Living with water stress: evolution of osmolyte systems

Impact of environmental salinity on the MAPK-NFAT5 pathway in Trachemys scripta elegans and its role in osmoregulaton

Globally, sea level rise (SLR) leads to salinization of coastal freshwater, in where organisms might be affected and in turn promote osmoregulation and adaptation in response to freshwater salinization. Trachemys scripta elegans a freshwater turtle species, exhibits remarkable tolerance to varying salinity environments, yet the underlying regulatory mechanisms remain poorly understood. This study aimed to elucidate the molecular mechanisms of osmoregulation in this species based on previous RNA-seq data. Our findings revealed that when exposed to 5 PSU (5 ‰) and 15 PSU (15 ‰) salinities, the turtles exhibited increased concentrations of ions (Na+, K+) and urea in urine, along with elevated osmotic pressures in both plasma and urine. Additionally, the protein levels of aquaporins (AQPs) and transporters of ions and organic osmolytes in the kidney were upregulated in saline water. Notably, the transcriptional level of the hypertonic regulator NFAT5 was significantly elevated, accompanied by an increase in phosphorylated NFAT5 levels in the nucleus of renal tubular epithelial cells. Furthermore, we observed upregulated phosphorylated levels of MAPKs in saline water. The use of MAPK inhibitors effectively blocked the transcription of NFAT5 and osmoregulatory target genes. Collectively, these results suggest that T. scripta elegans activates the MAPK-NFAT5 signaling pathway to modulate osmotic pressure in adaptation to saline water environments. Our study provides valuable insights into the osmoregulatory responses of aquatic organisms to saline environments and aids in understanding the adaptability of organisms inhabiting coastal areas facing rising sea levels.

Biophysical insights into osmolytes-driven enhancements in urate oxidase activity and stability

The thermal instability of pharmaceutical enzymes such as uricase or urate oxidase (UOX) in liquid solutions is a major problem. Notably, compatible osmolytes are a specific class of osmolytes that can preferentially stabilize the folded state of proteins. However, the detailed molecular interactions that enable them to affect protein stability are still not completely elucidated. This study aimed to investigate how the enzyme environment could be altered using osmolytes to improve its catalytic activity and stability. Initially, experimental conditions were optimized using response surface methodology (RSM). Then, kinetic and thermodynamic properties, as well as structural changes of urate oxidase, were assessed using spectroscopic and computational techniques in the presence and absence of mixed osmolytes. Kinetic parameters indicated an improvement in the catalytic function of urate oxidase and the results of thermodynamic analysis indicated that the van der Waals forces and hydrogen bonding network played a crucial role in the UOX-osmolytes interactions. Fluorescence measurements suggested that osmolyte-UOX interactions alter the enzyme's structure. The data revealed a complex quenching mechanism between the enzyme and osmolyte. Molecular dynamics (MD) simulations showed an increase in stability and structural compactness of the enzyme in the presence of mixed osmolytes. Furthermore, it depicted an increase in the abundance of secondary structure contents of the enzyme, which in turn maintained the integrity of its active site. Also, the molecular docking analysis further supported the experimental results. These findings revealed mechanisms by which binary-compatible osmolytes could have relevant effects on the catalytic function and stability of urate oxidase.

Function in disorder: A review on the roles of the disordered dehydrin proteins in conferring stress tolerance

Water scarcity as a result of drought is considered to be among the most common forms of abiotic stress which directly hampers plant health. Such conditions often lead to various interlinked physiological conditions, including oxidative stress resulting from increased ROS levels that in turn, induce membranes dysfunction, leading to disruption in cellular ionic balance, and oxidation of macromolecules. Plants employ several mechanisms to counter these hostile conditions, which help them adapt to such unforgiving environments. Accumulation of specific types of proteins called dehydrins (DHNs) represents one such mechanism of adaptation. DHNs are ubiquitous in distribution and have been reported in different life forms; accumulating under a wide spectrum of stress. An important role of DHNs is to protect and maintain cell's macromolecular structure and function, thereby preserving membrane integrity, stabilizing proteins and nucleic acid, and conferring protection against oxidative stress. The present article explores different aspects of DHNs, including their structural compositions, architectures and conformational flexibility, and their role in combating a plethora of stress environments, with specific focus towards drought. Possible involvements of DHNs in intracellular biocondensates formation through phase separation and their role in stress sensing are also provided.

Effect of osmolytes on the conformational stability of Aβ(25-35): A circular dichroism analysis

Alzheimer's (AD) is a neurodegenerative disease characterized by the onset and progression of mental decline. AD aetiopathogenesis is still questioned; however, according to one of the most accredited hypotheses, the accumulation of amyloid plaques formed by aggregated Aβ peptides is the primary cause of neuronal function loss. Accordingly, hundreds of molecules have been screened for their possible action to prevent or destroy amyloid aggregates. Following this track, osmolytes, naturally occurring small molecules produced by several organisms in response to external stressors, were recently evaluated as modulators of Aβ aggregation. In this study, we examined the conformational stability of Aβ(25-35) when exposed to the osmolytes acetylcholine (ACh), succinylcholine (SCh), and betaine (Bet). Aβ(25-35) is the shortest fragment known for replicating the aggregation process seen in Aβ peptides. By collecting circular dichroism (CD) spectra in water and different membrane-mimicking systems, we investigated the potential of the mentioned osmolytes to stabilize the soluble conformations of Aβ(25-35) and preserve them from denaturing conditions. Our data suggest that Bet is a promising small molecule that can safeguard the soluble form of Aβ peptide and is effective in counteracting environmental conditions by favoring the amyloid aggregation associated with pathology progression.

Chemical control of colloidal self-assembly driven by the electrosolvation force

Self-assembly of matter in solution generally relies on attractive interactions that overcome entropy and drive the formation of higher-order molecular and particulate structures. Such interactions are central to a variety of molecular processes, e.g., crystallisation, biomolecular folding and condensation, pathological protein aggregation and biofouling. The electrosolvation force introduces a distinct conceptual paradigm to the existing palette of interactions that govern the spontaneous accretion and organisation of matter. However, an understanding of the underlying physical chemistry, and therefore the ability to exert control over and tune the interaction, remains incomplete. Here we provide further evidence that this force arises from the structure of the interfacial electrolyte. Neutral molecules such as a different solvent, osmolytes or surfactants, may - even at very low concentrations in the medium - disrupt or reinforce pre-existing interfacial solvent structure, thereby delivering unanticipated chemical tuning of the ability of matter to self-assemble. The observations present unexpected mechanistic elements that may explain the impact of co-solvents and osmolytes on protein structure, stability and biomolecular condensation. Our findings thus furnish insight into the microscopic mechanisms that drive the emergence of order and structure from molecular to macroscopic scales in the solution phase.

The bio-decolorization of methyl orange by S.putrefaciens CN32 and responding mechanism to salinity stress based on transcriptomic analysis

Salinity poses a significant obstacle to the bio-decolorization of azo dyes. However, the underlying responding mechanisms of bio-decolorization bacteria remain unclear. Shewanella putrefaciens CN32 (S.P CN32) can reduce azo dyes through special electron transfer pathways. Hence, this study used methyl orange (MO) as a representative of azo dyes to investigate azo dye decolorization by S.P CN32 and to explore the responding mechanism of S.P CN32 to salinity stress in the decolorization process. More than 95 % of MO was decolorized by S.P CN32 under the conditions of pH 6-10, MO concentration high than 850 mg/L, and salinity 0-2 %. Lactate was the optimal electron donor in MO decolorization process by S.P CN32. The complete decolorization time was lagged by 30 h under 2 % salinity. FTIR and LC-MS were utilized to identify metabolites and analysis possible metabolic pathways in MO decolorization process. The expression changes of genes involved in MO bio-decolorization and response to salinity stress were characterized by transcriptome analysis. The salinity inhibition on MO decolorization was linked to the down-regulation of azoreductase-associated electron transport pathways and electron transfer chains including Mtr pathway, NADH dehydrogenase, mequinones and heme synthesis. But the up-regulation of flavins synthesis could slightly remit the inhibition. When exposed to salinity, bacteria up-regulated genes expression associated with Na+/K+ transport, the transfer and biosynthesis of proline and glutamate. Most of genes related to energy production by lactate metabolism, TCA cycle and fatty acid metabolism also up-regulated, while most genes related to cell motility down-regulated. This is conducive to supply energy for adapting salinity stress to survive. This study demonstrated the potential role of S.P CN32 in MO decolorization process, and may provide some new insights into the bio-treatment of textile wastewater with high salinity from the perspective of the molecular mechanism.

Microscopic Heterogeneity Driven by Molecular Aggregation and Water Dynamics in Aqueous Osmolyte Solutions

Water dynamics are investigated in binary osmolyte-water mixtures, exhibiting a microscopic heterogeneity driven by molecular aggregation, on the basis of molecular dynamics (MD) simulation studies. The protecting osmolyte TMAO molecules in solution are evenly dispersed without the formation of noticeable osmolyte aggregates, while the denaturant TMU molecules aggregate readily, generating microscopic heterogeneity in the spatial distribution of component molecules in TMU-water mixtures. A combined study of MD simulation with graph theoretical analysis and spatial inhomogeneity measurement with h-values in the two osmolyte solutions revealed that the translational and rotational motions of water in the microheterogeneous environment of TMU-water mixtures are less hindered than those in the homogeneous media of TMAO-water mixtures. The analysis of the osmolyte-water H-bond lifetime in the binary solutions shows that destabilizing osmolyte TMU makes relatively weak osmolyte-water interaction, compared to that in protecting osmolyte TMAO, enabling the interplay of TMU-TMU or TMU-protein as well as TMU-water interaction. Taken together, the complementary contributions of the two hypotheses are proposed to elucidate the operating mechanism of the osmolyte on protein stability, encompassing a direct mechanism for the preferential interaction between the osmolyte and protein and an indirect mechanism for the modulation of the water structure and dynamics in the osmolyte solutions.

Direct ionic stress sensing and mitigation by the transcription factor NFAT5

Rising temperatures and water scarcity caused by climate change are increasingly exposing our cells and tissues to ionic stress, a consequence of elevated cytoplasmic ionic strength that can disrupt protein, organelle, and genome function. Here, we unveil a single-protein mechanism for ionic strength sensing and mitigation in animal cells, one that is notably different from the analogous high osmolarity glycerol kinase cascade in yeast. The Rel family transcription factor NFAT5 directly senses intracellular ionic strength using a C-terminal prion-like domain (PLD). In response to elevated intracellular ionic strength, this PLD is necessary and sufficient to coordinate an adaptive gene expression program by recruiting the transcriptional coactivator BRD4. The purified NFAT5 PLD forms condensates in response to elevated solution ionic strength in vitro, and human NFAT5 alone is sufficient to reconstitute a mammalian transcriptional response to ionic stress in yeast. We propose that ion-sensitive conformational changes in a PLD directly regulate transcription to maintain ionic strength homeostasis in animal cells.

Genome assembly, gene content, and plastic gene expression responses to salinity changes in the Brackishwater Clam (Corbicula japonica) from a dynamic estuarine environment

Estuaries are dynamic transition zones between marine and freshwater environments, where salinity varies greatly on spatial and temporal scales. The temporal salinity fluctuations of these habitats require organisms to rapidly regulate ionic concentrations and osmotic pressure to survive in these dynamic conditions. Understanding the extent of plasticity of euryhaline animals is vital for predicting their responses and resilience to salinity change. We generated the first high-resolution genome and transcriptome sequences of C. japonica. In comparison with 11 other molluscan genomes, the C. japonica genome displayed striking expansions of putative neuron-related genes and gene families. The involvement of these genes in the glutamate/GABA-glutamine and glycine cycle suggests a possible contribution to the excitation of neuronal networks, particularly under high salinity conditions. This study contributes to our understanding of mechanisms underlying the rapid responses of estuarine species to changing conditions and raises many intriguing hypotheses and questions for future investigation.

Preventing epileptogenesis by interaction between inositol isomers and proteins

OBJECTIVE

Inositols play significant roles in biological systems. Myo-inositol (MI), the most prevalent isomer, functions as an osmolyte and mediates cell signal transduction. Other notable isomers include Scyllo-inositol (SCI) and D-Chiro-inositol (DCHI). Our previous investigations have highlighted MI's potential antiepileptogenic effects, although its exact mechanisms of action during epileptogenesis remain unclear. A critical, unexplored area is how inositols interact with proteins. Additionally, the antiepileptogenic capabilities of SCI and DCHI have yet to be determined. This study seeks to address these gaps.

METHODS

Inositol interacting proteins were identified by cellular thermal shift assay. Status epilepticus (SE) in rats was induced using kainic acid (KA), followed by a 28-day treatment with either MI, SCI, DCHI, or saline. The duration and frequencies of behavioral spontaneous recurrent seizures (SRS) were scored for 8 weeks by 24 h video monitoring system. The effects of inositol treatment on spatial learning and memory deficits associated with epileptogenesis were evaluated by Morris water maze test. The changes in protein amounts were studied by Western immunoblotting.

RESULTS

We identified several proteins that interact with inositols, noting both commonalities and isomer-specific associations. For the first time, we demonstrated that the treatment with SCI and DCHI, alongside MI, significantly reduces the frequency and duration of behavioral SRS in a KA-induced post-status epilepsy model in rats. This reduction persisted for 4 weeks post-treatment. Moreover, all three inositol isomers mitigated spatial learning and memory deficits associated with epileptogenesis. Alterations in the inositol interacting proteins: alpha synuclein and 14-3-3 theta were further examined 8 weeks post-SE in the hippocampus and neocortex of rats.

SIGNIFICANCE

Myo-inositol, SCI and DCHI interact with a number of proteins involved in different biological pathways. All studied inositol isomers express long-term beneficial effects on KA-induced SRS and the associated comorbidities. Inositols can be successfully used in the future for translational research.

PLAIN LANGUAGE SUMMARY

Epilepsy is a common neurological disorder characterized by spontaneous recurrent seizures and a range of associated comorbidities. The process that leads to the development of epilepsy is called epileptogenesis, and currently, no medication can effectively prevent it. Our study investigated the effects of a group of compounds-myo-inositol, scyllo-inositol, and D-chiro-inositol-that have potential antiepileptogenic properties on epilepsy induced by kainic acid. We found that: (i) the three inositol isomers share some common target proteins and also have unique ones and (ii) all of them counteract epileptogenesis and the related cognitive impairments.

Abomasal Infusion of Deuterium-Labeled Choline Confirms that Choline is a Methyl Donor in Gestating and Lactating Holstein Dairy Cattle

BACKGROUND

In cattle, dietary choline is fed in a rumen-protected form to bypass ruminal degradation while allowing intestinal absorption of choline. We require data to help us define choline utilization in the dairy cow transitioning from gestation to lactation.

OBJECTIVES

The study examined choline methyl group transfer in dairy cattle transitioning from gestation to lactation.

METHODS

Six multiparous, rumen-cannulated Holstein cows were enrolled in a longitudinal study design where they were abomasally infused with choline chloride (CC) for a 5-d experimental period at -3 wk from the expected due date and again at 2 wk postpartum. Twenty percent of CC provided per day was replaced with the stable-isotope trimethyl-d9-CC. Plasma, milk, liver, urine, and fecal samples were analyzed for choline and choline metabolite concentrations and isotope enrichment.

RESULTS

Plasma betaine (P < 0.01) and liver choline and betaine concentrations were lower during lactation (P < 0.01). During lactation, cows had greater circulating enrichment of d3-choline, d3-betaine, d9-betaine, and d9-phosphatidylcholine (PC; P ≤ 0.05), and greater liver enrichment of d3-glycerophosphorylcholine and d9-sphingomyelin (P ≤ 0.02). Greater urinary and fecal losses of d3- and d9-trimethylamine (TMA), and d3- and d9-TMA N-oxide (TMAO) were observed during pregnancy (P ≤ 0.05). Total choline metabolites detected in urine from infused CC were greater during pregnancy, relative to lactation (P < 0.01). Total fecal choline metabolites from infused CC were greater during lactation than during pregnancy (P = 0.03).

CONCLUSIONS

Our data confirm that choline is a methyl donor (e.g., detected d3-choline), and choline is used by both the cytidine diphosphate-choline and phosphatidylethanolamine N-methyl transferase pathways in the cow during gestation and lactation. We also provide evidence for the endogenous recycling of absorbed choline via bile (i.e. presence of d3-TMA). Degradation of choline to TMA and TMAO must be considered when evaluating choline bioavailability.

Regulation of desiccation-immersion cycle on the rate and fate of dissolved organic carbon release by Ulva pertusa

Macroalgae widely distribute in intertidal zones, one of blue carbon organisms. However, the regulatory mechanisms of tide on the carbon sequestration of macroalgae are still unclear. This study explored the effects of desiccation-rewetting cycles induced by tide on dissolved organic carbon (DOC) release from Ulva pertusa, which is prevalent from high to low tidal zones. Results showed that during desiccation stage, the DOC release of U. pertusa varied with desiccation levels, releasing 0.082, 0.22, and 0.35 mg g-1 FW at 0%, 40%, and 80% water loss, respectively, DOC accumulated on the surface of U. pertusa at a rate of about 0.52 mg g-1 FW h-1. Following 4 h of rewetting, DOC released surges to 0.99, 2.51, and 2.10 mg g-1 FW h-1. Using a stable isotope (13C) tracer method, we found that most DOC released by U. pertusa come from early fixed carbon. At 40% water loss, partial DOC stemmed from newly fixed carbon. DOC composition varied with desiccation level, affecting its bioavailability. After 16 days of degradation, DOC concentrations from U. pertusa at 0%, 40%, and 80% desiccation were 1.99, 3.22, and 2.54 mg g-1 FW, respectively. The 80% water loss showed the highest degradation rate, while the non-water-loss treatment group had the most potential to form refractory DOC. This study underlines the complex relationship between tide and the dynamics of DOC release in U. pertusa, highlighting their role in coastal carbon cycling.

Two-month ketogenic diet alters systemic and brain metabolism in middle-aged female mice

The ketogenic diet (KD) is a very low-carbohydrate, high-fat diet that reduces glucose catabolism and enhances β-oxidation and ketogenesis. While research in female rodents is limited, research in male rodents suggests that ketogenic interventions initiated at midlife may slow age-related cognitive decline, as well as preserve muscle mass and physical function later in life. This study aimed to investigate the effects of a KD on global metabolic changes in middle-aged females to inform potential mechanisms behind the anti-aging effects of this diet in an understudied sex. Targeted 1H-NMR metabolomics was conducted on serum, the liver, the kidney, and the gastrocnemius muscle, as well as the cortex and the hippocampal brain regions in 16-month-old female mice after a 2-month KD. Analysis of the serum and liver metabolome revealed that the 2-month KD resulted in increased concentrations of fatty acid catabolism metabolites, as well as system-wide elevations in ketones, consistent with the ketogenic phenotype. Metabolites involved in the glucose-alanine cycle were altered in the gastrocnemius muscle, serum and the liver. Other tissue-specific alterations were detected, including distinct effects on hepatic and renal one-carbon metabolism, as well as region specific differences in metabolism across hippocampal and cortical parts of the brain. Alterations to hippocampal metabolites involved in myelinogenesis could relate to the potential beneficial effects of a KD on memory.

Interaction studies unveil potential binding sites on bovine serum albumin for gut metabolite trimethylamine n-oxide (TMAO)

Trimethylamine-N-oxide (TMAO) is gut microbiota-derived metabolite, plays a critical role in human health and diseases such as metabolic, cardiovascular, colorectal cancer and, neurological disorders. Binding interactions between TMAO and serum albumins are crucial to understand the impact of TMAO on disease mechanisms. However, detailed insights into the interaction mechanisms, preferred binding locations, and conformational changes in BSA upon binding TMAO are still unclear. TMAO interacts with serum albumin in human body and thus, a model study of interaction for TMAO-BSA conjugate is presented in support of it. Decrease in absorbance intensity of protein upon interaction with metabolites reveals conjugate formation, while fluorescence spectroscopy indicate static quenching. Contact angle measurements further reveal the hydrophilic nature of the TMAO-BSA complex, while CD and FTIR support conformational changes in BSA upon binding but structure remain intact. Computational studies, such as molecular docking, molecular dynamics simulation and, MM/GBSA, confirm a stable complex with a binding energy of - 3.6 kcal/mol. These findings provide a foundation for understanding the pharmacodynamics and pharmacokinetics of TMAO and may aid in developing strategies for treating diseases, such as chronic kidney disease and neurological disorder where TMAO-serum albumins interaction are implicated.

Enhancing osmotic stress tolerance of cell mimetics by modulating lipid bilayer

Seeking effective ways to maintain cellular homeostasis is crucial to the survival of organisms when they encounter osmotic stress. Glycine betaine (GB) is a widely generated natural osmolyte, but its endogenous production and action are limited. Herein, a kind of nonionic surfactant dodecyl-β-d-glucopyranoside (DG) and a common polymer polyethylene glycol (PEG) are proven to have the ability to enhance the osmotic stress (induced by sugar concentration changes) tolerance of cell and organism models, those are giant unilamellar vesicles (GUVs) and gram-negative Escherichia coli. DG or PEG only induces small size decrease and certain shape change of GUVs. Importantly, DG or PEG at the concentration 100 times lower than that of GB effectively increases the survival rate of bacteria under both hypoosmotic and hyperosmotic conditions. This intriguing result is attributed to the insertion of DG or adsorption of PEG in the lipid bilayer membrane, leading to enhanced membrane permeability. These exogenous substances can replace GB to facilely and highly efficiently augment adaptation of organisms to osmotic stress.

Characterization and metabolomic profiling of endophytic bacteria isolated from Moringa oleifera and Piper betel leaves

Endophytes are microorganisms residing in plant tissues without causing harm and their relevance in medicinal plants has grown due to their biomolecules used in pharmaceuticals. This study isolated two endophytic bacterial strains from the leaves of M. oleifera and P. betel collected from Junagadh Agricultural University. The isolates were characterized morphologically and physio-biochemically, confirming them as gram-positive or gram-negative rods and cocci. Identification using 16S rRNA gene sequencing identified isolates belonging to various genera, including Priestia aryabhattai and Kocuria rhizophila The SEM characterization of the five selected isolates revealed diverse morphological structures, including coccus and rod shapes, organized in various formations. Isolates varied in size, with N3 (Kocuria rhizophila) cocci and S5 (Priestia aryabhattai) rods. Metabolomic analysis using GC/MS and LC-MS revealed diverse metabolic profiles with key compounds like n-Hexadecanoic acid, Pyrrolo[1,2-a]pyrazine-1,4-dione, Dihydrocapsaicin, and β-Homoproline, highlighting the potential of these endophytic bacteria in agricultural applications due to their roles in membrane integrity, antioxidant properties, stress response, and antibacterial activity.

From propensities to patterns to principles in protein folding

As proposed here, β-turns play an essential role in protein self-assembly. This compact, four-residue motif affects protein conformation dramatically by reversing the overall chain direction. Turns are the "hinges" in globular proteins. This new proposal broadens a previous hypothesis that globular proteins solve the folding problem in part by filtering conformers with unsatisfied backbone hydrogen bonds, thereby preorganizing the folding population. Recapitulating that hypothesis: unsatisfied conformers would be dramatically destabilizing, shifting the U(nfolded) ⇌ N(ative) equilibrium far to the left. If even a single backbone polar group is satisfied by solvent when unfolded but buried and unsatisfied when folded, that energy penalty alone, approximately +5 kcal/mol, would rival almost the entire free energy of protein stabilization at room temperature. Consequently, globular proteins are built on scaffolds of hydrogen-bonded α-helices and/or strands of β-sheet, motifs that can be extended indefinitely, with intra-segment hydrogen bond partners for their backbone polar groups and without steric clash. Scaffolds foster a protein-wide hydrogen-bonded network, and, of thermodynamic necessity, they self-assemble cooperatively. Unlike elements of repetitive secondary structure, α-helices and β-sheet, a four-residue β-turn has only a single hydrogen bond (from i + 3 → i), not a cooperatively formed assembly of hydrogen bonds. As such, turns can form autonomously and are poised to initiate assembly of scaffold elements by bringing them together in an orientation and registration that promotes cooperative "zipping". The overall effect of this self-assembly mechanism is to induce substantial preorganization in the thermodynamically accessible folding population and, concomitantly, to reduce the folding entropy.

Integrated Transcriptomic, Proteomic, and Metabolomic Analyses Revealed Molecular Mechanism for Salt Resistance in Soybean (Glycine max L.) Seedlings

Salt stress poses a significant challenge to plant growth and restricts agricultural development. To delve into the intricate mechanisms involved in soybean's response to salt stress and find targets to improve the salt resistance of soybean, this study integrated transcriptomic, proteomic, and metabolomic analyses to explore the regulatory networks involved in soybean salt tolerance. Transcriptomic analysis revealed significant changes in transcription factors, hormone-related groups, and calcium ion signaling. Notably, the biosynthetic pathways of cutin, suberine, and wax biosynthesis play an important role in this process. Proteomic results indicated salt-induced DNA methylation and the enrichment of phosphopyruvate hydrase post-salt stress, as well as its interaction with enzymes from various metabolic pathways. Metabolomic data unveiled the synthesis of various metabolites, including lipids and flavonoids, in soybean following salt stress. Furthermore, the integrated multiomics results highlighted the activation of multiple metabolic pathways in soybean in response to salt stress, with six pathways standing out prominently: stilbenoid, diarylheptanoid, and gingerol biosynthesis; carotenoid biosynthesis; carbon fixation in photosynthetic organisms; alanine, aspartate, and glutamate metabolism; thiamine metabolism; and pyruvate metabolism. These findings not only offer valuable insights into leveraging multiomics profiling techniques for uncovering salt tolerance mechanisms but also identify candidate genes for soybean improvement.

Amino acids modulate liquid-liquid phase separation in vitro and in vivo by regulating protein-protein interactions

Liquid-liquid phase separation (LLPS) is an intracellular process widely used by cells for many key biological functions. It occurs in complex and crowded environments, where amino acids (AAs) are vital components. We have found that AAs render the net interaction between proteins more repulsive. Here, we find that some AAs efficiently suppress LLPS in test tubes (in vitro). We then screen all the proteinogenic AAs and find that three specific AAs, including proline, glutamine, and glycine, significantly suppressed the formation of stress granules (SGs) in U2OS and HeLa cell lines (in vivo) irrespective of stress types. We also observe the effect in primary fibroblast cells, a viable cell model for neurodegenerative disorders. Kinetic studies by live-cell microscopy show that the presence of AAs not only slows down the formation but also decreases the saturating number and prevents the coalescence of SGs. We finally use sedimentation-diffusion equilibrium analytical ultracentrifuge (SE-AUC) to demonstrate that the suppression effects of AAs on LLPS may be due to their modulation in protein-protein and RNA-RNA interactions. Overall, this study reveals an underappreciated role of cellular AAs, which may find biomedical applications, especially in treating SG-associated diseases.

Superhydrophobic sand mulch and date palm biochar boost growth of Moringa oleifera in sandy soils via enhanced irrigation and nutrient use efficiency

Introduction

It is desirable to rehabilitate desert ecosystems with a selection of native plant species that render ecosystem services and yield natural products for creating a high-value industry, e.g., pharmaceuticals or cosmetics. However, plant growth under arid and hyper-arid conditions, such as in the Arabian Peninsula, is constrained by heat, freshwater scarcity, and alkaline sandy soils with low nutrient and water holding capacity. Therefore, it is imperative to develop nature-based sustainable technologies to improve arid soil conditions, as well as increase irrigation and nutrient-use eficiency.

Methods

Here, we report on a study evaluating the effects of two complementary soil amendment technologies, namely Superhydrophobic sand (SHS) mulch and engineered biochar (EB) on the growth of Moringa oleifera plants. Effects of SHS (1cm-thick), EB (2% w/w), and SHS+EB treatments were tracked in greenhouse plants under normal (N, 100% field capacity) and reduced (R, 50% of N) irrigation scenarios for over 150 days, where EB treatments were pre-loaded with nutrients and remaining treatments received traditional NPK fertilizer.

Results

Significant benefits of the SHS, EB, and SHS+EB treatments were found in terms of increased plant height, trunk diameter, leaf area, leaf chlorophyll content index, stomatal conductance, and shoot and root biomass in comparison with the controls. Evaporation water savings due to SHS mulching significantly enhanced transpiration under N and R scenarios. Similarly, EB and SHS+EB treated plants experienced higher transpiration than in the control plants under N and R conditions (p< 0.05). In response to water stress due to excessive evaporation, metabolomics analysis showed a higher accumulation of amino acids in control plants than other treatments under both irrigation regimes. Meanwhile, a higher abundance of sugars (i.e., D-Mannose, D-Fructose, glucose) and organic acid (i.e., malic acid) was observed in SHS and EB-treatments for Variable Importance in Projection (VIP) scores >1.0 (i.e., the scores considered of significance in contributing to the differences between treatment groups).

Discussion

The results show the synergistic benefits of SHS and EB technologies for addressing the challenges of water scarcity and nutrient limitation in arid regions, which couldcontribute to the success and sustainability of agriculture and greening efforts in such regions.

Structure and function of skin barrier lipids: Effects of hydration and natural moisturizers in vitro

Lipid membranes play a crucial role in regulating the body's water balance by adjusting their properties in response to hydration. The intercellular lipid matrix of the stratum corneum (SC), the outermost skin layer, serves as the body's primary defense against environmental factors. Osmolytes, including urocanic acid (UCA) and glycerol, are key components of the natural moisturizing factor that help the SC resist osmotic stress from dry environments. This study examines the effects of UCA and glycerol (each at 5 mol %) on isolated human SC lipids. For this, different techniques were employed, offering complementary information of the system's multiscale characteristics, including humidity-scanning quartz crystal microbalance with dissipation monitoring, infrared spectroscopy, x-ray diffraction, electrical impedance spectroscopy, and studies of water loss and permeability. Our results show that UCA increases water sorption and makes lipid films more liquid-like at high relative humidity, without significantly altering the lipid lamellar structure, chain order, or orthorhombic chain packing. Lipid films containing UCA exhibited higher water loss and significantly higher model drug permeability compared to lipid films without UCA. Further, incorporation of UCA resulted in kinetically faster changes in electrical properties upon contact with aqueous solution compared with control lipids. These observations suggest that UCA reduces lipid cohesion in regions other than the acyl chain-rich leaflets, which may impact SC desquamation. In contrast, glycerol did not influence the hydration or permeability of the SC lipid matrix. However, it increased the proportion of orthorhombic domains at high humidities and slowed the kinetics of the hydration process, as evidenced by slower changes in the dielectric properties of the lipid film. These findings suggest that glycerol enhances lipid cohesion rather than increasing water uptake, which is typically the expected function of humectants. Consequently, UCA and glycerol appear to have distinct roles in maintaining epidermal homeostasis.

HES1 potentiates high salt stress response as an enhancer of NFAT5-DNA binding

High salt conditions and subsequent hyperosmolarity are injurious cellular stresses that can activate immune signaling. Nuclear factor of activated T-cells 5 (NFAT5) is an essential transcription factor that induces osmoprotective genes such as aldose reductase (AR) and betaine-GABA transporter 1 (BGT1). High salt stress-mediated NFAT5 activation is also reported to accelerate the inflammatory response and autoimmune diseases. However, the systemic regulation of NFAT5 remains unclear. Here, we performed a genome-wide siRNA screen to comprehensively identify the regulators of NFAT5. We monitored NFAT5 nuclear translocation and identified one of the Notch signaling effectors, Hairy and enhancer of split-1 (HES1), as a positive regulator of NFAT5. HES1 was induced by high salinity via ERK signaling and facilitated NFAT5 recruitment to its target promoter region, resulting in the proper induction of osmoprotective genes and cytoprotection under high salt stress. These findings suggest that, though HES1 is well known as a transcriptional repressor, it positively regulates NFAT5-dependent transcription in the context of a high salinity/hyperosmotic response.

Integrating Transcriptome and Metabolome Analyses Revealed Salinity Induces Arsenobetaine Biosynthesis in Marine Medaka (Oryzias melastigma)

Marine fish exhibit elevated levels of arsenobetaine (AsB), while the impact and underlying mechanism of salinity on AsB biosynthesis remain inadequately explored. In this study, marine medaka (Oryzias melastigma), typically inhabiting 30‰ high salinity, were gradually acclimated to low salinities of 20, 10, and 0‰. Following acclimation, the fish were exposed to arsenate (As(V)) in their diet for 30 days. Results showed a significant accumulation of total arsenic (As) and AsB concentrations in the muscle and head tissues of the exposed fish, with these accumulations exhibiting a positive correlation with water salinity. Transcriptome analyses revealed that exposure to As(V) at low salinity may disrupt membrane components and induce cytoskeletal injuries, while at high salinity, it triggered oxidoreductase activity and transmembrane transport. Metabolome analyses indicated that low salinity induced osmotic stress, resulting in an increased requirement for amino acids to upload intracellular osmotic equilibrium in O. melastigma. Furthermore, the key organic osmolytes and amino acids, including taurine, l-methionine, guanidinoethyl sulfonate, and N-acetyl-l-aspartic acid, exhibited a negative correlation with the AsB concentration. These findings indicated that salinity can regulate osmotic balance by influencing amino acid synthesis under low salinity and stimulating AsB synthesis under high salinity conditions in O. melastigma. This study provides insights into the impact of high salinity on AsB biosynthesis, the underlying regulatory mechanisms, and implications for managing As(V) risk.

Extreme makeover: the incredible cell membrane adaptations of extremophiles to harsh environments

The existence of life beyond Earth has long captivated humanity, and the study of extremophiles-organisms surviving and thriving in extreme environments-provides crucial insights into this possibility. Extremophiles overcome severe challenges such as enzyme inactivity, protein denaturation, and damage of the cell membrane by adopting several strategies. This feature article focuses on the molecular strategies extremophiles use to maintain the cell membrane's structure and fluidity under external stress. Key strategies include homeoviscous adaptation (HVA), involving the regulation of lipid composition, and osmolyte-mediated adaptation (OMA), where small organic molecules protect the lipid membrane under stress. Proteins also have direct and indirect roles in protecting the lipid membrane. Examining the survival strategies of extremophiles provides scientists with crucial insights into how life can adapt and persist in harsh conditions, shedding light on the origins of life. This article examines HVA and OMA and their mechanisms in maintaining membrane stability, emphasizing our contributions to this field. It also provides a brief overview of the roles of proteins and concludes with recommendations for future research directions.

Carbohydrate accumulation patterns in mangrove and halophytic plant species under seasonal variation

This study investigates the impact of carbohydrate accumulation in mangrove and halophytic plants on their response to abiotic stress. Using soil analysis and FT-IR spectroscopy, key species (Sueda nudiflora, Aeluropus lagopoides, Avicennia marina) were examined for seasonal changes in sugar content (reducing sugars, total soluble sugars, starch). The elevated carbohydrate levels may serve as an indication of the plant's ability to adapt to different environmental conditions throughout the year. This accumulation enables plants to adapt to variations in their environment, assuring their survival and functionality during periods of environmental fluctuation. Halophytic plants' sugar content peaked during the monsoon, suggesting biotic adaptations. The mangrove Avicennia marina had year-round sugar levels. PCA and Hierarchical Cluster Analysis revealed sugar accumulation trends across species and seasons. Partial Least Squares (PLS) analysis revealed correlations between soil characteristics and sugar content, suggesting plant-microbe interactions. K-means clustering and correlation analysis of FT-IR data revealed sugar composition and resource allocation trade-offs. These findings shed light on the role of carbohydrate metabolism in enabling coastal plants to endure stress. Gaining insight into these mechanisms can enhance sustainable agriculture in challenging environments and shed light on plant adaptations to evolving environmental conditions, especially biotic interactions.

Oxygen- and proton-transporting open framework ionomer for medium-temperature fuel cells

Medium-temperature proton exchange membrane fuel cells (MT PEMFCs) operating at 100° to 120°C have improved kinetics, simplified thermal and water management, and broadened fuel tolerance compared with low-temperature PEMFCs. However, high temperatures lead to Nafion ionomer dehydration and exacerbate gas transportation limitations. Inspired by osmolytes found in hyperthermophiles, we developed α-aminoketone-linked covalent organic framework (COF) ionomers, interwoven with Nafion, to act as "breathable" proton conductors. This approach leverages synergistic hydrogen bonding to retain water, enhancing hydration and proton transport while reducing oxygen transport resistance. For commercial Pt/C, the MT PEMFCs achieved peak and rated power densities of 18.1 and 9.5 Watts per milligram of Pt at the cathode at 105°C fueled with H2 and air, marking increases of 101 and 187%, respectively, compared with cells lacking the COF.

Network analysis of metabolomics, transcriptome and hormones reveals propionic acid-mediated novel survival strategy against drought in wheat

Propionic acid (PA), a low-molecular-weight organic acid, is crucial to plant life metabolism. However, the regulatory mechanism of PA-mediated drought resistance in wheat remains largely unknown. Herein, we reported on a regulatory network of PA-mediated drought resistance in wheat using integrated transcriptome and metabolomics analysis and verified genes associated with drought resistance. Compared to the water-treated group, the application of PA alleviated the damage of drought by increasing plant water content, antioxidant enzyme activities and decreasing the malondialdehyde level (MDA). Transcriptome and metabolomics analysis revealed that PA triggered upregulation of key genes and metabolites, including TaBCAT, TaALDH6A1, TaALDH7A1, TaCHI, TaFLS, chrysin, and galangin, which were involved in valine, leucine and isoleucine degradation or flavonoid biosynthesis, respectively. In addition, the expression of genes encoding auxin-related transcription factors (TFs) strikingly increased, such as auxin/indoleacetic acid (AUX/IAA) and auxin response factor (ARF). Moreover, PA activated abscisic acid (ABA) and indole-3-acetic acid (IAA) signalling pathways. Taken together, our findings suggest that PA promotes energy metabolism and antioxidant activities to confer wheat drought resistance by introducing comprehensive and systemic effects of valine, leucine and isoleucine degradation flavonoid biosynthesis. Furthermore, activated AUX/IAA and ARF TFs might serve vital roles in drought resistance via modulating IAA signalling. This study provides novel insights into PA-mediated crop resistance and the improvement of the agroecological environment.

Transcriptional upregulation of the myo-inositol biosynthesis pathway is enhanced by NFAT5 in hyperosmotically stressed tilapia cells

Euryhaline fish experience variable osmotic environments requiring physiological adjustments to tolerate elevated salinity. Mozambique tilapia (Oreochromis mossambicus) possess one of the highest salinity tolerance limits of any fish. In tilapia and other euryhaline fish species, the myo-inositol biosynthesis (MIB) pathway enzymes, myo-inositol phosphate synthase (MIPS) and inositol monophosphatase 1 (IMPA1.1), are among the most upregulated mRNAs and proteins indicating the high importance of this pathway for hyperosmotic (HO) stress tolerance. These abundance changes must be precluded by HO perception and signaling mechanism activation to regulate the expression of MIPS and IMPA1.1 genes. In previous work using a O. mossambicus cell line (OmB), a reoccurring osmosensitive enhancer element (OSRE1) in both MIPS and IMPA1.1 was shown to transcriptionally upregulate these enzymes in response to HO stress. The OSRE1 core consensus (5'-GGAAA-3') matches the core binding sequence of the predominant mammalian HO response transcription factor, nuclear factor of activated T-cells (NFAT5). HO-challenged OmB cells showed an increase in NFAT5 mRNA suggesting NFAT5 may contribute to MIB pathway regulation in euryhaline fish. Ectopic expression of wild-type NFAT5 induced an IMPA1.1 promoter-driven reporter by 5.1-fold (P < 0.01). Moreover, expression of dominant negative NFAT5 in HO media resulted in a 47% suppression of the reporter signal (P < 0.005). Furthermore, reductions of IMPA1.1 (37-49%) and MIPS (6-37%) mRNA abundance were observed in HO-challenged NFAT5 knockout cells relative to control cells. Collectively, these multiple lines of experimental evidence establish NFAT5 as a tilapia transcription factor contributing to HO-induced activation of the MIB pathway.NEW & NOTEWORTHY In our study, we use a multi-pronged synthetic biology approach to demonstrate that the fish homolog of the predominant mammalian osmotic stress transcription factor nuclear factor of activated T-cells (NFAT5) also contributes to the activation of hyperosmolality inducible genes in cells of extremely euryhaline fish. However, in addition to NFAT5 the presence of other strong osmotically inducible signaling mechanisms is required for full activation of osmoregulated tilapia genes.

The contrasting roles of co-solvents in protein formulations and food products

Protein aggregation is a major hurdle in developing biopharmaceuticals, in particular protein formulation area, but plays a pivotal role in food products. Co-solvents are used to suppress protein aggregation in pharmaceutical proteins. On the contrary, aggregation is encouraged in the process of food product making. Thus, it is expected that co-solvents play a contrasting role in biopharmaceutical formulation and food products. Here, we show several examples that utilize co-solvents, e.g., salting-out salts, sugars, polyols and divalent cations in promoting protein-protein interactions. The mechanisms of co-solvent effects on protein aggregation and solubility have been studied on aqueous protein solution and applied to develop pharmaceutical formulation based on the acquired scientific knowledge. On the contrary, co-solvents have been used in food industries based on empirical basis. Here, we will review the mechanisms of co-solvent effects on protein-protein interactions that can be applied to both pharmaceutical and food industries and hope to convey knowledge acquired through research on co-solvent interactions in aqueous protein solution and formulation to those involved in food science and provide those involved in protein solution research with the observations on aggregation behavior of food proteins.

Interaction of anionic Fe3O4 nanoparticles with lipid vesicles: a review on deformation and poration under various conditions

This review focuses on the deformation and poration of lipid vesicles caused by the interaction of anionic magnetite nanoparticles (MNPs). Effects of various factors, such as surface charge density, salt and sugar concentrations in buffer, membrane cholesterol content, polymer-grafted phospholipid, and membrane potential have been discussed for the interaction of MNPs with lipid vesicles. To quantify these effects on the vesicles, compactness, fraction of deformation and poration, dynamics of membrane permeation, and kinetics of membrane permeation have been critically evaluated. The review explores the potential advancements as well as future directions of the research field in the biomedical application of MNPs.

Structure and mechanism of the osmoregulated choline transporter BetT

The choline-glycine betaine pathway plays an important role in bacterial survival in hyperosmotic environments. Osmotic activation of the choline transporter BetT promotes the uptake of external choline for synthesizing the osmoprotective glycine betaine. Here, we report the cryo-electron microscopy structures of Pseudomonas syringae BetT in the apo and choline-bound states. Our structure shows that BetT forms a domain-swapped trimer with the C-terminal domain (CTD) of one protomer interacting with the transmembrane domain (TMD) of a neighboring protomer. The substrate choline is bound within a tryptophan prism at the central part of TMD. Together with functional characterization, our results suggest that in Pseudomonas species, including the plant pathogen P. syringae and the human pathogen Pseudomonas aeruginosa, BetT is locked at a low-activity state through CTD-mediated autoinhibition in the absence of osmotic stress, and its hyperosmotic activation involves the release of this autoinhibition.

Enhancing protein stability under stress: osmolyte-based deep eutectic solvents as a biocompatible and robust stabilizing medium for lysozyme under heat and cold shock

In biomedical and biotechnological domains, liquid protein formulations are vital tools, offering versatility across various fields. However, maintaining protein stability in a liquid form presents challenges due to environmental factors, driving research to refine formulations for broader applications. In our recent study, we investigated the relationship between deep eutectic solvents (DESs) and the natural presence of osmolytes in specific combinations, showcasing the effectiveness of a bioinspired osmolyte-based DES in stabilizing a model protein. Recognizing the need for a more nuanced understanding of osmolyte-based DES stabilization capabilities under different storage conditions, here we broadened the scope of our osmolyte-based DES experimental screening, and delved deeper into structural changes in the enzyme under these conditions. We subjected lysozyme solutions in DESs based on various kosmotropic osmolytes (TMAO, betaine, sarcosine, DMSP, ectoine, GPC, proline, sorbitol and taurine) paired either with another kosmotropic (glycerol) or with chaotropic osmolyte urea to rigorous conditions: heat shock (at 80 °C) and repetitive freeze-thaw cycles (at -20 and -80 °C). Changes in enzyme activity, colloidal stability, and conformational alterations were then monitored using bioassays, aggregation tests, and spectroscopic techniques (FT-IR and CD). Our results demonstrate the remarkable effectiveness of osmolyte-based DES in stabilizing lysozyme under stress conditions, with sarcosine- and betaine-based DESs containing glycerol as a hydrogen bond donor showing the highest efficacy, even at high enzyme loadings up to 200 mg ml-1. Investigation of the individual and combined effects of the DES components on enzyme stability confirmed the synergistic behavior of the kosmotrope-urea mixtures and the cumulative effects in kosmotrope-glycerol mixtures. Additionally, we have shown that the interplay between the enzyme's active and stable (but inactive) states is highly influenced by the water content in DESs. Finally, toxicity assessments of osmolyte-based DESs using cell lines (Caco-2, HaCaT, and HeLa) revealed no risks to human health.

Solvent accessible surface area-assessed molecular basis of osmolyte-induced protein stability

In solvent-modulated protein folding, under certain physiological conditions, an equilibrium exists between the unfolded and folded states of the protein without any need to break or make a covalent bond. In this process, interactions between various protein groups (peptides) and solvent molecules are known to play a major role in determining the directionality of the chemical reaction. However, an understanding of the mechanism of action of the co(solvent) by a generic theoretical underpinning is lacking. In this study, a generic solvation model is developed based on statistical mechanics and the thermodynamic transfer free energy model by considering the microenvironment polarity of the interacting co(solvent)-protein system. According to this model, polarity and the fractional solvent-accessible surface areas contribute to the interaction energies. The present model includes various orientations of participating interactant solvent surfaces of suitable areas. As model systems, besides the backbone we consider naturally occurring amino acid residues solvated in ten different osmolytes, small organic compounds known to modulate protein stability. The present model is able to predict the correct trend of the osmolyte-peptide interactions ranging from stabilizing to destabilizing not only for the backbone but also for side chains. Our model predicts Asn, Gln, Asp, Glu, Arg and Pro to be highly stable in most of the protecting osmolytes while Ala, Val, Ile, Leu, Thr, Met, Lys, Phe, Trp and Tyr are predicted to be moderately stable, and Ser, Cys and Histidine are predicted to be least stable. However, in denaturing solvents, both backbone and side chain models show similar stabilities in urea and guanidine. One of the important aspects of this model is that it is essentially parameter-free and consistent with the electrostatics of the interaction partners that make this model suitable for estimating any solute-solvent interaction energies.

Trimethylamine N-oxide (TMAO) doubly locks the hydrophobic core and surfaces of protein against desiccation stress

Interactions between proteins and osmolytes are ubiquitous within cells, assisting in response to environmental stresses. However, our understanding of protein-osmolyte interactions underlying desiccation tolerance is limited. Here, we employ solid-state NMR (ssNMR) to derive information about protein conformation and site-specific interactions between the model protein, SH3, and the osmolyte trimethylamine N-oxide (TMAO). The data show that SH3-TMAO interactions maintain key structured regions during desiccation and facilitate reversion to the protein's native state once desiccation stress is even slightly relieved. We identify 10 types of residues at 28 sites involved in the SH3-TMAO interactions. These sites comprise hydrophobic, positively charged, and aromatic amino acids located in SH3's hydrophobic core and surface clusters. TMAO locks both the hydrophobic core and surface clusters through its zwitterionic and trimethyl ends. This double locking is responsible for desiccation tolerance and differs from ideas based on exclusion, vitrification, and water replacement. ssNMR is a powerful tool for deepening our understanding of extremely weak protein-osmolyte interactions and providing insight into the evolutionary mechanism of environmental tolerance.

Enhanced catabolism of glycine betaine and derivatives provides improved osmotic stress protection in Methylorubrum extorquens PA1

Integration of metabolites into the overall metabolic network of a cell requires careful coordination dependent upon the ultimate usage of the metabolite. Different stoichiometric needs, and thus pathway fluxes, must exist for compounds destined for diverse uses, such as carbon sources, nitrogen sources, or stress-protective agents. Herein, we expand upon our previous work that highlighted the nature of glycine betaine (GB) metabolism in Methylobacteria to examine the utilization of GB-derivative compounds dimethylglycine (DMG) and sarcosine into Methylorubrum extorquens in different metabolic capacities, including as sole nitrogen and/or carbon sources. We isolated gain-of-function mutations that allowed M. extorquens PA1 to utilize dimethylglycine as a carbon source and dimethylglycine and sarcosine as nitrogen source. Characterization of mutants demonstrated selection for variants of the AraC-like regulator Mext_3735 that confer constitutive expression of the GB metabolic gene cluster, allowing direct utilization of the downstream GB derivatives. Finally, among the distinct isolates examined, we found that catabolism of the osmoprotectant used for selection (GB or dimethylglycine) enhanced osmotic stress resistance provided in the presence of that particular osmolyte. Thus, access to the carbon and nitrogen and osmoprotective effects of GB and DMG are made readily accessible through adaptive mutations. In M. extorquens PA1, the limitations to exploiting this group of compounds appear to exist predominantly at the levels of gene regulation and functional activity, rather than being constrained by transport or toxicity.IMPORTANCEOsmotic stress is a common challenge for bacteria colonizing the phyllosphere, where glycine betaine (GB) can be found as a prevalent osmoprotectant. Though Methylorubrum extorquens PA1 cannot use GB or its demethylation products, dimethylglycine (DMG) and sarcosine, as a sole carbon source, utilization is highly selectable via single nucleotide changes for both GB and DMG growth. The innate inability to use these compounds is due to limited flux through steps in the pathway and regulatory constraints. Herein, the characterization of the transcriptional regulator, Mext_3735 (GbdR), expands our understanding of the various roles in which GB derivatives can be used in M. extorquens PA1. Interestingly, increased catabolism of GB and derivatives does not interfere with, but rather improves, the ability of cells to thrive under increased salt stress conditions, suggesting that metabolic flux improves stress tolerance rather than providing a distinct tension between uses.

Essential dynamics of ubiquitin in water and in a natural deep eutectic solvent

Natural deep eutectic solvents (NADESs) comprised of osmolytes are of interest as potential biomolecular (cryo)protectants. However, the way these solvents influence the structure and dynamics of biomolecules as well as the role of water remains poorly understood. We carried out principal component analysis of various secondary structure elements of ubiquitin in water and a betaine : glycerol : water (1 : 2 : ζ; ζ = 0, 1, 2, 5, 10, 20, 45) NADES, from molecular dynamics trajectories, to gain insight into the protein dynamics as it undergoes a transition from a highly viscous anhydrous to an aqueous environment. A crossover of the protein's essential dynamics at ζ ∼ 5, induced by solvent-shell coupled fluctuations, is observed, indicating that ubiquitin might (re)fold in the NADES upon water addition at ζ > ∼5. Further, in contrast to water, the anhydrous NADES preserves ubiquitin's essential modes at high temperatures explaining the protein's seemingly enhanced thermal stability.

The dynamic hypoosmotic response of Vibrio cholerae relies on the mechanosensitive channel MscS

Vibrio cholerae adapts to osmotic down-shifts by releasing metabolites through two mechanosensitive (MS) channels, low-threshold MscS and high-threshold MscL. To investigate each channel's contribution to the osmotic response, we generated ΔmscS, ΔmscL, and double ΔmscL ΔmscS mutants in V. cholerae O395. We characterized their tension-dependent activation in patch-clamp, and the millisecond-scale osmolyte release kinetics using a stopped-flow light scattering technique. We additionally generated numerical models describing osmolyte and water fluxes. We illustrate the sequence of events and define the parameters that characterize discrete phases of the osmotic response. Survival is correlated to the extent of cell swelling, the rate of osmolyte release, and the completeness of post-shock membrane resealing. Not only do the two channels interact functionally, but there is also an up-regulation of MscS in the ΔmscL strain, suggesting transcriptional crosstalk. The data reveal the role of MscS in the termination of the osmotic permeability response in V. cholerae.

Transcriptome Analysis of the Regulatory Mechanisms of Holly (Ilex dabieshanensis) under Salt Stress Conditions

The holly Ilex dabieshanensis K. Yao & M. B. Deng, a tree endemic to the Dabieshan Mountains region in China, is a commonly used landscaping plant. Like other crops, its growth is affected by salt stress. The molecular mechanism underlying salt tolerance in holly is still unclear. In this study, we used NaCl treatment and RNA sequencing (RNA-seq) at different times to identify the salt stress response genes of holly. A total of 4775 differentially expressed genes (DEGs) were identified. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of the DEGs obtained at different salt treatment times (3, 6, 9, 12, and 24 h), as compared to control (ck, 0 h), showed that plant hormone signal transduction and carotenoid biosynthesis were highly enriched. The mechanism by which holly responds to salt stress involves many plant hormones, among which the accumulation of abscisic acid (ABA) and its signal transduction may play an important role. In addition, ion homeostasis, osmotic metabolism, accumulation of antioxidant enzymes and nonenzymatic antioxidant compounds, and transcription factors jointly regulate the physiological balance in holly, providing important guarantees for its growth and development under conditions of salt stress. These results lay the foundation for studying the molecular mechanisms of salt tolerance in holly and for the selection of salt-tolerant varieties.

Electrostatics introduce a trade-off between mesophilic stability and adaptation in halophilic proteins

Extremophile organisms have adapted to extreme physicochemical conditions. Halophilic organisms, in particular, survive at very high salt concentrations. To achieve this, they have engineered the surface of their proteins to increase the number of short, polar and acidic amino acids, while decreasing large, hydrophobic and basic residues. While these adaptations initially decrease protein stability in the absence of salt, they grant halophilic proteins remarkable stability in environments with extremely high salt concentrations, where non-adapted proteins unfold and aggregate. The molecular mechanisms by which halophilic proteins achieve this, however, are not yet clear. Here, we test the hypothesis that the halophilic amino acid composition destabilizes the surface of the protein, but in exchange improves the stability in the presence of salts. To do that, we have measured the folding thermodynamics of various protein variants with different degrees of halophilicity in the absence and presence of different salts, and at different pH values to tune the ionization state of the acidic amino acids. Our results show that halophilic amino acids decrease the stability of halophilic proteins under mesophilic conditions, but in exchange improve salt-induced stabilization and solubility. We also find that, in contrast to traditional assumptions, contributions arising from hydrophobic effect and preferential ion exclusion are more relevant for haloadaptation than electrostatics. Overall, our findings suggest a trade-off between folding thermodynamics and halophilic adaptation to optimize proteins for hypersaline environments.

Literature Review of Proteomics Approach Associated with Coffee

As a significant crop growing all across the world, coffee is mostly produced in the bean belt of our global atlas. Worldwide variations in environmental conditions are causing a decline in the yield and quality of coffee varieties. Coffee production is the main emphasis of several traditional breeding techniques. But conventional breeding methods are not sufficient to tackle the problems related to coffee. The field of genomics, which includes transcriptomics, proteomics, and metabolomics, has made great paces in the last ten years. Proteomics is a well-known technique used to enhance the growth, yield, breeding, and quality of different plants under stable and shifting environments. The regulation of specific enzymes, genes, protein expression, modification, translation, and other features played an important role in the enhancement of important plants. However, relatively less research on the proteomics approach for coffee has been published in the last few years. For this reason, some of the most important aspects of proteome profiling for coffee plants have been covered in this review, including growth, the somatic embryo technique, altitude, environmental adoption, drought, and the role that proteins and important enzymes play in the flavor and taste of coffee. This review can aid in the breeding of new cultivars and improve coffee attributes. Furthermore, the present literature can pave the way for proteomics research on coffee.

Rotational Dynamics of Water near Osmolytes by Molecular Dynamics Simulations

The behavior of water molecules around organic molecules has attracted considerable attention as a crucial factor influencing the properties and functions of soft matter and biomolecules. Recently, it has been suggested that the change in protein stability upon the addition of small organic molecules (osmolytes) is dominated by the change in the water dynamics caused by the osmolyte, where the dynamics of not only the directly interacting water molecules but also the long-range hydration layer affect the protein stability. However, the relation between the long-range structure of hydration water in various solutions and the water dynamics remains unclear at the molecular level. We performed density-functional tight-binding molecular dynamics simulations to elucidate the varying rotational dynamics of water molecules in 15 osmolyte solutions. A positive correlation was observed between the rotational relaxation time and our proposed normalized parameter obtained by dividing the number of hydrogen bonds between water molecules by the number of nearest-neighbor water molecules. For the 15 osmolyte solutions, an increase or a decrease in the value of the normalized parameter for the second hydration shell tended to result in water molecules with slow and fast rotational dynamics, respectively, thus illustrating the importance of the second hydration shell for the rotational dynamics of water molecules. Our simulation results are anticipated to advance the current understanding of water dynamics around organic molecules and the long-range structure of water molecules.

The biophysics of water in cell biology: perspectives on a keystone for both marine sciences and cancer research

The biophysics of water, has been debated over more than a century. Although its importance is still underestimated, significant breakthroughs occurred in recent years. The influence of protein condensation on water availability control was documented, new findings on water-transport proteins emerged, and the way water molecules rearrange to minimize free energy at interfaces was deciphered, influencing membrane thermodynamics. The state of knowledge continued to progress in the field of deep-sea marine biology, highlighting unknown effects of high hydrostatic pressure and/or temperature on interactions between proteins and ligands in extreme environments, and membrane structure adaptations. The role of osmolytes in protein stability control under stress is also discussed here in relation to fish egg hydration/buoyancy. The complexity of water movements within the cell is updated, all these findings leading to a better view of their impact on many cellular processes. The way water flow and osmotic gradients generated by ion transport work together to produce the driving force behind cell migration is also relevant to both marine biology and cancer research. Additional common points concern water dynamic changes during the neoplastic transformation of cells and tissues, or embryo development. This could improve imaging techniques, early cancer diagnosis, and understanding of the molecular and physiological basis of buoyancy for many marine species.

Protecting Proteins from Desiccation Stress Using Molecular Glasses and Gels

Faced with desiccation stress, many organisms deploy strategies to maintain the integrity of their cellular components. Amorphous glassy media composed of small molecular solutes or protein gels present general strategies for protecting against drying. We review these strategies and the proposed molecular mechanisms to explain protein protection in a vitreous matrix under conditions of low hydration. We also describe efforts to exploit similar strategies in technological applications for protecting proteins in dry or highly desiccated states. Finally, we outline open questions and possibilities for future explorations.

Long-term health outcomes associated with hydration status

Body water balance is determined by fundamental homeostatic mechanisms that maintain stable volume, osmolality and the composition of extracellular and intracellular fluids. Water balance is maintained by multiple mechanisms that continuously match water losses through urine, the skin, the gastrointestinal tract and respiration with water gains achieved through drinking, eating and metabolic water production. Hydration status is determined by the state of the water balance. Underhydration occurs when a decrease in body water availability, due to high losses or low gains, stimulates adaptive responses within the water balance network that are aimed at decreasing losses and increasing gains. This stimulation is also accompanied by cardiovascular adjustments. Epidemiological and experimental studies have linked markers of low fluid intake and underhydration - such as increased plasma concentration of vasopressin and sodium, as well as elevated urine osmolality - with an increased risk of new-onset chronic diseases, accelerated aging and premature mortality, suggesting that persistent activation of adaptive responses may be detrimental to long-term health outcomes. The causative nature of these associations is currently being tested in interventional trials. Understanding of the physiological responses to underhydration may help to identify possible mechanisms that underlie potential adverse, long-term effects of underhydration and inform future research to develop preventative and treatment approaches to the optimization of hydration status.

Effects of CRISPR/Cas9 targeting of the myo-inositol biosynthesis pathway on hyper-osmotic tolerance of tilapia cells

Myo-inositol is an important compatible osmolyte in vertebrates. This osmolyte is produced by the myo-inositol biosynthesis (MIB) pathway composed of myo-inositol phosphate synthase and inositol monophosphatase. These enzymes are among the highest upregulated proteins in tissues and cell cultures from teleost fish exposed to hyperosmotic conditions indicating high importance of this pathway for tolerating this type of stress. CRISPR/Cas9 gene editing of tilapia cells produced knockout lines of MIB enzymes and control genes. Metabolic activity decreased significantly for MIB KO lines in hyperosmotic media. Trends of faster growth of the MIB knockout lines in isosmotic media and faster decline of MIB knockout lines in hyperosmotic media were also observed. These results indicate a decline in metabolic fitness but only moderate effects on cell survival when tilapia cells with disrupted MIB genes are exposed to hyperosmolality. Therefore MIB genes are required for full osmotolerance of tilapia cells.

Trimethylamine-N-oxide depletes urea in a peptide solvation shell

Trimethylamine-N-oxide (TMAO) and urea are metabolites that are used by some marine animals to maintain their cell volume in a saline environment. Urea is a well-known denaturant, and TMAO is a protective osmolyte that counteracts urea-induced protein denaturation. TMAO also has a general protein-protective effect, for example, it counters pressure-induced protein denaturation in deep-sea fish. These opposing effects on protein stability have been linked to the spatial relationship of TMAO, urea, and protein molecules. It is generally accepted that urea-induced denaturation proceeds through the accumulation of urea at the protein surface and their subsequent interaction. In contrast, it has been suggested that TMAO's protein-stabilizing effects stem from its exclusion from the protein surface, and its ability to deplete urea from protein surfaces; however, these spatial relationships are uncertain. We used neutron diffraction, coupled with structural refinement modeling, to study the spatial associations of TMAO and urea with the tripeptide derivative glycine-proline-glycinamide in aqueous urea, aqueous TMAO, and aqueous urea-TMAO (in the mole ratio 1:2 TMAO:urea). We found that TMAO depleted urea from the peptide's surface and that while TMAO was not excluded from the tripeptide's surface, strong atomic interactions between the peptide and TMAO were limited to hydrogen bond donating peptide groups. We found that the repartition of urea, by TMAO, was associated with preferential TMAO-urea bonding and enhanced urea-water hydrogen bonding, thereby anchoring urea in the bulk solution and depleting urea from the peptide surface.

Do Ionic Liquids Exhibit the Required Characteristics to Dissolve, Extract, Stabilize, and Purify Proteins? Past-Present-Future Assessment

Proteins are highly labile molecules, thus requiring the presence of appropriate solvents and excipients in their liquid milieu to keep their stability and biological activity. In this field, ionic liquids (ILs) have gained momentum in the past years, with a relevant number of works reporting their successful use to dissolve, stabilize, extract, and purify proteins. Different approaches in protein-IL systems have been reported, namely, proteins dissolved in (i) neat ILs, (ii) ILs as co-solvents, (iii) ILs as adjuvants, (iv) ILs as surfactants, (v) ILs as phase-forming components of aqueous biphasic systems, and (vi) IL-polymer-protein/peptide conjugates. Herein, we critically analyze the works published to date and provide a comprehensive understanding of the IL-protein interactions affecting the stability, conformational alteration, unfolding, misfolding, and refolding of proteins while providing directions for future studies in view of imminent applications. Overall, it has been found that the stability or purification of proteins by ILs is bispecific and depends on the structure of both the IL and the protein. The most promising IL-protein systems are identified, which is valuable when foreseeing market applications of ILs, e.g., in "protein packaging" and "detergent applications". Future directions and other possibilities of IL-protein systems in light-harvesting and biotechnology/biomedical applications are discussed.

A comparative analysis of TonEBP conditional knockout mouse models reveals inter-dependency between compartments of the intervertebral disc

Interactions between notochord and sclerotome are required for normal embryonic spine patterning, but whether the postnatal derivatives of these tissues also require interactions for postnatal intervertebral disc (IVD) growth and maintenance is less established. We report here the comparative analysis of four conditional knockout mice deficient for TonEBP, a transcription factor known to allow cells to adapt to changes in extracellular osmotic pressure, in specific compartments of the IVD. We show that TonEBP deletion in nucleus pulposus (NP) cells does not affect their survival or aggrecan expression, but promoted cell proliferation in the NP and in adjacent vertebral growth plates (GPs). In cartilage end plates/GPs, TonEBP deletion induced cell death, but also structural alterations in the adjacent NP cells and vertebral bodies. Embryonic or postnatal TonEBP loss generated similar IVD changes. In addition to demonstrating the requirement of TonEBP in the different compartments of the IVD, this comparative analysis uncovers the in vivo interdependency of the different IVD compartments during the growth of the postnatal IVD-vertebral units.

Macromolecular Crowding, Phase Separation, and Homeostasis in the Orchestration of Bacterial Cellular Functions

Macromolecular crowding affects the activity of proteins and functional macromolecular complexes in all cells, including bacteria. Crowding, together with physicochemical parameters such as pH, ionic strength, and the energy status, influences the structure of the cytoplasm and thereby indirectly macromolecular function. Notably, crowding also promotes the formation of biomolecular condensates by phase separation, initially identified in eukaryotic cells but more recently discovered to play key functions in bacteria. Bacterial cells require a variety of mechanisms to maintain physicochemical homeostasis, in particular in environments with fluctuating conditions, and the formation of biomolecular condensates is emerging as one such mechanism. In this work, we connect physicochemical homeostasis and macromolecular crowding with the formation and function of biomolecular condensates in the bacterial cell and compare the supramolecular structures found in bacteria with those of eukaryotic cells. We focus on the effects of crowding and phase separation on the control of bacterial chromosome replication, segregation, and cell division, and we discuss the contribution of biomolecular condensates to bacterial cell fitness and adaptation to environmental stress.

The impact of chronic Trimethylamine N-oxide administration on liver oxidative stress, inflammation, and fibrosis

TMAO, a gut microbiota derived byproduct, has been associated with various cardiometabolic diseases by promoting oxidative stress and inflammation. The liver is the main organ for TMAO production and chronic exposure to high doses of TMAO could alter its function. In this study, we evaluated the effect of chronic exposure of high TMAO doses on liver oxidative stress, inflammation, and fibrosis. TMAO was administered daily via gastric gavage to laboratory rats for 3 months. Blood was drawn for the quantification of TMAO, and liver tissues were harvested for the assessment of oxidative stress (MDA, GSH, GSSG, GPx, CAT, and 8-oxo-dG) and inflammation by quantification of IL-1α, TNF-α, IL-10, TGF-β, NOS and COX-2 expression. The evaluation of fibrosis was made by Western blot analysis of α-SMA and Collagen-3 protein expression. Histological investigation and immunohistochemical staining of iNOS were performed in order to assess the liver damage. After 3 months of TMAO exposure, TMAO serum levels enhanced in parallel with increases in MDA and GSSG levels in liver tissue and lower values of GSH and GSH/GSSG ratio as well as a decrease in GPx and CAT activities. Inflammation was also highlighted, with enhanced iNOS, COX-2, and IL-10 expression, without structural changes and without induction of liver fibrosis.