Proteomic Analysis of the Protein Expression Profile in the Mature <Emphasis Type="Italic">Nigella sativa</Emphasis> (Black Seed)

Nigella sativa (N. sativa) seed has been used as an important nutritional flavoring agent and in traditional medicine for treating many illnesses since ancient times. Understanding the proteomic component of the seed may lead to enhance the understanding of its structural and biological functional complexity. In this study, we have analyzed its proteome profile based on gel-based proteome mapping technique that includes one-dimensional gel electrophoresis followed by liquid chromatography and tandem mass spectrometry strategy. We have not come across any such studies that have been performed in N. sativa seeds up to date. A total of 277 proteins were identified, and their functional, metabolic, and location-wise annotations were carried out using the UniProt database. The majority of proteins identified in the proteome dataset based on their function were those involved in enzyme catalytic activity, nucleotide binding, and protein binding while the major cellular processes included regulation of biological process followed by regulation of secondary biological process, cell organization and biogenesis, protein metabolism, and transport. The identified proteome was localized mainly to the nucleus then to the cytoplasm, plasma membrane, mitochondria, plastid, and others. A majority of the proteins were involved in biochemical pathways involving carbohydrate metabolism, amino acid and shikimate pathway, lipid metabolism, nucleotide, cell organization and biogenesis, transport, and defense processes. The identified proteins in the dataset help to improve our understanding of the pathways involved in N. sativa seed metabolism and its biochemical features and detail out useful information that may help to utilize these proteins. This study could thus pave a way for future further high-throughput studies using a more targeted proteomic approach.     

Biochemical reactions in metabolite-protein interaction

An update on the recently developed chemical proteomics called activity-based protein profiling (ABPP) has been reviewed. ABPP is able to identify proteins interacted either covalently or non-covalently with metabolites significantly, which will facilitate the characterization of specific metabolite regulating proteins in human disease progression.     

AtTrxh3, a Thioredoxin,Is Identified as an Abscisic AcidBinding Protein in Arabidopsis thaliana

Abscisic acid (ABA, 1) is a plant hormone that regulates various plant physiological processes such as seed developing and stress responses. The ABA signaling system has been elucidated; binding of ABA with PYL proteins triggers ABA signaling. We have previously reported a new method to isolate a protein targeted with a bioactive small molecule using a biotin linker with alkyne and amino groups, a protein cross-linker, and a bioactive small molecule with an azido group (azido probe). This method was used to identify the unknown ABA binding protein of Arabidopsis thaliana. As a result, AtTrxh3, a thioredoxin, was isolated as an ABA binding protein. Our developed method can be applied to the identification of binding proteins of bioactive compounds.     

Synthesis and Characterization of <Emphasis Type="Italic">Sygyzium cumini</Emphasis> Nanoparticles for Its Protective Potential in High Glucose-Induced Cardiac Stress: a Green Approach

There exists a complex and multifactorial relationship between diabetes and cardiovascular disease. Hyperglycemia is an important factor imposing damage (glucose toxicity) on cardiac cell leading to diabetic cardiomyopathy. There are substantial clinical evidences on the adverse effects of conventional therapies in the prevention/treatment of diabetic cardiovascular complications. Currently, green-synthesized nanoparticles have emerged as a safe, efficient, and inexpensive alternative for therapeutic uses. The present study discloses the silver nanoparticle biosynthesizing capability and cardioprotective potential of Syzygium cumini seeds already reported to have antidiabetic properties. Newly generated silver nanoparticles S. cumini MSE silver nanoparticles (SmSNPs) were characterized by UV-visible spectroscopy, scanning electron microscopy (SEM), zeta sizer, X-ray diffraction (XRD), and Fourier transform infrared (FTIR) spectroscopy. Using methanolic extract of S. cumini seeds, an average size of 40–100-nm nanoparticles with 43.02 nm and ?19.6 mV zeta potential were synthesized. The crystalline nature of SmSNPs was identified by using XRD. 2,2-Diphenyl-1-picrylhydrazyl (DPPH) and 2,2′-azino-bis(3-ethylbenzthiazoline-6-sulfonic acid (ABTS) assays revealed the antioxidative potential to be 66.87 (±0.7) % and 86.07 (±0.92) % compared to 60.29 (±0.02) % and 85.67 (±1.27) % for S. cumini MSE. In vitro study on glucose-stressed H9C2 cardiac cells showed restoration in cell size, nuclear morphology, and lipid peroxide formation upon treatment of SmSNPs. Our findings concluded that S. cumini MSE SmSNPs significantly suppress the glucose-induced cardiac stress in vitro by maintaining the cellular integrity and reducing the oxidative damages therefore establishing its therapeutic potential in diabetic cardiomyopathy.     

Integrating Pharmacological and Computational Approaches for the Phytochemical Analysis of Syzygium cumini and Its Anti-Diabetic Potential

Diabetes mellitus (DM) is a metabolic disease caused by improper insulin secretion leading to hyperglycemia. Syzygium cumini has excellent therapeutic properties due to its high levels of phytochemicals. The current research aimed to evaluate the anti-diabetic potential of S. cumini plant’s seeds and the top two phytochemicals (kaempferol and gallic acid) were selected for further analysis. These phytochemicals were selected via computational tools and evaluated for α-Glucosidase inhibitory activity via enzymatic assay. Gallic acid (IC₅₀ 0.37 µM) and kaempferol (IC₅₀ 0.87 µM) have shown a stronger α-glucosidase inhibitory capacity than acarbose (5.26 µM). In addition, these phytochemicals demonstrated the highest binding energy, hydrogen bonding, protein–ligand interaction and the best MD simulation results at 100 ns compared to acarbose. Furthermore, the ADMET properties of gallic acid and kaempferol also fulfilled the safety criteria. Thus, it was concluded that S. cumini could potentially be used to treat DM. The potential bioactive molecules identified in this study (kaempferol and gallic acid) may be used as lead drugs against diabetes.     

Spatial regulation of a common precursor from two distinct genes generates metabolite diversity

In secondary metabolite biosynthesis, core synthetic genes such as polyketide synthase genes usually encode proteins that generate various backbone precursors. These precursors are modified by other tailoring enzymes to yield a large variety of different secondary metabolites. The number of core synthesis genes in a given species correlates, therefore, with the number of types of secondary metabolites the organism can produce. In our study, heterologous expression of all the A. terreus NRPS-like genes showed that two NRPS-like proteins, encoded by atmelA and apvA, release the same natural product, aspulvinone E. In hyphae this compound is converted to aspulvinones whereas in conidia it is converted to melanin. The genes are expressed in different tissues and this spatial control is probably regulated by their own specific promoters. Comparative genomics indicates that atmelA and apvA might share a same ancestral gene and the gene apvA is located in a highly conserved region in Aspergillus species that contains genes coding for life-essential proteins. Our data reveal the first case in secondary metabolite biosynthesis in which the tissue specific production of a single compound directs it into two separate pathways, producing distinct compounds with different functions. Our data also reveal that a single trans-prenyltransferase, AbpB, prenylates two substrates, aspulvinones and butyrolactones, revealing that genes outside of contiguous secondary metabolism gene clusters can modify more than one compound thereby expanding metabolite diversity. Our study raises the possibility of incorporation of spatial, cell-type specificity in expression of secondary metabolites of biological interest and provides new insight into designing and reconstituting their biosynthetic pathways.     

GC/MS Analysis of Essential Oil and Enzyme Inhibitory Activities of Syzygium cumini (Pamposia) Grown in Egypt: Chemical Characterization and Molecular Docking Studies

Syzygium cumini (Pomposia) is a well-known aromatic plant belonging to the family Myrtaceae, and has been reported for its various traditional and pharmacological potentials, such as its antioxidant, antimicrobial, anti-inflammatory, and antidiarrheal properties. The chemical composition of the leaf essential oil via gas chromatography–mass spectrometry (GC/MS) analysis revealed the identification of fifty-three compounds representing about 91.22% of the total oil. The identified oil was predominated by α-pinene (21.09%), followed by β-(E)-ocimene (11.80%), D-limonene (8.08%), β-pinene (7.33%), and α-terpineol (5.38%). The tested oil revealed a moderate cytotoxic effect against human liver cancer cells (HepG2) with an IC₅₀ value of 38.15 ± 2.09 µg/mL. In addition, it effectively inhibited acetylcholinesterase with an IC₅₀ value of 32.9 ± 2.1 µg/mL. Furthermore, it showed inhibitory properties against α-amylase and α-glucosidase with IC₅₀ values of 57.80 ± 3.30 and 274.03 ± 12.37 µg/mL, respectively. The molecular docking studies revealed that (E)-β-caryophyllene, one of the major compounds, achieved the best docking scores of −6.75, −5.61, and −7.75 for acetylcholinesterase, α-amylase, and α-glucosidase, respectively. Thus, it is concluded that S. cumini oil should be considered as a food supplement for the elderly to enhance memory performance and for diabetic patients to control blood glucose.     

Global profiling of ultraviolet-induced metabolic disruption in Melissa officinalis by using gas chromatography-mass spectrometry

Melissa officinalis contains various secondary metabolites that have health benefits. Generally, irradiating plants with ultraviolet (UV)-B induces the accumulation of secondary metabolites in plants. To understand the effect of UV-B irradiation on the metabolism of M. officinalis, metabolomics based on gas chromatography-mass spectrometry (GC-MS) was used in this study. The GC-MS analysis revealed 37 identified metabolites from various chemical classes, including alcohols, amino acids, inorganic acids, organic acids, and sugars. The metabolite profiles of the groups of M. officinalis irradiated with UV-B were separated and differentiated according to their irradiation times (i.e., 0, 1, and 2 h), using principal component analysis (PCA) and hierarchical clustering analysis (HCA), respectively. The PCA score plots of PC1 and PC2 showed that the three groups with different irradiation times followed a certain trajectory with increasing UV-B irradiation. HCA revealed that metabolic patterns differed among the three groups, and the 1 h-irradiated group was more similar to the control group (0 h) than the 2 h-irradiated group. In particular, UV-B irradiation of plants led to a decrease in sugars such as fructose, galactose, sucrose, and trehalose and an increase in metabolites in the tricarboxylic acid cycle, the proline-linked pentose phosphate pathway, and the phenylpropanoid pathway. This study demonstrated that metabolite profiling with GC-MS is useful for gaining a holistic understanding of UV-induced changes in plant metabolism.     

Extraction and chemical investigation of Kulthi (Macrotylona uniflorus,Lam.) seed protein

Studies have been carried out on the protein solubility profile of Kulthi (Macrotylona uniflorus, Lam.) seed in aqueous solution over various pHs and at different concentrations of NaCl, Na₂SO₃, CaCl₂, and MgCl₂ at pH 8.0. Amino acid analysis of isolated protein identified 17 amino acids, 9 of which are essential. Gel-permeation chromatography on Sephadex G-200 revealed the presence of seven components in the protein fraction. Their molecular weights were determined by two comparable standard methods. Extractable Kulthi seed proteins in salt solutions were separated electrophoretically into eight fractions whose molecular weights were found to be 186,200, 131,800, 108,400, 91,200, 53,700, 44,700, 38,000, and 27,500.     

Insights into structure and function of 30S Ribosomal Protein S2 (30S2) in Chlamydophila pneumoniae: A potent target of pneumonia

The gene 30S ribosomal protein S2 (30S2) is identified as a potential drug and vaccine target for Pneumonia. Its structural characterization is an important to understand the mechanism of action for identifying its receptor and/or other binding partners. The comparative genomics and proteomics studies are useful for structural characterization of 30S2 in C. Pneumoniae using different bioinformatics tools and web servers. In this study, the protein 30S2 structure was modelled and validated by Ramachandran plot. It is found that the modelled protein under most favoured “core” region was 88.7% and overall G-factor statistics with average score was −0.20. However, seven sequential motifs have been identified for 30S2 with reference codes (PR0095, PF0038, TIGR01012, PTHR11489, SSF52313 and PTHR11489). In addition, seven structural highly conserved residues have been identified in the large cleft are Lys160, Gly161and Arg162 with volume 1288.83 Å³ and average depth of the cleft was 10.75 Å. Moreover, biological functions, biochemical process and structural constituents of ribosome are also explored. The study will be helped us to understand the sequential, structural, functional and evolutionary clues of unknown proteins available in C. Pneumoniae.     

Anti-Alzheimer,antidiabetic and antioxidant potential of Satureja cuneifolia and analysis of its phenolic contents by LC-MS/MS

Many chronic diseases such as diabetes and Alzheimer’s disease are related to the type and quality of foods, which are consumed. Particularly, various plant origin products are stated as beneficial against such kind of chronic diseases with secondary metabolites such as their phenolic structures. Satureja cuneifolia is a plant, which is consumed as an herbal tea in some regions of Turkey and that’s why investigate of its biological activity is important. In our study, the anti-diabetic and anti-Alzheimer potentials of the methanol and water extracts of S. cuneifolia plant were measured via some enzymes inhibition experiments as in vitro. The antioxidant ability of the same extracts was measured via radical scavenging and reducing power methods. Also, the total phenolics and flavonoids of the plant were identified. Finally, the extracts were analyzed by the LC-MS/MS analysis and the phenolic content of S. cuneifolia was clarified.     

Synergistic Effects of Drought Stress and Photoperiods on Phenology and Secondary Metabolism of Silybum marianum

Silybum marianum is an important medicinal plant of the family Asteraceae, well known for its set of bioactive isomeric mixture of secondary metabolites “silymarin”, primarily acting as a hepato-protective agent. Abiotic stress augments plant secondary metabolism in different plant tissues to withstand harsh environmental fluctuations. In the current study, our aim was to induce drought stress in vitro on S. marianum under the influence of different photoperiod treatments to study the effects, with respect to variations in secondary metabolic profile and plant growth and development. S. marianum was extremely vulnerable to different levels of mannitol-induced drought stress. Water deficiency inhibited root induction completely and retarded plant growth was observed; however, phytochemical analysis revealed enhanced accumulation of total phenolic content (TPC), total flavonoid content (TFC), and total protein content along with several antioxidative enzymes. Secondary metabolic content was positively regulated with increasing degree of drought stress. A dependent correlation of seed germination frequency at mild drought stress and antioxidative activities was established with 2 weeks dark?+?2 weeks 16/8 h photoperiod treatment, respectively, whereas a positive correlation existed for TPC and TFC when 4 weeks 16/8 h photoperiod treatment was applied. The effects of drought stress are discussed in relation to phenology, seed germination frequency, biomass build up, antioxidative potential, and secondary metabolites accumulation.     

Thiophilic interaction chromatography of mammalian and avian transferrins

Transferrins are a class of iron-binding proteins widely distributed in biological fluids. All transferrins possess two metal binding sites, each of which can bind a ferric iron. Transferrins play a major role in plasma iron transport and have anti-bacterial, anti-inflammatory, and immunological functions. Lactoferrin is an iron-binding bilobal protein of the transferrin family found in neutrophilic leukocytes and external secretion of mammals. In an earlier communication, we have shown that both human serum transferrin and lactoferrin bind to 3S-gel. Ovotransferrin, the major egg-white protein, is an avian transferrin. In this paper, the details of the binding of mammalian and avian transferrins to 2S gel is presented. Both, apo and holo ovotransferrin, bind to 2S T-gel. Holo and apo lactoferrin from other mammalian species such as cow, rabbit, dog, mouse, and rat bind to T-gel.     

Comprehensive profiling of lysine acetylome in Staphylococcus aureus

The Gram-positive bacterium Staphylococcus aureus(S.aureus)is a wide spread common opportunistic pathogen that causes a wide variety of infectious diseases,from benign skin infections to life-threatening diseases such as the methicillin-resistant Staphylococcus aureus(MRSA)infection.Although emerging evidence suggests that lysine acetylation may play critical roles in bacterial physiology,the atlas of acetylome in S.aureus has not been studied.To comprehensively profile protein lysine acetylation in S.aureus,we used an integrated approach that combined immune affinity peptide enrichment using anti-lysine acetylation antibody,high-pH HPLC fractionation,and HPLC/mass spectrometry analysis.This study led to the identification of 1361 non-redundant acetylation sites on 412 proteins found in a search of S.aureus protein database extracted from the Swiss-Prot database.We further performed bioinformatic analysis to characterize this modification,including gene ontology annotation,protein-protein interaction,and domain analysis of the acetylation sites.We found that the acetylated proteins were enriched in multiple biological pathways,such as ribosomal function and energy metabolism.Our data provides a rich source for functional studies of lysine acetylation in S.aureus.     

Protein C-Mannosylation and C-Mannosyl Tryptophan in Chemical Biology and Medicine

C-Mannosylation is a post-translational modification of proteins in the endoplasmic reticulum. Monomeric α-mannose is attached to specific Trp residues at the first Trp in the Trp-x-x-Trp/Cys (W-x-x-W/C) motif of substrate proteins, by the action of C-mannosyltransferases, DPY19-related gene products. The acceptor substrate proteins are included in the thrombospondin type I repeat (TSR) superfamily, cytokine receptor type I family, and others. Previous studies demonstrated that C-mannosylation plays critical roles in the folding, sorting, and/or secretion of substrate proteins. A C-mannosylation-defective gene mutation was identified in humans as the disease-associated variant affecting a C-mannosylation motif of W-x-x-W of ADAMTSL1, which suggests the involvement of defects in protein C-mannosylation in human diseases such as developmental glaucoma, myopia, and/or retinal defects. On the other hand, monomeric C-mannosyl Trp (C-Man-Trp), a deduced degradation product of C-mannosylated proteins, occurs in cells and extracellular fluids. Several studies showed that the level of C-Man-Trp is upregulated in blood of patients with renal dysfunction, suggesting that the metabolism of C-Man-Trp may be involved in human kidney diseases. Together, protein C-mannosylation is considered to play important roles in the biosynthesis and functions of substrate proteins, and the altered regulation of protein C-manosylation may be involved in the pathophysiology of human diseases. In this review, we consider the biochemical and biomedical knowledge of protein C-mannosylation and C-Man-Trp, and introduce recent studies concerning their significance in biology and medicine.     

Analysis of bioaccessible concentration of trace elements in plant based edible materials by INAA and ICPMS methods

The total metal concentration and bioaccessible concentration of Cr, Mn, Fe, Cu, Zn, Se in Momordica charantia, Asparagus racemosus, Terminalia arjuna and Syzyzium cumini were measured by instrumental neutron activation analysis and by inductively coupled plasma mass spectrometry analysis (ICP-MS). The bioaccessible concentrations were determined in the gastrointestinal digest obtained after treating dried powdered samples sequentially in gastric and intestinal fluid of porcine origin at physiological conditions. The bioaccessible concentration of Fe was in the range of 58–67 mg kg^?1, Mn was 10.2–14.6 mg kg^?1, Cu was 3.7–4.8 mg kg^?1 and Zn was 10.6–18.4 mg kg^?1, were within the safety limits set for vegetable food stuff set by Joint FAO/WHO. The bioaccessibility of Zn, an essential element, was high (40–50 %) in M. charantia and in S. cumini. In addition, the total metal contents and bioaccessible concentration of Ni, Se, Cd and Pb in these samples were measured by ICP-MS. The total Cd content in S. cumini (2.6 ± 0.2 mg kg^?1) and its bioaccessible concentration (0.6 mg kg^?1) were strikingly high as compared to the other samples. Though total Hg contents were determined by ICP-MS, but their bioaccessible concentrations were below the detection limit (0.036 mg kg^?1).