B, Fnr, NarX/L, RpoS, and (p)ppGpp for stringent response, where the timescales for enzyme-level and gene-level regulations are different. Moreover, multiple regulations are coordinated by the intracellular metabolites, where fructose 1,6-bisphosphate (FBP), phosphoenolpyruvate (PEP), and acetyl-CoA (AcCoA) play important roles for enzyme-level regulation as well as transcriptional control, while α-ketoacids such as α-ketoglutaric acid (αKG), pyruvate (PYR), and oxaloacetate (OAA) play important roles for the coordinated regulation between carbon source uptake rate and other nutrient uptake rate such as nitrogen or sulfur uptake rate by modulation of cAMP via Cya.

Absolute quantification of the Kdp subunits of Escherichia coli by multiple reaction monitoring

The sensor kinase/response regulator system KdpD/KdpE of Escherichia coli regulates the expression of the kdpFABC operon, encoding the high-affinity KdpFABC potassium (K(+) )-transport complex. Additionally, it has been suggested that the kdpDE operon itself is subjected to autoregulation by its gene products KdpD and KdpE. However, since kdpFABC and kdpDE expression has mainly been studied on the transcriptional level, accurate information on absolute amounts and the stoichiometric subunit composition of KdpFABC and KdpD/KdpE under K(+) -limiting and K(+) -nonlimiting growth conditions are lacking. In this study, we used highly sensitive mass spectrometric methods to quantify the amount of subunits of the Kdp(F)ABC complex and KdpD/KdpE. Data-dependent shotgun MS was used to assess protein coverage and accessible peptides. Absolute amounts of Kdp(F)ABC and KdpD/KdpE were quantified by targeted MRM analysis in the presence of corresponding heavy labeled standard peptides. Baseline synthesis of Kdp(F)ABC and KdpD/KdpE was found to be in the attomolar range under K(+) -nonlimiting conditions. Under K(+) -limitation, synthesis of Kdp(F)ABC (KdpA:KdpB:KdpC ratio of 1:1:1) was amplified more than 100-fold, whereas only a tenfold amplification of KdpD/KdpE (KdpD:KdpE ratio of 1:4) was observed. The results obtained provide a solid basis for follow-up studies on the dynamic regulation of the Kdp system.

Transcriptomic and functional analysis of NaCl-induced stress in Enterococcus faecalis

The robust physiology of Enterococcus faecalis facilitates tolerance to various stresses. We here report the transcriptional response of E. faecalis V583 to growth in the presence of 6.5% NaCl. Among the early responses observed was an immediate down-regulation of mscL, accompanied by an up-regulation of genes predicted to be involved in uptake of extracellular potassium and glycine betaine. The high NaCl concentration also induced expression of chaperons and cell envelope related traits, such as the enterococcal polysaccharide antigen (epa) locus. Functional genetic analysis revealed reduced salt stress resistance in both epaB and epaE mutants. The reduced salt resistance phenotype associated with the epaB mutant was restored by complementation, hence demonstrating a role of Epa in the physiological robustness of E. faecalis. Furthermore, we demonstrate that Epa confers increased resistance towards multiple cell envelope stress-inducing factors. Accordingly, these findings delineate a potential link between the robust nature of E. faecalis and its ability to perform as a human pathogen, and provide a new perspective on the mechanisms by which Epa contributes to virulence. Notably, the high NaCl concentration also resulted in strict repression of the gelE-sprE operon and impaired gelatinase activity. We demonstrate that NaCl antagonize the GBAP-pheromone dependent induction in a concentration dependent manner.

Small proteins can no longer be ignored

Small proteins, here defined as proteins of 50 amino acids or fewer in the absence of processing, have traditionally been overlooked due to challenges in their annotation and biochemical detection. In the past several years, however, increasing numbers of small proteins have been identified either through the realization that mutations in intergenic regions are actually within unannotated small protein genes or through the discovery that some small, regulatory RNAs encode small proteins. These insights, together with comparative sequence analysis, indicate that tens if not hundreds of small proteins are synthesized in a given organism. This review summarizes what has been learned about the functions of several of these bacterial small proteins, most of which act at the membrane, illustrating the astonishing range of processes in which these small proteins act and suggesting several general conclusions. Important questions for future studies of these overlooked proteins are also discussed.

Dynamics of an interactive network composed of a bacterial two-component system, a transporter and K+ as mediator

KdpD and KdpE form a histidine kinase/response regulator system that senses K⁺ limitation and induces the kdpFABC operon, which encodes a high-affinity K⁺ uptake complex. To define the primary stimulus perceived by KdpD we focused in this study on the dynamics of the Kdp response. Escherichia coli cells were subjected to severe K⁺ limitation, and all relevant parameters of the Kdp response, i.e., levels of kdpFABC transcripts and KdpFABC proteins, as well as extra- and intracellular K⁺ concentrations, were quantitatively analysed over time (0 to 180 min). Unexpectedly, induction of kdpFABC was found to follow a non-monotonic time-course. To interpret this unusual behaviour, a mathematical model that adequately captures the dynamics of the Kdp system was established and used for simulations. We found a strong correlation between KdpD/KdpE activation and the intracellular K⁺ concentration, which is influenced by the uptake of K⁺ via the KdpFABC complex. Based on these results a model is proposed in which KdpD/KdpE phosphorylation is inversely correlated with the intracellular K⁺ concentration. To corroborate this hypothesis an isogenic mutant that produces a defective KdpFABC complex, and the trans-complemented mutant that expresses the KtrAB high-affinity K⁺ uptake system of Vibrio alginolyticus were quantitatively analysed. Experimental data and simulations for the mutants consistently support the tight correlation between KdpD/KdpE activation and the intracellular K⁺ concentration. This study presents a striking example of the non-intuitive dynamics of a functional unit comprising signalling proteins and a transporter with K⁺ as mediator.

Overexpression of the KdpF membrane peptide in Mycobacterium bovis BCG results in reduced intramacrophage growth and altered cording morphology

Membrane peptides appear as an emerging class of regulatory molecules in bacteria, which can interact with membrane proteins, such as sensor kinases. To date, regulatory membrane peptides have been completely overlooked in mycobacteria. The 30 amino-acid-long KdpF peptide, which is co-transcribed with kdpABC genes and regulated by the KdpDE two-component system, is supposed to stabilize the KdpABC potassium transporter complex but may also exhibit unsuspected regulatory function(s) towards the KdpD sensor kinase. Herein, we showed by quantitative RT-PCR that the Mycobacterium bovis BCG kdpAB and kdpDE genes clusters are differentially induced in potassium-deprived broth medium or within infected macrophages. We have overexpressed the kdpF gene in M. bovis BCG to investigate its possible regulatory role and effect on mycobacterial virulence. Our results indicate that KdpF does not play a critical regulatory role on kdp genes expression despite the fact that KdpF interacts with the KdpD sensor kinase in a bacterial two-hybrid assay. However, overexpression of kdpF results in a significant reduction of M. bovis BCG growth in both murine and human primary macrophages, and is associated with a strong alteration of colonial morphology and impaired cording formation. To identify novel KdpF interactants, a mycobacterial library was screened using KdpF as bait in the bacterial two-hybrid system. This allowed us to identify members of the MmpL family of membrane proteins, known to participate in the biosynthesis/transport of various cell wall lipids, thus highlighting a possible link between KdpF and cell wall lipid metabolism. Taken together, these data suggest that KdpF overexpression reduces intramacrophage growth which may result from alteration of the mycobacterial cell wall.

Fast, multiphase volume adaptation to hyperosmotic shock by Escherichia coli

All living cells employ an array of different mechanisms to help them survive changes in extra cellular osmotic pressure. The difference in the concentration of chemicals in a bacterium's cytoplasm and the external environment generates an osmotic pressure that inflates the cell. It is thought that the bacterium Escherichia coli use a number of interconnected systems to adapt to changes in external pressure, allowing them to maintain turgor and live in surroundings that range more than two-hundred-fold in external osmolality. Here, we use fluorescence imaging to make the first measurements of cell volume changes over time during hyperosmotic shock and subsequent adaptation on a single cell level in vivo with a time resolution on the order of seconds. We directly observe two previously unseen phases of the cytoplasmic water efflux upon hyperosmotic shock. Furthermore, we monitor cell volume changes during the post-shock recovery and observe a two-phase response that depends on the shock magnitude. The initial phase of recovery is fast, on the order of 15–20 min and shows little cell-to-cell variation. For large sucrose shocks, a secondary phase that lasts several hours adds to the recovery. We find that cells are able to recover fully from shocks as high as 1 Osmol/kg using existing systems, but that for larger shocks, protein synthesis is required for full recovery.

The two-component sensor kinase KdpD is required for Salmonella typhimurium colonization of Caenorhabditis elegans and survival in macrophages

The ability of enteric pathogens to perceive and adapt to distinct environments within the metazoan intestinal tract is critical for pathogenesis; however, the preponderance of interactions between microbe- and host-derived factors remain to be fully understood. Salmonella enterica serovar Typhimurium is a medically important enteric bacterium that colonizes, proliferates and persists in the intestinal lumen of the nematode Caenorhabditis elegans. Several Salmonella virulence factors important in murine and tissue culture models also contribute to worm mortality and intestinal persistence. For example, PhoP and the virulence plasmid pSLT are virulence factors required for resistance to the C. elegans antimicrobial peptide SPP-1. To uncover additional determinants required for Salmonella typhimurium pathogenesis in vivo, we devised a genetic screen to identify bacterial mutants defective in establishing a persistent infection in the intestine of C. elegans. Here we report on identification of 14 loci required for persistence in the C. elegans intestine and characterization of KdpD, a sensor kinase of a two-component system in S. typhimurium pathogenesis. We show that kdpD mutants are profoundly attenuated in intestinal persistence in the nematode and in macrophage survival. These findings may be attributed to the essential role KdpD plays in promoting resistance to osmotic, oxidative and antimicrobial stresses.

Transcriptional responses of Bacillus cereus towards challenges with the polysaccharide chitosan

The antibacterial activity of the polysaccharide chitosan towards different bacterial species has been extensively documented. The response mechanisms of bacteria exposed to this biopolymer and the exact molecular mechanism of action, however, have hardly been investigated. This paper reports the transcriptome profiling using DNA microarrays of the type-strain of Bacillus cereus (ATCC 14579) exposed to subinhibitory concentrations of two water-soluble chitosan preparations with defined chemical characteristics (molecular weight and degree of acetylation (F(A))). The expression of 104 genes was significantly altered upon chitosan A (weight average molecular weight (M(w)) 36.0 kDa, F(A) = 0.01) exposure and 55 genes when treated with chitosan B (M(w) 28.4 kDa, F(A) = 0.16). Several of these genes are involved in ion transport, especially potassium influx (BC0753-BC0756). Upregulation of a potassium transporting system coincides with previous studies showing a permeabilizing effect on bacterial cells of this polymer with subsequent loss of potassium. Quantitative PCR confirmed the upregulation of the BC0753 gene encoding the K(+)-transporting ATPase subunit A. A markerless gene replacement method was used to construct a mutant strain deficient of genes encoding an ATP-driven K(+) transport system (Kdp) and the KdpD sensor protein. Growth of this mutant strain in potassium limiting conditions and under salt stress did not affect the growth pattern or growth yield compared to the wild-type strain. The necessity of the Kdp system for potassium acquisition in B. cereus is therefore questionable. Genes involved in the metabolism of arginine, proline and other cellular constituents, in addition to genes involved in the gluconeogenesis, were also significantly affected. BC2798 encoding a chitin binding protein was significantly downregulated due to chitosan exposure. This study provides insight into the response mechanisms of B. cereus to chitosan treatment and the significance of the Kdp system in potassium influx under challenging conditions.

Bacterial stimulus perception and signal transduction: response to osmotic stress

When exposed to osmotic stress from the environment, bacteria act to maintain cell turgor and hydration by responding both on the level of gene transcription and protein activity. Upon a sudden decrease in external osmolality, internal solutes are released by the action of membrane embedded mechanosensitive channels. In response to an osmotic upshift, the concentration of osmolytes in the cytoplasm is increased both by de novo synthesis and by active uptake. In order to coordinate these processes of osmoregulation, cells are equipped with systems and mechanisms of sensing physical stimuli correlated to changes in the external osmolality (osmosensing), with pathways to transduce these stimuli into useful signals which can be processed in the cell (signal transduction), and mechanisms of regulating proper responses in the cell to recover from the environmental stress and to maintain all necessary physiological functions (osmoregulation). These processes will be described by a number of representative examples, mainly of osmoreactive transport systems with a focus on available data of their molecular mechanism.

Involvement of EupR, a response regulator of the NarL/FixJ family, in the control of the uptake of the compatible solutes ectoines by the halophilic bacterium Chromohalobacter salexigens

BACKGROUND

Osmosensing and associated signal transduction pathways have not yet been described in obligately halophilic bacteria. Chromohalobacter salexigens is a halophilic bacterium with a broad range of salt tolerance. In response to osmotic stress, it synthesizes and accumulates large amounts of the compatible solutes ectoine and hydroxyectoine. In a previous work, we showed that ectoines can be also accumulated upon transport from the external medium, and that they can be used as carbon sources at optimal, but not at low salinity. This was related to an insufficient ectoine(s) transport under these conditions.

RESULTS

A C. salexigens Tn1732-induced mutant (CHR95) showed a delayed growth with glucose at low and optimal salinities, could not grow at high salinity, and was able to use ectoines as carbon sources at low salinity. CHR95 was affected in the transport and/or metabolism of glucose, and showed a deregulated ectoine uptake at any salinity, but it was not affected in ectoine metabolism. Transposon insertion in CHR95 caused deletion of three genes, Csal0865-Csal0867: acs, encoding an acetyl-CoA synthase, mntR, encoding a transcriptional regulator of the DtxR/MntR family, and eupR, encoding a putative two-component response regulator with a LuxR_C-like DNA-binding helix-turn-helix domain. A single mntR mutant was sensitive to manganese, suggesting that mntR encodes a manganese-dependent transcriptional regulator. Deletion of eupR led to salt-sensitivity and enabled the mutant strain to use ectoines as carbon source at low salinity. Domain analysis included EupR as a member of the NarL/FixJ family of two component response regulators. Finally, the protein encoded by Csal869, located three genes downstream of eupR was suggested to be the cognate histidine kinase of EupR. This protein was predicted to be a hybrid histidine kinase with one transmembrane and one cytoplasmic sensor domain.

CONCLUSIONS

This work represents the first example of the involvement of a two-component response regulator in the osmoadaptation of a true halophilic bacterium. Our results pave the way to the elucidation of the signal transduction pathway involved in the control of ectoine transport in C. salexigens.

Osmolytes contribute to pH homeostasis of Escherichia coli

Background

Cytoplasmic pH homeostasis in Escherichia coli includes numerous mechanisms involving pH-dependent catabolism and ion fluxes. An important contributor is transmembrane K⁺ flux, but the actual basis of K⁺ compensation for pH stress remains unclear. Osmoprotection could mediate the pH protection afforded by K⁺ and other osmolytes.

Methods and Principal Findings

The cytoplasmic pH of E. coli K-12 strains was measured by GFPmut3 fluorimetry. The wild-type strain Frag1 was exposed to rapid external acidification by HCl addition. Recovery of cytoplasmic pH was enhanced equally by supplementation with NaCl, KCl, proline, or sucrose. A triple mutant strain TK2420 defective for the Kdp, Trk and Kup K⁺ uptake systems requires exogenous K⁺ for steady-state pH homeostasis and for recovery from sudden acid shift. The K⁺ requirement however was partly compensated by supplementation with NaCl, choline chloride, proline, or sucrose. Thus, the K⁺ requirement was mediated in part by osmolarity, possibly by relieving osmotic stress which interacts with pH stress. The rapid addition of KCl to strain TK2420 suspended at external pH 5.6 caused a transient decrease in cytoplasmic pH, followed by slow recovery to an elevated steady-state pH. In the presence of 150 mM KCl, however, rapid addition of another 150 mM KCl caused a transient increase in cytoplasmic pH. These transient effects may arise from secondary K⁺ fluxes occurring through other transport processes in the TK2420 strain.

Conclusions

Diverse osmolytes including NaCl, KCl, proline, or sucrose contribute to cytoplasmic pH homeostasis in E. coli, and increase the recovery from rapid acid shift. Osmolytes other than K⁺ restore partial pH homeostasis in a strain deleted for K⁺ transport.

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.

Influence of K+-dependent membrane lipid composition on the expression of the kdpFABC operon in Escherichia coli

The membrane-bound sensor kinase KdpD and the cytoplasmic response regulator KdpE regulate the expression of the kdpFABC operon coding for the high affinity potassium uptake system KdpFABC in Escherichia coli. The signal transduction cascade of this two component system is activated under K(+)-limiting conditions in the medium, but is less sensitive to high osmolality. In order to test whether K(+) limitation affects membrane phospholipid composition and whether this change affects kdpFABC expression, we analysed the phospholipid composition of E. coli under these conditions. Our measurements revealed that there is an increase in the cardiolipin (CL) content during the exponential growth phase at the expense of the zwitterionic phospholipid phosphatidylethanolamine. The higher anionic phospholipid content occurs along with an increase of transcriptional activity of the cls gene coding for CL synthase. Furthermore, in vivo studies with E. coli derivatives carrying mutations in genes coding for enzymes involved in phospholipid biosynthesis revealed that the increase in the anionic lipid composition enhances the expression rate of the kdpFABC operon. Finally, we show that kinase activity of KdpD is stimulated in its native membrane environment by fusion with liposomes of anionic, but reduced with liposomes of zwitterionic phospholipids.

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.

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 DeltauspC 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.