Protein and Peptide Letters - Volume 32, Issue 9, 2025

Diabetic hyperglycemia is often associated with elevated levels of trimethylamine-N-oxide (TMAO), a gut microbiota-derived metabolite that was recently identified as a risk factor for cardiovascular diseases. The combined presence of hyperglycemia and TMAO can aggravate cardiac dysfunction in diabetic patients. This study aimed to evaluate the protective effects of the methanolic extract of Syzygium aromaticum against the toxic effects induced by TMAO and hyperglycemia in cultured rat cardiomyocytes.

Rat cardiomyocytes, H9C2 were exposed to high glucose and TMAO, individually and in combination to simulate diabetic and dysbiotic stress conditions. Cells were treated with optimized doses of Syzygium aromaticum extract under dual-stress conditions. Cellular and nuclear morphology were assessed microscopically. Oxidative stress markers were evaluated. Proteomic profiling using liquid chromatography-mass spectrometry (LC-MS) was conducted to identify differentially expressed proteins. Crucial targets were identified and functionally annotated using integrated bioinformatics tools and databases. Expression of the critical transcription factor Yin-Yang-1 (YY1) was analysed using quantitative PCR (qPCR).

Dual exposure to TMAO and hyperglycemia resulted in greater morphological and oxidative damage compared to exposure to either individual stressor alone. Treatment with Syzygium aromaticum extract significantly reduced cellular and nuclear damage as well as oxidative stress under dual-stress conditions. Proteomic analysis revealed several differentially expressed proteins, with YY1 identified as a key regulatory factor. qPCR confirmed the suppression of YY1 expression by Syzygium aromaticum treatment.

Our findings suggest that Syzygium aromaticum mitigates cardiomyocyte injury caused by metabolic and microbial stress. Its protective effect may be mediated through antioxidant activity and transcriptional regulation, particularly via the downregulation of YY1, a key player in cardiac stress responses.

Syzygium aromaticum exhibits multifaceted cardioprotective and prebiotic potential by mitigating TMAO and hyperglycemia-induced toxicity, highlighting its therapeutic promise in managing gut dysbiosis linked to diabetic cardiomyopathy.

The present study aims to compare the monotherapy of diosmetin and 5-hydroxydecanoate (5-HD) against the therapeutic effect of their combination therapy in the unilaterally injected rotenone-induced neurotoxicity in the male rats. Motor deficits accompany Parkinson's Disease (PD), while Bioflavonoids like diosmetin, which are antioxidants and anti-inflammatories, protect against neurotoxins. Moreover, mitochondrial dysfunction contributes to PD. The mitochondrial ATP-sensitive potassium channel [mito(KATP)] regulates reactive species and 5-HD, meaning decreasing it may lessen mitochondrial injury. To evaluate the effect of diosmetin, alone and in combination with 5-HD, on Oxidative Stress (OS) markers, mitochondrial function, and dopaminergic preservation in the SNpc.

Male Wistar rats were divided into seven groups, including normal control, sham, rotenone-treated, and treatment groups receiving diosmetin, 5-HD, their combination, or selegiline as a standard drug. Biochemical assays were conducted to assess OS markers, mitochondrial complex-I activity, and dopaminergic neuroprotection. Behavioral tests were performed to evaluate motor deficits.

Rotenone administration significantly increased OS, impaired mitochondrial complex-I activity, and reduced motor coordination. Diosmetin treatment significantly reverses the effects of rotenone. Combined treatment with diosmetin and 5-HD showed enhanced neuroprotective effects compared to individual treatments.

This study demonstrates that both diosmetin and 5-HD monotherapies alleviate rotenone-induced behavioral impairments in the experimental rats. Additionally, the individual treatment of diosmetin and 5-HD reduces dopaminergic toxicity induced by rotenone. At the sub-cellular level, diosmetin and 5-HD monotherapies counteract rotenone’s impact on antioxidant markers, DA metabolites, and mitochondrial function in the SNpc region of the brain. Notably, combining diosmetin and 5-HD yielded superior therapeutic effects on rotenone-induced behavioral and molecular changes compared to either monotherapy alone. These findings suggest that diosmetin and 5-HD may offer a promising alternative for PD management.

Diosmetin exhibits potent antioxidant and neuroprotective properties against rotenone-induced PD-like pathology. The combination of diosmetin and 5-HD offers a synergistic therapeutic potential, suggesting a promising approach for managing oxidative stress and mitochondrial dysfunction in PD.

The skin of amphibians performs some vital roles, such as camouflage, ion and water transport, and gas exchange. Additionally, it plays a significant role in the immune system by preventing pathogen invasion. The secretions produced by the granular glands in the skin possess antimicrobial properties, which help prevent harmful microorganisms from entering the animal's body. The study aims to determine the total protein amounts in the secretion of Pelophylax bedriagae (Levant water frog) distributed in Türkiye and to reveal whether it has antimicrobial properties. In this context, it is a pioneering study on antimicrobial peptides in the skin secretion of Pelophylax.

Field research was carried out at İzmir, Türkiye’s Homeros Valley. Because AMPs are species-specific, not sex-specific peptides, both male and female adults were used, regardless of sex. The average weight of the animals used in the experiment was 21 grams. Granular glands were stimulated using a specialized device, and the secretions were collected for analysis. The collected secretions were lyophilized after centrifugation. Then, the total protein amount in the secretion was determined by Bicinchoninic Acid (BCA). The antibacterial activities of the skin secretions against Escherichia coli and Staphylococcus aureus were assessed using a plate well diffusion assay. The peptide profiles in the skin secretions were determined using the Tricine-SDS-PAGE electrophoresis method.

The plate well diffusion assay demonstrated that the skin secretions created a 21 mm inhibition zone against E. coli and a 20 mm inhibition zone against S. aureus. The results of the Tricine-SDS-PAGE electrophoresis revealed the presence of peptides with five different molecular weights, including one smaller than 5 kDa. As a result of the analysis, it was determined that P. bedriagae secretion exhibits antimicrobial properties, and many proteins with different molecular masses were identified in the skin secretion.

There are no skin secretion studies on P. bedriage in the literature. However, activity studies were also conducted on the skin secretion of another Pelophylax species, P. ridibundus. The study examined the antibacterial activities of the skin secretion against some gram-positive and gram-negative bacteria using a plate well diffusion assay. Their study showed that E. coli formed a 21 mm zone and S. aureus formed a 24 mm zone.

This study is preliminary, and in future studies, AMPs in skin secretions can be isolated by chromatographic methods, such as HPLC, and peptides can be sequenced and identified in detail.

Pleckstrin homology and RhoGEF domain-containing G7 (PLEKHG7) is a largely uncharacterized gene whose role in diffuse large B-cell lymphoma (DLBCL) remains unexplored. Thus, we aimed to profile PLEKHG7 expression, assess its prognostic value, and explore therapeutic implications.

RNA-seq data from TCGA-DLBCL (n=48) and GTEx normal tissues were analyzed via UCSC XENA. Differential expression was tested using the Wilcoxon rank-sum test and FDR correction. Prognostic significance was evaluated by Kaplan–Meier and multivariate Cox regression (nomogram). Gene set enrichment analysis (GSEA) mapped PLEKHG7-associated pathways. Drug sensitivity correlations were extracted from RNAactDrug. qRT-PCR validated expression in DLBCL cell lines (OCI-Ly3, SU-DHL-4) versus normal B lymphocytes (GM12878).

PLEKHG7 was markedly up-regulated in DLBCL tissues (P < 0.001) and cell lines versus normal controls (AUC = 0.739). High PLEKHG7 expression predicted inferior overall survival (HR = 8.88; 95% CI: 1.09–72.27; P = 0.041) and remained an independent prognostic factor (HR = 10.109; P = 0.033). GSEA linked PLEKHG7 to ribosome, oxidative phosphorylation, proteasome, cytokine-cytokine receptor interaction, spliceosome, and ECM-receptor pathways. Elevated PLEKHG7 negatively correlated with sensitivity to idelalisib, omipalisib, belinostat, methotrexate, and dacinostat.

The study's limitations include reliance on bioinformatics data and the lack of functional validation. Further research is needed to elucidate the molecular mechanisms underlying PLEKHG7's role in DLBCL and validate its clinical utility.

PLEKHG7 is significantly overexpressed in DLBCL and independently predicts poor prognosis. Its association with key oncogenic pathways and drug resistance underscores its potential as both a prognostic biomarker and a therapeutic target, warranting further functional validation.

Superoxide Dismutases (SODs) are enzymes that catalyzes the conversion of toxic free radicals generated during stress conditions into nontoxic forms. Thus, the enzyme superoxide dismutase contributes to the adaptation and survival of microorganisms across a variety of environmental conditions, making it an indispensable enzyme during the response to stress. In this study, we embarked upon investigating and characterizing a Superoxide Dismutase (SOD) from DNA extracted directly from garden soil, where the average temperature ranges from 4°C- 45°C.

Metagenomic DNA was extracted by employing a kit. The gene was amplified using PCR. The amplified PCR product was gel eluted and ligated into the pGEMT-easy vector, followed by its subcloning in an expression vector. The protein was purified using Ni-NTA chromatography and characterized using biophysical, biochemical, and computational approaches.

The recombinant SOD was expressed and purified; the purified protein exhibited activity and stability over a broad pH and temperature range, with optimal activity observed at 40°C and pH 8, respectively. The enzyme remains completely stable at 40°C for 3 h. However, in contrast, it loses 50% of its activity when incubated at 50°C and 60°C for 3 h. The biophysical investigation revealed stable conformation of the secondary structure of the protein, as evident from circular dichroism and intrinsic Tryptophan (Trp) fluorescence studies. In silico sequence and structural analysis revealed a close similarity of the SOD reported in this study to the Mn SOD of multi-Bacillus species. Molecular simulation dynamics experiments revealed the all-over conformational stability of protein structures at varying pH, indicating broad pH functioning of the enzyme.

The study provides a comprehensive analysis of the structure and function of a superoxide dismutase enzyme derived from a soil metagenome. A Mn²⁺ binding site identified in the study offers an opportunity to further facilitate engineering and design of mutant SOD.

The enzyme exhibits distinct attributes that hold significant industrial relevance. Owing to the wide functionality of SOD at different pH and temperature, it can be tailored for its potential industrial applications, including therapeutic potential, thus opening new avenues for enhanced antioxidant therapies and novel biocatalyst designing.

Numerous X-ray crystal structures of the c-Src SH3 domain have provided a large sampling of atomic-level information for this important signaling domain. Multiple crystal forms have been reported, with variable crystal lattice contacts and chemical crystallization conditions.

We crystallized the c-Src SH3 domain in a crystallization buffer containing NiCl2.

A unique crystal structure of the Src SH3 domain in the trigonal space group H32 is determined to 1.45 Å resolution. Crystal packing and anomalous scattering reveal that this crystal form is mediated by two ordered nickel ions provided by the crystallization buffer. Nickel coordination occurs in a 2:2 stoichiometry, which dimerizes two SH3 domain monomers across a pseudo-twofold rotation axis and involves the native N-terminal c-Src SH3 amino acid sequence, a surface-exposed histidine residue, and ordered water molecules.

This study provides an example of metal-mediated crystallization and metal binding by N-terminal protein residues, contrasting with the Amino-Terminal Copper and Nickel Binding (ATCUN) motif.

Alternative avenues help widen the potential for future crystallography-based studies of the c-Src SH3 domain.