Low External Concentrations Research Articles

Mutation of the K+ transporter SlHAK5 of tomato alters pistil morphology, ionome, metabolome and transcriptome in flowers.

K+ accumulation in plant tissues is a crucial factor for plant growth and development. The tomato high-affinity K+ transporter SlHAK5 is essential for root K+ acquisition from low external concentrations. It is also involved in K+ accumulation in pollen and plant fertility as slhak5 KO plants show a low rate of pollen germination, impaired pollen tube growth and parthenocarpic fruits. Here, we present a thorough analysis of slhak5 flowers, which showed relevant defects at the anatomic, ionomic, metabolomic and transcriptomic levels. First, slhak5 flowers exhibited shorter styles and enlarged ovaries that, together with a low number of seeds in fruits from slhak5 X WT crosses, indicated an effect of the slhak5 mutation on female fertility. Second, a lower accumulation of Ca2+, as well as of several metabolites such as amino acids, citric acid and sugars, was observed in mutant flowers, whereas indole-3-acetic acid content was increased when compared to the wild-type. Third, RNAseq conducted on pistils and stamens of wild-type and slhak5 plants revealed that transport and signalling pathways are significantly enriched in the gene expression analyses of stamens. Thus, it can be concluded that a functional SlHAK5 transporter is required to maintain appropriate Ca2+, metabolite and gene expression levels in flowers, and its absence leads to important reductions in both male and female fertility.

Knockout of OsNRAMP5 enhances rice tolerance to cadmium toxicity in response to varying external cadmium concentrations via distinct mechanisms

OsNRAMP5 is a transporter responsible for cadmium (Cd) and manganese (Mn) uptake and root-to-shoot translocation of Mn in rice plants. Knockout of OsNRAMP5 is regarded as an effective approach to minimize Cd uptake and accumulation in rice. It is vital to evaluate the effects of knocking out OsNRAMP5 on Cd and Mn accumulation, as well as Cd tolerance of rice plants in response to varying environmental Cd concentrations, and to uncover the underlying mechanism, which until now, has remained largely unexplored. This study showed that knockout of OsNRAMP5 decreased Cd uptake, but simultaneously facilitated Cd translocation from roots to shoots. The effect of OsNRAMP5 knockout on reducing root Cd uptake weakened, however its effect on improving root-to-shoot Cd translocation was constant with increasing environmental Cd concentrations. As a result, its mutation dramatically reduced Cd accumulation in shoots under low and moderate Cd stress, but inversely increased that under high Cd conditions. Interestingly, Cd tolerance of its knockout mutants was persistently enhanced, irrespective of lower or higher Cd concentrations in shoots, compared with that of wild-type plants. Knockout of OsNRAMP5 mitigated Cd toxicity by dramatically diminishing Cd uptake at low or moderate external Cd concentrations. Remarkably, its knockout effectively complemented deficient mineral nutrients in shoots, thereby indirectly enhancing rice tolerance to severe Cd stress. Additionally, its mutation conferred preferential delivery of Mn to young leaves and grains. These results have important implications for the application of the OsNRAMP5 mutation in mitigating Cd toxicity and lowering the risk of excessive Cd accumulation in rice grains.

The functional characterization of LjNRT2.4 indicates a novel, positive role of nitrate for an efficient nodule N2 -fixation activity.

Atmospheric nitrogen (N2) -fixing nodules are formed on the roots of legume plants as result of the symbiotic interaction with rhizobia. Nodule functioning requires high amounts of carbon and energy, and therefore legumes have developed finely tuned mechanisms to cope with changing external environmental conditions, including nutrient availability and flooding. The investigation of the role of nitrate as regulator of the symbiotic N2 fixation has been limited to the inhibitory effects exerted by high external concentrations on nodule formation, development and functioning. We describe a nitrate-dependent route acting at low external concentrations that become crucial in hydroponic conditions to ensure an efficient nodule functionality. Combined genetic, biochemical and molecular studies are used to unravel the novel function of the LjNRT2.4 gene. Two independent null mutants are affected by the nitrate content of nodules, consistent with LjNRT2.4 temporal and spatial profiles of expression. The reduced nodular nitrate content is associated to a strong reduction of nitrogenase activity and a severe N-starvation phenotype observed under hydroponic conditions. We also report the effects of the mutations on the nodular nitric oxide (NO) production and content. We discuss the involvement of LjNRT2.4 in a nitrate-NO respiratory chain taking place in the N2 -fixing nodules.

Evidence that human and equine erythrocytes could have significant roles in the transport and delivery of amino acids to organs and tissues

Erythrocytes have a well-defined role in the gaseous exchange of oxygen and carbon dioxide in the mammalian body. The erythrocytes can contain more than half of the free amino acids present in whole blood. Based on measures showing that venous erythrocyte levels of amino acids are much less than arterial erythrocyte levels, it has previously been proposed that erythrocytes also play a role in the delivery of amino acids to tissues in the body. This role has been dismissed because it has been assumed that to act as an amino acid transport vehicle, the erythrocytes should release their entire amino acid content in the capillary beds at the target tissues with kinetic studies showing that this would take too long to achieve. This investigation set out to investigate whether the equine erythrocytes could rapidly take up and release smaller packages of amino acids when exposed to high or low external concentrations of amino acids, because it seemed very unlikely that cells would be able to release all of their amino acids without serious impacts on osmotic balance. Freshly prepared erythrocytes were placed in alternating solutions of high and low amino acid concentrations in PBS to assess the capacities of these cells to rapidly take up and release amino acids depending on the nature of the external environment. It was found that amino acids were rapidly taken up and released in small quantities in each cycle representing 15% of their total load in equine erythrocytes and 16% in human erythrocytes. The capacity for rapid uptake/release of amino acids by equine and human erythrocytes provided evidence to support the theory that mammalian erythrocytes have a significant role in transport of amino acids from the liver to tissues, muscles and organs.

Two Ways To Convert a Low-Affinity Potassium Channel to High Affinity: Control of Bacillus subtilis KtrCD by Glutamate.

Potassium and glutamate are the major cation and anion, respectively, in every living cell. Due to the high concentrations of both ions, the cytoplasm of all cells can be regarded as a potassium glutamate solution. This implies that the concentrations of both ions need to be balanced. While the control of potassium uptake by glutamate is well established for eukaryotic cells, much less is known about the mechanisms that link potassium homeostasis to glutamate availability in bacteria. Here, we have discovered that the availability of glutamate strongly decreases the minimal external potassium concentration required for the highly abundant Bacillus subtilis potassium channel KtrCD to accumulate potassium. In contrast, the inducible KtrAB and KimA potassium uptake systems have high apparent affinities for potassium even in the absence of glutamate. Experiments with mutant strains revealed that the KtrD subunit responds to the presence of glutamate. For full activity, KtrD synergistically requires the presence of the regulatory subunit KtrC and of glutamate. The analysis of suppressor mutants of a strain that has KtrCD as the only potassium uptake system and that experiences severe potassium starvation identified a mutation in the ion selectivity filter of KtrD (Gly282 to Val) that similarly results in a strongly glutamate-independent increase of the apparent affinity for potassium. Thus, this work has identified two conditions that increase the apparent affinity of KtrCD for potassium, i.e., external glutamate and the acquisition of a single point mutation in KtrD.IMPORTANCE In each living cell, potassium is required for maintaining the intracellular pH and for the activity of essential enzymes. Like most other bacteria, Bacillus subtilis possesses multiple low- and high-affinity potassium uptake systems. Their activity is regulated by the second messenger cyclic di-AMP. Moreover, the pools of the most abundant ions potassium and glutamate must be balanced. We report two conditions under which the low-affinity potassium channel KtrCD is able to mediate potassium uptake at low external potassium concentrations: physiologically, the presence of glutamate results in a severely increased potassium uptake. Moreover, this is achieved by a mutation affecting the selectivity filter of the KtrD channel. These results highlight the integration between potassium and glutamate homeostasis in bacteria.

Root architecture traits variation and nitrate-influx responses in diverse wheat genotypes under different external nitrogen concentrations

In order to identify the genetic variations in root system architecture traits and their probable association with high- and low-affinity nitrate transport system, we performed several experiments on a genetically diverse set of wheat genotypes grown under two external nitrogen levels (optimum and limited nitrate conditions) at two growth points of the seedling stage. Further, we also examined the nitrate uptake and its transport under different combinations of nitrate availability in the external media using 15N-labelled N-source (15NO3−), and gene expression pattern of different high- and low-affinity nitrate transporters. We observed that nitrate starvation invariably increases the total root size in all genotypes. However, the variation of component traits of total root size under nitrate starvation is genotype-specific at both stages. Further, we also observed genotypic variation in both nitrate uptake and translocation depending on the growth stage, external nitrate concentration and growing conditions. The expression of the TaNRT2.1 gene was invariably up-regulated under low external nitrate concentration; however, it gets reduced after a longer period (21 days) of starvation than the early stage (14 days). Among the four NRT1.1 orthologs, TaNPF6.3 and TaNPF6.4 consistently showed higher expression than TaNPF6.1 and TaNPF6.2 at higher nitrate concentration at both the growth stages. TaNPF6.3 and TaNPF6.4 apparently showed a feature of typical low-affinity nitrate transporter gene at higher external nitrate concentration at 14 and 21 days growth stages, respectively. The present study reveals the complex root system of wheat that has genotype-specific N-foraging along with highly coordinated high- and low-affinity nitrate transport systems for nitrate uptake and transport.

A Na+ leak channel cloned from Trichoplax adhaerens extends extracellular pH and Ca2+ sensing for the DEG/ENaC family close to the base of Metazoa

Acid-sensitive ion channels belonging to the degenerin/epithelial sodium channel (DEG/ENaC) family activate in response to extracellular protons and are considered unique to deuterostomes. However, sensitivity to pH/protons is more widespread, where, for example, human ENaC Na+ leak channels are potentiated and mouse BASIC and Caenorhabditis elegans ACD-1 Na+ leak channels are blocked by extracellular protons. For many DEG/ENaC channels, extracellular Ca2+ ions modulate gating, and in some cases, the binding of protons and Ca2+ is interdependent. Here, we functionally characterize a DEG/ENaC channel from the early-diverging animal Trichoplax adhaerens, TadNaC6, that conducts Na+-selective leak currents in vitro sensitive to blockade by both extracellular protons and Ca2+. We determine that proton block is enhanced in low external Ca2+ concentration, whereas calcium block is enhanced in low external proton concentration, indicative of competitive binding of these two ligands to extracellular sites of the channel protein. TadNaC6 lacks most determinant residues for proton and Ca2+ sensitivity in other DEG/ENaC channels, and a mutation of one conserved residue (S353A) associated with Ca2+ block in rodent BASIC channels instead affected proton sensitivity, all indicative of independent evolution of H+ and Ca2+ sensitivity. Strikingly, TadNaC6 was potently activated by the general DEG/ENaC channel blocker amiloride, a rare feature only reported for the acid-activated channel ASIC3. The sequence and structural divergence of TadNaC6, coupled with its noncanonical functional features, provide unique opportunities for probing the proton, Ca2+, and amiloride regulation of DEG/ENaC channels and insight into the possible core-gating features of ancestral ion channels.

Response of Plantago major to cesium and strontium in hydroponics: Absorption and effects on morphology, physiology and photosynthesis

Human activities lead to increasing concentration of the stable elements cesium (Cs) and strontium (Sr) and their radioactive isotopes in the food chain, where plants play an important part. Here we investigated Plantago major under the influence of long-term exposure to stable Cs and Sr.The plants were cultivated hydroponically in different concentrations of cesium sulfate (between 0.002 and 20 mM) and strontium nitrate (between 0.001 and 100 mM).Uptake of Cs and Sr into leaves was analyzed from extracts by inductively coupled plasma mass spectrometry (ICP-MS). It was increased with increasing external Cs and Sr concentrations. However, the efficiency of Cs and Sr transfer from solution to plants was higher for low external concentrations. Highest transfer factors were 6.78 for Cs and 71.13 for Sr. Accumulation of Sr was accompanied by a slight decrease of potassium (K) and calcium (Ca) in leaves, whereas the presence of Cs in the medium affected only uptake of K.The toxic effects of Cs and Sr were estimated from photosynthetic reactions and plant growth.In leaves, Cs and Sr affected the chlorophyll fluorescence even at their low concentrations. Low and high concentrations of both ions reduced dry weight and length of roots and leaves.The distribution of the elements between the different tissues of leaves and roots was investigated using Energy Dispersive X-Ray microanalysis (EDX) with scanning electron microscope (SEM). Overall, observations suggested differential patterns in accumulating Cs and Sr within the roots and leaves.When present in higher concentrations the amount of Cs and Sr transferred from environment to plants was sufficient to affect some physiological processes. The experimental model showed a potential for P. major to study the influence of radioactive contaminants and their removal from hotspots.

Knock-Down of CsNRT2.1, a Cucumber Nitrate Transporter, Reduces Nitrate Uptake, Root length, and Lateral Root Number at Low External Nitrate Concentration.

Nitrogen (N) is a macronutrient that plays a crucial role in plant growth and development. Nitrate () is the most abundant N source in aerobic soils. Plants have evolved two adaptive mechanisms such as up-regulation of the high-affinity transport system (HATS) and alteration of the root system architecture (RSA), allowing them to cope with the temporal and spatial variation of . However, little information is available regarding the nitrate transporter in cucumber, one of the most important fruit vegetables in the world. In this study we isolated a nitrate transporter named CsNRT2.1 from cucumber. Analysis of the expression profile of the CsNRT2.1 showed that CsNRT2.1 is a high affinity nitrate transporter which mainly located in mature roots. Subcellular localization analysis revealed that CsNRT2.1 is a plasma membrane transporter. In N-starved CsNRT2.1 knock-down plants, both of the constitutive HATS (cHATS) and inducible HATS (iHATS) were impaired under low external concentration. Furthermore, the CsNRT2.1 knock-down plants showed reduced root length and lateral root numbers. Together, our results demonstrated that CsNRT2.1 played a dual role in regulating the HATS and RSA to acquire effectively under N limitation.

Salt concentration dependence of ionic conductivity in ion exchange membranes

Electric field driven ion transport in ion exchange membranes, often quantified by membrane resistance or ionic conductivity, is important for membrane-based technologies such as electrodialysis, batteries, fuel cells, etc. Various methods for measuring membrane ionic conductivity have been reported in the literature, but no widely accepted, standard protocol exists. Consequently, conflicting ionic conductivity results for widely studied commercial ion exchange membranes have been reported, leading to confusion regarding, for example, the salt concentration dependence of membrane ionic conductivity, especially for membranes equilibrated with dilute aqueous salt solutions. In this study, we report a simple, fast, reliable technique for measuring ionic conductivity based on direct contact between the membrane and electrodes. The technique was used to measure ionic conductivity values for a series of commercial ion exchange membranes as a function of external solution NaCl concentration (ranging from 0.001 to 5M). The salt concentration dependence of membrane ionic conductivity was rationalized within the Nernst-Einstein framework. At low external solution salt concentrations (< 0.3M), ionic conductivity values were essentially constant since mobile ion concentrations in the membranes approached a constant value (i.e., the fixed charge group concentration). At high salt concentrations (> 0.3M), ionic conductivity values increased with increasing salt concentration for three of the membranes, presumably due to increased ion sorption owing to weaker Donnan exclusion, and decreased for one membrane, presumably due to decreased ion diffusion coefficients resulting from osmotic deswelling.

Production of low-Cs+ rice plants by inactivation of the K+ transporter OsHAK1 with the CRISPR-Cas system.

The occurrence of radiocesium in food has raised sharp health concerns after nuclear accidents. Despite being present at low concentrations in contaminated soils (below μm), cesium (Cs+ ) can be taken up by crops and transported to their edible parts. This plant capacity to take up Cs+ from low concentrations has notably affected the production of rice (Oryza sativa L.) in Japan after the nuclear accident at Fukushima in 2011. Several strategies have been put into practice to reduce Cs+ content in this crop species such as contaminated soil removal or adaptation of agricultural practices, including dedicated fertilizer management, with limited impact or pernicious side-effects. Conversely, the development of biotechnological approaches aimed at reducing Cs+ accumulation in rice remain challenging. Here, we show that inactivation of the Cs+ -permeable K+ transporter OsHAK1 with the CRISPR-Cas system dramatically reduced Cs+ uptake by rice plants. Cs+ uptake in rice roots and in transformed yeast cells that expressed OsHAK1 displayed very similar kinetics parameters. In rice, Cs+ uptake is dependent on two functional properties of OsHAK1: (i) a poor capacity of this system to discriminate between Cs+ and K+ ; and (ii) a high capacity to transport Cs+ from very low external concentrations that is likely to involve an active transport mechanism. In an experiment with a Fukushima soil highly contaminated with 137 Cs+ , plants lacking OsHAK1 function displayed strikingly reduced levels of 137 Cs+ in roots and shoots. These results open stimulating perspectives to smartly produce safe food in regions contaminated by nuclear accidents.

Mitochondrial ATP-Mg/phosphate carriers transport divalent inorganic cations in complex with ATP.

The ATP-Mg/phosphate carriers (APCs) modulate the intramitochondrial adenine nucleotide pool size. In this study the concentration-dependent effects of Mg2+ and other divalent cations (Me2+) on the transport of [3H]ATP in liposomes reconstituted with purified human and Arabidopsis APCs (hAPCs and AtAPCs, respectively, including some lacking their N-terminal domains) have been investigated. The transport of Me2+ mediated by these proteins was also measured. In the presence of a low external concentration of [3H]ATP (12μM) and increasing concentrations of Me2+, Mg2+ stimulated the activity (measured as initial transport rate of [3H]ATP) of hAPCs and decreased that of AtAPCs; Fe2+ and Zn2+ stimulated markedly hAPCs and moderately AtAPCs; Ca2+ and Mn2+ markedly AtAPCs and moderately hAPCs; and Cu2+ decreased the activity of both hAPCs and AtAPCs. All the Me2+-dependent effects correlated well with the amount of ATP-Me complex present. The transport of [14C]AMP, which has a much lower ability of complexation than ATP, was not affected by the presence of the Me2+ tested, except Cu2+. Furthermore, the transport of [3H]ATP catalyzed by the ATP/ADP carrier, which is known to transport only free ATP and ADP, was inhibited by all the Me2+ tested in an inverse relationship with the formation of the ATP-Me complex. Finally, direct measurements of Mg2+, Mn2+, Fe2+, Zn2+ and Cu2+ showed that they are cotransported with ATP by both hAPCs and AtAPCs. It is likely that in vivo APCs transport free ATP and ATP-Mg complex to different degrees, and probably trace amounts of other Me2+ in complex with ATP.

A systems-level model reveals that 1,2-Propanediol utilization microcompartments enhance pathway flux through intermediate sequestration

The spatial organization of metabolism is common to all domains of life. Enteric and other bacteria use subcellular organelles known as bacterial microcompartments to spatially organize the metabolism of pathogenicity-relevant carbon sources, such as 1,2-propanediol. The organelles are thought to sequester a private cofactor pool, minimize the effects of toxic intermediates, and enhance flux through the encapsulated metabolic pathways. We develop a mathematical model of the function of the 1,2-propanediol utilization microcompartment of Salmonella enterica and use it to analyze the function of the microcompartment organelles in detail. Our model makes accurate estimates of doubling times based on an optimized compartment shell permeability determined by maximizing metabolic flux in the model. The compartments function primarily to decouple cytosolic intermediate concentrations from the concentrations in the microcompartment, allowing significant enhancement in pathway flux by the generation of large concentration gradients across the microcompartment shell. We find that selective permeability of the microcompartment shell is not absolutely necessary, but is often beneficial in establishing this intermediate-trapping function. Our findings also implicate active transport of the 1,2-propanediol substrate under conditions of low external substrate concentration, and we present a mathematical bound, in terms of external 1,2-propanediol substrate concentration and diffusive rates, on when active transport of the substrate is advantageous. By allowing us to predict experimentally inaccessible aspects of microcompartment function, such as intra-microcompartment metabolite concentrations, our model presents avenues for future research and underscores the importance of carefully considering changes in external metabolite concentrations and other conditions during batch cultures. Our results also suggest that the encapsulation of heterologous pathways in bacterial microcompartments might yield significant benefits for pathway flux, as well as for toxicity mitigation.

Uneven HAK/KUP/KT Protein Diversity Among Angiosperms: Species Distribution and Perspectives.

HAK/KUP/KT K+ transporters have been widely associated with K+ transport across membranes in bacteria, fungi, and plants. Indeed some members of the plant HAK/KUP/KT family contribute to root K+ uptake, notably at low external concentrations. Besides such role in acquisition, several studies carried out in Arabidopsis have shown that other members are also involved in developmental processes. With the publication of new plant genomes, a growing interest on plant species other than Arabidopsis has become evident. In order to understand HAK/KUP/KT diversity in these new plant genomes, we discuss the evolutionary trends of 913 HAK/KUP/KT sequences identified in 46 genomes revealing five major groups with an uneven distribution among angiosperms, notably between dicotyledonous and monocotyledonous species. This information evidenced the richness of crop genomes in HAK/KUP/KT transporters and supports their study for unraveling novel physiological roles of such transporters in plants.

The role of the intra- and extracellular protons in the photosynthetic response induced by the variation potential in pea seedlings

Local burning induces generation and propagation of variation potential (VP) in higher plants. VP induces transient inactivation of photosynthesis, which is possibly connected with proton signal in plant cell. Analysis of the role of changes in intracellular and extracellular pH in the VP-induced photosynthetic response in pea seedlings was the aim of this work. It was shown that local burning induced VP propagation, which was accompanied with a decrease of intracellular pH and increase of extracellular pH. VP induced photosynthesis inactivation that included an increase in the nonphotochemical fluorescence quenching and a decrease in the CO2 assimilation rate. Analysis of photosynthetic responses under control and low external CO2 concentration and changes in pH showed that there were two components in the responses. The first component appeared as a fast decrease of the CO2 assimilation and increase of nonphotochemical quenching. It depended on the activity of the dark stage of photosynthesis and was connected with apoplast alkalization. The second component was presented as a slow increase of nonphotochemical quenching. It weakly depended on a dark stage and was connected with a decrease of intracellular pH.

CATION EXCHANGER1 Cosegregates with Cadmium Tolerance in the Metal Hyperaccumulator Arabidopsis halleri and Plays a Role in Limiting Oxidative Stress in Arabidopsis Spp.

Arabidopsis halleri is a model species for the study of plant adaptation to extreme metallic conditions. In this species, cadmium (Cd) tolerance seems to be constitutive, and the mechanisms underlying the trait are still poorly understood. A previous quantitative trait loci (QTL) analysis performed on A. halleri × Arabidopsis lyrata backcross population1 identified the metal-pump gene Heavy Metal ATPase4 as the major genetic determinant for Cd tolerance. However, although necessary, Heavy Metal ATPase4 alone is not sufficient for determining this trait. After fine mapping, a gene encoding a calcium(2+)/hydrogen(+) antiporter, cation/hydrogen(+) exchanger1 (CAX1), was identified as a candidate gene for the second QTL of Cd tolerance in A. halleri. Backcross population1 individuals displaying the A. halleri allele for the CAX1 locus exhibited significantly higher CAX1 expression levels compared with the ones with the A. lyrata allele, and a positive correlation between CAX1 expression and Cd tolerance was observed. Here, we show that this QTL is conditional and that it is only detectable at low external Ca concentration. CAX1 expression in both roots and shoots was higher in A. halleri than in the close Cd-sensitive relative species A. lyrata and Arabidopsis thaliana. Moreover, CAX1 loss of function in A. thaliana led to higher Cd sensitivity at low concentration of Ca, higher sensitivity to methylviologen, and stronger accumulation of reactive oxygen species after Cd treatment. Overall, this study identifies a unique genetic determinant of Cd tolerance in the metal hyperaccumulator A. halleri and offers a new twist for the function of CAX1 in plants.

Simulating the effects of light intensity and carbonate system composition on particulate organic and inorganic carbon production in Emiliania huxleyi.

Coccolithophores play an important role in the marine carbon cycle. Variations in light intensity and external carbonate system composition alter intracellular carbon fluxes and therewith the production rates of particulate organic and inorganic carbon. Aiming to find a mechanistic explanation for the interrelation between dissolved inorganic carbon fluxes and particulate carbon production rates, we develop a numerical cell model for Emiliania huxleyi, one of the most abundant coccolithophore species. The model consists of four cellular compartments, for each of which the carbonate system is resolved dynamically. The compartments are connected to each other and to the external medium via substrate fluxes across the compartment-confining membranes. By means of the model we are able to explain several pattern observed in particulate organic and inorganic carbon production rates for different strains and under different acclimation conditions. Particulate organic and inorganic carbon production rates for instance decrease at very low external CO2 concentrations. Our model suggests that this effect is caused mainly by reduced HCO3(-) uptake rates, not by CO2 limitation. The often observed decrease in particulate inorganic carbon production rates under Ocean Acidification is explained by a downregulation of cellular HCO3(-) uptake.

Breaking conceptual locks in modelling root absorption of nutrients: reopening the thermodynamic viewpoint of ion transport across the root.

The top-down analysis of nitrate influx isotherms through the Enzyme-Substrate interpretation has not withstood recent molecular and histochemical analyses of nitrate transporters. Indeed, at least four families of nitrate transporters operating at both high and/or low external nitrate concentrations, and which are located in series and/or parallel in the different cellular layers of the mature root, are involved in nitrate uptake. Accordingly, the top-down analysis of the root catalytic structure for ion transport from the Enzyme-Substrate interpretation of nitrate influx isotherms is inadequate. Moreover, the use of the Enzyme-Substrate velocity equation as a single reference in agronomic models is not suitable in its formalism to account for variations in N uptake under fluctuating environmental conditions. Therefore, a conceptual paradigm shift is required to improve the mechanistic modelling of N uptake in agronomic models. An alternative formalism, the Flow-Force theory, was proposed in the 1970s to describe ion isotherms based upon biophysical 'flows and forces' relationships of non-equilibrium thermodynamics. This interpretation describes, with macroscopic parameters, the patterns of N uptake provided by a biological system such as roots. In contrast to the Enzyme-Substrate interpretation, this approach does not claim to represent molecular characteristics. Here it is shown that it is possible to combine the Flow-Force formalism with polynomial responses of nitrate influx rate induced by climatic and in planta factors in relation to nitrate availability. Application of the Flow-Force formalism allows nitrate uptake to be modelled in a more realistic manner, and allows scaling-up in time and space of the regulation of nitrate uptake across the plant growth cycle.

Phytotoxicity of Sodium Fluoride and Uptake of Fluoride in Willow Trees

The willow tree (Salix viminalis) toxicity test and a cress seed germination test (Lepidium sativum) were used to determine uptake of F and phytotoxicity of NaF. Concentrations in hydroponic solutions were 0–1000 mg F/L and 0–400 mg F/L in the preliminary and definitive test. A third test was done with soils collected from a fluoride-contaminated site at Fredericia, Denmark. The EC10, EC20 and EC50-values for inhibition of transpiration were determined to 38.0, 59.6 and 128.7 mg F/L, respectively. The toxicity test with soil showed strong inhibition for the sample with the highest fluoride concentration (405 mg free F per kg soil, 75 mg F per L soil solution). The seed germination and root elongation test with cress gave EC10, EC20 and EC50-values of 61.4, 105.0 and 262.8 mg F/L, respectively. At low external concentrations, fluoride was taken up more slowly than water and at high external concentrations at the same velocity. This indicates that an efflux pump becomes overloaded at concentrations above 210 mg F/L. Uptake kinetics were simulated with a non-linear mathematical model, and the Michaelis-Menten parameters were determined to half-saturation constant KM near 2 g F/L and maximum enzymatic removal rate vmax at 9 g/(kg d).

Monte-Carlo modeling of the central carbon metabolism of Lactococcus lactis: insights into metabolic regulation.

Metabolic pathways are complex dynamic systems whose response to perturbations and environmental challenges are governed by multiple interdependencies between enzyme properties, reactions rates, and substrate levels. Understanding the dynamics arising from such a network can be greatly enhanced by the construction of a computational model that embodies the properties of the respective system. Such models aim to incorporate mechanistic details of cellular interactions to mimic the temporal behavior of the biochemical reaction system and usually require substantial knowledge of kinetic parameters to allow meaningful conclusions. Several approaches have been suggested to overcome the severe data requirements of kinetic modeling, including the use of approximative kinetics and Monte-Carlo sampling of reaction parameters. In this work, we employ a probabilistic approach to study the response of a complex metabolic system, the central metabolism of the lactic acid bacterium Lactococcus lactis, subject to perturbations and brief periods of starvation. Supplementing existing methodologies, we show that it is possible to acquire a detailed understanding of the control properties of a corresponding metabolic pathway model that is directly based on experimental observations. In particular, we delineate the role of enzymatic regulation to maintain metabolic stability and metabolic recovery after periods of starvation. It is shown that the feedforward activation of the pyruvate kinase by fructose-1,6-bisphosphate qualitatively alters the bifurcation structure of the corresponding pathway model, indicating a crucial role of enzymatic regulation to prevent metabolic collapse for low external concentrations of glucose. We argue that similar probabilistic methodologies will help our understanding of dynamic properties of small-, medium- and large-scale metabolic networks models.