Why Nature Chose Potassium

Origin of the RNA World in Cold Hadean Geothermal Fields Enriched in Zinc and Potassium: Abiogenesis as a Positive Fallout from the Moon-Forming Impact?

The ubiquitous, evolutionarily oldest RNAs and proteins exclusively use rather rare zinc as transition metal cofactor and potassium as alkali metal cofactor, which implies their abundance in the habitats of the first organisms. Intriguingly, lunar rocks contain a hundred times less zinc and ten times less potassium than the Earth's crust; the Moon is also depleted in other moderately volatile elements (MVEs). Current theories of impact formation of the Moon attribute this depletion to the MVEs still being in a gaseous state when the hot post-impact disk contracted and separated from the nascent Moon. The MVEs then fell out onto juvenile Earth's protocrust; zinc, as the most volatile metal, precipitated last, just after potassium. According to our calculations, the top layer of the protocrust must have contained up to 1019 kg of metallic zinc, a powerful reductant. The venting of hot geothermal fluids through this MVE-fallout layer, rich in metallic zinc and radioactive potassium, both capable of reducing carbon dioxide and dinitrogen, must have yielded a plethora of organic molecules released with the geothermal vapor. In the pools of vapor condensate, the RNA-like molecules may have emerged through a pre-Darwinian selection for low-volatile, associative, mineral-affine, radiation-resistant, nitrogen-rich, and polymerizable molecules.

Morphological, anatomical, and bioactive properties of Hypericum scabrum L.: effects on diabetes mellitus, Alzheimer's disease, and HDFa fibroblasts and U87-MG cancer cells

Diabetes mellitus (DM) and cancer are multifactorial diseases with significant health consequences, and their relationship with aging makes them particularly challenging. Epidemiological data suggests that individuals with DM are more susceptible to certain cancers. This study examined the bioactive properties of Hypericum scabrum extracts, including methanol, hexane, and others, focusing on their inhibitory effects on key enzymes associated with DM and neurodegenerative diseases, such as acetylcholinesterase, butyrylcholinesterase, α-amylase, and α-glucosidase. Additionally, the impact of these extracts on human fibroblast (HDFa) and glioblastoma (U87MG) cancer cells was evaluated. The methanol extract was analyzed for elemental composition using ICP-MS, secondary metabolites, and amino acids via LC-MS/MS and underwent morphological and anatomical characterization. The methanol extract demonstrated notable inhibitory activity, with an IC50 value of < 1 µg/mL against α-glucosidase, surpassing acarbose in efficacy. The flower essential oil exhibited the highest inhibition (79.95%) of butyrylcholinesterase and the strongest acetylcholinesterase inhibition (21.62%). Elemental analysis revealed high concentrations of Na and K, while quinic acid and proline were identified as major metabolites, with proline concentrations reaching 494.0482 nmol/mL in the aerial part extract. The anticancer assays revealed higher cytotoxicity in U87MG glioblastoma cells compared to HDFa fibroblasts, suggesting potential applications for cancer therapy. The plant grows 20-50 cm tall, with yellow flowers and ovoid-ribbed capsules containing brown, reniform seeds. Its leaves are amphistomatic and ornamented, while stems feature striate cuticles and paracytic stomata. The pollen grains are microreticulate with syncolporate apertures. These results underscore the promising therapeutic potential of H. scabrum in managing DM, cancer, and neurodegenerative diseases, with its ability to inhibit key enzymes and show selective cytotoxicity against cancer cells.

Preliminary Research on Dietary Supplementation of Potassium Magnesium Sulphate on Transport Stress in Finishing Pigs Prior to Slaughter

Transport stress prior to slaughter frequently induces a stress response, negatively affecting meat quality. This study investigated the impact of dietary potassium magnesium sulphate (PMS) supplementation during the fattening stage on the stress response and meat quality in finishing pigs subjected to transport stress. The experiment involved two phases. Initially, 48 finishing pigs (68.00 ± 0.40 kg) were randomly allocated into two groups: a control group receiving a basal diet (CON) and a PMS-supplemented group receiving the basal diet with 0.50% PMS. Each group was housed in six pens, with four pigs per pen. After 60 days of feeding, in the second phase, two pigs from each pen were randomly selected for slaughter, with one pig subjected to a 4 h transportation stress prior to slaughter. Pigs were categorized into four treatment groups based on diet and stress: (1) control without transport stress, (2) control with transport stress, (3) PMS-supplemented without transport stress, and (4) PMS-supplemented with transport stress. Serum, jejunum, and longissimus thoracis muscle (LM) samples were collected. The results indicated that dietary PMS supplementation did not significantly affect growth performance during the fattening stage (p > 0.05). However, following transport, the PMS pigs showed a reduction in norepinephrine and cortisol concentrations (p = 0.09, p < 0.05) and a significant increase in serum glutathione peroxidase (GSH-Px) activity (p < 0.05). Furthermore, PMS supplementation significantly increased serum catalase (CAT), total antioxidant capacity (T-AOC), alkaline phosphatase (AKP) activity, and high-density lipoprotein cholesterol (HDL-C) levels (p < 0.05), while significantly reducing cholesterol (CHO) levels (p < 0.05). Transport stress adversely affected the intestinal health of finishing pigs, as evidenced by a decrease in intestinal villus height (0.05 < p < 0.1), a condition ameliorated by PMS supplementation. Additionally, transported pigs exhibited a higher drip loss24h in LM (p < 0.05), which was also alleviated through PMS supplementation. In conclusion, PMS supplementation mitigates transport stress and improves meat quality in finishing pigs.

Metals in Motion: Understanding Labile Metal Pools in Bacteria

Metal ions are essential for all life. In microbial cells, potassium (K+) is the most abundant cation and plays a key role in maintaining osmotic balance. Magnesium (Mg2+) is the dominant divalent cation and is required for nucleic acid structure and as an enzyme cofactor. Microbes typically require the transition metals manganese (Mn), iron (Fe), copper (Cu), and zinc (Zn), although the precise set of metal ions needed to sustain life is variable. Intracellular metal pools can be conceptualized as a chemically complex mixture of rapidly exchanging (labile) ions, complemented by those reservoirs that exchange slowly relative to cell metabolism (sequestered). Labile metal pools are buffered by transient interactions with anionic metabolites and macromolecules, with the ribosome playing a major role. Sequestered metal pools include many metalloproteins, cofactors, and storage depots, with some pools redeployed upon metal depletion. Here, I review the size, composition, and dynamics of intracellular metal pools and highlight the major gaps in understanding.

Potassium extrusion by plant cells: evolution from an emergency valve to a driver of long-distance transport

The ability to accumulate nutrients is a hallmark for living creatures and plants evolved highly effective nutrient transport systems, especially for the uptake of potassium (K+). However, plants also developed mechanisms that enable the rapid extrusion of K+ in combination with anions. The combined release of K+ and anions is probably an ancient extrusion system, as it is found in the Characeae that are closely related to land plants. We postulate that the ion extrusion mechanisms have developed as an emergency valve, which enabled plant cells to rapidly reduce their turgor, and prevent them from bursting. Later in evolution, seed plants adapted this system for various responses, such as the closure of stomata, long-distance stress waves, dropping of leaves by pulvini, and loading of xylem vessels. We discuss the molecular nature of the transport proteins that are involved in ion extrusion-based functions of plants and describe the functions that they obtained during evolution.

Disentangling the Regulatory Response of Agrobacterium tumefaciens CHLDO to Glyphosate for Engineering Whole-Cell Phosphonate Biosensors

Phosphonates (PHTs), organic compounds with a stable C-P bond, are widely distributed in nature. Glyphosate (GP), a synthetic PHT, is extensively used in agriculture and has been linked to various human health issues and environmental damage. Given the prevalence of GP, developing cost-effective, on-site methods for GP detection is key for assessing pollution and reducing exposure risks. We adopted Agrobacterium tumefaciens CHLDO, a natural GP degrader, as a host and the source of genetic parts for constructing PHT biosensors. In this bacterial species, the phn gene cluster, encoding the C-P lyase pathway, is regulated by the PhnF transcriptional repressor. We selected the phnG promoter, which displays a dose-dependent response to GP, to build a set of whole-cell biosensors. Through stepwise genetic optimization of the transcriptional cascade, we created a whole-cell biosensor capable of detecting GP in the 0.25-50 μM range in various samples, including soil and water.

Regulation of potassium uptake in Caulobacter crescentus

Potassium (K+) is an essential physiological element determining membrane potential, intracellular pH, osmotic/turgor pressure, and protein synthesis in cells. Here, we describe the regulation of potassium uptake systems in the oligotrophic α-proteobacterium Caulobacter crescentus known as a model for asymmetric cell division. We show that C. crescentus can grow in concentrations from the micromolar to the millimolar range by mainly using two K+ transporters to maintain potassium homeostasis, the low-affinity Kup and the high-affinity Kdp uptake systems. When K+ is not limiting, we found that the kup gene is essential while kdp inactivation does not impact the growth. In contrast, kdp becomes critical but not essential and kup dispensable for growth in K+-limited environments. However, in the absence of kdp, mutations in kup were selected to improve growth in K+-depleted conditions, likely by increasing the affinity of Kup for K+. In addition, mutations in the KdpDE two-component system, which regulates kdpABCDE expression, suggest that the inner membrane sensor regulatory component KdpD mainly works as a phosphatase to limit the growth when cells reach late exponential phase. Our data therefore suggest that KdpE is phosphorylated by another non-cognate histidine kinase. On top of this, we determined the KdpE-dependent and independent K+ transcriptome. Together, our work illustrates how an oligotrophic bacterium responds to fluctuation in K+ availability.IMPORTANCEPotassium (K+) is a key metal ion involved in many essential cellular processes. Here, we show that the oligotroph Caulobacter crescentus can support growth at micromolar concentrations of K+ by mainly using two K+ uptake systems, the low-affinity Kup and the high-affinity Kdp. Using genome-wide approaches, we also determined the entire set of genes required for C. crescentus to survive at low K+ concentration as well as the full K+-dependent regulon. Finally, we found that the transcriptional regulation mediated by the KdpDE two-component system is unconventional since unlike Escherichia coli, the inner membrane sensor regulatory component KdpD seems to work rather as a phosphatase on the phosphorylated response regulator KdpE~P.

Formation of methylglyoxal (CH3C(O)CHO) in interstellar analog ices - a key intermediate in cellular metabolism

Ketoaldehydes are key intermediates in biochemical processes including carbohydrate, lipid, and amino acid metabolism. Despite their crucial role in the interstellar synthesis of essential biomolecules necessary for the Origins of Life, their formation mechanisms have largely remained elusive. Here, we report the first bottom-up formation of methylglyoxal (CH3C(O)CHO)-the simplest ketoaldehyde-through the barrierless recombination of the formyl (HĊO) radical with the acetyl (CH3ĊO) radical in low-temperature interstellar ice analogs upon exposure to energetic irradiation as proxies of galactic cosmic rays. Utilizing vacuum ultraviolet photoionization reflectron time-of-flight mass spectrometry and isotopic substitution studies, methylglyoxal and its enol tautomer 2-hydroxypropenone (CH3C(OH)CO) were identified in the gas phase during the temperature-programmed desorption of irradiated carbon monoxide-acetaldehyde (CO-CH3CHO) ices, suggesting their potential as promising candidates for future astronomical searches. Once synthesized in cold molecular clouds, methylglyoxal can serve as a key precursor to sugars, sugar acids, and amino acids. Furthermore, this work provides the first experimental evidence for tautomerization of a ketoaldehyde in interstellar ice analogs, advancing our fundamental knowledge of how ketoaldehydes and their enol tautomers can be synthesized in deep space.

Membrane potential dynamics unveil the promise of bioelectrical antimicrobial susceptibility Testing (BeAST) for anti-fungal screening

Membrane potential is a useful marker for antimicrobial susceptibility testing (AST) due to its fundamental roles in cell function. However, the difficulties associated with measuring the membrane potential in microbes restrict its broad application. In this study, we present bioelectrical AST (BeAST) using the model fungus Saccharomyces cerevisiae. Using fluorescent indicators [DiBAC4(3), ThT, and TMRM], we measured plasma and mitochondrial membrane-potential dynamics upon electric stimulation. We find that a 2.5 second electric stimulation induces hyperpolarization of plasma membrane lasting 20 minutes in vital S. cerevisiae, but depolarization in inhibited cells. The numerical simulation of FitzHugh-Nagumo model successfully recapitulates vitality-dependent dynamics. The model also suggests that the magnitude of plasma-membrane potential dynamics (PMD) correlates with the degree of inhibition. To test this prediction and to examine if BeAST can be used for assessing novel anti-fungal compounds, we treat cells with biogenic silver nanoparticles (bioAgNPs) synthesized using orange fruit flavonoids and Fusarium oxysporum. Comparing BeAST with optical density assay alongside various stressors, we show that PMD correlates with the magnitude of growth inhibitions. These results suggest that BeAST holds promise for screening anti-fungal compounds, offering a valuable approach to tackling antimicrobial resistance.

IMPORTANCE

Rapid assessment of the efficacy of antimicrobials is important for optimizing treatments, avoiding misuse and facilitating the screening of new antimicrobials. The need for rapid antimicrobial susceptibility testing (AST) is growing with the rise of antimicrobial resistance. Here, we present bioelectrical AST (BeAST). Combining time-lapse microscopy and mathematical modeling, we show that electrically induced membrane potential dynamics of yeast cells correspond to the strength of growth inhibition. Furthermore, we demonstrate the utility of BeAST for assessing antimicrobial activities of novel compounds using biogenic silver nanoparticles.

DarA-the central processing unit for the integration of osmotic with potassium and amino acid homeostasis in Bacillus subtilis

Cyclic di-adenosine monophosphate (c-di-AMP) is a second messenger involved in diverse metabolic processes including osmolyte uptake, cell wall homeostasis, as well as antibiotic and heat resistance. This study investigates the role of the c-di-AMP receptor protein DarA in the osmotic stress response in Bacillus subtilis. Through a series of experiments, we demonstrate that DarA plays a central role in the cellular response to osmotic fluctuations. Our findings show that DarA becomes essential under extreme potassium limitation as well as upon salt stress, highlighting its significance in mediating osmotic stress adaptation. Suppressor screens with darA mutants reveal compensatory mechanisms involving the accumulation of osmoprotectants, particularly potassium and citrulline. Mutations affecting various metabolic pathways, including the citric acid cycle as well as glutamate and arginine biosynthesis, indicate a complex interplay between the osmotic stress response and metabolic regulation. In addition, the growth defects of the darA mutant during potassium starvation and salt stress in a strain lacking the high-affinity potassium uptake systems KimA and KtrAB can be rescued by increased affinity of the remaining potassium channel KtrCD or by increased expression of ktrD, thus resulting in increased potassium uptake. Finally, the darA mutant can respond to salt stress by the increased expression of MleN , which can export sodium ions.IMPORTANCEEnvironmental bacteria are exposed to rapidly changing osmotic conditions making an effective adaptation to these changes crucial for the survival of the cells. In Gram-positive bacteria, the second messenger cyclic di-AMP plays a key role in this adaptation by controlling (i) the influx of physiologically compatible organic osmolytes and (ii) the biosynthesis of such osmolytes. In several bacteria, cyclic di-adenosine monophosphate (c-di-AMP) can bind to a signal transduction protein, called DarA, in Bacillus subtilis. So far, no function for DarA has been discovered in any organism. We have identified osmotically challenging conditions that make DarA essential and have identified suppressor mutations that help the bacteria to adapt to those conditions. Our results indicate that DarA is a central component in the integration of osmotic stress with the synthesis of compatible amino acid osmolytes and with the homeostasis of potassium, the first response to osmotic stress.

Fluorescent Protein-Based Sensors for Detecting Essential Metal Ions across the Tree of Life

Genetically encoded fluorescent metal ion sensors are powerful tools for elucidating metal dynamics in living systems. Over the last 25 years since the first examples of genetically encoded fluorescent protein-based calcium indicators, this toolbox of probes has expanded to include other essential and non-essential metal ions. Collectively, these tools have illuminated fundamental aspects of metal homeostasis and trafficking that are crucial to fields ranging from neurobiology to human nutrition. Despite these advances, much of the application of metal ion sensors remains limited to mammalian cells and tissues and a limited number of essential metals. Applications beyond mammalian systems and in vivo applications in living organisms have primarily used genetically encoded calcium ion sensors. The aim of this Perspective is to provide, with the support of historical and recent literature, an updated and critical view of the design and use of fluorescent protein-based sensors for detecting essential metal ions in various organisms. We highlight the historical progress and achievements with calcium sensors and discuss more recent advances and opportunities for the detection of other essential metal ions. We also discuss outstanding challenges in the field and directions for future studies, including detecting a wider variety of metal ions, developing and implementing a broader spectral range of sensors for multiplexing experiments, and applying sensors to a wider range of single- and multi-species biological systems.

Energy optimisation predicts the capacity of ion buffering in the brain

Neurons store energy in the ionic concentration gradients they build across their cell membrane. The amount of energy stored, and hence the work the ions can do by mixing, can be enhanced by the presence of ion buffers in extra- and intracellular space. Buffers act as sources and sinks of ions, however, and unless the buffering capacities for different ion species obey certain relationships, a complete mixing of the ions may be impeded by the physical conditions of charge neutrality and isotonicity. From these conditions, buffering capacities were calculated that enabled each ion species to mix completely. In all valid buffer distributions, the [Formula: see text] ions were buffered most, with a capacity exceeding that of [Formula: see text] and [Formula: see text] buffering by at least an order of magnitude. The similar magnitude of the (oppositely directed) [Formula: see text] and [Formula: see text] gradients made extracellular space behave as a [Formula: see text]-[Formula: see text] exchanger. Anions such as [Formula: see text] were buffered least. The great capacity of the extra- and intracellular [Formula: see text] buffers caused a large influx of [Formula: see text] ions as is typically observed during energy deprivation. These results explain many characteristics of the physiological buffer distributions but raise the question how the brain controls the capacity of its ion buffers. It is suggested that neurons and glial cells, by their great sensitivity to gradients of charge and osmolarity, respectively, sense deviations from electro-neutral and isotonic mixing, and use these signals to tune the chemical composition, and buffering capacity, of the extra- and intracellular matrices.

Essential and non-essential elements in tuna and billfish around the world: Distribution patterns and influencing factors

Tuna and billfish are widely distributed in oceans worldwide. Their survival is relied on a decent share of essential and non-essential elements. We conducted a comprehensive evaluation of essential and non-essential elements in livers of tuna and billfish collected from global oceans. The individual element consistently shown similar orders of magnitude in both tuna and billfish, with essential elements generally being 1-3 orders of magnitude higher than non-essential elements. Various physicochemical properties and behaviors contributed to four distinct clusters of these elements. Also, element distribution pattern indicated the presence of four sample groups based on regions and categories. Nine elements served as characteristic indicators. Among them, fish category was the most important influencing factor. Hg, Fe, Tl, Co, and Se were influenced by body size, trophic level, and feeding habits. Ni was influenced by sampling regions, while Mg, Mn and As were influenced by body size and local primary production.

The many roles of cyclic di-AMP to control the physiology of Bacillus subtilis

The dinucleotide cyclic di-AMP (c-di-AMP) is synthesized as a second messenger in the Gram-positive model bacterium Bacillus subtilis as well as in many bacteria and archaea. Bacillus subtilis possesses three diadenylate cyclases and two phosphodiesterases that synthesize and degrade the molecule, respectively. Among the second messengers, c-di-AMP is unique since it is essential for B. subtilis on the one hand but toxic upon accumulation on the other. This role as an "essential poison" is related to the function of c-di-AMP in the control of potassium homeostasis. C-di-AMP inhibits the expression and activity of potassium uptake systems by binding to riboswitches and transporters and activates the activity of potassium exporters. In this way, c-di-AMP allows the adjustment of uptake and export systems to achieve a balanced intracellular potassium concentration. C-di-AMP also binds to two dedicated signal transduction proteins, DarA and DarB. Both proteins seem to interact with other proteins in their apo state, i.e. in the absence of c-di-AMP. For DarB, the (p)ppGpp synthetase/hydrolase Rel and the pyruvate carboxylase PycA have been identified as targets. The interactions trigger the synthesis of the alarmone (p)ppGpp and of the acceptor molecule for the citric acid cycle, oxaloacetate, respectively. In the absence of c-di-AMP, many amino acids inhibit the growth of B. subtilis. This feature can be used to identify novel players in amino acid homeostasis. In this review, we discuss the different functions of c-di-AMP and their physiological relevance.

Modulation of potassium transport to increase abiotic stress tolerance in plants

Potassium is the major cation responsible for the maintenance of the ionic environment in plant cells. Stable potassium homeostasis is indispensable for virtually all cellular functions, and, concomitantly, viability. Plants must cope with environmental changes such as salt or drought that can alter ionic homeostasis. Potassium fluxes are required to regulate the essential process of transpiration, so a constraint on potassium transport may also affect the plant's response to heat, cold, or oxidative stress. Sequencing data and functional analyses have defined the potassium channels and transporters present in the genomes of different species, so we know most of the proteins directly participating in potassium homeostasis. The still unanswered questions are how these proteins are regulated and the nature of potential cross-talk with other signaling pathways controlling growth, development, and stress responses. As we gain knowledge regarding the molecular mechanisms underlying regulation of potassium homeostasis in plants, we can take advantage of this information to increase the efficiency of potassium transport and generate plants with enhanced tolerance to abiotic stress through genetic engineering or new breeding techniques. Here, we review current knowledge of how modifying genes related to potassium homeostasis in plants affect abiotic stress tolerance at the whole plant level.

The Na+,K+-ATPase and its stoichiometric ratio: some thermodynamic speculations

 Almost seventy years after its discovery, the sodium-potassium adenosine triphosphatase (the sodium pump) located in the cell plasma membrane remains a source of novel mechanistic and physiologic findings. A noteworthy feature of this enzyme/transporter is its robust stoichiometric ratio under physiological conditions: it sequentially counter-transports three sodium ions and two potassium ions against their electrochemical potential gradients per each hydrolyzed ATP molecule. Here we summarize some present knowledge about the sodium pump and its physiological roles, and speculate whether energetic constraints may have played a role in the evolutionary selection of its characteristic stoichiometric ratio.

Uncovering the significance of the ratio of food K:Na in bee ecology and evolution

Bees provide important ecological services, and many species are threatened globally, yet our knowledge of wild bee ecology and evolution is limited. While evolving from carnivorous ancestors, bees had to develop strategies for coping with limitations imposed on them by a plant-based diet, with nectar providing energy and essential amino acids and pollen as an extraordinary, protein- and lipid-rich food nutritionally similar to animal tissues. Both nectar and pollen display one characteristic common to plants, a high ratio of potassium to sodium (K:Na), potentially leading to bee underdevelopment, health problems, and death. We discuss why and how the ratio of K:Na contributes to bee ecology and evolution and how considering this factor in future studies will provide new knowledge, more accurately depicting the relationship of bees with their environments. Such knowledge is essential for understanding how plants and bees function and interact and is needed to effectively protect wild bees.

A model industrial workhorse: Bacillus subtilis strain 168 and its genome after a quarter of a century

The vast majority of genomic sequences are automatically annotated using various software programs. The accuracy of these annotations depends heavily on the very few manual annotation efforts that combine verified experimental data with genomic sequences from model organisms. Here, we summarize the updated functional annotation of Bacillus subtilis strain 168, a quarter century after its genome sequence was first made public. Since the last such effort 5 years ago, 1168 genetic functions have been updated, allowing the construction of a new metabolic model of this organism of environmental and industrial interest. The emphasis in this review is on new metabolic insights, the role of metals in metabolism and macromolecule biosynthesis, functions involved in biofilm formation, features controlling cell growth, and finally, protein agents that allow class discrimination, thus allowing maintenance management, and accuracy of all cell processes. New 'genomic objects' and an extensive updated literature review have been included for the sequence, now available at the International Nucleotide Sequence Database Collaboration (INSDC: AccNum AL009126.4).

The elements of life: A biocentric tour of the periodic table

Living systems are built from a small subset of the atomic elements, including the bulk macronutrients (C,H,N,O,P,S) and ions (Mg,K,Na,Ca) together with a small but variable set of trace elements (micronutrients). Here, we provide a global survey of how chemical elements contribute to life. We define five classes of elements: those that are (i) essential for all life, (ii) essential for many organisms in all three domains of life, (iii) essential or beneficial for many organisms in at least one domain, (iv) beneficial to at least some species, and (v) of no known beneficial use. The ability of cells to sustain life when individual elements are absent or limiting relies on complex physiological and evolutionary mechanisms (elemental economy). This survey of elemental use across the tree of life is encapsulated in a web-based, interactive periodic table that summarizes the roles chemical elements in biology and highlights corresponding mechanisms of elemental economy.

Challenges and opportunities in bringing nonbiological atoms to life with synthetic metabolism

The relatively narrow spectrum of chemical elements within the microbial 'biochemical palate' limits the reach of biotechnology, because several added-value compounds can only be produced with traditional organic chemistry. Synthetic biology offers enabling tools to tackle this issue by facilitating 'biologization' of non-canonical chemical atoms. The interplay between xenobiology and synthetic metabolism multiplies routes for incorporating nonbiological atoms into engineered microbes. In this review, we survey natural assimilation routes for elements beyond the essential biology atoms [i.e., carbon (C), hydrogen (H), nitrogen (N), oxygen (O), phosphorus (P), and sulfur (S)], discussing how these mechanisms could be repurposed for biotechnology. Furthermore, we propose a computational framework to identify chemical elements amenable to biologization, ranking reactions suitable to build synthetic metabolism. When combined and deployed in robust microbial hosts, these approaches will offer sustainable alternatives for smart chemical production.

Two Trk/Ktr/HKT-type potassium transporters, TrkG and TrkH, perform distinct functions in Escherichia coli K-12

Escherichia coli K-12 possesses two versions of Trk/Ktr/HKT-type potassium ion (K⁺) transporters, TrkG and TrkH. The current paradigm is that TrkG and TrkH have largely identical characteristics, and little information is available regarding their functional differences. Here, we show using cation uptake experiments with K⁺ transporter knockout mutants that TrkG and TrkH have distinct ion transport activities and physiological roles. K⁺-transport by TrkG required Na⁺, whereas TrkH-mediated K⁺ uptake was not affected by Na⁺. An aspartic acid located five residues away from a critical glycine in the third pore-forming region might be involved in regulation of Na⁺-dependent activation of TrkG. In addition, we found that TrkG but not TrkH had Na⁺ uptake activity. Our analysis of K⁺ transport mutants revealed that TrkH supported cell growth more than TrkG; however, TrkG was able to complement loss of TrkH-mediated K⁺ uptake in E. coli. Furthermore, we determined that transcription of trkG in E. coli was downregulated but not completely silenced by the xenogeneic silencing factor H-NS (histone-like nucleoid structuring protein or heat-stable nucleoid-structuring protein). Taken together, the transport function of TrkG is clearly distinct from that of TrkH, and TrkG seems to have been accepted by E. coli during evolution as a K⁺ uptake system that coexists with TrkH.

Significance of two transmembrane ion gradients for human erythrocyte volume stabilization

Functional effectiveness of erythrocytes depends on their high deformability that allows them to pass through narrow tissue capillaries. The erythrocytes can deform easily due to discoid shape provided by the stabilization of an optimal cell volume at a given cell surface area. We used mathematical simulation to study the role of transport Na/K-ATPase and transmembrane Na+ and K+ gradients in human erythrocyte volume stabilization at non-selective increase in cell membrane permeability to cations. The model included Na/K-ATPase activated by intracellular Na+, Na+ and K+ transmembrane gradients, and took into account contribution of glycolytic metabolites and adenine nucleotides to cytoplasm osmotic pressure. We found that this model provides the best stabilization of the erythrocyte volume at non-selective increase in the permeability of the cell membrane, which can be caused by an oxidation of the membrane components or mechanical stress during circulation. The volume of the erythrocyte deviates from the optimal value by no more than 10% with a change in the non-selective permeability of the cell membrane to cations from 50 to 200% of the normal value. If only one transmembrane ion gradient is present (Na+), the cell loses the ability to stabilize volume and even small changes in membrane permeability cause dramatic changes in the cell volume. Our results reveal that the presence of two oppositely directed transmembrane ion gradients is fundamentally important for robust stabilization of cellular volume in human erythrocytes.

Role of the CrcB transporter of Pseudomonas putida in the multi-level stress response elicited by mineral fluoride

The presence of mineral fluoride (F^- ) in the environment has both a geogenic and anthropogenic origin, and the halide has been described to be toxic in virtually all living organisms. While the evidence gathered in different microbial species supports this notion, a systematic exploration of the effects of F^- salts on the metabolism and physiology of environmental bacteria remained underexplored thus far. In this work, we studied and characterized tolerance mechanisms deployed by the model soil bacterium Pseudomonas putida KT2440 against NaF. By adopting systems-level omic approaches, including functional genomics and metabolomics, we gauged the impact of this anion at different regulatory levels under conditions that impair bacterial growth. Several genes involved in halide tolerance were isolated in a genome-wide Tn-Seq screening-among which crcB, encoding an F^- -specific exporter, was shown to play the predominant role in detoxification. High-resolution metabolomics, combined with the assessment of intracellular and extracellular pH values and quantitative physiology experiments, underscored the key nodes in central carbon metabolism affected by the presence of F^- . Taken together, our results indicate that P. putida undergoes a general, multi-level stress response when challenged with NaF that significantly differs from that caused by other saline stressors. While microbial stress responses to saline and oxidative challenges have been extensively studied and described in the literature, very little is known about the impact of fluoride (F^- ) on bacterial physiology and metabolism. This state of affairs contrasts with the fact that F^- is more abundant than other halides in the Earth crust (e.g. in some soils, the F^- concentration can reach up to 1 mg g_soil ^-1 ). Understanding the global effects of NaF treatment on bacterial physiology is not only relevant to unveil distinct mechanisms of detoxification but it could also guide microbial engineering approaches for the target incorporation of fluorine into value-added organofluorine molecules. In this regard, the soil bacterium P. putida constitutes an ideal model to explore such scenarios, since this species is particularly known for its high level of stress resistance against a variety of physicochemical perturbations.

Socializing Models During Lactation Alter Colonic Mucosal Gene Expression and Fecal Microbiota of Growing Piglets

The enrichment of the social environment during lactation alleviates the stress of weaned piglets. It is significant to understand how the enriched social environment improves the weaning stress of piglets. RNA sequencing (RNA-seq) of colonic mucosa, 16S rRNA sequencing of feces, and short-chain fatty acids (SCFAs) of colonic content were used to determine the effects of social contact during lactation. In this study, thirty litter lactating piglets were divided into intermittent social contact (ISC) group that contacted with neighbors intermittently, continuous social contact (CSC) group that contacted with neighbors starting at day (D) 14 after birth, and control (CON) group in which piglets were kept in their original litter. The piglets were weaned at D35 and regrouped at D36. The colonic mucosal RNA-seq, fecal microbes, and SCFAs of colonic contents of 63-day-old piglets were analyzed. The results of RNA-seq showed that compared with the CON group, the pathways of digestion and absorption of minerals, protein, and vitamins of piglets were changed in the ISC group, whereas the pathways of retinol metabolism and nitrogen metabolism in the colonic mucosal were affected and stimulated the immune response in the CSC group. Compared with the CON group, the abundances of pernicious microorganisms (Desulfovibrio, Pseudomonas, Brevundimonas, etc.) in the CSC group and pernicious microorganisms (Desulfovibrio, Neisseria, Sutterella, etc.) and beneficial bacteria (Bifidobacterium, Megamonas, and Prevotella_9) in the ISC group were significantly higher (p < 0.05). The abundances of proinflammatory bacteria (Coriobacteriaceae_unclassified, Coprococcus_3, and Ruminococcus_2) in the CSC group were significantly increased (p < 0.05), but the abundances of SCFAs producing bacteria (Lachnospiraceae_UCG-010, Parabacteroides, Anaerotruncus, etc.) and those of anti-inflammatory bacteria (Eubacterium, Parabacteroides, Ruminiclostridium_9, and Alloprevotella) were significantly reduced (p < 0.05) in the CSC group. Compared with the CON group, the concentrations of microbial metabolites, acetate, and propionate in the colonic contents were reduced (p < 0.05) in the ISC group, whereas the concentration of acetate was reduced (p < 0.05) in the CSC group. Therefore, both ISC and CSC during lactation affected the composition of fecal microbes and changed the expression of intestinal mucosal genes related to nutrient metabolism and absorption of piglets.

L-Proline Synthesis Mutants of Bacillus subtilis Overcome Osmotic Sensitivity by Genetically Adapting L-Arginine Metabolism

The accumulation of the compatible solute L-proline by Bacillus subtilis via synthesis is a cornerstone in the cell’s defense against high salinity as the genetic disruption of this biosynthetic process causes osmotic sensitivity. To understand how B. subtilis could potentially cope with high osmolarity surroundings without the functioning of its natural osmostress adaptive L-proline biosynthetic route (ProJ-ProA-ProH), we isolated suppressor strains of proA mutants under high-salinity growth conditions. These osmostress-tolerant strains carried mutations affecting either the AhrC transcriptional regulator or its operator positioned in front of the argCJBD-carAB-argF L-ornithine/L-citrulline/L-arginine biosynthetic operon. Osmostress protection assays, molecular analysis and targeted metabolomics showed that these mutations, in conjunction with regulatory mutations affecting rocR-rocDEF expression, connect and re-purpose three different physiological processes: (i) the biosynthetic pathway for L-arginine, (ii) the RocD-dependent degradation route for L-ornithine, and (iii) the last step in L-proline biosynthesis. Hence, osmostress adaptation without a functional ProJ-ProA-ProH route is made possible through a naturally existing, but inefficient, metabolic shunt that allows to substitute the enzyme activity of ProA by feeding the RocD-formed metabolite γ-glutamate-semialdehyde/Δ¹-pyrroline-5-carboxylate into the biosynthetic route for the compatible solute L-proline. Notably, in one class of mutants, not only substantial L-proline pools but also large pools of L-citrulline were accumulated, a rather uncommon compatible solute in microorganisms. Collectively, our data provide an example of the considerable genetic plasticity and metabolic resourcefulness of B. subtilis to cope with everchanging environmental conditions.

The PTS Ntr -KdpDE-KdpFABC Pathway Contributes to Low Potassium Stress Adaptation and Competitive Nodulation of Sinorhizobium fredii

In all ecological niches, potassium is actively consumed by diverse prokaryotes and their interacting eukaryote hosts. It is only just emerging that potassium is a key player in host-pathogen interactions, and the role of potassium in mutualistic interactions remains largely unknown.

Potassium at the Origins of Life: Did Biology Emerge from Biotite in Micaceous Clay?

Intracellular potassium concentrations, [K+], are high in all types of living cells, but the origins of this K+ are unknown. The simplest hypothesis is that life emerged in an environment that was high in K+. One such environment is the spaces between the sheets of the clay mineral mica. The best mica for life's origins is the black mica, biotite, because it has a high content of Mg++ and because it has iron in various oxidation states. Life also has many of the characteristics of the environment between mica sheets, giving further support for the possibility that mica was the substrate on and within which life emerged. Here, a scenario for life's origins is presented, in which the necessary processes and components for life arise in niches between mica sheets; vesicle membranes encapsulate these processes and components; the resulting vesicles fuse, forming protocells; and eventually, all of the necessary components and processes are encapsulated within individual cells, some of which survive to seed the early Earth with life. This paper presents three new foci for the hypothesis of life's origins between mica sheets: (1) that potassium is essential for life's origins on Earth; (2) that biotite mica has advantages over muscovite mica; and (3) that micaceous clay is a better environment than isolated mica for life's origins.

A Soft Evaporation and Ionization Technique for Mass Spectrometric Analysis and Bio-Imaging of Metal Ions in Plants Based on Metal-Iodide Cluster Ionization

Protonation/deprotonation is the well-recognized mass spectrometric mechanism in matrix-assisted laser desorption ionization of organic molecules but not for metal ions with different oxidation states. We describe herein a soft evaporation and ionization technique for metal ions based on iodination/de-iodination in metal-iodide cluster ionization (MICI). It is not only able to determine identities and oxidation states of metal ions but also reveal spatial distributions and isotope ratios in response to physiological or environmental changes. A long chain alcohol 1-tetradecanol with no functional groups that can absorb laser irradiation was used to cover and prevent samples from direct laser ablation. Upon the irradiation of the third harmonic Nd³⁺:YAG (355 nm, 3 ns), iohexol containing three covalently bonded iodine atoms instantly generates negative iodide ions that can quantitatively form clusters with at least 14 essential metal ions present in plants. The detection limits vary with different metal ions down to low fmol. MICI eliminates the atomization process that obscures metal charges in inductively coupled plasma mass spectrometry. Because only metal ions can be iodinated with iohexol, interferences from the abundant organic molecules of plants that are confronted by secondary ion mass spectrometry (SIMS) are also greatly decreased.

Engineering potassium activation into biosynthetic thiolase

Activation of enzymes by monovalent cations (M+) is a widespread phenomenon in biology. Despite this, there are few structure-based studies describing the underlying molecular details. Thiolases are a ubiquitous and highly conserved family of enzymes containing both K+-activated and K+-independent members. Guided by structures of naturally occurring K+-activated thiolases, we have used a structure-based approach to engineer K+-activation into a K+-independent thiolase. To our knowledge, this is the first demonstration of engineering K+-activation into an enzyme, showing the malleability of proteins to accommodate M+ ions as allosteric regulators. We show that a few protein structural features encode K+-activation in this class of enzyme. Specifically, two residues near the substrate-binding site are sufficient for K+-activation: A tyrosine residue is required to complete the K+ coordination sphere, and a glutamate residue provides a compensating charge for the bound K+ ion. Further to these, a distal residue is important for positioning a K+-coordinating water molecule that forms a direct hydrogen bond to the substrate. The stability of a cation-π interaction between a positively charged residue and the substrate is determined by the conformation of the loop surrounding the substrate-binding site. Our results suggest that this cation-π interaction effectively overrides K+-activation, and is, therefore, destabilised in K+-activated thiolases. Evolutionary conservation of these amino acids provides a promising signature sequence for predicting K+-activation in thiolases. Together, our structural, biochemical and bioinformatic work provide important mechanistic insights into how enzymes can be allosterically activated by M+ ions.

Potassium physiology from Archean to Holocene: A higher-plant perspective

In this paper, we discuss biological potassium acquisition and utilization processes over an evolutionary timescale, with emphasis on modern vascular plants. The quintessential osmotic and electrical functions of the K⁺ ion are shown to be intimately tied to K⁺-transport systems and membrane energization. Several prominent themes in plant K⁺-transport physiology are explored in greater detail, including: (1) channel mediated K⁺ acquisition by roots at low external [K⁺]; (2) K⁺ loading of root xylem elements by active transport; (3) variations on the theme of K⁺ efflux from root cells to the extracellular environment; (4) the veracity and utility of the "affinity" concept in relation to transport systems. We close with a discussion of the importance of plant-potassium relations to our human world, and current trends in potassium nutrition from farm to table.

The ups and downs of ectoine: structural enzymology of a major microbial stress protectant and versatile nutrient

Ectoine and its derivative 5-hydroxyectoine are compatible solutes and chemical chaperones widely synthesized by Bacteria and some Archaea as cytoprotectants during osmotic stress and high- or low-growth temperature extremes. The function-preserving attributes of ectoines led to numerous biotechnological and biomedical applications and fostered the development of an industrial scale production process. Synthesis of ectoines requires the expenditure of considerable energetic and biosynthetic resources. Hence, microorganisms have developed ways to exploit ectoines as nutrients when they are no longer needed as stress protectants. Here, we summarize our current knowledge on the phylogenomic distribution of ectoine producing and consuming microorganisms. We emphasize the structural enzymology of the pathways underlying ectoine biosynthesis and consumption, an understanding that has been achieved only recently. The synthesis and degradation pathways critically differ in the isomeric form of the key metabolite N-acetyldiaminobutyric acid (ADABA). γ-ADABA serves as preferred substrate for the ectoine synthase, while the α-ADABA isomer is produced by the ectoine hydrolase as an intermediate in catabolism. It can serve as internal inducer for the genetic control of ectoine catabolic genes via the GabR/MocR-type regulator EnuR. Our review highlights the importance of structural enzymology to inspire the mechanistic understanding of metabolic networks at the biological scale.

A meet-up of two second messengers: the c-di-AMP receptor DarB controls (p)ppGpp synthesis in Bacillus subtilis

Many bacteria use cyclic di-AMP as a second messenger to control potassium and osmotic homeostasis. In Bacillus subtilis, several c-di-AMP binding proteins and RNA molecules have been identified. Most of these targets play a role in controlling potassium uptake and export. In addition, c-di-AMP binds to two conserved target proteins of unknown function, DarA and DarB, that exclusively consist of the c-di-AMP binding domain. Here, we investigate the function of the c-di-AMP-binding protein DarB in B. subtilis, which consists of two cystathionine-beta synthase (CBS) domains. We use an unbiased search for DarB interaction partners and identify the (p)ppGpp synthetase/hydrolase Rel as a major interaction partner of DarB. (p)ppGpp is another second messenger that is formed upon amino acid starvation and under other stress conditions to stop translation and active metabolism. The interaction between DarB and Rel only takes place if the bacteria grow at very low potassium concentrations and intracellular levels of c-di-AMP are low. We show that c-di-AMP inhibits the binding of DarB to Rel and the DarB–Rel interaction results in the Rel-dependent accumulation of pppGpp. These results link potassium and c-di-AMP signaling to the stringent response and thus to the global control of cellular physiology.

In several bacteria, cyclic di-AMP mediates potassium (K+) and osmotic homeostasis. Here, the authors show that DarB, a Bacillus subtilis protein previously reported to bind cyclic di-AMP, interacts with the (p)ppGpp synthetase/hydrolase Rel in a K+-dependent manner in turn leading to Rel-dependent accumulation of pppGpp under conditions of K+ starvation.

Deflating the RNA Mg2+ bubble. Stereochemistry to the rescue!

Proper evaluation of the ionic structure of biomolecular systems through X ray and cryo-EM techniques remains challenging but is essential for advancing our understanding of the underlying structure/activity/solvent relationships. However, numerous studies overestimate the number of Mg2+ in deposited structures due to assignment errors finding their origin in improper consideration of stereochemical rules. Herein, to tackle such issues, we re-evaluate the PDBid 6QNR and 6SJ6 models of the ribosome ionic structure. We establish that stereochemical principles need to be carefully pondered when evaluating ion binding features, even when K+ anomalous signals are available as it is the case for the 6QNR PDB entry. For ribosomes, assignment errors can result in misleading conceptions of their solvent structure. For instance, present stereochemical analysis result in a significant decrease of the number of assigned Mg2+ in 6QNR, suggesting that K+ and not Mg2+ is the prevalent ion in the ribosome 1st solvation shell. We stress that the use of proper stereochemical guidelines in combination or not with other identification techniques, such as those pertaining to the detection of transition metals, of some anions and of K+ anomalous signals, is critical for deflating the current Mg2+ bubble witnessed in many ribosome and other RNA structures. We also stress that for the identification of lighter ions such as Mg2+, Na+, …, for which no anomalous signals can be detected, stereochemistry coupled with high resolution structures (<2.4 Å) remain the best currently available option.

How potassium came to be the dominant biological cation: of metabolism, chemiosmosis, and cation selectivity since the beginnings of life

In the cytoplasm of practically all living cells, potassium is the major cation while sodium dominates in the media (seawater, extracellular fluids). Both prokaryotes and eukaryotes have elaborate mechanisms and spend significant energy to maintain this asymmetric K⁺ /Na⁺ distribution. This essay proposes an original line of evidence to explain how bacteria selected potassium at the very beginning of the evolutionary process and why it remains essential for eukaryotes.

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.

One-carbon metabolism, folate, zinc and translation

The translation process, central to life, is tightly connected to the one-carbon (1-C) metabolism via a plethora of macromolecule modifications and specific effectors. Using manual genome annotations and putting together a variety of experimental studies, we explore here the possible reasons of this critical interaction, likely to have originated during the earliest steps of the birth of the first cells. Methionine, S-adenosylmethionine and tetrahydrofolate dominate this interaction. Yet, 1-C metabolism is unlikely to be a simple frozen accident of primaeval conditions. Reactive 1-C species (ROCS) are buffered by the translation machinery in a way tightly associated with the metabolism of iron-sulfur clusters, zinc and potassium availability, possibly coupling carbon metabolism to nitrogen metabolism. In this process, the highly modified position 34 of tRNA molecules plays a critical role. Overall, this metabolic integration may serve both as a protection against the deleterious formation of excess carbon under various growth transitions or environmental unbalanced conditions and as a regulator of zinc homeostasis, while regulating input of prosthetic groups into nascent proteins. This knowledge should be taken into account in metabolic engineering.

Intersecting Xenobiology and Neometabolism To Bring Novel Chemistries to Life

The diversity of life relies on a handful of chemical elements (carbon, oxygen, hydrogen, nitrogen, sulfur and phosphorus) as part of essential building blocks; some other atoms are needed to a lesser extent, but most of the remaining elements are excluded from biology. This circumstance limits the scope of biochemical reactions in extant metabolism - yet it offers a phenomenal playground for synthetic biology. Xenobiology aims to bring novel bricks to life that could be exploited for (xeno)metabolite synthesis. In particular, the assembly of novel pathways engineered to handle nonbiological elements (neometabolism) will broaden chemical space beyond the reach of natural evolution. In this review, xeno-elements that could be blended into nature's biosynthetic portfolio are discussed together with their physicochemical properties and tools and strategies to incorporate them into biochemistry. We argue that current bioproduction methods can be revolutionized by bridging xenobiology and neometabolism for the synthesis of new-to-nature molecules, such as organohalides.

Interferon-Gamma Stimulated Murine Macrophages In Vitro: Impact of Ionic Composition and Osmolarity and Therapeutic Implications

Background: Injections of osmolytes are promising immunomodulatory treatments for medical benefit, although the rationale and underlying mechanisms are often lacking. The goals of the present study were twofold: (1) to clarify the anti-inflammatory role of the potassium ion and (2) to begin to decouple the effects that ionic strength, ionic species, and osmolarity have on macrophage biology. Materials and Methods: RAW 264.7 murine macrophages were encapsulated in three-dimensional, poly(ethylene glycol) diacrylate hydrogels and activated with interferon-gamma to yield M(IFN). Gene and protein profiles were made of M(IFN) exposed to different hyperosmolar treatments (80 mM potassium gluconate, 80 mM sodium gluconate, and 160 mM sucrose). Results: Relative to M(IFN), all hyperosmolar treatments suppressed expression of pro-inflammatory markers (nitric oxide synthase-2 [NOS-2], tumor necrosis factor-alpha, monocyte chemoattractant protein-1 [MCP-1]) and increased messenger RNA (mRNA) expression of the pleiotropic and angiogenic markers interleukin-6 (IL-6) and vascular endothelial growth factor-A (VEGF), respectively. Ionic osmolytes also demonstrated a greater level of change compared to the nonionic treatments, with mRNA levels of IL-6 the most significantly affected. M(IFN) exposed to K+ exhibited the lowest levels of NOS-2 and MCP-1, and this ion limited IL-6 release induced by osmolarity. Conclusion: Cumulatively, these data suggest that osmolyte composition, ionic strength, and osmolarity are all parameters that can influence therapeutic outcomes. Future work is necessary to further decouple and mechanistically understand the influence that these biophysical parameters have on cell biology, including their impact on other macrophage functions, intracellular osmolyte composition, and cellular and organellular membrane potentials.