Heavy metal ions are potent inhibitors of protein folding

Correlation of NADH/NAD+ electrochemical potential and enzymatic activity for investigating protein folding and kinetics

The biological activity of a protein is determined by its native three-dimensional structure. Various stress factors induce structural changes in the proteins that leads to altered protein homeostasis with the accumulation of misfolded and aggregated protein conformers. Standard methods such as spectrophotometry, luminometry and fluorimetry are conventionally used to study protein activity. Here, an electrochemical method has been developed to measure the change in anodic peak current (Ip,a) of NADH generated during the oxidation reaction. The method showed a linear range of detection from 62.5 μM to 1.0 mM (R2 = 0.999) for NADH with calculated detection limit of 16.02 μM and sensitivity of 1.75 × 103 μA mM-1 cm-2. The method was further employed to investigate the enzymatic activity and folding kinetics of malate dehydrogenase (MDH) and glucose-6-phosphate dehydrogenase (G6PDH). Also, the effect of aluminium ion (Al3+) on the activity and folding kinetics was investigated electrochemically. The Al3+ induced structural alterations in MDH and G6PDH were assessed using circular dichroism (CD), Thioflavin-T (ThT) and nuclear magnetic resonance (NMR). The developed label-free electrochemical method provides an alternative method for investigating protein activity and folding kinetics.

Production of minicell-like structures by Escherichia coli biosynthesizing cadmium fluorescent nanoparticles: a novel response to heavy metal exposure

The bacterial synthesis of fluorescent semiconductor nanoparticles or quantum dots (QDs), presents a sustainable method for producing nanomaterials with customized optical properties and significant technological potential. However, the underlying cellular mechanisms for this process remain elusive. Specifically, the role of cellular structures in QD generation has not been thoroughly investigated. In this study, we examined the morphological changes in Escherichia coli during the biosynthesis of cadmium sulfide (CdS) QDs, using a strain overexpressing the gshA gene to promote QD biosynthesis through increased glutathione (GSH) levels. Microscopy analyses revealed that fluorescence emission associated with QDs was concentrated at the cell poles, along with fluorescence emission from small spherical cells, a phenomenon exclusively detectable during QD biosynthesis. Transmission electron microscopy (TEM) revealed electron-dense nanomaterials localized at the cell poles. Furthermore, it was demonstrated the formation of minicell-like structures (∼ 0.5 μm in diameter) originating from these poles under biosynthesis conditions. These minicells encapsulated nanometric electron-dense material. Additional analyses indicated that minicells contained inclusion bodies, likely formed due to gshA overexpression and cadmium stress. Our findings confirms the role of minicells as a bacterial mechanism for sequestering cadmium at the cell poles and expelling the metal in the form of nanoparticles. This underscores the importance of minicells in bacterial physiology and stress responses, introducing a novel mechanism for heavy metal detoxification in bacteria.

Molecular interactions, structural effects, and binding affinities between silver ions (Ag+) and amyloid beta (Aβ) peptides

Because silver is toxic to microbes, but not considered toxic to humans, the metal has been used as an antimicrobial agent since ancient times. Today, silver nanoparticles and colloidal silver are used for antibacterial purposes, and silver-peptide and similar complexes are being developed as therapeutic agents. Yet, the health effects of silver exposure are not fully understood, nor are the molecular details of silver-protein interactions. In Alzheimer's disease, the most common form of dementia worldwide, amyloid-β (Aβ) peptides aggregate to form soluble oligomers that are neurotoxic. Here, we report that monovalent silver ions (Ag+) bind wildtype Aβ40 peptides with a binding affinity of 25 ± 12 µM in MES buffer at 20 °C. Similar binding affinities are observed for wt Aβ40 peptides bound to SDS micelles, for an Aβ40(H6A) mutant, and for a truncated Aβ(4-40) variant containing an ATCUN (Amino Terminal Cu and Ni) motif. Weaker Ag+ binding is observed for the wt Aβ40 peptide at acidic pH, and for an Aβ40 mutant without histidines. These results are compatible with Ag+ ions binding to the N-terminal segment of Aβ peptides with linear bis-his coordination. Because the Ag+ ions do not induce any changes in the size or structure of Aβ42 oligomers, we suggest that Ag+ ions have a minor influence on Aβ toxicity.

Expression optimization and characterization of a novel amylopullulanase from the thermophilic Cohnella sp. A01

Amylopullulanase (EC. 3.2.1.41/1) is an enzyme that hydrolyzes starch and pullulan, capable of breaking (4 → 1)-α and (6 → 1)-α bonds in starch. Here, the Amy1136 gene (2166 base pairs) from the thermophilic bacterium Cohnella sp. A01 was cloned into the expression vector pET-26b(+) and expressed in Escherichia coli BL21. The enzyme was purified using heat shock at 90 °C for 15 min. The expression optimization of Amy1136 was performed using Plackett-Burman and Box-Behnken design as follows: temperature of 26.7 °C, rotational speed of 180 rpm, and bacterial population of 1.25. The Amy1136 displayed the highest activity at a temperature of 50 °C (on pullulan) and a pH of 8.0 (on starch) and, also exhibited stability at high temperatures (90 °C) and over a range of pH values. Ag+ significantly increased enzyme activity, while Co2+ completely inhibited amylase activity. The enzyme was found to be calcium-independent. The kinetic parameters Km, Vmax, kcat, and kcat/Km for amylase activity were 2.4 mg/mL, 38.650 μmol min-1 mg-1, 38.1129 S-1, and 0.09269 S-1mg mL-1, respectively, and for pullulanase activity were 173.1 mg/mL, 59.337 μmol min-1 mg-1, 1.586 S-1, and 1.78338 S-1mg mL-1, respectively. The thermodynamic parameters Kin, t1/2, Ea#, ΔH#, ΔG# and ΔS# were calculated equal to 0.20 × 10-2 (m-1), 462.09 (min), 16.87 (kJ/mol), 14.18 (kJ/mol), 47.34 (kJ/mol) and 102.60 (Jmol K-1), respectively. The stability of Amy1136 under high temperature, acidic and alkaline pH, surfactants, organic solvents, and calcium independence, suggests its suitability for industrial applications.

Quantum Dot Reporters Designed for CRISPR-Based Detection of Viral Nucleic Acids

Diagnostic methods based on CRISPR technology have shown great potential due to their highly specific, efficient, and sensitive detection capabilities. Although the majority of the current studies rely on fluorescent dye-quencher reporters, the limitations of fluorescent dyes, such as poor photostability and small Stokes shifts, urgently necessitate the optimization of reporters. In this study, we developed innovative quantum dot (QD) reporters for the CRISPR/Cas systems, which not only leveraged the advantages of high photoluminescence quantum yield and large Stokes shifts of QDs but were also easily synthesized through a simple one-step hydrothermal method. Based on the trans-cleavage characteristics of Cas12a and Cas13a, two types of QD reporters were designed, the short DNA strand and the hybridization-based QD reporters, achieving the detection of DNA and RNA at the pM level, respectively, and validating the performance in the analysis of clinical samples. Furthermore, based on the unique property of QDs that allowed multicolor emission under one excitation, the application potential for simultaneous detection of diseases was further investigated. Taken together, this work proposed novel QD reporters that could be applied to the various CRISPR/Cas systems, providing a new toolbox to expand the diagnosis of bioanalytical and biomedical fields.

Promising New Methods Based on the SOD Enzyme and SAUR36 Gene to Screen for Canola Materials with Heavy Metal Resistance

Canola is the largest self-produced vegetable oil source in China, although excessive levels of cadmium, lead, and arsenic seriously affect its yield. Therefore, developing methods to identify canola materials with good heavy metal tolerance is a hot topic for canola breeding. In this study, canola near-isogenic lines with different oil contents (F338 (40.62%) and F335 (46.68%) as the control) and heavy metal tolerances were used as raw materials. In an experiment with 100 times the safe standard values, the superoxide dismutase (SOD) and peroxidase (POD) activities of F335 were 32.02 mmol/mg and 71.84 mmol/mg, while the activities of F338 were 24.85 mmol/mg and 63.86 mmol/mg, exhibiting significant differences. The DEGs and DAPs in the MAPK signaling pathway of the plant hormone signal transduction pathway and other related pathways were analyzed and verified using RT-qPCR. SAUR36 and SAUR32 were identified as the key differential genes. The expression of the SAUR36 gene in canola materials planted in the experimental field was significantly higher than in the control, and FY958 exhibited the largest difference (27.82 times). In this study, SOD and SAUR36 were found to be closely related to heavy metal stress tolerance. Therefore, they may be used to screen for new canola materials with good heavy metal stress tolerance for canola breeding.

Mitigation of the Deleterious Effect of Heavy Metals on the Conformational Stability of Ubiquitin through Osmoprotectants

The Ubiquitin-Proteasome System (UPS) is important in protein homeostasis and is involved in many cell processes. UPS's wide range of regulatory activities is based on the unique and diverse signals transmitted through all-encompassing processes. Cells need a fully functional UPP to cope with oxidative stress, so cellular redox status modulates ubiquitin activity. However, these protein quality control systems are compromised under adverse conditions such as heavy metal stress, resulting in pathological conditions. Heavy metals disrupt the physiological action of sensitive proteins by forming complexes with side-chain functional groups or by dislocating critical metal ions in metalloproteins. In addition, perturbation in the structure of Ubiquitin may affect the ubiquitin-proteasome pathway. In this study, it has been investigated the effects of heavy metals likewise chromium (Cr), cadmium (Cd), and mercury chloride (HgCl2) on the conformational stability of Ubiquitin as well as overcome their hazardous effect, the interaction of osmo-protectants such as Sesamol, gallic acid, Glycine, and ascorbic acid have also been explored in the study. The near and far UV-circular dichroism measurements deduced the secondary and tertiary structural changes. The size of the Ubiquitin before and after exposure to heavy metals was measured by DLS (dynamic light scattering). Docking research was also used to investigate the interaction of Ubiquitin with various heavy metals. Near and far UV-circular dichroism (CD) measurements revealed that mercury, chromium, and cadmium disrupt Ubiquitin's secondary and tertiary structure. The effect of chromium, even at low concentrations, was significantly deleterious compared to cadmium and mercury chloride. Ubiquitin's far-UV circular dichroism spectra subjected to heavy metals were recorded in several osmo-protectants, such as ascorbic acid, Glycine, gallic acid, and Sesamol, which offset the adverse effects of heavy metals. DLS studies revealed a noteworthy change in the hydrodynamic radius of Ubiquitin in the presence of heavy metals. Docking analysis revealed a significant binding affinity of mercury and cadmium ions with Ubiquitin. This study can infer the heavy metals' disruption of Ubiquitin's secondary and tertiary structure. Osmo-protectants produced by animal cells are more effective against heavy metals than plant antioxidants.

Minicells as an Escherichia coli mechanism for the accumulation and disposal of fluorescent cadmium sulphide nanoparticles

BACKGROUND

Bacterial biosynthesis of fluorescent nanoparticles or quantum dots (QDs) has emerged as a unique mechanism for heavy metal tolerance. However, the physiological pathways governing the removal of QDs from bacterial cells remains elusive. This study investigates the role of minicells, previously identified as a means of eliminating damaged proteins and enhancing bacterial resistance to stress. Building on our prior work, which unveiled the formation of minicells during cadmium QDs biosynthesis in Escherichia coli, we hypothesize that minicells serve as a mechanism for the accumulation and detoxification of QDs in bacterial cells.

RESULTS

Intracellular biosynthesis of CdS QDs was performed in E. coli mutants ΔminC and ΔminCDE, known for their minicell-producing capabilities. Fluorescence microscopy analysis demonstrated that the generated minicells exhibited fluorescence emission, indicative of QD loading. Transmission electron microscopy (TEM) confirmed the presence of nanoparticles in minicells, while energy dispersive spectroscopy (EDS) revealed the coexistence of cadmium and sulfur. Cadmium quantification through flame atomic absorption spectrometry (FAAS) demonstrated that minicells accumulated a higher cadmium content compared to rod cells. Moreover, fluorescence intensity analysis suggested that minicells accumulated a greater quantity of fluorescent nanoparticles, underscoring their efficacy in QD removal. Biosynthesis dynamics in minicell-producing strains indicated that biosynthesized QDs maintained high fluorescence intensity even during prolonged biosynthesis times, suggesting continuous QD clearance in minicells.

CONCLUSIONS

These findings support a model wherein E. coli utilizes minicells for the accumulation and removal of nanoparticles, highlighting their physiological role in eliminating harmful elements and maintaining cellular fitness. Additionally, this biosynthesis system presents an opportunity for generating minicell-coated nanoparticles with enhanced biocompatibility for diverse applications.

An Overview of Diverse Strategies To Inactivate Enterobacteriaceae-Targeting Bacteriophages

Bacteriophages are viruses that infect bacteria and thus threaten industrial processes relying on the production executed by bacterial cells. Industries bear huge economic losses due to such recurring and resilient infections. Depending on the specificity of the process, there is a need for appropriate methods of bacteriophage inactivation, with an emphasis on being inexpensive and high efficiency. In this review, we summarize the reports on antiphagents, i.e., antibacteriophage agents on inactivation of bacteriophages. We focused on bacteriophages targeting the representatives of the Enterobacteriaceae family, as its representative, Escherichia coli, is most commonly used in the bio-industry. The review is divided into sections dealing with bacteriophage inactivation by physical factors, chemical factors, and nanotechnology-based solutions.

Soft-metal(loid)s induce protein aggregation in Escherichia coli

Metal(loid) salts were used to treat infectious diseases in the past due to their exceptional biocidal properties at low concentrations. However, the mechanism of their toxicity has yet to be fully elucidated. The production of reactive oxygen species (ROS) has been linked to the toxicity of soft metal(loid)s such as Ag(I), Au(III), As(III), Cd(II), Hg(II), and Te(IV). Nevertheless, few reports have described the direct, or ROS-independent, effects of some of these soft-metal(loid)s on bacteria, including the dismantling of iron-sulfur clusters [4Fe-4S] and the accumulation of porphyrin IX. Here, we used genome-wide genetic, proteomic, and biochemical approaches under anaerobic conditions to evaluate the direct mechanisms of toxicity of these metal(loid)s in Escherichia coli. We found that certain soft-metal(loid)s promote protein aggregation in a ROS-independent manner. This aggregation occurs during translation in the presence of Ag(I), Au(III), Hg(II), or Te(IV) and post-translationally in cells exposed to Cd(II) or As(III). We determined that aggregated proteins were involved in several essential biological processes that could lead to cell death. For instance, several enzymes involved in amino acid biosynthesis were aggregated after soft-metal(loid) exposure, disrupting intracellular amino acid concentration. We also propose a possible mechanism to explain how soft-metal(loid)s act as proteotoxic agents.

Mechanisms of genotoxicity and proteotoxicity induced by the metalloids arsenic and antimony

Arsenic and antimony are metalloids with profound effects on biological systems and human health. Both elements are toxic to cells and organisms, and exposure is associated with several pathological conditions including cancer and neurodegenerative disorders. At the same time, arsenic- and antimony-containing compounds are used in the treatment of multiple diseases. Although these metalloids can both cause and cure disease, their modes of molecular action are incompletely understood. The past decades have seen major advances in our understanding of arsenic and antimony toxicity, emphasizing genotoxicity and proteotoxicity as key contributors to pathogenesis. In this review, we highlight mechanisms by which arsenic and antimony cause toxicity, focusing on their genotoxic and proteotoxic effects. The mechanisms used by cells to maintain proteostasis during metalloid exposure are also described. Furthermore, we address how metalloid-induced proteotoxicity may promote neurodegenerative disease and how genotoxicity and proteotoxicity may be interrelated and together contribute to proteinopathies. A deeper understanding of cellular toxicity and response mechanisms and their links to pathogenesis may promote the development of strategies for both disease prevention and treatment.

A fully π-conjugated covalent organic framework with dual binding sites for ultrasensitive detection and removal of divalent heavy metal ions

Covalent organic frameworks (COFs) have become a promising candidate for the remediation of heavy metal pollution. However, researches on COF adsorbents still have challenges on maintaining good optical properties and adsorption performance under harsh conditions. Herein, a fully π-conjugated COF with dual binding sites (Bpy-sp2c-COF) is reported for rapid fluorescence recognition and enhanced adsorption towards divalent heavy metal ions. The vinylene-linkage lattice shows strong luminescence and excellent stability in both strong acidity and basicity. Bpy-sp2c-COF demonstrates not only nanomolar-scale detection of divalent heavy metal ions, but also good adsorption capacity (Hg2+ 718.48, Ni2+ 278.64, Cu2+ 260.11, and Co2+ 126.23 mg/g). Experimental and theoretical studies reveal the intramolecular charge transfer as the fluorescence quenching mechanism. Further simulation results demonstrate the cyano and bipyridine groups on the lattice can act as dual binding sites for divalent heavy metal ions. Experimental results confirmed the adsorption capacity of Bpy-sp2c-COF superior to that of COFs with either cyano groups (Hg2+ 415.34, Ni2+ 165.60, Cu2+ 160.55, and Co2+ 73.14 mg/g), or bipyridine groups (Hg2+ 369.25, Ni2+ 133.41, Cu2+ 133.32, and Co2+ 69.23 mg/g). Besides, robust regeneration of the adsorbent could be achieved over 10 cycles. The fully π-conjugated COF with dual binding sites provides a new approach for designing next-generation sensors and adsorbents with excellent performances.

Characterization of Uranyl (UO22+) Ion Binding to Amyloid Beta (Aβ) Peptides: Effects on Aβ Structure and Aggregation

Uranium (U) is naturally present in ambient air, water, and soil, and depleted uranium (DU) is released into the environment via industrial and military activities. While the radiological damage from U is rather well understood, less is known about the chemical damage mechanisms, which dominate in DU. Heavy metal exposure is associated with numerous health conditions, including Alzheimer's disease (AD), the most prevalent age-related cause of dementia. The pathological hallmark of AD is the deposition of amyloid plaques, consisting mainly of amyloid-β (Aβ) peptides aggregated into amyloid fibrils in the brain. However, the toxic species in AD are likely oligomeric Aβ aggregates. Exposure to heavy metals such as Cd, Hg, Mn, and Pb is known to increase Aβ production, and these metals bind to Aβ peptides and modulate their aggregation. The possible effects of U in AD pathology have been sparsely studied. Here, we use biophysical techniques to study in vitro interactions between Aβ peptides and uranyl ions, UO22+, of DU. We show for the first time that uranyl ions bind to Aβ peptides with affinities in the micromolar range, induce structural changes in Aβ monomers and oligomers, and inhibit Aβ fibrillization. This suggests a possible link between AD and U exposure, which could be further explored by cell, animal, and epidemiological studies. General toxic mechanisms of uranyl ions could be modulation of protein folding, misfolding, and aggregation.

MsDjB4, a HSP40 Chaperone in Alfalfa (Medicago sativa L.), Improves Alfalfa Hairy Root Tolerance to Aluminum Stress

The toxicity of aluminum (Al) in acidic soils poses a significant limitation to crop productivity. In this study, we found a notable increase in DnaJ (HSP40) expression in the roots of Al-tolerant alfalfa (WL-525HQ), which we named MsDjB4. Transient conversion assays of tobacco leaf epidermal cells showed that MsDjB4 was targeted to the membrane system including Endoplasmic Reticulum (ER), Golgi, and plasma membrane. We overexpressed (MsDjB4-OE) and suppressed (MsDjB4-RNAi) MsDjB4 in alfalfa hairy roots and found that MsDjB4-OE lines exhibited significantly better tolerance to Al stress compared to wild-type and RNAi hairy roots. Specifically, MsDjB4-OE lines had longer root length, more lateral roots, and lower Al content compared to wild-type and RNAi lines. Furthermore, MsDjB4-OE lines showed lower levels of lipid peroxidation and ROS, as well as higher activity of antioxidant enzymes SOD, CAT, and POD compared to wild-type and RNAi lines under Al stress. Moreover, MsDjB4-OE lines had higher soluble protein content compared to wild-type and RNAi lines after Al treatment. These findings provide evidence that MsDjB4 contributes to the improved tolerance of alfalfa to Al stress by facilitating protein synthesis and enhancing antioxidant capacity.

Chimeric MerR-Family Regulators and Logic Elements for the Design of Metal Sensitive Genetic Circuits in Bacillus subtilis

Whole-cell biosensors are emerging as promising tools for monitoring environmental pollutants such as heavy metals. These sensors constitute a genetic circuit comprising a sensing module and an output module, such that a detectable signal is produced in the presence of the desired analyte. The MerR family of metal-responsive regulators offers great potential for the construction of metal sensing circuits, due to their high sensitivity, tight transcription control, and large diversity in metal-specificity. However, the sensing diversity is broadest in Gram-negative systems, while chassis organisms are often selected from Gram-positive species, particularly sporulating bacilli. This can be problematic, because Gram-negative biological parts, such as promoters, are frequently observed to be nonfunctional in Gram-positive hosts. Herein, we combined construction of synthetic genetic circuits and chimeric MerR regulators, supported by structure-guided design, to generate metal-sensitive biosensor modules that are functional in the biotechnological work-horse species Bacillus subtilis. These chimeras consist of a constant Gram-positive derived DNA-binding domain fused to variable metal binding domains of Gram-negative origins. To improve the specificity of the whole-cell biosensor, we developed a modular "AND gate" logic system based on the B. subtilis two-subunit σ-factor, SigO-RsoA, designed to maximize future use for synthetic biology applications in B. subtilis. This work provides insights into the use of modular regulators, such as the MerR family, in the design of synthetic circuits for the detection of heavy metals, with potentially wider applicability of the approach to other systems and genetic backgrounds.

Differential interactions of α-synuclein conformers affect refolding and activity of proteins

The accumulation of protein aggregates as intracellular inclusions interferes with cellular protein homeostasis leading to protein aggregation diseases. Protein aggregation results in the formation of several protein conformers including oligomers and fibrils, where each conformer has its own structural characteristic and proteotoxic potential. The present study explores the effect of alpha-synuclein (α-syn) conformers on the activity and spontaneous refolding of firefly luciferase. Of the different conformers, α-syn monomers delayed the inactivation of luciferase under thermal stress conditions and enhanced the spontaneous refolding of luciferase. In contrast, the α-syn oligomers and fibrils adversely affected luciferase activity and refolding, where the oligomers inhibited spontaneous refolding, whereas a pronounced effect on the inactivation of native luciferase was observed in the case of fibrils. These results indicate that the oligomers and fibrils of α-syn interfere with the refolding of luciferase and promote its misfolding and aggregation. The study reveals the differential propensities of various conformers of a pathologically relevant protein in causing inactivation, structural modifications and misfolding of other proteins, consequently resulting in altered protein homeostasis.

Barley metallothionein isoforms, MT2b2 and MT4, differentially respond to photohormones in barley aleurone layer and their recombinant forms show different affinity for binding to zinc and cadmium

Metallothioneins (MTs) are metal-binding proteins that have important roles in the homeostasis of heavy metals. In this study, the two MT genes was studied in response to phytohormones using the barley aleurone layer as a kind of model system. The aleurone layer was isolated from barley embryo-less half grains and was incubated for 24 h with different phytohormones. Based on the results the genes encoding HvMT2b2 and HvMT4 were down-regulated through gibberellic acid (GA), while they were and up-regulated through salicylic acid (SA). Despite this, these two genes were differentially expressed to other hormones. Furthermore, the proteins HvMT2b2 and HvMT4 were heterologous expressed as GST-fusion proteins in E. coli. The HvMT4 and HvMT2b2 heterologous expression in E. coli gives rise to 10- and 3-fold improvements in the accumulation capacity for Zn2+, respectively. Whereas the transgenic E. coli strain that expresses HvMT2b2 could accumulate Cd2+ three-fold higher than control. The expression of HvMT4 did not affect the accumulation of Cd2+. HvMT4 which is known as seed-specific isoform seems to be able to bind to Zn2+ with good affinity and cannot bind Cd2+. In comparison, HvMT2b2 was able to bind both Zn2+ and Cd2+. Therefore HvMT4 could serve a noteworthy role in zinc storage in barley seeds. The expression of HvMT4 is induced by SA 30-fold, concerning the untreated aleurone layer. Such results could provide good insights for the assessment of the effects of phytohormones in the molecular mechanism involved in essential metal storage in cereal seeds.

Bioaccumulation of industrial heavy metals and interactive biochemical effects on two tropical medicinal plant species

Concentrations of heavy metals (Cr, Cu, Fe, Mn, Ni, Pb, and Zn) accumulation were studied in the leaves of two medicinal plant species, namely Holarrhena pubescens and Wrightia tinctoria, from two industrial areas and a control area. Our comparison study revealed that industrialization significantly increased the accumulation of heavy metals in both plant species. A comparison study in control and industrial areas exhibited that heavy metal accumulation was higher in the industrially affected area than in the control area. Heavy metal concentration exceeded the permissible limit recommended by the WHO in both species of two industrial areas. However, both species accumulated the least heavy metal concentration in the control area. Biochemical investigation specifies that in response to heavy metal accumulation, both species increased the activity of hydrogen peroxide (H₂O₂), malondialdehyde content, the activity of enzymatic (superoxide dismutase and peroxidase) and nonenzymatic (ascorbic acid) antioxidant, but decreased the primary (soluble carbohydrate and total protein), secondary metabolites (phenol and flavonoid) content and free radical scavenging (DPPH) activity. This study indicates that industrialization potentially harms medicinal plants by reducing the efficacy of their medicinal property.

Effects of External Perturbations on Protein Systems: A Microscopic View

Protein folding can be viewed as the origami engineering of biology resulting from the long process of evolution. Even decades after its recognition, research efforts worldwide focus on demystifying molecular factors that underlie protein structure-function relationships; this is particularly relevant in the era of proteopathic disease. A complex co-occurrence of different physicochemical factors such as temperature, pressure, solvent, cosolvent, macromolecular crowding, confinement, and mutations that represent realistic biological environments are known to modulate the folding process and protein stability in unique ways. In the current review, we have contextually summarized the substantial efforts in unveiling individual effects of these perturbative factors, with major attention toward bottom-up approaches. Moreover, we briefly present some of the biotechnological applications of the insights derived from these studies over various applications including pharmaceuticals, biofuels, cryopreservation, and novel materials. Finally, we conclude by summarizing the challenges in studying the combined effects of multifactorial perturbations in protein folding and refer to complementary advances in experiment and computational techniques that lend insights to the emergent challenges.

Biofilm-mediated decolorization, degradation and detoxification of synthetic effluent by novel biofilm-producing bacteria isolated from textile dyeing effluent

Biofilm-mediated bioremediation of xenobiotic pollutants is an environmental friendly biological technique. In this study, 36 out of 55 bacterial isolates developed biofilms in glass test tubes containing salt-optimized broth plus 2% glycerol (SOBG). Scanning electron microscopy, Fourier transform infrared (FTIR) spectroscopy, and Congo red- and Calcofluor binding results showed biofilm matrices contain proteins, curli, nanocellulose-rich polysaccharides, nucleic acids, lipids, and peptidoglycans. Several functional groups including -OH, N-H, C-H, CO, COO^-, -NH_2, PO, C-O, and C-C were also predicted. By sequencing, ten novel biofilm-producing bacteria (BPB) were identified, including Exiguobacterium indicum ES31G, Kurthia gibsonii ES43G, Kluyvera cryocrescens ES45G, Cedecea lapagei ES48G, Enterobacter wuhouensis ES49G, Aeromonas caviae ES50G, Lysinibacillus sphaericus ES51G, Acinetobacter haemolyticus ES52G, Enterobacter soli ES53G, and Comamonas aquatica ES54G. The Direct Red (DR) 28 (a carcinogenic and mutagenic dye used in dyeing and biomedical processes) decolorization process was optimized in selected bacterial isolates. Under optimum conditions (SOBG medium, 75 mg L^-1 dye, pH 7, 28 °C, microaerophilic condition and within 72 h of incubation), five of the bacteria tested could decolorize 97.8% ± 0.56-99.7% ± 0.45 of DR 28 dye. Azoreductase and laccase enzymes responsible for biodegradation were produced under the optimum condition. UV-Vis spectral analysis revealed that the azo (-NN-) bond peak at 476 nm had almost disappeared in all of the decolorized samples. FTIR data revealed that the foremost characteristic peaks had either partly or entirely vanished or were malformed or stretched. The chemical oxygen demand decreased by 83.3-91.3% in the decolorized samples, while plant probiotic bacterial growth was indistinguishable in the biodegraded metabolites and the original dye. Furthermore, seed germination (%) was higher in the biodegraded metabolites than the parent dye. Thus, examined BPB could provide potential solutions for the bioremediation of industrial dyes in wastewater.

Mycosynthesis of Metal-Containing Nanoparticles-Fungal Metal Resistance and Mechanisms of Synthesis

In the 21st century, nanomaterials play an increasingly important role in our lives with applications in many sectors, including agriculture, biomedicine, and biosensors. Over the last two decades, extensive research has been conducted to find ways to synthesise nanoparticles (NPs) via mediation with fungi or fungal extracts. Mycosynthesis can potentially be an energy-efficient, highly adjustable, environmentally benign alternative to conventional physico-chemical procedures. This review investigates the role of metal toxicity in fungi on cell growth and biochemical levels, and how their strategies of resistance, i.e., metal chelation, biomineral formation, biosorption, bioaccumulation, compartmentalisation, and efflux of metals from cells, contribute to the synthesis of metal-containing NPs used in different applications, e.g., biomedical, antimicrobial, catalytic, biosensing, and precision agriculture. The role of different synthesis conditions, including that of fungal biomolecules serving as nucleation centres or templates for NP synthesis, reducing agents, or capping agents in the synthesis process, is also discussed. The authors believe that future studies need to focus on the mechanism of NP synthesis, as well as on the influence of such conditions as pH, temperature, biomass, the concentration of the precursors, and volume of the fungal extracts on the efficiency of the mycosynthesis of NPs.

Genetic variation and molecular characterization of Zygophyllum coccineum L. ecotypes of the iron mining area of El-Wahat El-Bahariya in Egypt

Remediation and mitigation processes can recover the ecosystems affected by mining operations. Zygophyllum coccineum L. is a native indigenous xerophyte that grows in Egypt's Western Desert, particularly around the iron mining ore deposits, and accumulates high rates of potentially toxic elements (PTEs) in its succulent leaves. The present study evaluated the genetic variation and molecular responses of Z. coccineum to heavy metal stressful conditions in three sites. Results revealed that Z. coccineum bioaccumulation capacity was greater than unity and varied amongst the three locations. In response to heavy metal toxicity, Z. coccineum plants boosted their antioxidative enzymes activity and glutathione levels as a tolerance strategy. Anatomically, a compact epidermis, a thick spongy mesophyll with water storage cells, and a thicker vascular system were observed. Protein electrophoretic analysis yielded 20 fragments with a polymorphism rate of 85%. The antioxidant genes (CAT: catalase, POD: peroxidase and GST: polyphenol oxidase) showed greater levels of expression. In addition, DNA-based molecular genetic diversity analyses using Start Codon Targeted (SCoT) and Inter Simple Sequence Repeat (ISSR) markers yielded 54 amplified fragments (i.e. 24 monomorphic and 30 polymorphic), with 12 unique fragments and a polymorphism rate of 55.5%. The greatest PIC values were recorded for SCoT-6 (0.36) and for both of the 14 A and 44 B ISSR primers (0.25). Diversity index (DI) of all SCoT and ISSR amplified primers was 0.23. The present findings reveal the distinct heavy metal's adaption attributes of Z. coccineum, indicating its improved survival in severely arid mining environments.

Importance of Metal Biotransformation in Cell Response to Metallic Nanoparticles: A Transcriptomic Meta-analysis Study

Metallic nanoparticles are increasingly present in our environment, raising concerns on their interactions with living organisms and potential toxicity. Indeed, metallic nanoparticles release metal ions that can be toxic, bioessential, therapeutically active, or combine several of these features. However, human cell responses to different metallic nanoparticles and ions have rarely been compared so far. We propose here a meta-analysis of the transcriptomic responses of human cells to nanoparticles and ions of various metals (titanium, iron, copper, zinc, silver, cadmium, platinum, gold), in order to identify the commonalities and differences between cell responses to these compounds. This analysis revealed that the chemical properties of metals are more important than their known biological functions (i.e., essential metals, toxicity) in governing the cell transcriptome. Particularly, we evidence that the response to nanoparticles is dominated by the response to the ions they contain, and depend on the nanoparticles' solubility. The formulation as nanoparticles impacts the cell response at lower intensity than the released ions, by altering genes related to vesicle intracellular transport and the cytoskeleton. Moreover, we put into light that several metals (i.e., copper, zinc, silver, cadmium, and gold) trigger a common cell response governed by metallothioneins, which coexist with singular signatures that are specific to a given element.

Mercury Ion Binding to Apolipoprotein E Variants ApoE2, ApoE3, and ApoE4: Similar Binding Affinities but Different Structure Induction Effects

Mercury intoxication typically produces more severe outcomes in people with the APOE-ε4 gene, which codes for the ApoE4 variant of apolipoprotein E, compared to individuals with the APOE-ε2 and APOE-ε3 genes. Why the APOE-ε4 allele is a risk factor in mercury exposure remains unknown. One proposed possibility is that the ApoE protein could be involved in clearing of heavy metals, where the ApoE4 protein might perform this task worse than the ApoE2 and ApoE3 variants. Here, we used fluorescence and circular dichroism spectroscopies to characterize the in vitro interactions of the three different ApoE variants with Hg(I) and Hg(II) ions. Hg(I) ions displayed weak binding to all ApoE variants and induced virtually no structural changes. Thus, Hg(I) ions appear to have no biologically relevant interactions with the ApoE protein. Hg(II) ions displayed stronger and very similar binding affinities for all three ApoE isoforms, with K _D values of 4.6 μM for ApoE2, 4.9 μM for ApoE3, and 4.3 μM for ApoE4. Binding of Hg(II) ions also induced changes in ApoE superhelicity, that is, altered coil-coil interactions, which might modify the protein function. As these structural changes were most pronounced in the ApoE4 protein, they could be related to the APOE-ε4 gene being a risk factor in mercury toxicity.

Efficiency of Multifunctional Antibacterial Hydrogels for Chronic Wound Healing in Diabetes: A Comprehensive Review

Diabetic chronic wounds or amputation, which are complications of diabetes mellitus (DM), are a cause of great suffering for diabetics. In addition to the lack of oxygen, elevated reactive oxygen species (ROS) and reduced vascularization, microbial invasion is also a critical factor that induces non-healing chronic diabetic wounds, ie, wounds still remaining in the stage of inflammation, after which the wound tissue begins to age and becomes necrotic. To clear up the infection, alleviate the inflammation in the wound and prevent necrosis, many kinds of hydrogel have been fabricated to eliminate infections with pathogens. The unique properties of hydrogels make them ideally suited to wound dressings because they provide a moist environment for wound healing and act as a barrier against bacteria. This review article will mainly cover the recent developments and innovations of antibacterial hydrogels for diabetic chronic wound healing.

A Comparative Analysis of Heavy Metal Effects on Medicinal Plants

Popularity of herbal drugs has always been in high demand, but recently it has been increasing all over the world, especially in India, because of the lower range of adverse health effects as compared to synthetic or man-made drugs. Not only this but their cost-effectiveness and easy availability to the poor people and the masses, particularly in developing countries, are major causes for their demand. But there lies a huge problem during the process of plant collection that affects their medicinal properties to certain degrees. This is caused by heavy metal toxicity in soil in different locations of the Indian subcontinent. This was correlated with their potential to cause health damage. Exposure of humans to heavy metals includes diverse pathways from food to water to consumption and inhalation of polluted air to permanent damage to exposed skin and even by occupational exposure at workplaces. As we can understand, the main mechanisms of heavy metal toxicity include the production of free radicals to affect the host by oxidative stress, damaging biological molecules such as enzymes, proteins, lipids, and even nucleic acids and finally damaging DNA which is the fastest way to carcinogenesis and in addition, neurotoxicity. Therefore, in this paper, we have researched how the plants/herbs are affected due to heavy metal deposition in their habitat and how it can lead to serious clinical complications.

The Modulatory Role of sti-1 in Methylmercury-Induced Toxicity in Caenorhabditis elegans

Human exposure to the neurotoxin methylmercury (MeHg) poses a significant health risk to the development of the nervous system. The mechanisms of MeHg-induced neurotoxicity are associated with the disruption of cellular homeostasis, and include oxidative stress, loss of calcium homeostasis, and impaired protein quality control. The stress inducible protein 1 (STI-1) is involved in the regulation of protein quality control by acting as a protein cochaperone to maintain optimal protein unfolding and refolding. Here, we utilized the Caenorhabditis elegans (C. elegans) model of MeHg toxicity to characterize the role of the sti-1 gene in MeHg-induced toxicity. We showed that lifespan and developmental milestone timings were significantly altered in sti-1 knockout (KO) animals with MeHg exposure. However, knocking down sti-1 by RNAi did not result in an analogous effect for lifespan, but did still sensitize to delays in developmental milestone progression by acute MeHg, suggesting that insufficiency of sti-1 does not recapitulate all phenotypes of the null mutation. Furthermore, inhibition of ATP levels by MeHg exposure was modulated by sti-1. Considering that the skn-1/gst-4 pathway is highly involved in metal's toxicity, such pathway was also explored in our model. We showed that sti-1 mutant worms exhibited impaired capacity to upregulate the antioxidant genes skn-1/gst-4, highlighting a central role of sti-1 in modulating antioxidant response. Lastly, we showed that loss-of-function mutation in the rrf-3 gene, which encodes a putative RNA-directed RNA polymerase, has significant effect in altering MeHg-induced toxicity by potentiating the animal's detoxification system. Altogether, our novel data show an indispensable role of protein quality control in the defense against MeHg toxicity.

OFF-switching property of quorum sensor LuxR via As(III)-induced insoluble form

Whole-cell sensors for arsenite detection have been developed exclusively based on the natural arsenite (As(III)) sensory protein ArsR for arsenic metabolism. This study reports that the quorum-sensing LuxR/Plux system from Vibrio fischeri, which is completely unrelated to arsenic metabolism, responds to As(III) in a dose-dependent manner. Due to as many as 9 cysteine residues, which has a high binding affinity with As(III), LuxR underwent As(III)-induced insoluble form, thereby reducing its effective cellular concentration. Accordingly, the expression level of green fluorescent protein under the control of Plux gradually decreased with increasing As(III) concentration in the medium. This is a novel As(III)-detection system that has never been proposed before, with a unique ON-to-OFF transfer function.

Environmental factors modulating protein conformations and their role in protein aggregation diseases

The adverse physiological conditions have been long known to impact protein synthesis, folding and functionality. Major physiological factors such as the effect of pH, temperature, salt and pressure are extensively studied for their impact on protein structure and homeostasis. However, in the current scenario, the environmental risk factors (pollutants) have gained impetus in research because of their increasing concentrations in the environment and strong epidemiologic link with protein aggregation disorders. Here, we review the physiological and environmental risk factors for their impact on protein conformational changes, misfolding, aggregation, and associated pathological conditions, especially environmental risk factors associated pathologies.

Effect of Divalent Metal Ion on the Structure, Stability and Function of Klebsiella pneumoniae Nicotinate-Nucleotide Adenylyltransferase: Empirical and Computational Studies

The continuous threat of drug-resistant Klebsiella pneumoniae justifies identifying novel targets and developing effective antibacterial agents. A potential target is nicotinate nucleotide adenylyltransferase (NNAT), an indispensable enzyme in the biosynthesis of the cell-dependent metabolite, NAD+. NNAT catalyses the adenylation of nicotinamide/nicotinate mononucleotide (NMN/NaMN), using ATP to form nicotinamide/nicotinate adenine dinucleotide (NAD+/NaAD). In addition, it employs divalent cations for co-substrate binding and catalysis and has a preference for different divalent cations. Here, the biophysical structure of NNAT from K. pneumoniae (KpNNAT) and the impact of divalent cations on its activity, conformational stability and substrate-binding are described using experimental and computational approaches. The experimental study was executed using an enzyme-coupled assay, far-UV circular dichroism, extrinsic fluorescence spectroscopy, and thermal shift assays, alongside homology modelling, molecular docking, and molecular dynamic simulation. The structure of KpNNAT revealed a predominately α-helical secondary structure content and a binding site that is partially hydrophobic. Its substrates ATP and NMN share the same binding pocket with similar affinity and exhibit an energetically favourable binding. KpNNAT showed maximum activity and minimal conformational changes with Mg2+ as a cofactor compared to Zn2+, Cu2+ and Ni2+. Overall, ATP binding affects KpNNAT dynamics, and the dynamics of ATP binding depend on the presence and type of divalent cation. The data obtained from this study would serve as a basis for further evaluation towards designing structure-based inhibitors with therapeutic potential.

Molecular Biology of Cadmium Toxicity in Saccharomyces cerevisiae

Cadmium (Cd) is a toxic heavy metal mainly originating from industrial activities and causes environmental pollution. To better understand its toxicity and pollution remediation, we must understand the effects of Cd on living beings. Saccharomyces cerevisiae (budding yeast) is an eukaryotic unicellular model organism. It has provided much scientific knowledge about cellular and molecular biology in addition to its economic benefits. Effects associated with copper and zinc, sulfur and selenium metabolism, calcium (Ca2+) balance/signaling, and structure of phospholipids as a result of exposure to cadmium have been evaluated. In yeast as a result of cadmium stress, "mitogen-activated protein kinase," "high osmolarity glycerol," and "cell wall integrity" pathways have been reported to activate different signaling pathways. In addition, abnormalities and changes in protein structure, ribosomes, cell cycle disruption, and reactive oxygen species (ROS) following cadmium cytotoxicity have also been detailed. Moreover, the key OLE1 gene that encodes for delta-9 FA desaturase in relation to cadmium toxicity has been discussed in more detail. Keeping all these studies in mind, an attempt has been made to evaluate published cellular and molecular toxicity data related to Cd stress, and specifically published on S. cerevisiae.

Effects of the Toxic Metals Arsenite and Cadmium on α-Synuclein Aggregation In Vitro and in Cells

Exposure to heavy metals, including arsenic and cadmium, is associated with neurodegenerative disorders such as Parkinson’s disease. However, the mechanistic details of how these metals contribute to pathogenesis are not well understood. To search for underlying mechanisms involving α-synuclein, the protein that forms amyloids in Parkinson’s disease, we here assessed the effects of arsenic and cadmium on α-synuclein amyloid formation in vitro and in Saccharomyces cerevisiae (budding yeast) cells. Atomic force microscopy experiments with acetylated human α-synuclein demonstrated that amyloid fibers formed in the presence of the metals have a different fiber pitch compared to those formed without metals. Both metal ions become incorporated into the amyloid fibers, and cadmium also accelerated the nucleation step in the amyloid formation process, likely via binding to intermediate species. Fluorescence microscopy analyses of yeast cells expressing fluorescently tagged α-synuclein demonstrated that arsenic and cadmium affected the distribution of α-synuclein aggregates within the cells, reduced aggregate clearance, and aggravated α-synuclein toxicity. Taken together, our in vitro data demonstrate that interactions between these two metals and α-synuclein modulate the resulting amyloid fiber structures, which, in turn, might relate to the observed effects in the yeast cells. Whilst our study advances our understanding of how these metals affect α-synuclein biophysics, further in vitro characterization as well as human cell studies are desired to fully appreciate their role in the progression of Parkinson’s disease.

A non-lethal method to assess element content in the endangered Pinna nobilis

The fan shell Pinna nobilis is the largest bivalve endemic to the Mediterranean and is actually a strongly endangered species. Due to the biological, ecological, and historical relevance of this species, the research of a non-lethal method to relate the element content in organism's tissues and environment can provide information potentially useful to evaluate environmental pollution and organism physiological status. In this study, a screening on element concentration in the animal growing environment (seawater and sediments) and in four soft tissues (hepatopancreas, gills, mantle, and muscle), and two acellular tissues (calcite shell layer, and byssus) was performed. The comparison among these results was used to assess whether the no-lethal acellular tissue element concentration can be used to reveal the element presence in the environment and soft tissues. Elements, such as B, Ag, As, Mn, Mo, Pb, or Se, showed a possible relationship between their presence in the byssus and soft tissues. In the byssus Cr, Sb, Sn, and V have shown to be mostly related to the environment, more than the soft tissues, and might be used to draw a historical record of the exposure of the organism. The element concentration in the calcite shell layer did not relate with environmental element concentrations. Essential elements, like Cu, Fe, Ni, and Zn, were present in calcite shell layer and byssus and are likely related to their biological activity in the organism. The research also gave an overview on the presence of pollution and on the preferential intake route of the element. In summary, this study, performed on a limited number of specimens of this protected species, indicated that element concentration in the byssus can be applied as non-lethal method to monitor this endangered species and its interaction with the elements in the growing environment.

Reactivity of Thiol-Rich Zn Sites in Diacylglycerol-Sensing PKC C1 Domain Probed by NMR Spectroscopy

Conserved homology 1 (C1) domains are peripheral zinc finger domains that are responsible for recruiting their host signaling proteins, including Protein Kinase C (PKC) isoenzymes, to diacylglycerol-containing lipid membranes. In this work, we investigated the reactivity of the C1 structural zinc sites, using the cysteine-rich C1B regulatory region of the PKCα isoform as a paradigm. The choice of Cd²⁺ as a probe was prompted by previous findings that xenobiotic metal ions modulate PKC activity. Using solution NMR and UV-vis spectroscopy, we found that Cd²⁺ spontaneously replaced Zn²⁺ in both structural sites of the C1B domain, with the formation of all-Cd and mixed Zn/Cd protein species. The Cd²⁺ substitution for Zn²⁺ preserved the C1B fold and function, as probed by its ability to interact with a potent tumor-promoting agent. Both Cys₃His metal-ion sites of C1B have higher affinity to Cd²⁺ than Zn²⁺, but are thermodynamically and kinetically inequivalent with respect to the metal ion replacement, despite the identical coordination spheres. We find that even in the presence of the oxygen-rich sites presented by the neighboring peripheral membrane-binding C2 domain, the thiol-rich sites can successfully compete for the available Cd²⁺. Our results indicate that Cd²⁺ can target the entire membrane-binding regulatory region of PKCs, and that the competition between the thiol- and oxygen-rich sites will likely determine the activation pattern of PKCs.

Recent advances in the biodegradation of azo dyes

As dye demand continues to rapidly increase in the food, pharmaceutical, cosmetic, paper, textile, and leather industries, an industrialization increase is occurring. Meanwhile, the degradation and removal of azo dyes have raised broad concern regarding the hazards posed by these dyes to the ecological environment and human health. Physicochemical treatments have been applied but are hindered by high energy and economic costs, high sludge production, and chemicals handling. Comparatively, the bioremediation technique is an eco-friendly, removal-efficient, and cost-competitive method to resolve the problem. This paper provides scientific and technical information about recent advances in the biodegradation of azo dyes. It expands the biodegradation efficiency, characteristics, and mechanisms of various microorganisms containing bacteria, fungi, microalgae, and microbial consortia, which have been reported to biodegrade azo dyes. In addition, information about physicochemical factors affecting dye biodegradation has been compiled. Furthermore, this paper also sketches the recent development and characteristics of advanced bioreactors.

Genome-wide imaging screen uncovers molecular determinants of arsenite-induced protein aggregation and toxicity

The toxic metalloid arsenic causes widespread misfolding and aggregation of cellular proteins. How these protein aggregates are formed in vivo, the mechanisms by which they affect cells and how cells prevent their accumulation is not fully understood. To find components involved in these processes, we performed a genome-wide imaging screen and identified Saccharomyces cerevisiae deletion mutants with either enhanced or reduced protein aggregation levels during arsenite exposure. We show that many of the identified factors are crucial to safeguard protein homeostasis (proteostasis) and to protect cells against arsenite toxicity. The hits were enriched for various functions including protein biosynthesis and transcription, and dedicated follow-up experiments highlight the importance of accurate transcriptional and translational control for mitigating protein aggregation and toxicity during arsenite stress. Some of the hits are associated with pathological conditions, suggesting that arsenite-induced protein aggregation may affect disease processes. The broad network of cellular systems that impinge on proteostasis during arsenic stress identified in this current study provides a valuable resource and a framework for further elucidation of the mechanistic details of metalloid toxicity and pathogenesis. This article has an associated First Person interview with the first authors of the paper.

Positive Selection Inhibits Plasmid Coexistence in Bacterial Genomes

Plasmids play an important role in bacterial evolution by transferring niche-adaptive functional genes between lineages, thus driving genomic diversification. Bacterial genomes commonly contain multiple, coexisting plasmid replicons, which could fuel adaptation by increasing the range of gene functions available to selection and allowing their recombination. However, plasmid coexistence is difficult to explain because the acquisition of plasmids typically incurs high fitness costs for the host cell. Here, we show that plasmid coexistence was stably maintained without positive selection for plasmid-borne gene functions and was associated with compensatory evolution to reduce fitness costs. In contrast, with positive selection, plasmid coexistence was unstable despite compensatory evolution. Positive selection discriminated between differential fitness benefits of functionally redundant plasmid replicons, retaining only the more beneficial plasmid. These data suggest that while the efficiency of negative selection against plasmid fitness costs declines over time due to compensatory evolution, positive selection to maximize plasmid-derived fitness benefits remains efficient. Our findings help to explain the forces structuring bacterial genomes: coexistence of multiple plasmids in a genome is likely to require either rare positive selection in nature or nonredundancy of accessory gene functions among the coexisting plasmids.

The deubiquitinating enzyme USP7 regulates the transcription factor Nrf1 by modulating its stability in response to toxic metal exposure

The nuclear factor E2-related factor 1 (Nrf1) transcription factor performs a critical role in regulating cellular homeostasis as part of the cellular stress response and drives the expression of antioxidants and detoxification enzymes among many other functions. Ubiquitination plays an important role in controlling the abundance and thus nuclear accumulation of Nrf1 proteins, but the regulatory enzymes that act on Nrf1 are not fully defined. Here, we identified ubiquitin specific protease 7 (USP7), a deubiquitinating enzyme, as a novel regulator of Nrf1 activity. We found that USP7 interacts with Nrf1a and TCF11—the two long protein isoforms of Nrf1. Expression of wildtype USP7, but not its catalytically defective mutant, resulted in decreased ubiquitination of TCF11 and Nrf1a, leading to their increased stability and increased transactivation of reporter gene expression by TCF11 and Nrf1a. In contrast, knockdown or pharmacologic inhibition of USP7 dramatically increased ubiquitination of TCF11 and Nrf1a and reduction of their steady state levels. Loss of USP7 function attenuated the induction of Nrf1 protein expression in response to treatment with arsenic and other toxic metals, and inhibition of USP7 activity significantly sensitized cells to arsenic treatment. Collectively, these findings suggest that USP7 may act to modulate abundance of Nrf1 protein to induce gene expression in response to toxic metal exposure.

Proteomics in systems toxicology

Proteins are the ultimate product of gene expression. As they hinge between gene transcription and phenotype, they offer a more realistic perspective of toxicopathic effects, responses and even susceptibility to insult than targeting genes and mRNAs while dodging some inter-individual variability that hinders measuring downstream endpoints like metabolites or enzyme activity. Toxicologists have long focused on proteins as biomarkers but the advent of proteomics shifted risk assessment from narrow single-endpoint analyses to whole-proteome screening, enabling deriving protein-centric adverse outcome pathways (AOPs), which are pivotal for the derivation of Systems Biology informally named Systems Toxicology. Especially if coupled pathology, the identification of molecular initiating events (MIEs) and AOPs allow predictive modeling of toxicological pathways, which now stands as the frontier for the next generation of toxicologists. Advances in mass spectrometry, bioinformatics, protein databases and top-down proteomics create new opportunities for mechanistic and effects-oriented research in all fields, from ecotoxicology to pharmacotoxicology.

Metal pollution as a potential threat to shell strength and survival in marine bivalves

Marine bivalve molluscs, such as scallops, mussels and oysters, are crucial components of coastal ecosystems, providing a range of ecosystem services, including a quarter of the world's seafood. Unfortunately, coastal marine areas often suffer from high levels of metals due to dumping and disturbance of contaminated material. We established that increased levels of metal pollution (zinc, copper and lead) in sediments near the Isle of Man, resulting from historical mining, strongly correlated with significant weakening of shell strength in king scallops, Pecten maximus. This weakness increased mortality during fishing and left individuals more exposed to predation. Comparative structural analysis revealed that shells from the contaminated area were thinner and exhibited a pronounced mineralisation disruption parallel to the shell surface within the foliated region of both the top and bottom valves. Our data suggest that these disruptions caused reduced fracture strength and hence increased mortality, even at subcritical contamination levels with respect to current international standards. This hitherto unreported effect is important since such non-apical responses rarely feed into environmental quality assessments, despite potentially significant implications for the survival of organisms exposed to contaminants. Hence our findings highlight the impact of metal pollution on shell mineralisation in bivalves and urge a reappraisal of currently accepted critical contamination levels.

Blood donation and heavy metal poisoning in developing nations: Any link?

Long term health effects of heavy metal exposure from both occupational and environmental settings involve multi-organ toxicities including but not limited to disturbances of neurological, cognitive, and metabolic processes, immune system dysregulation, carcinogenesis and sometimes permanent disabilities. Humans are exposed to toxic metals through various sources and routes of entry. The risk of heavy metal poisoning from donor blood has been the subject of many scientific investigations. In this review we highlight how the access to a safe and adequate blood transfusion with minimal risk of toxic metals to recipients is a public health challenge, especially in developing nations. For quality assurance purposes, blood donors are screened for various blood-borne pathogens, but screening for toxic metal levels is not routine. Evidence from scientific studies used in this review lends credence to the risk of heavy metal poisoning from donors with high blood concentrations of these heavy metals. The risk of toxicity is exceptionally high in vulnerable populations such as neonates and preterm infants, as well as in pregnant women and other individuals with conditions requiring multiple blood transfusions. This is worse in developing countries where some members of the population engage in illegal refining and artisanal mining activities. In order to reduce toxic metal exposure in vulnerable populations, blood meant for transfusion in vulnerable subjects, e.g. children, should be routinely screened for heavy metal concentrations. Patients receiving multiple blood transfusions should also be monitored for iron overload and its attendant toxicities.

Cysteine: an overlooked energy and carbon source

Biohybrids composed of microorganisms and nanoparticles have emerged as potential systems for bioenergy and high-value compound production from CO₂ and light energy, yet the cellular and metabolic processes within the biological component of this system are still elusive. Here we dissect the biohybrid composed of the anaerobic acetogenic bacterium Moorella thermoacetica and cadmium sulphide nanoparticles (CdS) in terms of physiology, metabolism, enzymatics and transcriptomic profiling. Our analyses show that while the organism does not grow on l-cysteine, it is metabolized to acetate in the biohybrid system and this metabolism is independent of CdS or light. CdS cells have higher metabolic activity, despite an inhibitory effect of Cd²⁺ on key enzymes, because of an intracellular storage compound linked to arginine metabolism. We identify different routes how cysteine and its oxidized form can be innately metabolized by the model acetogen and what intracellular mechanisms are triggered by cysteine, cadmium or blue light.

Pesticide interactions induce alterations in secondary structure of malate dehydrogenase to cause destability and cytotoxicity

Environmental exposure to pesticides increases the risk of neurotoxicity and neurodegenerative diseases. The mechanism of pesticide-induced toxicity is attributed to the increased reactive oxygen species, mitochondrial dysfunction, inhibition of key cellular enzymes and accelerated pathogenic protein aggregation. The structural basis of pesticide-protein interaction is limited to pathogenic proteins such as α-synuclein, Tau and amyloid-beta. However, the effect of pesticides on metabolic proteins is still unexplored. Here, we used rotenone and chlorpyrifos to understand the interaction of these pesticides with a metabolic protein, malate dehydrogenase (MDH) and the consequent pesticide-induced cytotoxicity. We found that rotenone and chlorpyrifos strongly bind to MDH, interferes with protein folding and triggers alteration in its secondary structure. Both pesticides showed high binding affinities for MDH as observed by NMR and LCMS. Rotenone and chlorpyrifos induced structural alterations during MDH refolding resulting in the formation of cytotoxic conformers that generated oxidative stress and reduced cell viability. Our findings suggest that pesticides, in general, interact with proteins resulting in the formation of cytotoxic conformers that may have implications in neurotoxicity and neurodegenerative diseases.

Substitution of the Native Zn(II) with Cd(II), Co(II) and Ni(II) Changes the Downhill Unfolding Mechanism of Ros87 to a Completely Different Scenario

The structural effects of zinc replacement by xenobiotic metal ions have been widely studied in several eukaryotic and prokaryotic zinc-finger-containing proteins. The prokaryotic zinc finger, that presents a bigger βββαα domain with a larger hydrophobic core with respect to its eukaryotic counterpart, represents a valuable model protein to study metal ion interaction with metallo-proteins. Several studies have been conducted on Ros87, the DNA binding domain of the prokaryotic zinc finger Ros, and have demonstrated that the domain appears to structurally tolerate Ni(II), albeit with important structural perturbations, but not Pb(II) and Hg(II), and it is in vitro functional when the zinc ion is replaced by Cd(II). We have previously shown that Ros87 unfolding is a two-step process in which a zinc binding intermediate converts to the native structure thorough a delicate downhill folding transition. Here, we explore the folding/unfolding behaviour of Ros87 coordinated to Co(II), Ni(II) or Cd(II), by UV-Vis, CD, DSC and NMR techniques. Interestingly, we show how the substitution of the native metal ion results in complete different folding scenarios. We found a two-state unfolding mechanism for Cd-Ros87 whose metal affinity K_d is comparable to the one obtained for the native Zn-Ros87, and a more complex mechanism for Co-Ros87 and Ni-Ros87, that show higher K_d values. Our data outline the complex cross-correlation between the protein-metal ion equilibrium and the folding mechanism proposing such an interplay as a key factor in the proper metal ion selection by a specific metallo-protein.

Mechanisms of sensing and response to proteotoxic stress

Cells are continuously subject to various stresses, battling both exogenous insults as well as toxic by-products of normal cellular metabolism and nutrient deprivation. Throughout the millennia, cells developed a core set of general stress responses that promote survival and reproduction under adverse circumstances. Past and current research efforts have been devoted to understanding how cells sense stressors and how that input is deciphered and transduced, resulting in stimulation of stress management pathways. A prime element of cellular stress responses is the increased transcription and translation of proteins specialized in managing and mitigating distinct types of stress. In this review, we focus on recent developments in our understanding of cellular sensing of proteotoxic stressors that impact protein synthesis, folding, and maturation provided by the model eukaryote the budding yeast, Saccharomyces cerevisiae, with reference to similarities and differences with other model organisms and humans.

A portable microfluidic device-based Fe3O4-urease nanoprobe-enhanced colorimetric sensor for the detection of heavy metals in fish tissue

A portable microfluidic device with highly sensitive enzyme nanoprobe (Fe₃O₄ MNPs-urease, average size 34.6 nm) was demonstrated for the analysis of heavy metals ions (Hg²⁺, Cd²⁺ and Pb²⁺) in fish gill and muscle tissue. The immobilized urease nanoprobe (K_m = 0.05 mM) exhibited twofold sensitivity over the free enzyme assay (apparent K_m = 0.1 mM). The nanoprobe was characterized using SEM, EDAX, PSA and FT-IR. The inhibition measurements were carried out for individual as well as the mixture of metal ions (CRM standards of 9 elements (CRM_mix-9)). The lower limit of quantification (LOQ) (0.5, 0.1, and 0.1 ng L^-1 for Hg²⁺, Cd²⁺, and Pb²⁺) and lower limit of detection (LOD) was achieved at 0.1 ng L^-1 with sensitivity 8-14% per decade for Hg²⁺, Cd²⁺, and Pb²⁺ ions. A visual result can be observed by the naked eye through the microfluidic device as well as with 96 transparent microwell plates. The order of relative inhibition was found to be CRM_mix-9 > (Hg²⁺ + Cd²⁺ + Pb²⁺) > (Cd²⁺ + Pb²⁺) > (Pb²⁺ + Hg²⁺) > (Hg²⁺ + Cd²⁺) > Pb²⁺ > Cd²⁺ > Hg²⁺, respectively. The recovery % in fish tissues were found to be 88-98% for Hg²⁺, Cd²⁺ and Pb²⁺ ions.

<i>Syzygium samarangense</i> Volatile Oil Inhibited Bacteria Growth and Extracellular Protease of <i>Salmonella typhimurium</i>

BACKGROUND AND OBJECTIVE

Medicinal plants are fast becoming essential pharmaceuticals for disease and infection management. The vast antimicrobial properties of these plants reside in the inhibitory properties of their endogenous secondary metabolites. Therefore, this study aimed to assess if the volatile oil of Syzygium samarangense inhibits enteric bacteria growth and its effect against the caseinolytic activity of the extracellular protease of Salmonella typhimurium.

MATERIALS AND METHODS

The volatile oil was extracted by hydrodistillation, while the antimicrobial assay was assessed with the microdilution method. The extracellular protease was partially purified by salting out, followed by size-exclusion chromatography. The mode of inhibition of this enzyme was deduced from the enzyme-substrate kinetics using a line-weaver burke plot.

RESULTS

The antimicrobial properties of the oil were reported against ten enteric bacteria. Proteus vulgaris has the highest IC50 value of 0.75±0.004% v/v, while S. typhimurium, the most sensitive bacterium, showed the lowest IC50 value of 0.17±0.005% v/v. The extracellular protease of S. typhimurium was partially purified to achieve 3.73 purification fold and 314.2 μmol min-1 mg-1 protein. The optimal caseinolytic activity of this enzyme was found at pH 7.5 and 40 °C. The protease showed significantly higher activity in the presence of Zn2+ (9.3±0.33 U min-1) as compared to the control (7.0±0.58 U min-1) (p<0.05), however, K+, Ca2+, Co2+, Ba2+, Pb2+ and Hg2+ considerably reduced the enzyme activity. The activity of this enzyme was competitively inhibited by the volatile oil as an inhibitor.

CONCLUSION

The volatile oil of S. samarangense inhibited a wide range of enteric bacteria and, therefore proposed as a potential antimicrobial agent. Inhibiting the extracellular protease of S. typhimurium may be one of its modes of action against these pathogens.