Enzymes activated by monovalent cations

Cyclic di-AMP traps proton-coupled K+ transporters of the KUP family in an inward-occluded conformation

Cyclic di-AMP is the only known essential second messenger in bacteria and archaea, regulating different proteins indispensable for numerous physiological processes. In particular, it controls various potassium and osmolyte transporters involved in osmoregulation. In Bacillus subtilis, the K⁺/H⁺ symporter KimA of the KUP family is inactivated by c-di-AMP. KimA sustains survival at potassium limitation at low external pH by mediating potassium ion uptake. However, at elevated intracellular K⁺ concentrations, further K⁺ accumulation would be toxic. In this study, we reveal the molecular basis of how c-di-AMP binding inhibits KimA. We report cryo-EM structures of KimA with bound c-di-AMP in detergent solution and reconstituted in amphipols. By combining structural data with functional assays and molecular dynamics simulations we reveal how c-di-AMP modulates transport. We show that an intracellular loop in the transmembrane domain interacts with c-di-AMP bound to the adjacent cytosolic domain. This reduces the mobility of transmembrane helices at the cytosolic side of the K⁺ binding site and therefore traps KimA in an inward-occluded conformation.

The interplay between Cs and K in Pseudanabaena catenata; from microbial bloom control strategies to bioremediation options for radioactive waters

Pseudanabaena dominates cyanobacterial blooms in the First-Generation Magnox Storage Pond (FGMSP) at a UK nuclear site. The fission product Cs is a radiologically significant radionuclide in the pond, and understanding the interactions between Cs and Pseudanabaena spp. is therefore important for determining facility management strategies, as well as improving understanding of microbiological responses to this non-essential chemical analogue of K. This study evaluated the fate of Cs following interactions with Pseudanabaena catenata, a laboratory strain most closely related to that dominating FGMSP blooms. Experiments showed that Cs (1 mM) exposure did not affect the growth of P. catenata, while a high concentration of K (5 mM) caused a significant reduction in cell yield. Scanning transmission X-ray microscopy elemental mapping identified Cs accumulation to discrete cytoplasmic locations within P. catenata cells, indicating a potential bioremediation option for Cs. Proteins related to stress responses and nutrient limitation (K, P) were stimulated by Cs treatment. Furthermore, selected K⁺ transport proteins were mis-regulated by Cs dosing, which indicates the importance of the K⁺ transport system for Cs accumulation. These findings enhance understanding of Cs fate and biological responses within Pseudanabaena blooms, and indicate that K exposure might provide a microbial bloom control strategy.

Electrodeposition of Calcium Phosphate Coatings on Metallic Substrates for Bone Implant Applications: A Review

This review summaries more than three decades of scientific knowledge on electrodeposition of calcium phosphate coatings. This low-temperature process aims to make the surface of metallic bone implants bioactive within a physiological environment. The first part of the review describes the reaction mechanisms that lead to the synthesis of a bioactive coating. Electrodeposition occurs in three consecutive steps that involve electrochemical reactions, pH modification, and precipitation of the calcium phosphate coating. However, the process also produces undesired dihydrogen bubbles during the deposition because of the reduction of water, the solvent of the electrolyte solution. To prevent the production of large amounts of dihydrogen bubbles, the current density value is limited during deposition. To circumvent this issue, the use of pulsed current has been proposed in recent years to replace the traditional direct current. Thanks to breaking times, dihydrogen bubbles can regularly escape from the surface of the implant, and the deposition of the calcium phosphate coating is less disturbed by the accumulation of bubbles. In addition, the pulsed current has a positive impact on the chemical composition, morphology, roughness, and mechanical properties of the electrodeposited calcium phosphate coating. Finally, the review describes one of the most interesting properties of electrodeposition, i.e., the possibility of adding ionic substituents to the calcium phosphate crystal lattice to improve the biological performance of the bone implant. Several cations and anions are reviewed from the scientific literature with a description of their biological impact on the physiological environment.

Potassium dependency of enzymes in plant primary metabolism

Potassium is a macroelement essential to many aspects of plant life, such as photosynthesis, phloem transport or cellular electrochemistry. Many enzymes in animals or microbes are known to be stimulated or activated by potassium (K⁺ ions). Several plant enzymes are also strictly K⁺-dependent, and this can be critical when plants are under K deficiency and thus intracellular K⁺ concentration is low. Although metabolic effects of low K conditions have been documented, there is presently no review focusing on roles of K⁺ for enzyme catalysis or activation in plants. In this mini-review, we compile the current knowledge on K⁺-requirement of plant enzymes and take advantage of structural data to present biochemical roles of K⁺. This information is instrumental to explain direct effects of low K⁺ content on metabolism and this is illustrated with recent metabolomics data.

Nitrogen Assimilation and Transport by Ex Planta Nitrogen-Fixing Bradyrhizobium diazoefficiens Bacteroids Is Modulated by Oxygen, Bacteroid Density and l-Malate

Symbiotic nitrogen fixation requires the transfer of fixed organic nitrogen compounds from the symbiotic bacteria to a host plant, yet the chemical nature of the compounds is in question. Bradyrhizobium diazoefficiens bacteroids were isolated anaerobically from soybean nodules and assayed at varying densities, varying partial pressures of oxygen, and varying levels of l-malate. Ammonium was released at low bacteroid densities and high partial pressures of oxygen, but was apparently taken up at high bacteroid densities and low partial pressures of oxygen in the presence of l-malate; these later conditions were optimal for amino acid excretion. The ratio of partial pressure of oxygen/bacteroid density of apparent ammonium uptake and of alanine excretion displayed an inverse relationship. Ammonium uptake, alanine and branch chain amino acid release were all dependent on the concentration of l-malate displaying similar K0.5 values of 0.5 mM demonstrating concerted regulation. The hyperbolic kinetics of ammonium uptake and amino acid excretion suggests transport via a membrane carrier and also suggested that transport was rate limiting. Glutamate uptake displayed exponential kinetics implying transport via a channel. The chemical nature of the compounds released were dependent upon bacteroid density, partial pressure of oxygen and concentration of l-malate demonstrating an integrated metabolism.

K+ promotes the favorable effect of polyamine on gene expression better than Na

BACKGROUND

Polyamines are involved in a wide variety of biological processes including a marked effect on the structure and function of DNA. During our study on the interaction of polyamines with DNA, we found that K+ enhanced in vitro gene expression in the presence of polyamine more strongly than Na+. Thus, we sought to clarify the physico-chemical mechanism underlying this marked difference between the effects of K+ and Na+.

PRINCIPAL FINDINGS

It was found that K+ enhanced gene expression in the presence of spermidine, SPD(3+), much more strongly than Na+, through in vitro experiments with a Luciferase assay on cell extracts. Single-DNA observation by fluorescence microscopy showed that Na+ prevents the folding transition of DNA into a compact state more strongly than K+. 1H NMR measurement revealed that Na+ inhibits the binding of SPD to DNA more strongly than K+. Thus, SPD binds to DNA more favorably in K+-rich medium than in Na+-rich medium, which leads to favorable conditions for RNA polymerase to access DNA by decreasing the negative charge.

CONCLUSION AND SIGNIFICANCE

We found that Na+ and K+ exhibit markedly different effects through competitive binding with a cationic polyamine, SPD, to DNA, which causes a large difference in the higher-order structure of genomic DNA. It is concluded that the larger favorable effect of Na+ than K+ on in vitro gene expression observed in this study is well attributable to the significant difference between Na+ and K+ on the competitive binding inducing conformational transition of DNA.

Applications of Abscisic Acid and Increasing Concentrations of Calcium Affect the Partitioning of Mineral Nutrients between Tomato Leaf and Fruit Tissue

This study examined how abscisic acid (ABA) and calcium (Ca) concentrations in nutrient solution affect concentrations of mineral nutrients in tomato leaves and fruit. Tomato plants were grown in a greenhouse at 25/20 °C (day/night) under a 16 h photoperiod. Plants were treated with different concentrations of ABA and Ca. Calcium was applied via the irrigation lines at 60, 90, or 180 mg·L−1. ABA was applied as a combination of foliar sprays and root applications. For foliar ABA applications, treatments consisted of deionized (DI) water control (0.0 mg·L−1 ABA) or 500 mg·L−1 ABA. For ABA root applications, treatments consisted of no ABA control (0.0 mg·L−1 ABA) or 50 mg·L−1 ABA applied via the irrigation lines. Results indicate that mineral nutrient concentrations in tomato leaf and fruit tissue varied in connection with each exogenous application of ABA. Variability in mineral nutrient concentration depended on if ABA was applied to the leaf or root tissue. Additionally, increasing Ca treatment concentrations either decreased or did not change mineral nutrients in tomato and fruit tissue. Thus, tomato plants react to acquiring mineral nutrients in numerous mechanisms and, depending on how the applications of exogenous ABA are applied, can have varying effects on these mechanisms.

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.

Mesophyll cells' ability to maintain potassium is correlated with drought tolerance in tea (Camellia sinensis)

Tea plant is an important economic crop and is vulnerable to drought. A good understanding of tea drought tolerance mechanisms is required for breeding robust drought tolerant tea varieties. Previous studies showed mesophyll cells' ability to maintain K⁺ is associated with its stress tolerance. Here, in this study, 12 tea varieties were used to investigate the role of mesophyll K⁺ retention ability towards tea drought stress tolerance. A strong and negative correlation (R² = 0.8239, P < 0.001) was found between PEG (mimic drought stress)-induced K⁺ efflux from tea mesophyll cells and overall drought tolerance in 12 tea varieties. In agreement with this, a significantly higher retained leaf K⁺ content was found in drought tolerant than the sensitive tea varieties. Furthermore, exogenous applied K⁺ (5 mM) significantly alleviated drought-induced symptom in tea plants, further supporting our finding that mesophyll K⁺ retention is an important component for drought tolerance mechanisms in tea plants. Moreover, pharmacological experiments showed that the contribution of K⁺ outward rectifying channels and non-selective cation channels in controlling PEG-induced K⁺ efflux from mesophylls cells are varied between drought tolerant and sensitive tea varieties.

Potassium fertilization arrests malate accumulation and alters soluble sugar metabolism in apple fruit

Effects of different potassium (K) levels, which were K0 (no fertilizer), K1 (71.5 g KCl plant-1 year-1), K2 (286.7 g KCl plant-1 year-1), and K3 (434 g KCl plant-1 year-1), were evaluated based on sugar and organic acid metabolism levels from 70-126 days after bloom (DAB) in the developing fruit of potted five-year-old apple (Malus domestica, Borkh.) trees. The results indicate that K fertilization promoted greater fruit mass, higher Ca2+ and soluble solid levels, and lower titratable acid levels, as well as increased pH values at harvest. With the application of different levels of K fertilizer, fructose, sorbitol, glucose and sucrose accumulation rates significantly changed during fruit development. Fruit in the K2 group had higher fructose, sucrose and glucose levels than those in other treatment groups at 126 DAB. These changes in soluble sugar are related to the activity of metabolic enzymes. Sucrose synthase (SS) and sorbitol dehydrogenase (SDH) activity in the K2 treated fruit was significantly higher than those in other treatment groups from 70-126 DAB. Malate levels in K-supplemented fruit were notably lower than those in non K-supplemented fruit, and K3 treated fruit had the lowest malate levels during fruit development. Cytosolic malic enzyme (ME) and phosphoenolpyruvate carboxykinase (PEPCK) activity significantly increased in fruit under the K2 treatment during 112-126 DAB and 98-126 DAB, respectively. In addition, Ca2+ concentration increased with increasing K fertilization levels, which promoted a maximum of 11.72 mg g-1 dry weight in apple fruit. These results show that K levels can alter soluble sugar and malate levels due to the interaction between sugars and acid-metabolic enzymes in fruit.

Biochemical composition and antioxidant activity affected by spraying potassium sulfate in black grape (Vitis vinifera L. cv. Rasha)

BACKGROUND

The physiological and metabolic processes involved with grapevine growth and production are influenced by key macro- and micronutrients. Potassium is an essential plant nutrient that affects growth and fruit quality. In this study, the impact of foliar spraying of potassium sulfate (K₂ SO₄ ) on qualitative characteristics of grape berries was evaluated in the cultivar 'Rasha', a commonly cultivated cultivar in Kurdistan province of Iran. Leaves of the fully grown vines were sprayed with each of the 1.5 and 3 g L^-1 K₂ SO₄ solutions once (1 month after petal senescence) and twice (15 days after first spraying). The control plants were sprayed with distilled water. Various biochemical contents and enzyme activities on the ripe berries were analyzed.

RESULTS

Significant increases in anthocyanin, total protein content, and antioxidant enzyme activities were observed in the berries treated twice with 3 g L^-1 K₂ SO₄ . Concentrations of total carbohydrate, phenol, and antioxidant activity in berries sprayed with K₂ SO₄ were higher than in the controls. We observed a strong correlation between antioxidant activity and different phenolic compounds.

CONCLUSION

These findings suggest that K₂ SO₄ treatment influences biosynthesis of phenolic compounds and antioxidant enzymes. Thus, treatment by K₂ SO₄ could improve nutritional and qualitative attributes of grape. © 2018 Society of Chemical Industry.

The cost of surviving nitrogen excess: energy and protein demand in the lichen Cladonia portentosa as revealed by proteomic analysis

Different nitrogen forms affect different metabolic pathways in lichens. In particular, the most relevant changes in protein expression were observed in the fungal partner, with NO ₃^- mostly affecting the energetic metabolism and NH ₄⁺ affecting transport and regulation of proteins and the energetic metabolism much more than NO ₃^- did. Excess deposition of reactive nitrogen is a well-known agent of stress for lichens, but which symbiont is most affected and how, remains a mystery. Using proteomics can expand our understanding of stress effects on lichens. We investigated the effects of different doses and forms of reactive nitrogen, with and without supplementary phosphorus and potassium, on the proteome of the lichen Cladonia portentosa growing in a 'real-world' simulation of nitrogen deposition. Protein expression changed with the nitrogen treatments but mostly in the fungal partner, with NO₃^- mainly affecting the energetic metabolism and NH₄⁺ also affecting the protein synthesis machinery. The photobiont mainly responded overexpressing proteins involved in energy production. This suggests that in response to nitrogen stress, the photobiont mainly supports the defensive mechanisms initiated by the mycobiont with an increased energy production. Such surplus energy is then used by the cell to maintain functionality in the presence of NO₃^-, while a futile cycle of protein production can be hypothesized to be induced by NH₄⁺ excess. External supply of potassium and phosphorus influenced differently the responses of particular enzymes, likely reflecting the many processes in which potassium exerts a regulatory function.

Molecular Mechanisms of Enzyme Activation by Monovalent Cations

Regulation of enzymes through metal ion complexation is widespread in biology and underscores a physiological need for stability and high catalytic activity that likely predated proteins in the RNA world. In addition to divalent metals such as Ca²⁺, Mg²⁺, and Zn²⁺, monovalent cations often function as efficient and selective promoters of catalysis. Advances in structural biology unravel a rich repertoire of molecular mechanisms for enzyme activation by Na⁺ and K⁺ Strategies range from short-range effects mediated by direct participation in substrate binding, to more distributed effects that propagate long-range to catalytic residues. This review addresses general considerations and examples.

Roles and Transport of Sodium and Potassium in Plants

The two alkali cations Na(+) and K(+) have similar relative abundances in the earth crust but display very different distributions in the biosphere. In all living organisms, K(+) is the major inorganic cation in the cytoplasm, where its concentration (ca. 0.1 M) is usually several times higher than that of Na(+). Accumulation of Na(+) at high concentrations in the cytoplasm results in deleterious effects on cell metabolism, e.g., on photosynthetic activity in plants. Thus, Na(+) is compartmentalized outside the cytoplasm. In plants, it can be accumulated at high concentrations in vacuoles, where it is used as osmoticum. Na(+) is not an essential element in most plants, except in some halophytes. On the other hand, it can be a beneficial element, by replacing K(+) as vacuolar osmoticum for instance. In contrast, K(+) is an essential element. It is involved in electrical neutralization of inorganic and organic anions and macromolecules, pH homeostasis, control of membrane electrical potential, and the regulation of cell osmotic pressure. Through the latter function in plants, it plays a role in turgor-driven cell and organ movements. It is also involved in the activation of enzymes, protein synthesis, cell metabolism, and photosynthesis. Thus, plant growth requires large quantities of K(+) ions that are taken up by roots from the soil solution, and then distributed throughout the plant. The availability of K(+) ions in the soil solution, slowly released by soil particles and clays, is often limiting for optimal growth in most natural ecosystems. In contrast, due to natural salinity or irrigation with poor quality water, detrimental Na(+) concentrations, toxic for all crop species, are present in many soils, representing 6 % to 10 % of the earth's land area. Three families of ion channels (Shaker, TPK/KCO, and TPC) and 3 families of transporters (HAK, HKT, and CPA) have been identified so far as contributing to K(+) and Na(+) transport across the plasmalemma and internal membranes, with high or low ionic selectivity. In the model plant Arabidopsis thaliana, these families gather at least 70 members. Coordination of the activities of these systems, at the cell and whole plant levels, ensures plant K(+) nutrition, use of Na(+) as a beneficial element, and adaptation to saline conditions.

Expression of the Genes Encoding the Trk and Kdp Potassium Transport Systems of Mycobacterium tuberculosis during Growth In Vitro

Two potassium (K(+))-uptake systems, Trk and Kdp, are operative in Mycobacterium tuberculosis (Mtb), but the environmental factors triggering their expression have not been determined. The current study has evaluated the expression of these genes in the Mtb wild-type and a trk-gene knockout strain at various stages of logarithmic growth in relation to extracellular K(+) concentrations and pH. In both strains, mRNA levels of the K(+)-uptake encoding genes were relatively low compared to those of the housekeeping gene, sigA, at the early- and mid-log phases, increasing during late-log. Increased gene expression coincided with decreased K(+) uptake in the context of a drop in extracellular pH and sustained high extracellular K(+) concentrations. In an additional series of experiments, the pH of the growth medium was manipulated by the addition of 1N HCl/NaOH. Decreasing the pH resulted in reductions in both membrane potential and K(+) uptake in the setting of significant induction of genes encoding both K(+) transporters. These observations are consistent with induction of the genes encoding the active K(+) transporters of Mtb as a strategy to compensate for loss of membrane potential-driven uptake of K(+) at low extracellular pH. Induction of these genes may promote survival in the acidic environments of the intracellular vacuole and granuloma.

Higher Potassium Concentration in Shoots Reduces Gray Mold in Sweet Basil

Nutritional elements can affect plant susceptibility to plant pathogens, including Botrytis cinerea. We tested the effect of potassium (K) fertilization on gray mold in sweet basil grown in pots, containers, and soil. Increased K in the irrigation water and in the sweet basil tissue resulted in an exponential decrease in gray mold severity. Potassium supplied to plants by foliar application resulted in a significant decrease in gray mold in plants grown with a low rate of K fertigation. Lower K fertigation resulted in a significant increase in B. cinerea infection under semi-commercial conditions. Gray mold severity in harvested shoots was significantly negatively correlated with K concentration in the irrigation solution, revealing resistance to B. cinerea infection as a result of high K concentration in sweet basil tissue. Gray mold was reduced following K foliar application of the plants. In general, there was no synergy between the fertigation and foliar spray treatments. Proper K fertilization can replace some of the required chemical fungicide treatments and it may be integrated into gray mold management for improved disease suppression.

Higher-order human telomeric G-quadruplex DNA metalloenzyme catalyzed Diels–Alder reaction: an unexpected inversion of enantioselectivity modulated by K+ and NH4+ ions

K⁺ and NH₄⁺, bearing approximately equal ionic radius, present different allosteric activation for higher-order human telomeric G-quadruplex DNA metalloenzyme.

Durum and bread wheat differ in their ability to retain potassium in leaf mesophyll: implications for salinity stress tolerance

Understanding the intrinsic mechanisms involved in the differential salinity tolerance between bread wheat and durum wheat is essential for breeding salt-tolerant varieties to cope with the global salinity issue threatening future food supply. In the past, higher salinity tolerance in bread wheat compared with durum wheat has been attributed to its better ability to exclude Na(+) from uptake. Here we show that another mechanism, namely more superior K(+) retention ability in the leaf mesophyll, also contributes to this difference. A strong positive correlation (R(2) > 0.41, P < 0.001) was found between NaCl-induced K(+) efflux in the leaf mesophyll and overall salinity tolerance in 48 wheat varieties. However, while the above correlation was strong in bread wheat, it was statistically insignificant in durum wheat. Consistent with these findings, a significantly higher relative leaf K(+) content was found in bread wheat than in durum wheat. In contrast to root tissues, the role of voltage-gated K(+) channels in K(+) retention in the wheat mesophyll was relatively small, and non-selective cation channels played a major role in controlling intracellular K(+) homeostasis. Moreover, a significant negative correlation between NaCl-induced mesophyll H(+) flux and mesophyll K(+) retention was found, and interpreted as a compensatory mechanism employed by sensitive varieties to regain K(+) leaked into the apoplast. It is concluded that bread wheat and durum wheat show different strategies of coping with salinity, and that targeting mechanisms conferring K(+) retention in the leaf mesophyll may be a promising way to improve the overall salinity tolerance in these species.

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.

Ability of leaf mesophyll to retain potassium correlates with salinity tolerance in wheat and barley

This work investigated the importance of the ability of leaf mesophyll cells to control K(+) flux across the plasma membrane as a trait conferring tissue tolerance mechanism in plants grown under saline conditions. Four wheat (Triticum aestivum and Triticum turgidum) and four barley (Hordeum vulgare) genotypes contrasting in their salinity tolerance were grown under glasshouse conditions. Seven to 10-day-old leaves were excised, and net K(+) and H(+) fluxes were measured from either epidermal or mesophyll cells upon acute 100 mM treatment (mimicking plant failure to restrict Na(+) delivery to the shoot) using non-invasive microelectrode ion flux estimation (the MIFE) system. To enable net ion flux measurements from leaf epidermal cells, removal of epicuticular waxes was trialed with organic solvents. A series of methodological experiments was conducted to test the efficiency of different methods of wax removal, and the impact of experimental procedures on cell viability, in order to optimize the method. A strong positive correlation was found between plants' ability to retain K(+) in salt-treated leaves and their salinity tolerance, in both wheat and especially barley. The observed effects were related to the ionic but not osmotic component of salt stress. Pharmacological experiments have suggested that voltage-gated K(+) -permeable channels mediate K(+) retention in leaf mesophyll upon elevated NaCl levels in the apoplast. It is concluded that MIFE measurements of NaCl-induced K(+) fluxes from leaf mesophyll may be used as an efficient screening tool for breeding in cereals for salinity tissue tolerance.

Coherent Behavior and the Bound State of Water and K(+) Imply Another Model of Bioenergetics: Negative Entropy Instead of High-energy Bonds

Observations of coherent cellular behavior cannot be integrated into widely accepted membrane (pump) theory (MT) and its steady state energetics because of the thermal noise of assumed ordinary cell water and freely soluble cytoplasmic K(+). However, Ling disproved MT and proposed an alternative based on coherence, showing that rest (R) and action (A) are two different phases of protoplasm with different energy levels. The R-state is a coherent metastable low-entropy state as water and K(+) are bound to unfolded proteins. The A-state is the higher-entropy state because water and K(+) are free. The R-to-A phase transition is regarded as a mechanism to release energy for biological work, replacing the classical concept of high-energy bonds. Subsequent inactivation during the endergonic A-to-R phase transition needs an input of metabolic energy to restore the low entropy R-state. Matveev's native aggregation hypothesis allows to integrate the energetic details of globular proteins into this view.

The bacterial actin MamK: in vitro assembly behavior and filament architecture

It is now recognized that actin-like proteins are widespread in bacteria and, in contrast to eukaryotic actins, are highly diverse in sequence and function. The bacterial actin, MamK, represents a clade, primarily found in magnetotactic bacteria, that is involved in the proper organization of subcellular organelles, termed magnetosomes. We have previously shown that MamK from Magnetospirillum magneticum AMB-1 (AMB-1) forms dynamic filaments in vivo. To gain further insights into the molecular mechanisms that underlie MamK dynamics and function, we have now studied the in vitro properties of MamK. We demonstrate that MamK is an ATPase that, in the presence of ATP, assembles rapidly into filaments that disassemble once ATP is depleted. The mutation of a conserved active site residue (E143A) abolishes ATPase activity of MamK but not its ability to form filaments. Filament disassembly depends on both ATPase activity and potassium levels, the latter of which results in the organization of MamK filaments into bundles. These data are consistent with observations indicating that accessory factors are required to promote filament disassembly and for spatial organization of filaments in vivo. We also used cryo-electron microscopy to obtain a high resolution structure of MamK filaments. MamK adopts a two-stranded helical filament architecture, but unlike eukaryotic actin and other actin-like filaments, subunits in MamK strands are unstaggered giving rise to a unique filament architecture. Beyond extending our knowledge of the properties and function of MamK in magnetotactic bacteria, this study emphasizes the functional and structural diversity of bacterial actins in general.

Probing mechanism of metal catalyzed hydrolysis of Thymidylyl (3'-O, 5'-S) thymidine phosphodiester derivatives

Hydrolysis of nucleic acids is of fundamental importance in biological sciences. Kinetic and theoretical studies on different substrates wherein the phosphodiester bond combined with alkyl or aryl groups and sugar moiety have been the focus of attention in recent literature. The present work focuses on understanding the mechanism and energetics of alkali metal (Li, Na, and K) catalyzed hydrolysis of phosphodiester bond in modeled substrates including Thymidylyl (3'-O, 5'-S) thymidine phosphodiester (Tp-ST) (1), 3'-Thymidylyl (1-trifluoroethyl) phosphodiester (Tp-OCH(2)CF(3)) (2), 3'-Thymidylyl (o-cholorophenyl) phosphodiester (Tp-OPh(o-Cl)) (3) and 3'-Thymidylyl(p-nitrophenyl) phosphodiester (Tp-OPh(p-NO(2))) (4) employing density functional theory. Theoretical calculations reveal that the reaction follows a single-step (A(N)D(N)) mechanism where nucleophile attack and leaving group departure take place simultaneously. Activation barrier for potassium catalyzed Tp-ST hydrolysis (12.0 kcal mol(-1)) has been nearly twice as large compared to that for hydrolysis incorporating lithium or sodium. Effect of solvent (water) on activation energies has further been analyzed by adding a water molecule to each metal ion of the substrate. It has been shown that activation barrier of phosphodiester hydrolysis correlates well with basicity of leaving group.

Potassium acts as a GTPase-activating element on each nucleotide-binding domain of the essential Bacillus subtilis EngA

EngA proteins form a unique family of bacterial GTPases with two GTP-binding domains in tandem, namely GD1 and GD2, followed by a KH (K-homology) domain. They have been shown to interact with the bacterial ribosome and to be involved in its biogenesis. Most prokaryotic EngA possess a high GTPase activity in contrast to eukaryotic GTPases that act mainly as molecular switches. Here, we have purified and characterized the GTPase activity of the Bacillus subtilis EngA and two shortened EngA variants that only contain GD1 or GD2-KH. Interestingly, the GTPase activity of GD1 alone is similar to that of the whole EngA, whereas GD2-KH has a 150-fold lower GTPase activity. At physiological concentration, potassium strongly stimulates the GTPase activity of each protein construct. Interestingly, it affects neither the affinities for nucleotides nor the monomeric status of EngA or the GD1 domain. Thus, potassium likely acts as a chemical GTPase-activating element as proposed for another bacterial GTPase like MnmE. However, unlike MnmE, potassium does not promote dimerization of EngA. In addition, we solved two crystal structures of full-length EngA. One of them contained for the first time a GTP-like analogue bound to GD2 while GD1 was free. Surprisingly, its overall fold was similar to a previously solved structure with GDP bound to both sites. Our data indicate that a significant structural change must occur upon K⁺ binding to GD2, and a comparison with T. maritima EngA and MnmE structures allowed us to propose a model explaining the chemical basis for the different GTPase activities of GD1 and GD2.

HAK transporters from Physcomitrella patens and Yarrowia lipolytica mediate sodium uptake

The widespread presence of Na(+)-specific uptake systems across plants and fungi is a controversial topic. In this study, we identify two HAK genes, one in the moss Physcomitrella patens and the other in the yeast Yarrowia lipolytica, that encode Na(+)-specific transporters. Because HAK genes are numerous in plants and are duplicated in many fungi, our findings suggest that some HAK genes encode Na(+) transporters and that Na(+) might play physiological roles in plants and fungi more extensively than is currently thought.

Characterization of Halomonas sp. strain H11 α-glucosidase activated by monovalent cations and its application for efficient synthesis of α-D-glucosylglycerol

An α-glucosidase (HaG) with the following unique properties was isolated from Halomonas sp. strain H11: (i) high transglucosylation activity, (ii) activation by monovalent cations, and (iii) very narrow substrate specificity. The molecular mass of the purified HaG was estimated to be 58 kDa by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). HaG showed high hydrolytic activities toward maltose, sucrose, and p-nitrophenyl α-D-glucoside (pNPG) but to almost no other disaccharides or malto-oligosaccharides higher than trisaccharides. HaG showed optimum activity to maltose at 30°C and pH 6.5. Monovalent cations such as K(+), Rb(+), Cs(+), and NH(4)(+) increased the enzymatic activity to 2- to 9-fold of the original activity. These ions shifted the activity-pH profile to the alkaline side. The optimum temperature rose to 40°C in the presence of 10 mM NH(4)(+), although temperature stability was not affected. The apparent K(m) and k(cat) values for maltose and pNPG were significantly improved by monovalent cations. Surprisingly, k(cat)/K(m) for pNPG increased 372- to 969-fold in their presence. HaG used some alcohols as acceptor substrates in transglucosylation and was useful for efficient synthesis of α-d-glucosylglycerol. The efficiency of the production level was superior to that of the previously reported enzyme Aspergillus niger α-glucosidase in terms of small amounts of by-products. Sequence analysis of HaG revealed that it was classified in glycoside hydrolase family 13. Its amino acid sequence showed high identities, 60%, 58%, 57%, and 56%, to Xanthomonas campestris WU-9701 α-glucosidase, Xanthomonas campestris pv. raphani 756C oligo-1,6-glucosidase, Pseudomonas stutzeri DSM 4166 oligo-1,6-glucosidase, and Agrobacterium tumefaciens F2 α-glucosidase, respectively.

Rigidification of the autolysis loop enhances Na(+) binding to thrombin

Binding of Na(+) to thrombin ensures high activity toward physiological substrates and optimizes the procoagulant and prothrombotic roles of the enzyme in vivo. Under physiological conditions of pH and temperature, the binding affinity of Na(+) is weak due to large heat capacity and enthalpy changes associated with binding, and the K(d)=80 mM ensures only 64% saturation of the site at the concentration of Na(+) in the blood (140 mM). Residues controlling Na(+) binding and activation have been identified. Yet, attempts to improve the interaction of Na(+) with thrombin and possibly increase catalytic activity under physiological conditions have so far been unsuccessful. Here we report how replacement of the flexible autolysis loop of human thrombin with the homologous rigid domain of the murine enzyme results in a drastic (up to 10-fold) increase in Na(+) affinity and a significant improvement in the catalytic activity of the enzyme. Rigidification of the autolysis loop abolishes the heat capacity change associated with Na(+) binding observed in the wild-type and also increases the stability of thrombin. These findings have general relevance to protein engineering studies of clotting proteases and trypsin-like enzymes.

Redesigning allosteric activation in an enzyme

Enzyme activation by monovalent cations is widely documented in plants and the animal world. In type II enzymes, activation entails two steps: binding of the monovalent cation to its allosteric site and transduction of this event into enhanced catalytic activity. The effect has exquisite specificity for either Na(+) or K(+), the most abundant cations present in physiological environments. Enzymes requiring K(+) such as kinases and molecular chaperones are not activated as well or at all by the larger cation Cs(+) or the smaller cations Na(+) and Li(+). Enzymes requiring Na(+) such as β-galactosidase and clotting proteases are not activated as well by Li(+), or the larger cations K(+), Rb(+), and Cs(+). Efforts to switch specificity between Na(+) and K(+) in this large class of enzymes and completely redesign the mechanism of allosteric transduction leading to enhanced catalytic activity have so far been unsuccessful. Here we show how mutagenesis of two loops defining the Na(+) binding site of thrombin, a Na(+)-activated clotting protease, generates a construct that is most active in the presence of K(+) toward synthetic and physiological substrates. The effect is the result of a higher binding affinity and more efficient allosteric transduction of binding into enhanced catalytic activity for K(+) compared to Na(+), which represents a complete reversal of the properties of wild type. In addition, the construct features altered specificity toward physiological substrates resulting in a significant anticoagulant profile. The findings are relevant to all Na(+)-activated proteases involved in blood coagulation and the complement system.

Activity, folding and Z-DNA formation of the 8-17 DNAzyme in the presence of monovalent ions

The effect of monovalent ions on both the reactivity and global folding of the 8-17 DNAzyme is investigated, and the results are compared with those of the hammerhead ribozyme, which has similar size and secondary structure. In contrast to the hammerhead ribozyme, the 8-17 DNAzyme activity is not detectable in the presence of 4 M K(+), Rb(+), or Cs(+) or in the presence of 80 mM, [Co(NH(3))(6)](3+). Only 4 M Li(+), NH(4)(+) and, to a lesser extent, Na(+) conferred detectable activity. The observed rate constants (k(obs) approximately 10(-3) min(-1) for Li(+) and NH(4)(+)) are approximately 1000-fold lower than that in the presence of 10 mM Mg(2+), and approximately 200,000-fold slower than that in the presence of 100 microM Pb(2+). Since the hammerhead ribozyme displays monovalent ion-dependent activity that is often within approximately 10-fold of divalent metal ion-dependent activity, these results suggest that the 8-17 DNAzyme, obtained by in vitro selections, has evolved to have a more stringent divalent metal ion requirement for high activity as compared to the naturally occurring ribozymes, making the 8-17 DNAzyme an excellent choice as a Pb(2+) sensor with high selectivity. In contrast to the activity data, folding was observed in the presence of all the monovalent ions investigated, although those monovalent ions that do not support DNAzyme activity have weaker binding affinity (K(d) approximately 0.35 M for Rb(+) and Cs(+)), while those that confer DNAzyme activity possess stronger affinity (K(d) approximately 0.22 M for Li(+), Na(+) and NH(4)(+)). In addition, a correlation between metal ion charge density, binding affinity and enzyme activity was found among mono- and divalent metal ions except Pb(2+); higher charge density resulted in stronger affinity and higher activity, suggesting that the observed folding and activity is at least partially due to electrostatic interactions between ions and the DNAzyme. Finally, circular dichroism (CD) study has revealed Z-DNA formation with the monovalent metal ions, Zn(2+) and Mg(2+); the K(d) values obtained using CD were in the same range as those obtained from folding studies using FRET. However, Z-DNA formation was not observed with Pb(2+). These results indicate that Pb(2+)-dependent function follows a different mechanism from the monovalent metal ions and other divalent metal ions; in the presence of latter metal ions, metal-ion dependent folding and structural changes, including formation of Z-DNA, play an important role in the catalytic function of the 8-17 DNAzyme.

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.

Tryptophan synthase: structure and function of the monovalent cation site

The monovalent cation (MVC) site of the tryptophan synthase from Salmonella typhimurium plays essential roles in catalysis and in the regulation of substrate channeling. In vitro, MVCs affect the equilibrium distribution of intermediates formed in the reaction of l-Ser with the alpha(2)beta(2) complex; the MVC-free, Cs(+)-bound, and NH(4)(+)-bound enzymes stabilize the alpha-aminoacrylate species, E(A-A), while Na(+) binding stabilizes the l-Ser external aldimine species, E(Aex(1)). Two probes of beta-site reactivity and conformation were used herein, the reactive indole analogue, indoline, and the l-Trp analogue, l-His. MVC-bound E(A-A) reacts rapidly with indoline to give the indoline quinonoid species, E(Q)(indoline), which slowly converts to dihydroiso-l-tryptophan. MVC-free E(A-A) gives very little E(Q)(indoline), and turnover is strongly impaired; the fraction of E(Q)(indoline) formed is <3.5% of that given by the Na(+)-bound form. The reaction of l-Ser with the MVC-free internal aldimine species, E(Ain), initially gives small amounts of an active E(A-A) which converts to an inactive species on a slower, conformational, time scale. This inactivation is abolished by the binding of MVCs. The inactive E(A-A) appears to have a closed beta-subunit conformation with an altered substrate binding site that is different from the known conformations of tryptophan synthase. Reaction of l-His with E(Ain) gives an equilibrating mixture of external aldimine and quinonoid species, E(Aex)(his) and E(Q)(his). The MVC-free and Na(+) forms of the enzyme gave trace amounts of E(Q)(his) ( approximately 1% of the beta-sites). The Cs(+) and NH(4)(+) forms gave approximately 17 and approximately 14%, respectively. The reactivity of MVC-free E(Ain) was restored by the binding of an alpha-site ligand. These studies show MVCs and alpha-site ligands act synergistically to modulate the switching of the beta-subunit from the open to the closed conformation, and this switching is crucial to the regulation of beta-site catalytic activity. Comparison of the structures of Na(+) and Cs(+) forms of the enzyme shows Cs(+) favors complexes with open indole binding sites poised for the conformational transition to the closed state, whereas the Na(+) form does not. The beta-subunits of Cs(+) complexes exhibit preformed indole subsites; the indole subsites of the open Na(+) complexes are collapsed, distorted, and too small to accommodate indole.

Mutant N143P reveals how Na+ activates thrombin

The molecular mechanism of thrombin activation by Na(+) remains elusive. Its kinetic formulation requires extension of the classical Botts-Morales theory for the action of a modifier on an enzyme to correctly account for the contribution of the E*, E, and E:Na(+) forms. The extended scheme establishes that analysis of k(cat) unequivocally identifies allosteric transduction of Na(+) binding into enhanced catalytic activity. The thrombin mutant N143P features no Na(+)-dependent enhancement of k(cat) yet binds Na(+) with an affinity comparable to that of wild type. Crystal structures of the mutant in the presence and absence of Na(+) confirm that Pro(143) abrogates the important H-bond between the backbone N atom of residue 143 and the carbonyl O atom of Glu(192), which in turn controls the orientation of the Glu(192)-Gly(193) peptide bond and the correct architecture of the oxyanion hole. We conclude that Na(+) activates thrombin by securing the correct orientation of the Glu(192)-Gly(193) peptide bond, which is likely flipped in the absence of cation. Absolute conservation of the 143-192 H-bond in trypsin-like proteases and the importance of the oxyanion hole in protease function suggest that this mechanism of Na(+) activation is present in all Na(+)-activated trypsin-like proteases.

Alkali metals (Li, Na, and K) in methyl phosphodiester hydrolysis

The phosphodiester linkage central to biological systems has been modeled by methyl phosphodiester (MPDE) in various theoretical and experimental studies. Under physiological conditions, hydrolysis of the phosphodiester is negligible, however this process can be catalyzed in the presence of metal ions. To understand the role of alkali metals in MPDE hydrolysis and, in particular, how it influences the reaction pathway and the associated energetics, density functional calculations employing the 6-31+G(d,p) basis set have been carried out. Different pathways that include the reactant, intermediates and the products have been investigated for MPDE hydrolysis catalyzed by one or two lithium ions, characterized as stationary point geometries on the potential energy surface. The pathways A and B incorporate a single lithium ion bonded to different oxygens of the diester functionality. In pathway C, a six-membered ring was noticed wherein the nucleophile bridges two lithium ions interacting with different oxygens of the phosphoryl group. Furthermore, in the pathway (D) incorporating two lithium ions, one of the lithium ions interacts with the hydroxyl group and another with the methoxy oxygen; both metal ions are coordinated by the same phosphoryl oxygen. In addition to this, yet another pathway (E), where the metal ions are bound to different oxygens of the phosphoryl group, has also been dealt with. The calculations have shown that the A and B pathways lead to a single step reaction. A three-step mechanism including the nucleophilic (hydroxyl) attack, rotation of a methyl group and, finally, departure of the methoxy group has been predicted for the D and E profiles. Both D and E pathways are favored equally (with a marginal difference of 0.3 kJ mol(-1) in their activation energies) in the gas phase and a transition state corresponding to nucleophilic attack with an energy barrier of 32.5 kJ mol(-1) was located when lithium was used. A penta-coordinated phosphorous intermediate on the potential energy surface was characterized along these pathways. MPDE hydrolysis yielded a lower energy barrier for lithium than those for the remaining alkali metal ions. This agrees well with the experimentally observed trend for the hydrolysis rates: Li > Na > K. Self consistent reaction field (SCRF) calculations reveal the lower energy barrier between the reactant and the transition state for the nucleophilic attack in nonpolar solvents. The extent of bond formation (or cleavage) in different stationary point structures along the reaction path as estimated from the electron density at the bond critical point in the molecular electron density topography, has proven useful in distinguishing the associative or dissociative reaction pathways.

A novel potassium deficiency-induced stimulon in Anabaena torulosa

Potassium deficiency enhanced the synthesis of fifteen proteins in the nitrogen-fixing cyanobacterium Anabaena torulosa and of nine proteins in Escherichia coli. These were termed potassium deficiency-induced proteins or PDPs and constitute hitherto unknown potassium deficiency-induced stimulons. Potassium deficiency also enhanced the synthesis of certain osmotic stress-induced proteins. Addition of K+ repressed the synthesis of a majority of the osmotic stress-induced proteins and of PDPs in these bacteria. These proteins contrast with the dinitrogenase reductase of A. torulosa and the glycine betaine-binding protein of E. coli, both of which were osmo-induced to a higher level in potassium-supplemented conditions. The data demonstrate the occurrence of novel potassium deficiency-induced stimulons and a wider role of K+ in regulation of gene expression and stress responses in bacteria