Binding Of Transition Metal Ions Research Articles

The aromatic amino acid phenylalanine: a versatile tool for binding transition metal ions.

The human body contains many different types of transition metal ions, such as Zn2+, Cu2+, which are involved in many physiological processes. An excess or deficiency of these ions can cause diseases, such as Alzheimer's disease, which is closely related to the levels of these ions in the body. In-depth understanding of various physiological and pathological mechanisms related to metal ions requires understanding the interaction between metal ions and nearby amino acids at the atomic level. This article selected four transition metal ions: Zn2+, Cu2+, Fe2+, and Mn2+ and the aromatic amino acid Phe, known for its strong coordination capability, as study subjects, comprehensively examining their binding situations. The results show that there are multiple binding modes between them and Phe, and most of the binding modes involve benzene ring coordination. The coordination strength order of the four metal ions with benzene ring, carbonyl O, hydroxyl O and amino N is different. For the lowest energy structure formed by each ion with Phe, all four ions are bound to N, carbonyl O, and benzene ring. Zn2+ is combined with two C's of the benzene ring, Cu2+ with four C's of the benzene ring, and Fe2+ and Mn2+ with the benzene ring as a whole. Part of the reason for this phenomenon may be derived from the tendency of transition metal ions to reach 18e stable structures when bound to ligands. There is a strong binding force between the four ions and Phe, and the binding trend is Cu2+(-294.9kcal/mol) > Zn2+(-261.3kcal/mol) > Fe2+(-247.5kcal/mol) > Mn2+(-220.2kcal/mol). Mayer bond order analysis and molecular orbital localization analysis found that there are very strong chemical interactions between transition metal ions and surrounding atoms, especially with N and carbonyl O. Several initial structures with different coordination modes to Phe were created according to chemical intuition for each divalent cation. Then semiempirical MD simulations at GFN2 level were run on these structures. The numerous generated structures were classified according to some criteria, then representative geometries were preliminarily optimized by TPSSh/6-31G*/LanL2DZ. To get more accurate electronic energies, high-precision quantum chemistry calculations at the level of TPSSh/def2TZVPP//TPSSh/def2QZVPP were carried out on the selected low-lying structures. All the optimized structures were confirmed to be minima without imaginary frequency by performing frequency analyses. Further electronic structure analyses such as IRI, Mayer bond order, IBSI etc. were performed to get more insights into the binding between the transition metal ions and Phe.

Synthesis and Evaluation of Water-Soluble Antioxidants Derived from L-carnosine and Syringaldehyde (or Vanillin)

Polyphenols are well known for their health-related benefits, including antioxidant activities, but most of them are hydrophobic, decreasing their bioavailability. This study reports water-soluble trimeric antioxidants synthesized with L-carnosine and the hydrophobic ortho-methoxy-substituted phenolic unit, syringaldehyde or vanillin.In the DPPH assay, carnosine-syringaldehyde (7.5 μM) and carnosine-vanillin (19 μM) derivatives showed much lower IC50 values than ascorbic acid (27.5 μM) and sodium ascorbate (30.5 μM) standards. According to the AAPH assay, carnosine-syringaldehyde and carnosine-vanillin protect DNA at concentrations as low as 6.5 μM and 26 μM, respectively, while both sodium ascorbate and ascorbic acid protected until 52 μM. Another notable property of these antioxidants is they can protect DNA well against hydroxyl radicals, produced via the Fenton reaction: carnosine-syringaldehyde showed DNA protection at all tested concentrations (833−1.6 μM), but the protection was slightly weaker between 26−1.6 μM. Carnosine-vanillin showed strong protection in the 833−104 μM range and some protection between 52−3.2 μM. Conversely, both sodium ascorbate and ascorbic acid did not protect DNA at any test concentration. In the pro-oxidant potential assessments, the synthesized antioxidants did not show any pro-oxidant effects at all concentrations, whereas sodium ascorbate showed severe pro-oxidant effects between 833−13 μM and ascorbic acid, 833−52 μM.Our study stresses the importance of ortho-methoxy group(s) for antioxidants as its electron-donating nature contributes to enhancing antioxidant activities, while steric bulk eliminates pro-oxidant effects by preventing the effective binding of transition metal ions to the phenolic hydroxyl group. The hydrophobicity of hindered phenols can be overcome if attached to a water-soluble scaffold.

Quantitative proteomics investigating the intrinsic adaptation mechanism of Aeromonas hydrophila to streptomycin.

Aeromonas hydrophila, a prevalent pathogen in the aquaculture industry, poses significant challenges due to its drug-resistant strains. Moreover, residues of antibiotics like streptomycin, extensively employed in aquaculture settings, drive selective bacterial evolution, leading to the progressive development of resistance to this agent. However, the underlying mechanism of its intrinsic adaptation to antibiotics remains elusive. Here, we employed a quantitative proteomics approach to investigate the differences in protein expression between A. hydrophila under streptomycin (SM) stress and nonstress conditions. Notably, bioinformatics analysis unveiled the potential involvement of metal pathways, including metal cluster binding, iron-sulfur cluster binding, and transition metal ion binding, in influencing A. hydrophila's resistance to SM. Furthermore, we evaluated the sensitivity of eight gene deletion strains related to streptomycin and observed the potential roles of petA and AHA_4705 in SM resistance. Collectively, our findings enhance the understanding of A. hydrophila's response behavior to streptomycin stress and shed light on its intrinsic adaptation mechanism.

Dynamic Li+ Capture through Ligand-Chain Interaction for the Regeneration of Depleted LiFePO4 Cathode.

After application in electric vehicles, spent LiFePO4 (LFP) batteries are typically decommissioned. Traditional recycling methods face economic and environmental constraints. Therefore, direct regeneration has emerged as a promising alternative. However, irreversible phase changes can significantly hinder the efficiency of the regeneration process owing to structural degradation. Moreover, improper storage and treatment practices can lead to metamorphism, further complicating the regeneration process. In this study, a sustainable recovery method is proposed for the electrochemical repair of LFP batteries. A ligand-chain Zn-complex (ZnDEA) is utilized as a structural regulator, with its ─NH─ group alternatingly facilitating the binding of preferential transition metal ions (Fe3+ during charging and Zn2+ during discharging). This dynamic coordination ability helps to modulate volume changes within the recovered LFP framework. Consequently, the recovered LFP framework can store more Li-ions, enhance phase transition reversibility between LFP and FePO4 (FP), modify the initial Coulombic efficiency, and reduce polarization voltage differences. The recovered LFP cells exhibit excellent capacity retention of 96.30% after 1500 cycles at 2C. The ligand chain repair mechanism promotes structural evolution to facilitate ion migration, providing valuable insights into the targeted ion compensation for environmentally friendly recycling in practical applications.

–HH and –HAAAH motifs act as fishing nets for biologically relevant metal ions in metallopeptides

Histidine are one of the most common residues involved in transition metal ion binding in the active sites of metalloenzymes. In order to mimic enzymatic metal binding sites, it is crucial to understand the basic coordination modes of histidine residues, distributed at different positions in the peptide sequence. We show that: (i) the separation of two histidines has a large effect on complex stability – a sequence with adjusting histidine residues forms more stable complexes with Zn(II) than the one in which the residues are separated, while the contrary is observed for Cu(II) complexes, in which amide nitrogens participate in metal binding. No pronounced effect is observed for Ni(II) complexes, where the amides participate in binding at higher pH; (ii) non-coordinating amino acid residues (basic, acidic and aromatic ones) have a significant impact on complex stability; charged and aromatic residues may enhance Zn(II) binding, while the contrary is observed for the amide-binding Cu(II); (iii) cysteine containing sequences are much more effective Zn(II) and Ni(II) binding motifs at pH above 8, while histidine containing ligands are more suitable for effective Zn(II) and Ni(II) binding at lower pH.

Antioxidant and Anti-Glycation Potential of H2 Receptor Antagonists-In Vitro Studies and a Systematic Literature Review.

Background: Histamine H2 receptor antagonists are a group of drugs that inhibit gastric juice secretion in gastrointestinal diseases. However, there is evidence to suggest that H2 blockers have a broader spectrum of activity. The antioxidant properties of H2 blockers have not been fully elucidated, and their anti-glycation potential has not been studied to date. Therefore, this is the first study to compare the antioxidant and antiglycation potentials of the most popular H2 antagonists (ranitidine, cimetidine, and famotidine) on protein glycoxidation in vitro. Methods: Bovine serum albumin (BSA) was glycated using sugars (glucose, fructose, galactose, and ribose) as well as aldehydes (glyoxal and methylglyoxal). Results: In the analyzed group of drugs, ranitidine was the only H2 blocker that significantly inhibited BSA glycation in all tested models. The contents of protein carbonyls, protein glycoxidation products (↓dityrosine, ↓N-formylkynurenine), and early (↓Amadori products) and late-stage (↓AGEs) protein glycation products decreased in samples of glycated BSA with the addition of ranitidine relative to BSA with the addition of the glycating agents. The anti-glycation potential of ranitidine was comparable to those of aminoguanidine and Trolox. In the molecular docking analysis, ranitidine was characterized by the lowest binding energy for BSA sites and could compete with protein amino groups for the addition of carbonyl groups. H2 blockers also scavenge free radicals. The strongest antioxidant properties are found in ranitidine, which additionally has the ability to bind transition metal ions. The systematic literature review also revealed that the anti-glycation effects of ranitidine could be attributed to its antioxidant properties. Conclusions: Ranitidine showed anti-glycation and antioxidant properties. Further research is needed, particularly in patients with diseases that promote protein glycation.

Quantifying metal-binding specificity of CcNikZ-II from Clostridium carboxidivorans in the presence of competing metal ions

Many proteins bind transition metal ions as cofactors to carry out their biological functions. Despite binding affinities for divalent transition metal ions being predominantly dictated by the Irving-Williams series for wild-type proteins, in vivo metal ion binding specificity is ensured by intracellular mechanisms that regulate free metal ion concentrations. However, a growing area of biotechnology research considers the use of metal-binding proteins in vitro to purify specific metal ions from wastewater, where specificity is dictated by the protein's metal binding affinities. A goal of metalloprotein engineering is to modulate these affinities to improve a protein's specificity towards a particular metal; however, the quantitative relationship between the affinities and the equilibrium metal-bound protein fractions depends on the underlying binding mechanisms. Here we demonstrate a high-throughput intrinsic tryptophan fluorescence quenching method to validate binding models in multi-metal solutions for CcNikZ-II, a nickel-binding protein from Clostridium carboxidivorans. Using our validated models, we quantify the relationship between binding affinity and specificity in different classes of metal-binding models for CcNikZ-II. We further illustrate the potential relevance of data-informed models to predicting engineering targets for improved specificity.

The Structure of Cyclic Neuropeptide Somatostatin and Octapeptide Octreotide in the Presence of Copper Ions: Insights from Transition Metal Ion FRET and Native Ion Mobility-Mass Spectrometry.

The conformation and function of somatostatin (SST), a cyclic neuropeptide, was recently found to be altered in the presence of Cu(II) ions, which leads to self-aggregation and loss of biological function as a neurotransmitter. However, the impact of Cu(II) ions on the structure and function of SST is not fully understood. In this work, transition metal ion Förster resonance energy transfer (tmFRET) and native ion mobility-mass spectrometry (IM-MS) were utilized to study the structures of well-defined gas-phase ions of SST and of a smaller analogue, octreotide (OCT). The tmFRET results suggest two binding sites of Cu(II) ions in both native-like SST and OCT ions, either in close proximity to the disulfide bond or complexed by two aromatic residues, consistent with results obtained from collision-induced dissociation (CID). The former binding site was reported to initiate aggregation of SST, while the latter binding site could directly affect the essential motif for receptor binding and therefore impair the biological function of SST and OCT when bound to SST receptors. Our results demonstrate that tmFRET is capable of locating transition metal ion binding sites in neuropeptides. Furthermore, multiple distance constraints (tmFRET) and global shape (IM-MS) provide additional structural insights of SST and OCT ions upon metal binding, which is related to the self-aggregation mechanisms and overall biological functions.

Vaginal Birth Alters Gut Transcriptome of Neonatal Pigs

Background: Women at risk of preterm birth are routinely administered prenatal doses of glucocorticoids to facilitate lung maturation and improve pulmonary outcomes in preterm infants. Additionally, preterm infants are often administered low doses of glucocorticoids postnatally for prevention of bronchopulmonary dysplasia. However, there is limited understanding about the impact of perinatal glucocorticoid exposure on the gut and liver in preterm infants. In pigs, there is a spike in plasma cortisol in newborns during parturition. We previously showed in pigs that plasma cortisol levels positively correlate with plasma fibroblast growth factor 19 (FGF19), a gut hormone that negatively regulates hepatic bile acid synthesis. FGF19 is secreted by epithelial cells predominantly in the distal ileum in response to bile acids. However, in vaginally-born pigs, FGF19 mRNA levels were higher in the proximal jejunum. This led us to hypothesize that exposure to glucocorticoids in the perinatal period has a profound impact on the transcription of genes involved in the development of gut and liver. Objective: The objective of this study was to characterize the impact of spontaneous vaginal birth and the exposure to elevated cortisol on the transcriptome in gut and liver tissue of neonatal pigs Methods: Two sows underwent a cesarean section on gestation day 114 (“Term”; term=115 day), two sows underwent a cesarean section on gestation day 105 (“Preterm”) and two additional sows were allowed to farrow at term gestational age (“Vaginal”). Small intestine tissue and plasma was collected from newborn pigs (n= 10 Preterm; n=8 Term; n=6 Vaginal). RNA-seq analysis was performed on intestinal samples mapped to the latest Sus scrofa Sscrofa11.1 reference genome (NCBI). Results: Cortisol levels were statistically highest in the vaginally-born pigs (139 ng/mL), followed by the Term (101 ng/mL) and lowest in the Preterm (61 ng/mL) pigs. Gene Ontology (GO) analysis showed significant enrichment in pathways of upregulated genes involved in response to toxic substances, stress, detoxification and inorganic substances in the jejunum of Vaginal pigs compared to Preterm and Term pigs. KEGG analysis of the proximal jejunum indicated enrichment in pathways of upregulated genes in steroid hormone biosynthesis, bile secretion, TNF signaling and IL-17 Vaginal, compared to Term and Preterm pigs. The same pattern was not the same in the distal ileum where GO analysis showed pathway enrichment of upregulated genes in oxidation-reduction processes, and transition metal ion binding in Vaginal compared to Term and Preterm pigs. KEGG analysis of the distal ileum identified pathway enrichment of upregulated genes in complement and coagulation, bile acid synthesis and secretion, fatty acid metabolism, and amino acid metabolism in Vaginal pigs. Conclusion: Genes in metabolic and cellular signaling pathways associated with cortisol are upregulated in vaginally-born pigs. This work was supported in part by federal funds from the USDA, Agricultural Research Service under Cooperative Agreement Number 3092-51000-060-01, and grants from the National Institutes of Health Grant DK-094616 (D.G.B), and the Texas Medical Center Digestive Diseases Center (NIH Grant P30 DK-56338). Caitlin Vonderohe was supported by T32 DK007664 and Greg Guthrie was supported by K01 DK129408. 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.

Small DNAs That Specifically and Tightly Bind Transition Metal Ions.

Specific DNA-binding to metal ions is a long-standing fundamental research topic with great potential to transform into nano/biotechnology and therapeutics applications. Herein, based on the mobility change of DNA in denaturing gels, we develop a selection strategy to discover a series of 40-45 nt small DNAs that can bind Zn2+ and Cd2+ specifically and tightly. The Zn2+- and Cd2+-bound DNA complexes can even tolerate harsh denaturing conditions of 8 M urea and 50 mM EDTA. The discovery not only exposes a new class of transition metal ion-binding DNAs but also provides potentially a new tool for targeting drug therapies based on metal ions.

Ameliorative potential of quercetin and rutin on dextromethorphan-induced toxicity in Sprague-Dawley rats

Dextromethorphan as an antitussive has been reported to have deleterious effect on the testicular function. Quercetin is an extensive class of polyphenolic flavonoid compounds found in plant sources like green vegetables and tea. It is considered to be a strong antioxidant due to its ability scavenge free radicals and bind transition metal ions. Rutin is a flavonoid of the flavonol-type that is found in plant kingdom and a nutritional component of foodstuffs in apples, onions and black tea. In this study, we determined the effect of Quercetin and Rutin on Dextromethorphan-induced toxicity in males using Sprague-Dawley rats as models. Eighty male rats (150 ± 30 g) divided into four (N=20; A-D) were used for a duration of 16 weeks. Group A, control received distilled water (DW); group B-C received 20, 40 and 80 mg/kg of DM respectively. At the end of treatment period, 5 animals were selected and euthanized from each group. Seminal parameters and Hormonal milieu were analysed. The remaining 15 rats were divided into 3 groups (N=5; E-G). They received Quercetin (50 mg/kg) Rutin (25 mg/kg) and DW respectively for 16 weeks to ascertain recovery rate. The rats were sacrificed and the above parameters were analysed. Significant dose-dependent reduction in seminal parameters and hormones was observed in DM- treated groups. An increase in seminal parameters and hormonal milieu was observed when DM- treated and recovery-alone groups were compared to Rutin and Quercetin groups. The supplementation of Rutin and Quercetin showed significant increases in the parameters which could mitigate the toxic effect of Dextromethorphan and in turn translates into improved fertility in males.

Protective Role of Quercetin on Thioacetamide-Induced Renal Injury in Adult Male Albino Rats

Background: Thioacetamide (TAA) is a recognized industrial poisonous agent drastically used in animal studies for induction of hepatic necrosis, fibrosis and cirrhosis. It is additionally reported to be nephrotoxic through induction of oxidative stress. Quercetin (QE) has a high antioxidant capacity via free radical scavenging, transition metal ion binding, and lipid peroxidation inhibition. Aim of the work: The goal of this research was to see if QE may help reduce the negative effects of thioacetamide on renal tissue by histological examination of the kidney. Material and methods: Twenty four adult male Albino rats 7–9 weeks old around 180–200g body weight were allocated into 3 groups; Group I (n=8) receiving distilled water, Group II (n=8); rats receiving TAA and Group III (n=8); receiving TAA and QE. Results: Renal tissues were examined under a light microscope stained by Harris Hematoxylin & Eosin (H&E stain), Periodiceeacid Schiff (PAS) andjMasson’srTrichrome for TAA-treated groups revealed severe histopathological changes, whereas specimens obtained from QE-treated groups showed onlywmild changes. Immunohistochemical results corroborated these findings. Conclusion: This study demonstrated the ameliorative consequences of QE in opposition to TAA-induced renal injury in rats. The result of this study might contribute in the development of a novel complementary alternative medication in combating and therapeutic intervention of TAA-induced renal injury. KEY WORDS: Thioacetamide, renal, quercetin, albino rat and histopathology.

Comparative proteome and transcriptome analyses of the response of postharvest pears to Penicillium expansum infection

Penicillium expansum causes blue mold disease in pears during storage and transportation, causing huge economic losses. However, researches on the defense mechanisms of pears against P. expansum are still in the early stages. Therefore, many unknown disease-resistant factors have yet to be excavated, severely limiting the breakthrough progress of pear blue mold control strategies. The current study used transcriptome and proteome approaches to evaluate pear defense mechanisms following infection with P. expansum. 96% of pear proteins were associated with the transcriptome data. Gene Ontology (GO) enrichment analysis determined that the remaining associated genes/proteins were significantly enriched in 80 GO terms. The significantly enriched GO terms included oxyacid metabolism, aldehyde-lyase activity, transition metal ion binding, terpenoid metabolic process, response to stimulus, etc. An enrichment analysis conducted by the Kyoto Encyclopedia of Genes and Genomes (KEGG) showed that 122 metabolic pathways were enriched, of which 11 were closely related to other metabolic pathways. In these 11 metabolic pathways, the genes/proteins (such as peroxidase, histidinol-phosphate aminotransferase (hisC), prephenate dehydratase (ADT), etc.) related to the biosynthesis of plant secondary metabolites, and the genes/proteins (such as ethylene-responsive transcription factor 1 (ERF), BR-signaling kinase (BSK), brassinosteroid insensitive 1-associated receptor kinase 1 (BAK1), etc.) related to plant hormones were significantly enriched. Overall, this study provides a deep understanding of pear’s defense response, which could be used in future research to develop strategies to control fungal diseases.

A Proteomic Study of the Effect of N-acetylcysteine on the Regulation of Early Pregnancy in Goats.

Simple SummaryEarly pregnancy regulation is an extremely complex process that is influenced by various factors. We previously mined the differentially expressed genes affected by N-acetyl-L-cysteine (NAC) in early pregnancy in goats via transcriptome sequencing. We found that NAC increased the number of lambs by affecting the immune pathway in ewes and enhancing antioxidation. Based on this, we here explored the effect of NAC on early pregnancy in goats at the protein level. The results showed a difference in the expression of uterine keratin and increases in the levels of antioxidant indices and hormones in doe serum.Dietary supplementation with N-acetyl-L-cysteine (NAC) may support early pregnancy regulation and fertility in female animals. The purpose of this study was to investigate the effect of supplementation with 0.07% NAC on the expression of the uterine keratin gene and protein in Qianbei-pockmarked goats during early pregnancy using tandem mass spectrometry (TMT) relative quantitative proteomics. The results showed that there were significant differences in uterine keratin expression between the experimental group (NAC group) and the control group on day 35 of gestation. A total of 6271 proteins were identified, 6258 of which were quantified by mass spectrometry. There were 125 differentially expressed proteins (DEPs), including 47 upregulated and 78 downregulated proteins, in the NAC group. Bioinformatic analysis showed that these DEPs were mainly involved in the transport and biosynthesis of organic matter and were related to the binding of transition metal ions, DNA and proteins and the catalytic activity of enzymes. They were enriched in the Jak-STAT signalling pathway, RNA monitoring pathway, amino acid biosynthesis, steroid biosynthesis and other pathways that may affect the early pregnancy status of does through different pathways and thus influence early embryonic development. Immunohistochemistry, real-time quantitative PCR and Western blotting were used to verify the expression and localization of glial fibrillary acidic protein (GFAP) and pelota mRNA surveillance and ribosomal rescue factor (PELO) in uterine horn tissue. The results showed that both PELO and GFAP were localized to endometrial and stromal cells, consistent with the mass spectrometry data at the transcriptional and translational levels. Moreover, NAC supplementation increased the levels of the reproductive hormones follicle-stimulating hormone (FSH), luteinizing hormone (LH), oestradiol (E2), progesterone (P4), superoxide dismutase (SOD), glutamate peroxidase (GSH-Px) and nitric oxide (NO) in the serum of does. These findings provide new insight into the mechanism by which NAC regulates early pregnancy and embryonic development in goats.

A mechanistic investigation of the effect of dispersion phase protein type on the physicochemical stability of water–in–oil emulsions

In this study, effects of two animal–based and two plant–based proteins on the stability of W/O emulsions were evaluated. On physical stability, turbiscan stability index values showed that the trend of protein–added emulsion followed the order: whey protein isolate (WPI) < sodium caseinate (CAS) < pea protein isolation (PPI) < chickpea protein isolation (CPI). On chemical stability, the inhibition of lipid oxidation followed the order: CPI < CAS < WPI < PPI. The particle size, zeta potential, ability to increase emulsion viscosity and interfacial adsorption of proteins affected the emulsion physical stability. Among the effects of chemical stability, antioxidant properties, physical barrier effects and transition metal ion binding capacity were crucial for lipid oxidation. In improving the stability of W/O emulsions, we found great potential of CPI and PPI for the future combined application of both and to improve the stability of W/O emulsions.

Inhibition Molecular Mechanism of the Novel Fungicidal N-(Naphthalen-1-yl) phenazine-1-carboxamide against Rhizoctonia solani

To explore the molecular mechanism through which the novel fungicide N-(naphthalen-1-yl) phenazine-1-carboxamide (NNPCN) inhibits Rhizoctonia solani, we clarified the target and mode of action, explored lead compounds, and developed novel fungicides. Methods: Growth observation, scanning electron microscopy, transmission electron microscopy, transcriptome sequencing technology, quantitative real-time PCR (qRT-PCR), physiological and biochemical determination, and reverse molecular docking technology were used to study the effects of this compound on the microscopic morphology of R. solani. The differentially expressed genes (DEGs), functions, and metabolic pathways were analyzed. The genes displaying significant differences were randomly selected for qRT-PCR verification and confirmed by physiological and biochemical determination to construct their binding mode with key targets. The results showed that the mycelium treated with NNPCN produced a red secretion and exhibited progressive creeping growth. Under a scanning electron microscope, hyphal swelling, uneven thickness, fractures, deformities, and hyphal surface warts increased. Under a transmission electron microscope, the cell wall was separated, the subcellular organelles were disintegrated, and the septum disappeared. Furthermore, there were 6838 DEGs under NNPCN treatment, including 291 significant DEGs, of which 143 were upregulated and 148 downregulated. Ten DEGs were randomly selected for qRT-PCR verification, and the gene expression trend was consistent with the transcriptome sequencing results. Gene Ontology enrichment analysis showed that the DEGs were significantly enriched in cell wall glucan decomposition and metabolism, cell membrane synthesis, metabolism, composition, organic hydroxyl compounds, oxidoreductase activity, and transition metal ion binding. Metabolic pathway enrichment analysis showed that there were 16 significant metabolic pathways, such as steroid biosynthesis and ABC transporters. Further study found that genes, such as the glycosyl hydrolase family 10 domain-containing protein, which is related to glucan catabolic process function as tied to the cell wall, were downregulated. Lipid oxidation, modification, and other genes related to the cell membrane were also downregulated. Secondly, genes related to lipid modification, lipid metabolism processes, integral components of the membrane, and other ABC transporters were downregulated. Fatty-acid oxidation and carbohydrate metabolic processes, which are related to antioxidant and metabolic functions, displayed significant differences in their target genes. Nitrite reductase [NADH] activity and mitochondrial organization gene expression were downregulated. These results revealed that target genes may involved in the cell wall, cell membrane, antioxidant and metabolism, nitrogen metabolism, and mitochondria. The results of the physiological and biochemical tests showed that NNPCN decreased the β-1,3-glucanase, malondialdehyde, and ATPase activities and nucleic acid leakage but increased the activity of nitrate reductase. The results of the reverse molecular docking showed that NNPCN could freely bind to target proteins such as β-1,3-glucanase, ABC transporter, and NADPH nitrate reductase, whereby NNPCN could bind to glucanase via van der Waals and electrostatic forces and to ABC transporter and NADPH nitrate reductase via hydrogen bonding. Conclusion: The mechanism via which NNPCN inhibits R. solani may be related to the cell wall structure, cell membrane damage, antioxidant activity, and metabolism.

Transcriptome and metabolome analysis of stress tolerance to aluminium in Vitis quinquangularis.

Transcriptional and metabolic regulation of aluminium tolerance of Chinese wild Vitis quinquangularis after Al treatment for 12h: genes and pathways related to stress resistance are activated to cope with Al stress. The phytotoxicity of aluminium (Al) has become a major issue in inhibiting plant growth in acidic soils. Chinese wild Vitis species have excellent stress resistance. In this study, to explore the mechanism underlying Al tolerance in Chinese wild Vitis quinquangularis, we conducted a transcriptome analysis to understand the changes in gene expression and pathways in V. quinquangularis leaves after Al treatment for 12h (Al_12h). Compared with the control (CK) treatment, 2266 upregulated differentially expressed genes (DEGs) and 2943 downregulated DEGs were identified after Al treatment. We analysed the top 60 upregulated DEGs and found that these genes were related mostly to cell wall organization or biogenesis, transition metal ion binding, etc. Another analysis of all the upregulated DEGs showed that genes related to the ABC transport pathway, salicylic acid (SA), jasmonic acid (JA) and abscisic acid (ABA) hormone signalling pathway were expressed. Transcriptome and metabolome analysis revealed that genes and metabolites (phenylalanine, cinnamate and quercetin) related to the phenylalanine metabolic pathway were expressed. In summary, the results provide a new contribution to a better understanding of the metabolic changes that occur in grapes after Al stress as well as to research on improving the resistance of grape cultivars.

Melatonin-induced DNA demethylation of metal transporters and antioxidant genes alleviates lead stress in radish plants

Melatonin (MT) is a tryptophan-derived natural product that plays a vital role in plant response to abiotic stresses, including heavy metals (HMs). However, it remains elusive how exogenous MT mediates lead (Pb) accumulation and detoxification at the methylation and transcriptional levels in radish. In this study, decreased Pb accumulation and increased antioxidant enzyme activity were detected under MT treatment in radish. Single-base resolution maps of DNA methylation under Pb stress (Pb200) and Pb plus MT treatment (Pb_50MT) were first generated. The genome-wide methylation level was increased under Pb stress, while an overall loss of DNA methylation was observed under MT treatment. The differentially methylated region (DMR)-associated genes between Pb_50MT and Pb200 were uniquely enriched in ion binding terms, including cation binding, iron ion binding, and transition metal ion binding. Hyper-DMRs between Pb200 and Control exhibited a decreasing trend of methylation under Pb_50MT treatment. A few critical upregulated antioxidant genes (e.g., RsAPX2, RsPOD52 and RsGST) exhibited decreased methylation levels under MT treatment, which enabled the radish plants to scavenge lead-induced reactive oxygen species (ROS) and decrease oxidative stress. Notably, several MT-induced HM transporter genes with low methylation (e.g., RsABCF5, RsYSL7 and RsHMT) and transcription factors (e.g., RsWRKY41 and RsMYB2) were involved in reducing Pb accumulation in radish roots. These findings could facilitate comprehensive elucidation of the molecular mechanism underlying MT-mediated Pb accumulation and detoxification in radish and other root vegetable crops.

Binding of Divalent Transition Metal Ions to Immobilized Phosphinic Acid Ligands. Part I. Characterization by Fourier Transform Infrared Spectroscopy

ABSTRACT This report introduces a multi-part study on determining the fundamental mechanisms by which a range of phosphorus-based ligands bind metal ions. FTIR spectroscopy is utilized to propose the mechanism; in the subsequent paper, density functional theory is applied to interrogate the spectra and identify a definitive mechanism. In this report, we follow the binding of divalent metal ions (Pb(II), Cd(II), Cu(II), Zn(II), Ni(II)) to phosphinic acid immobilized on crosslinked polystyrene. Important issues include identifying the moieties involved in forming the phosphinate – metal bond, and whether metal ion valency affects the outcome. Phosphinic acid has bands at ≈1100 cm−1and 950 cm−1, each subdivided into two bands. Upon binding the metal ion, two new bands appear at ≈1000 cm−1 while only one band in each of the two sets shifts. An affinity sequence of Pb(II) > Cd(II) > Cu(II) > Zn(II) > Ni(II) follows the order of increasing ionic index indicating a dominant ion-exchange mechanism, unlike trivalent ions which follow an order of decreasing polarizability. FTIR spectra confirm that a higher than expected affinity for Cu(II) is due to a coupling of the ion-exchange mechanism to a redox reaction that results in the formation of Cu(0) and conversion of the phosphinic ligand to phosphonic acid, as indicated by a pronounced band at 926 cm−1 which is also present in the spectra of separately prepared phosphonic acid and Cu-loaded phosphonic acid. The behavior of the FTIR bands indicates that the phosphinic acid ligand follows the same mechanism with divalent and trivalent ions. DFT subsequently addresses: the bonds that give the metal phosphinate band, the lack of movement of bands not involved in the metal phosphinate, and hydrogen bonding among ligands.

Fluorogenic aptamers resolve the flexibility of RNA junctions using orientation-dependent FRET.

To further understand the transcriptome, new tools capable of measuring folding, interactions, and localization of RNA are needed. Although Förster resonance energy transfer (FRET) is an angle- and distance-dependent phenomenon, the majority of FRET measurements have been used to report distances, by assuming rotationally averaged donor–acceptor pairs. Angle-dependent FRET measurements have proven challenging for nucleic acids due to the difficulties in incorporating fluorophores rigidly into local substructures in a biocompatible manner. Fluorescence turn-on RNA aptamers are genetically encodable tags that appear to rigidly confine their cognate fluorophores, and thus have the potential to report angular-resolved FRET. Here, we use the fluorescent aptamers Broccoli and Mango-III as donor and acceptor, respectively, to measure the angular dependence of FRET. Joining the two fluorescent aptamers by a helix of variable length allowed systematic rotation of the acceptor fluorophore relative to the donor. FRET oscillated in a sinusoidal manner as a function of helix length, consistent with simulated data generated from models of oriented fluorophores separated by an inflexible helix. Analysis of the orientation dependence of FRET allowed us to demonstrate structural rigidification of the NiCo riboswitch upon transition metal-ion binding. This application of fluorescence turn-on aptamers opens the way to improved structural interpretation of ensemble and single-molecule FRET measurements of RNA.