High Salt Conditions Research Articles

Resourcefulness of propylprodigiosin isolated from Brevundimonas olei strain RUN-D1

A novel red-pigmented bacterium was isolated from a water sample collected at Osun River, Ede. Morphological and 16 S rRNA gene sequencing revealed that the bacterium is a strain of Brevundimonas olei, while its red pigment was identified using UV-visible, FTIR and GCMS as a derivative of propylprodigiosin. The maximum absorbance of 534 nm, the FTIR’s 1344 cm− 1 peak of prodigiosin’s methoxyl C-O interaction, and the molecular ions from GCMS confirmed the pigment’s identity. The pigments production was temperature-sensitive (25 °C), lost at > 28 °C, and in the presence of urea and humus. In addition, the pigment turned pink in the presence of hydrocarbons, while its red colour was retained with KCN and Fe2SO4, and enhanced by methylparaben. Furthermore, the pigment is stable in high temperature, salt, and acidic conditions, but changed to yellow in alkaline solution. The pigment, identified as propylprodigiosin (m/z 297), demonstrated broad-spectrum antibacterial activities against clinically important strains of Staphylococcus aureus (ATCC25923), Pseudomonas aeruginosa (ATCC9077), Bacillus cereus (ATCC10876), Salmonella typhi (ATCC13311), and Escherichia coli (DSM10974). The ethanol extract has the highest zones of inhibition of 29 ± 3.0, 26 ± 1.2, 22 ± 3.0, 22 ± 1.5, and 20 ± 2.0 mm, respectively. Furthermore, the acetone pigments interacted with cellulose and glucose such that increasing glucose concentrations showed linearity at 425 nm. Finally, the fastness of the pigments to fabrics was excellent, with percentage fadedness of 0 and − 43% light and washing tests, respectively, in the presence of Fe2SO4 as the mordant. The antibacterial nature of prodigiosin solutions and their good textile fastness to fabrics could be essential in manufacturing antiseptic materials such as bandages, hospital clothing and agricultural applications such as tubers preservation.Key points

Probiotic properties and antimicrobial evaluation of silymarin-enriched Lactobacillus bacteria isolated from traditional curd

Nowadays, the increasing use of medicinal plants in the treatment and prevention of diseases has attracted the attention of researchers. The aim of this work was to investigate the probiotic properties and antibacterial and antifungal activity of silymarin-enriched Lactobacillus bacteria against several important pathogenic bacteria and also Aspergillus flavus as one of the harmful molds in the food and health industries. For this purpose, 52 g-positive and catalase-negative bacteria were isolated from 60 traditional curd samples from Ilam province. Five of the 52 bacterial strains had more than 90% viability in high bile salt and acidic conditions and were selected for further investigation. The five strains with positive results showed good hydrophobicity (≥ 50.30%), auto-aggregation (≥ 53.70%), coaggregation (≥ 28.20%), and high cholesterol removal ability (from 09.20 to 67.20%) and therefore can be considered potential probiotics. The tested strains displayed acceptable antibacterial and antifungal activity against all 12 pathogenic bacteria and A. flavus. Also, the results of the simultaneous antifungal activity of probiotic strains and silymarin showed that the combination of silymarin and probiotics has a significantly better (P < 0.05) antifungal effect than the control group or the probiotic groups alone. Interestingly, in addition to the Limosilactobacillus fermentum C3 strain, the Limosilactobacillus fermentum C18 and Lactiplantibacillus pentosus C20 strains also had significant inhibitory effects against A. flavus when used with silymarin extract in methanol. Meanwhile, silymarin extract in DMSO and PEG increased the antagonistic activity of all five potential probiotic strains.

Impact of dark septate endophytes on salt stress alleviation of tomato plants.

Fungal endophytes can improve plant tolerance to abiotic stress conditions. Dark septate endophytes (DSEs) belong to phylogenetically non-related groups of root colonizing fungi among the Ascomycota with high melanin-producing activities. They can be isolated from roots of more than 600 plant species in diverse ecosystems. Still the knowledge about their interaction with host plants and their contribution to stress alleviation is limited. The current work aimed to test the abilities of three DSEs (Periconia macrospinosa, Cadophora sp., Leptodontidium sp.) to alleviate moderate and high salt stress in tomato plants. By including an albino mutant, the role of melanin for the interaction with plants and salt stress alleviation could also be tested. P. macrospinosa and Cadophora sp. improved shoot and root growth 6 weeks after inoculation under moderate and high salt stress conditions. No matter how much salt stress was applied, macroelement (P, N, and C) contents were unaffected by DSE inoculation. The four tested DSE strains successfully colonized the roots of tomato, but the colonization level was clearly reduced in the albino mutant of Leptodontidium sp. Any difference in the effects on plant growth between the Leptodontidium sp. wild type strain and the albino mutant could, however, not be observed. These results show that particular DSEs are able to increase salt tolerance as they promote plant growth specifically under stress condition. Increased plant biomasses combined with stable nutrient contents resulted in higher P uptake in shoots of inoculated plants at moderate and high salt conditions and higher N uptake in the absence of salt stress in all inoculated plants, in P. macrospinosa-inoculated plants at moderate salt condition and in all inoculated plants except the albino mutants at high salt condition. In summary, melanin in DSEs seems to be important for the colonization process, but does not influence growth, nutrient uptake or salt tolerance of plants.

Synthesis and Performance Evaluation of a Novel Nanoparticle Coupling Expanded Granule Plugging Agent.

This study focuses on the characteristics of fractured and vuggy high-temperature and high-salt reservoirs in the Tahe Oilfield. The Acrylamide/2-acrylamide-2-methylpropanesulfonic copolymer salt was selected as a polymer; the hydroquinone and hexamethylene tetramine was selected as the crosslinking agent with a ratio of 1:1; the nanoparticle SiO2 was selected, and its dosage was optimized to 0.3%; Additionally, a novel nanoparticle coupling polymer gel was independently synthesized. The surface of the gel was a three-dimensional network structure, with grids arranged in pieces and interlaced with each other, and the structure was very stable. The SiO2 nanoparticles were attached to the gel skeleton, forming effective coupling and enhancing the strength of the gel skeleton. To solve the problem of complex gel preparation and transportation, the novel gel is compressed, pelletized, and dried into expanded particles through industrial granulation, and the disadvantage of the rapid expansion of expanded particles is optimized through physical film coating treatment. Finally, a novel nanoparticle coupling expanded granule plugging agent was developed. Evaluation of the performance of the novel nanoparticle coupling expanded granule plugging agent. With an increase in temperature and mineralization, the expansion multiplier of granules decreases; aged under high-temperature and high-salt conditions for 30 days, the expansion multiplier of granules can still reach 3.5 times, the toughness index is 1.61, and the long-term stability of the granules can be good; the water plugging rate of granules is 97.84%, which is superior to other widely used particle-based plugging agents.

AcCRISPR: an activity-correction method for improving the accuracy of CRISPR screens

High throughput CRISPR screens are revolutionizing the way scientists unravel the genetic underpinnings of engineered and evolved phenotypes. One of the critical challenges in accurately assessing screening outcomes is accounting for the variability in sgRNA cutting efficiency. Poorly active guides targeting genes essential to screening conditions obscure the growth defects that are expected from disrupting them. Here, we develop acCRISPR, an end-to-end pipeline that identifies essential genes in pooled CRISPR screens using sgRNA read counts obtained from next-generation sequencing. acCRISPR uses experimentally determined cutting efficiencies for each guide in the library to provide an activity correction to the screening outcomes via calculation of an optimization metric, thus determining the fitness effect of disrupted genes. CRISPR-Cas9 and -Cas12a screens were carried out in the non-conventional oleaginous yeast Yarrowia lipolytica and acCRISPR was used to determine a high-confidence set of essential genes for growth under glucose, a common carbon source used for the industrial production of oleochemicals. acCRISPR was also used in screens quantifying relative cellular fitness under high salt conditions to identify genes that were related to salt tolerance. Collectively, this work presents an experimental-computational framework for CRISPR-based functional genomics studies that may be expanded to other non-conventional organisms of interest.

Translocation of Hydrophobic Polyelectrolytes under Electrical Field: Molecular Dynamics Study.

We studied the translocation of polyelectrolyte (PE) chains driven by an electric field through a pore by means of molecular dynamics simulations of a coarse-grained HP model mimicking high salt conditions. Charged monomers were considered as polar (P) and neutral monomers as hydrophobic (H). We considered PE sequences that had equally spaced charges along the hydrophobic backbone. Hydrophobic PEs were in the globular form in which H-type and P-type monomers were partially segregated and they unfolded in order to translocate through the narrow channel under the electric field. We provided a quantitative comprehensive study of the interplay between translocation through a realistic pore and globule unraveling. By means of molecular dynamics simulations, incorporating realistic force fields inside the channel, we investigated the translocation dynamics of PEs at various solvent conditions. Starting from the captured conformations, we obtained distributions of waiting times and drift times at various solvent conditions. The shortest translocation time was observed for the slightly poor solvent. The minimum was rather shallow, and the translocation time was almost constant for medium hydrophobicity. The dynamics were controlled not only by the friction of the channel, but also by the internal friction related to the uncoiling of the heterogeneous globule. The latter can be rationalized by slow monomer relaxation in the dense phase. The results were compared with those from a simplified Fokker-Planck equation for the position of the head monomer.

Global Transcriptome-Guided Identification of Neutral Sites for Engineering Synechococcus elongatus PCC 11801.

Engineered cyanobacteria are attractive hosts for the phototrophic conversion of CO2 to chemicals. Synechococcus elongatus PCC11801, a novel, fast-growing, and stress-tolerant cyanobacterium, has the potential to be a platform cell factory, and hence, it necessitates the development of a synthetic biology toolbox. Considering the widely followed cyanobacterial engineering strategy of chromosomal integration of heterologous DNA, it is of interest to discover and validate new chromosomal neutral sites (NSs) in this strain. To that end, global transcriptome analysis was performed using RNA Seq under the conditions of high temperature (HT), carbon (HC), and salt (HS) and ambient growth conditions. We found upregulation of 445, 138, and 87 genes and downregulation of 333, 125, and 132 genes, under HC, HT, and HS, respectively. Following nonhierarchical clustering, gene enrichment, and bioinformatics analysis, 27 putative NSs were predicted. Six of them were experimentally tested, and five showed confirmed neutrality, based on unaltered cell growth. Thus, global transcriptomic analysis was effectively exploited for NS annotation and would be advantageous for multiplexed genome editing.

Mechanism and Performance Analysis of Nanoparticle-Polymer Fluid for Enhanced Oil Recovery: A Review.

With the increasing energy demand, oil is still an important fuel source worldwide. The chemical flooding process is used in petroleum engineering to increase the recovery of residual oil. As a promising enhanced oil-recovery technology, polymer flooding still faces some challenges in achieving this goal. The stability of a polymer solution is easily affected by the harsh reservoir conditions of high temperature and high salt, and the influence of the external environment such as high salinity, high valence cations, pH value, temperature and its own structure is highlighted. This article also involves the introduction of commonly used nanoparticles, whose unique properties are used to improve the performance of polymers under harsh conditions. The mechanism of nanoparticle improvement on polymer properties is discussed, that is, how the interaction between them improves the viscosity, shear stability, heat-resistance and salt-tolerant performance of the polymer. Nanoparticle-polymer fluids exhibit properties that they cannot exhibit by themselves. The positive effects of nanoparticle-polymer fluids on reducing interfacial tension and improving the wettability of reservoir rock in tertiary oil recovery are introduced, and the stability of nanoparticle-polymer fluid is described. While analyzing and evaluating the research on nanoparticle-polymer fluid, indicating the obstacles and challenges that still exist at this stage, future research work on nanoparticle-polymer fluid is proposed.

Synthesis and mechanism of environmentally friendly high temperature and high salt resistant lubricants

With the exploration and development of deep and ultra-deep oil and gas, high torque and high friction during the drilling of deep and ultra-deep wells become one of the key issues affecting drilling safety and drilling speed. Meanwhile, the high temperature and high salt problem in deep formations is prominent, which poses a major challenge to the lubricity of drilling fluids under high temperature and high salt. This paper reports an organic borate ester SOP as an environmentally friendly drilling fluid lubricant. The performance evaluation results show that when 1% lubricant SOP is added to the fresh water-based mud, the lubrication coefficient decreases from 0.631 to 0.046, and the reduction rate of lubrication coefficient is 92.7%. Under the conditions of 210 °C and 30% NaCl, the reduction rate of lubricating coefficient of the base slurry with 1% SOP was still remain 81.5%. After adding 1% SOP, the wear volume decreased by 94.11% compared with the base slurry. The contact resistance experiment during the friction process shows that SOP can form a thick adsorption film on the friction surface under high temperature and high salt conditions, thus effectively reducing the friction resistance. Molecular dynamics simulation shows that lubricant SOP can be physically adsorbed on the surface of drilling tool and borehole wall through hydrogen bond and van der Waals force. XPS analysis further shows that SOP adsorbs on the friction surface and reacts with metal atoms on the friction surface to form a chemically reactive film. Therefore, under high temperature and high salt conditions, the synergistic effect of physical adsorption film and chemical reaction film effectively reduces the frictional resistance and wear of the friction surface. In addition, SOP is non-toxic and easy to degrade. Therefore, SOP is a highly effective and environmentally friendly lubricant in high temperature and high salt drilling fluid.

Purification and biochemical characterization of SM14est, a PET-hydrolyzing enzyme from the marine sponge-derived Streptomyces sp. SM14.

The successful enzymatic degradation of polyester substrates has fueled worldwide investigation into the treatment of plastic waste using bio-based processes. Within this realm, marine-associated microorganisms have emerged as a promising source of polyester-degrading enzymes. In this work, we describe the hydrolysis of the synthetic polymer PET by SM14est, a polyesterase which was previously identified from Streptomyces sp. SM14, an isolate of the marine sponge Haliclona simulans. The PET hydrolase activity of purified SM14est was assessed using a suspension-based assay and subsequent analysis of reaction products by UV-spectrophotometry and RP-HPLC. SM14est displayed a preference for high salt conditions, with activity significantly increasing at sodium chloride concentrations from 100 mM up to 1,000 mM. The initial rate of PET hydrolysis by SM14est was determined to be 0.004 s-1 at 45°C, which was increased by 5-fold to 0.02 s-1 upon addition of 500 mM sodium chloride. Sequence alignment and structural comparison with known PET hydrolases, including the marine halophile PET6, and the highly efficient, thermophilic PHL7, revealed conserved features of interest. Based on this work, SM14est emerges as a useful enzyme that is more similar to key players in the area of PET hydrolysis, like PHL7 and IsPETase, than it is to its marine counterparts. Salt-tolerant polyesterases such as SM14est are potentially valuable in the biological degradation of plastic particles that readily contaminate marine ecosystems and industrial wastewaters.

Porcine spermadhesin AQN-3 binds to negatively charged phospholipids

The spermadhesin AQN-3 is a major component of porcine seminal plasma. While various studies suggest that this protein binds to boar sperm cells, its attachment to the cells is poorly understood. Therefore, the capacity of AQN-3 to interact with lipids was investigated. For that purpose, AQN-3 was recombinantly expressed in E. coli and purified via the included His-tag. Characterizing the quaternary structure by size exclusion chromatography revealed that recombinant AQN-3 (recAQN-3) is largely present as multimer and/or aggregate. To determine the lipid specificity of recAQN-3, a lipid stripe method and a multilamellar vesicle (MLV)-based binding assay were used. Both assays show that recAQN-3 selectively interacts with negatively charged lipids, like phosphatidic acid, phosphatidylinositol phosphates, and cardiolipin. No interaction was observed with phosphatidylcholine, sphingomyelin, phosphatidylethanolamine, or cholesterol. The affinity to negatively charged lipids can be explained by electrostatic interactions because binding is partly reversed under high-salt condition. However, more factors have to be assumed like hydrogen bonds and/or hydrophobic forces because the majority of bound molecules was not released by high salt. To confirm the observed binding behavior for the native protein, porcine seminal plasma was incubated with MLVs comprising phosphatidic acid or phosphatidyl-4,5-bisphosphate. Attached proteins were isolated, digested, and analyzed by mass spectrometry. Native AQN-3 was detected in all samples analyzed and was – besides AWN – the most abundant protein. It remains to be investigated whether AQN-3, together with other sperm associated seminal plasma proteins, acts as decapacitation factor by targeting negative lipids with signaling or other functional roles in fertilization.

Susceptibility of Listeria monocytogenes and Staphylococcus aureus Grown Under High Salt Conditions to X-ray Irradiation

Susceptibility of Listeria monocytogenes and Staphylococcus aureus Grown Under High Salt Conditions to X-ray Irradiation

Signaling crosstalk between Dipeptidyl Peptidase 4 and Angiotensin II-AT1R plays a role in proximal tubule NHE3 regulation and salt sensitive hypertension

Background: Salt sensitivity to hypertension occurs in 50-60% of all hypertensive patients and is more common in overweight/obese, females and aging population. In salt sensitive hypertension, the renin-angiotensin system (RAS) is known to play a major role and in particular, Angiotensin II (Ang II) regulation of the sodium hydrogen exchanger (NHE3) in the proximal tubule may mediate the pathophysiology. Dipeptidyl peptidase 4 (DPP4), an exopeptidase expressed abundantly on the brush border, binds to NHE3 and DPP4 inhibition reduces NHE3-mediated sodium reabsorption in proximal tubule cells. Interestingly, we observed both in vitro and in vivo that Ang II stimulates DPP4 activity. However, the mechanisms mediating the interplay between Ang II and DPP4 and its role in NHE3 regulation remain unknown. Therefore, we hypothesized that Ang II stimulation of DPP4 activity via crosstalk between AT1R and DPP4 may account for NHE3 modulation and, consequently, salt-sensitive hypertension. Methods: To address this hypothesis, we stimulated OK-AT1R (stable expressing rat AT1R) proximal tubule cells with Ang II (10 -8 to 10 -10 M), OKP cells with Ang II 10 -8 M and microperfused rat nephrons (Ang II 10 -10 M). In addition, sodium balance studies were conducted on DPP4-/- mice with high salt (1% sodium choride in drinking water) and low salt (0.02% in diet) Results: In OK-AT1R cells, we observed a dose-dependent increase in DPP4 activity, which was inhibited with AT1R blockade, and a battery of kinase inhibitors, including those for Src, PI3K, mTOR, S6K, ERK, and EGFR. Blockade with the DPP4 inhibitor MK-0626 not only suppressed DPP4 activity but partially suppressed Ang II-mediated signaling via EGFR, src, PI3K, mTOR and S6K. Further dissection of the pathways revealed that the blockade of src, which binds to both AT1R and DPP4, mimicked many of the effects of AT1R and DPP4 blockade. Mechanistically, blockade of motor proteins myosin II and myosin VI, which have been shown to redistribute with DPP4 and NHE3 along the microvilli microdomains, did not inhibit Ang II-induced DPP4 activity suggesting other mechanisms (phosphorylation) may underlie Ang II-DPP4 crosstalk in proximal tubule cells. Importantly, we found that DPP4 inhibition blocked Ang II-mediated stimulation of NHE3 activity (pHi) in vitro (OKP cells) and JHCO 3 - in vivo (rat nephrons). In addition, we observed that DPP4 gene-deleted mice lose more salt under both high and low salt ingestion and that DPP4 deficiency lowers BP under conditions of high salt, suggesting that DPP4 may regulate salt-sensitive hypertension. In conclusion, Ang II-AT1R and DPP4 likely crosstalk via binding to src and/or PI3-K, and inhibition of DPP4 suppresses Ang II-AT1R signaling and downstream effectors, including NHE3. Moreover, inhibition of signaling downstream of AT1R can suppress DPP4 activity, suggesting that AT1R and DPP4 act in concert but not via subcellular redistribution via motor proteins. The Sao Paulo Research Foundation - FAPESP (2021/14534-3), Sao Paulo, SP, Brazil to Flavia Martins and Dr. Adriana Girardi; NIH/NIDDK - K08 DK115886 to Dr. Ravi Nistala This is the full abstract presented at the American Physiology Summit 2023 meeting and is only available in HTML format. There are no additional versions or additional content available for this abstract. Physiology was not involved in the peer review process.

Synthesis and properties of PNA containing a dicationic nucleobase based on N4-benzoylated cytosine

We report the synthesis of a peptide nucleic acid (PNA) monomer containing N4-bis(aminomethyl)benzoylated cytosine (BzC2+ base). The BzC2+ monomer was incorporated into PNA oligomers using Fmoc-based solid-phase synthesis. The BzC2+ base in PNA had two positive charges and exhibited greater affinity for DNA G base than the natural C base. The BzC2+ base stabilized PNA-DNA heteroduplexes through electrostatic attractions, even in high salt conditions. The two positive charges on the BzC2+ residue did not compromise the sequence specificity of PNA oligomers. These insights will aid the future design of cationic nucleobases.

The Relationship between Protein–Protein Interactions and Liquid–Liquid Phase Separation for Monoclonal Antibodies

Being able to predict and control concentrated solution properties for solutions of monoclonal antibodies (mAbs) is critical for developing therapeutic formulations. At higher protein concentrations, undesirable solution properties include high viscosities, opalescence, particle formation, and precipitation. The overall aim of this work is to understand the relationship between commonly measured dilute solution parameters, the reduced osmotic second virial coefficient b22 and the diffusion interaction parameter kD and liquid-liquid phase separation, which occurs at higher protein concentrations. For globular proteins such as lysozyme or γB-crystallin, the location of the liquid-liquid coexistence curve is controlled by the net protein-protein interaction, which is related to b22. Because many mAbs undergo reversible self-association due to forming highly directional interactions, it is not known if b22 can be used as a reliable predictor for LLPS since increasing the anisotropy in the interaction potential causes phase separation to occur at much stonger net protein-protein attractions or lower values of b22. Here, we map the coexistence curves for three mAbs, referred to as COE-01, COE-07, and COE-19, in terms of b22 and kD values. The measurements are carried out at a low salt condition near the pI, where protein-protein interactions are expected to be anisotropic due to the presence of electrostatic attractions, and under salting-out conditions at high ammonium sulfate concentrations, which is expected to reduce the anisotropy by screening electrostatic interactions. We also show that deviations from a linear correlation between b22 and kD can be used as an indicator of reversible self-association. Each of the mAbs under salting-out conditions follows the correlation supporting the hypothesis that protein-protein interactions are nonspecific, while deviations from the correlation occur for COE-01 and COE-19 under low salt conditions indicating the mAbs undergo reversible self-association. For five out of the six conditions, the onset of phase separation, as reflected by the reduced virial coefficient at the critical point b22c occurs in a small window -1.6 > b22c > -2.3, which is similar to what has been observed for lysozyme and for bovine γB-crystallin. Under low salt conditions, b22c ≈ -5.1 for COE-19, which we previously showed to self-associate into small oligomers. Our findings suggest that under conditions where mAb interactions are weakly anisotropic, such as occur at high salt conditions, phase separation will begin to occur in a small window of b22. Deviations from the window can occur when mAbs undergo reversible self-association, although this is not always the case and likely depends upon whether or not highly directional interactions are passivated in the oligomer formation. We expect fitting LLPS measurements to simplified interaction models for mAbs will provide additional insight into the nature of the protein-protein interactions and guide their development for calculating concentrated solution properties.

Improvement in salt-tolerance of Aspergillus oryzae γ-glutamyl transpeptidase via protein chimerization with Aspergillus sydowii homolog

γ-Glutamyl transpeptidase is one of the key enzymes involved in glutamate production during high-salt fermentation of soy sauce and miso by koji mold, Aspergillus oryzae. However, the activity of γ-glutamyl transpeptidase from A. oryzae (AOggtA) is markedly reduced in the presence of NaCl, thus classifying it as a non-salt-tolerant enzyme. In contrast, the homologous protein from the xerophilic mold, A. sydowii (ASggtA) maintains its activity under high-salt conditions. Therefore, in this study, a chimeric enzyme, ASAOggtA, was designed and engineered to improve salt-tolerance in AOggtA by swapping the N-terminal region, based on sequence and structure comparisons between salt-tolerant ASggtA and non-salt-tolerant AOggtA. The parental AOggtA and ASggtA and their chimera, ASAOggtA, were heterologously expressed in A. oryzae and purified. The chimeric enzyme inherited the superior activity and stability from each of the two parent enzymes. ASAOggtA showed > 2-fold greater tolerance than AOggtA in the presence of 18% NaCl. In addition, the chimera showed a broader range of pH stability and greater thermostability than ASggtA. AOggtA and ASAOggtA were sy over the range pH 3.0 to pH 10.5. Thermal stability was found to be in the order AOggtA (57.5 °C, t1/2 = 32.5 min) > ASAOggtA (55 °C, t1/2 = 20.5 min) > ASggtA (50 °C, t1/2 = 12.5 min). The catalytic and structural characteristics indicated that non-salt-tolerant AOggtA would not undergo irreversible structural changes in the presence of NaCl, but rather a temporary conformational change, which might result in reducing the substrate binding and catalytic activity, on the basis of kinetic properties. In addition, the chimeric enzyme showed hydrolytic activity toward L-glutamine that was as high as that of AOggtA. The newly-designed chimeric ASAOggtA might have potential applications in high-salt fermentation, such as miso and shoyu, to increase the content of the umami-flavor amino acid, L-glutamate.

Dietary sodium enhances the expression of SLC4 family transporters, IRBIT, L-IRBIT, and PP1 in rat kidney: Insights into the molecular mechanism for renal sodium handling.

The kidney plays a central role in maintaining the fluid and electrolyte homeostasis in the body. Bicarbonate transporters NBCn1, NBCn2, and AE2 are expressed at the basolateral membrane of the medullary thick ascending limb (mTAL). In a previous study, NBCn1, NBCn2, and AE2 are proposed to play as a regulatory pathway to decrease NaCl reabsorption in the mTAL under high salt condition. When heterologously expressed, the activity of these transporters could be stimulated by the InsP3R binding protein released with inositol 1,4,5-trisphosphate (IRBIT), L-IRBIT (collectively the IRBITs), or protein phosphatase PP1. In the present study, we characterized by immunofluorescence the expression and localization of the IRBITs, and PP1 in rat kidney. Our data showed that the IRBITs were predominantly expressed from the mTAL through the distal renal tubules. PP1 was predominantly expressed in the TAL, but is also present in high abundance from the distal convoluted tubule through the medullary collecting duct. Western blotting analyses showed that the abundances of NBCn1, NBCn2, and AE2 as well as the IRBITs and PP1 were greatly upregulated in rat kidney by dietary sodium. Co-immunoprecipitation study provided the evidence for protein interaction between NBCn1 and L-IRBIT in rat kidney. Taken together, our data suggest that the IRBITs and PP1 play an important role in sodium handling in the kidney. We propose that the IRBITs and PP1 stimulates NBCn1, NBCn2, and AE2 in the basolateral mTAL to inhibit sodium reabsorption under high sodium condition. Our study provides important insights into understanding the molecular mechanism for the regulation of sodium homeostasis in the body.

DNA rehybridization drives product release from Cas9 ribonucleoprotein to enable multiple-turnover cleavage.

The RNA-guided Cas9 endonuclease from Staphylococcus aureus (SauCas9) can catalyze multiple-turnover reactions whereas Cas9 from Streptococcus pyogenes (SpyCas9) is a single-turnover enzyme. Here we dissect the mechanism of multiple-turnover catalysis by SauCas9 and elucidate its molecular basis. We show that the multiple-turnover catalysis does not require more than stoichiometric RNA guides to Cas9 nuclease. Rather, the RNA-guide loaded ribonucleoprotein (RNP) is the reactive unity that is slowly released from product and recycled in the subsequent reaction. The mechanism that RNP is recycled for multiple-turnover reaction entails the unwinding of the RNA:DNA duplex in the R-loop. We argue that DNA rehybridization is required for RNP release by supplementing the energy cost in the process. Indeed, turnover is arrested when DNA rehybridization is suppressed. Further, under higher salt conditions, both SauCas9 and SpyCas9 showed increased turnover, and engineered SpyCas9 nucleases that form fewer direct or hydrogen bonding interactions with target DNA became multiple-turnover enzymes. Thus, these results indicate that for both SpyCas9 and SauCas9, turnover is determined by the energetic balance of the post-chemistry RNP-DNA interaction. Due to the conserved protein core folds, the mechanism underpinning turnover we establish here is likely operant in all Cas9 nucleases.

Saccharopolyspora sp. NFXS83 in Marine Biotechnological Applications: From Microalgae Growth Promotion to the Production of Secondary Metabolites.

Marine bacteria are a significant source of bioactive compounds for various biotechnological applications. Among these, actinomycetes have been found to produce a wide range of secondary metabolites of interest. Saccharopolyspora is one of the genera of actinomycetes that has been recognized as a potential source of these compounds. This study reports the characterization and genomic analysis of Saccharopolyspora sp. NFXS83, a marine bacterium isolated from seawater from the Sado estuary in Portugal. The NFXS83 strain produced multiple functional and stable extracellular enzymes under high-salt conditions, showed the ability to synthesize auxins such as indole-3-acetic acid, and produced diffusible secondary metabolites capable of inhibiting the growth of Staphylococcus aureus. Furthermore, when Phaeodactylum tricornutum was co-cultivated with strain NFXS83 a significant increase in microalgae cell count, cell size, auto-fluorescence, and fucoxanthin content was observed. Detailed analysis revealed the presence of clusters involved in the production of various secondary metabolites, including extracellular enzymes, antimicrobial compounds, terpenes, and carotenoids in the genome of strain NFXS83. Ultimately, these findings indicate that Saccharopolyspora sp. NFXS83 has a significant potential for a wide range of marine biotechnological applications.

How Single Amino Acid Substitutions Can Disrupt a Protein Hetero-Dimer Interface: Computational and Experimental Studies of the LigAB Dioxygenase from Sphingobium sp. Strain SYK-6.

Protocatechuate 4,5-dioxygenase (LigAB) is a heterodimeric enzyme that catalyzes the dioxygenation of multiple lignin derived aromatic compounds. The active site of LigAB is at the heterodimeric interface, with specificity conferred by the alpha subunit and catalytic residues contributed by the beta subunit. Previous research has indicated that the phenylalanine at the 103 position of the alpha subunit (F103α) controls selectivity for the C5 position of the aromatic substrates, and mutations of this residue can enhance the rate of catalysis for substrates with larger functional groups at this position. While several of the mutations to this position (Valine, V; Threonine, T; Leucine, L; and Histidine, H) were catalytically active, other mutations (Alanine, A; and Serine, S) were found to have reduced dimer interface affinity, leading to challenges in copurifing the catalytically active enzyme complex under high salt conditions. In this study, we aimed to experimentally and computationally interrogate residues at the dimer interface to discern the importance of position 103α for maintaining the integrity of the heterodimer. Molecular dynamic simulations and electrophoretic mobility assays revealed a preference for nonpolar/aromatic amino acids in this position, suggesting that while substitutions to polar amino acids may produce a dioxygenase with a useful substrate utilization profile, those considerations may be off-set by potential destabilization of the catalytically active oligomer. Understanding the dimerization of LigAB provides insight into the multimeric proteins within the largely uncharacterized superfamily and characteristics to consider when engineering proteins that can degrade lignin efficiently. These results shed light on the challenges associated with engineering proteins for broader substrate specificity.