Search Results (62)

Background/Objectives: Methicillin-resistant Staphylococcus aureus (MRSA) poses a significant global health threat due to its increasing resistance to conventional antibiotics. Antimicrobial peptides (AMPs) derived from natural sources represent a promising alternative. Fragments of spider membrane-active toxins can serve as AMPs with anti-MRSA activity. Methods: To demonstrate this, amino acid sequences of approximately 2000 linear spider venom peptides were fragmented into 9–22-residue-long moieties (75,235 in total) and pre-trained neural networks were used to predict their anti-MRSA activity. As many as 15 peptides with high predicted activity were synthesized, and three AMPs with high anti-MRSA and low hemolytic activities were selected. One of these peptides was studied using high-resolution ¹H-, ¹³C-, and ¹⁵N-NMR spectroscopy in an aqueous solution and lyso-palmitoylphosphatidylglycerol (LPPG) micelles. Wide-line ³¹P-NMR was applied to multilamellar phospholipid liposomes composed of phosphatidylcholine (PC) or phosphatidylglycerol (PG). Results: Low hemolytic activity is explained by non-specific interaction with PC whereas high antibacterial activity arises from specific interaction with PG accompanied with the formation of a tight complex between the N-terminal tripeptide fragment and PG headgroup. The structure of a such complex, stabilized by an ionic interaction between the N-terminal NH₃⁺ group and the lipid phosphate, was determined based on peptide–LPPG NOEs. The most favorable ratio between anti-MRSA and hemolytic activities, i.e., selectivity of the peptides, is attained when the tripeptide consists exclusively of phenylalanine and tryptophan residues. Confocal microscopy confirmed that the most selective peptide deteriorates the plasma membrane of S. aureus. Conclusions: This approach may enable the production of highly selective AMPs against Stapylococci, including MRSA. Full article

Nitrogen is an essential element required for bacterial homeostasis. It serves as a building block for the biosynthesis of macromolecules and provides precursors for secondary metabolites. Actinomycetes have developed the ability to use various nitrogen sources to ensure their survival in ecological niches with fluctuating nutrient availability. A complex nitrogen metabolism of Actinobacteria allows the utilization of various compounds as N sources, including ammonium, nitrate, urea, amino acids, amino sugars, and amines. One such adaptation is the ability to acquire nitrogen from alternative amine sources like monoamines or polyamines putrescine, cadaverine, spermidine, and spermine, ensuring both nutrient availability (C and N sources) and resistance against high polyamine concentrations. Actinobacterial nitrogen degradation, including the catabolism of amines, is not only important under low nitrogen availability, but also required to survive under high concentrations of these compounds. The purpose of this review is to summarize the knowledge on nitrogen degradation and, more specifically, catabolism of amines in Actinobacterial survival and its role in nitrogen metabolism. Applying critical analysis of the recent available literature and sequencing data, this work aims to explore strategies of pathogenic and non-pathogenic Actinobacteria to survive in the presence of different nitrogen sources, and their impact on primary and secondary metabolism. The knowledge about nitrogen degradation pathways in Actinobacteria including mono- and polyamine catabolism collected in the scope of this review paper is brought in connection with possibilities to combat pathogens by using their capability to metabolize polyamines as an antibiotic drug target. This might offer new directions for target-based drug design to combat Actinobacterial infections. Full article

Low-complexity domains (LCDs) are protein regions characterized by a simple amino acid composition and low sequence complexity, as they are typically composed of repeats or a limited set of a few amino acids. Historically dismissed as “garbage sequences”, these regions are now acknowledged as critical functional elements. This review systematically explores the structural characteristics, biological functions, pathological roles, and research methodologies associated with LCDs. Structurally, LCDs are marked by intrinsic disorder and conformational dynamics, with their amino acid composition (e.g., G/Y-rich, Q-rich, S/R-rich, P-rich) dictating structural tendencies (e.g., β-sheet formation, phase separation ability). Functionally, LCDs mediate protein–protein interactions, drive liquid–liquid phase separation (LLPS) to form biomolecular condensates, and play roles in signal transduction, transcriptional regulation, cytoskeletal organization, and nuclear pore transportation. Pathologically, LCD dysfunction—such as aberrant phase separation or aggregation—is implicated in neurodegenerative diseases (e.g., ALS, AD), cancer (e.g., Ewing sarcoma), and prion diseases. We also summarize the methodological advances in LCD research, including biochemical (CD, NMR), structural (cryo-EM, HDX-MS), cellular (fluorescence microscopy), and computational (MD simulations, AI prediction) approaches. Finally, we highlight current challenges (e.g., structural heterogeneity, causal ambiguity of phase separation) and future directions (e.g., single-molecule techniques, AI-driven LCD design, targeted therapies). This review provides a comprehensive perspective on LCDs, illuminating their pivotal roles in cellular physiology and disease, and offering insights for future research and therapeutic development. Full article

Intrinsically disordered regions (IDRs) are sometimes considered parts of the ‘dark proteomes’, i.e., protein parts that have been largely under-appreciated, as are the overlapping phenomena of low-complexity or compositionally biased regions (LCRs/CBRs). Experimentalists and computationalists alike are still learning how to decrypt the functionally meaningful features of such regions. Here, I report the creation of the support troupe Patterny to aid such protein cryptanalysis. The current troupe members are named Blocky, Bandy, Moduley, Repeaty, and Runny. To discern important features, protein regions are compared to ideal assortments wherein everything is sampled proportionally and dispersed randomly. Blocky discerns the segregation of amino-acids by type, and scores them for it. Bandy is focused on picking out compositional bands and calculating their evenness. Moduley labels the boundaries of optimized compositional modules (‘CModules’) and other possible boundary sets for compositionally biased regions. Repeaty concisely summarizes repetitiveness using an information entropy of amino-acid interval diversity. Runny enumerates homopeptide content and assesses its significance. Both original whole sequences and CModules from Moduley, are fed into the other Patterny members. Patterny is applied to some illustrative sample data from yeast proteome and the DISPROT database. It is available at Github, and might aid those aiming to intensify light-shedding and hypothesis generation for protein regions with function encoded in a distributed manner, such as IDRs and LCRs/CBRs more generally. Full article

Background/Objectives: Syphilis, a chronic sexually transmitted disease caused by the spirochete Treponema pallidum subspecies pallidum (T. pallidum), is still endemic in low- and middle-income countries and has been resurgent for decades in many high-income nations despite being treatable. Improving our understanding of syphilis pathogenesis, immunology, and T. pallidum biology could result in novel measures to curtail syphilis spread, including new therapeutics, a preventive vaccine, and, most importantly, improved diagnostics. Methods: Using overlapping synthetic peptides spanning the length of the T. pallidum Tp0435 mature lipoprotein, an abundant antigen known to induce an immunodominant humoral response during both natural and experimental infection, we evaluated which Tp0435 linear epitopes are most significantly recognized by antibodies from an infected host. Specifically, we used sera from 63 patients with syphilis at different stages, sera from non-syphilis patients (n = 40), and sera longitudinally collected from 10 rabbits infected with either the Nichols or SS14 isolates of T. pallidum, which represent the model strains for the two known circulating clades of this pathogen, to further evaluate the use of this animal model for syphilis studies. Recognized amino acid sequences were then mapped to the experimentally determined Tp0435 structure. Results: Reactive epitopes in both serum groups mapped predominantly to the α-helix preceding Tp0435 soluble β-barrel and the loops of the barrel. Conclusions: In the current effort to improve current syphilis diagnostics, the peptides corresponding to these immunodominant epitopes could help develop epitope-based assays such as peptide-based ELISAs and lateral flow point-of-care tests to improve the performance of treponemal tests and expedite diagnosis in low-income settings, where the infection is still a significant concern for public health and access to facilities with laboratories equipped to perform complex procedures might be challenging. Full article

Infectious bronchitis virus (IBV) of the GI-23 lineage, which first emerged in the Middle East in the late 1990s, has since spread worldwide. The factors driving its expansion, whether human involvement, wild bird migration, or the virus’s biological traits, are still unclear. This study aimed to trace the genome evolution of GI-23 IBV in chickens and its adaptability to quails, which are susceptible to both gamma- and deltacoronaviruses. Thirty specific-pathogen-free (SPF) birds, aged between two and three weeks, were used. Initially, three birds were inoculated with the G052/2016 IBV via the oculo-nasal route. On the third day post-infection (dpi), oropharyngeal swabs were collected from the whole group, pooled, and subsequently used to infect three next birds. This process was repeated nine more times during consecutive IBV passages (P-I–P-X), and eventually, virus sequencing was performed using Next-Generation Sequencing (NGS). The obtained results showed that quails were not susceptible to the IBV GI-23 lineage, as the virus RNA was detected in low amounts only during the first passage (QP-I) with no further detections in later rounds of IBV passaging. In chickens, only mild diarrhea symptoms appeared in a few individuals. The NGS analysis identified sixty-two single nucleotide variants (SNVs), thirty of which caused amino acid changes, twenty-eight were synonymous, and one SNV introduced a stop codon. Three SNVs were found in untranslated regions. However, none of these SNVs lasted beyond seven passages, with forty-four being unique SNVs. The Shannon entropy values measured during passages varied for pol1a, pol1b, S, 5a, 5b, and N genes, with overall genome complexity peaking at CP-VI and CP-X. The highest complexity was observed in the pol1a (CP-X) and S genes (CP-IV, CP-VI, CP-VIII, and CP-X). Along with the S gene that was under positive selection, eight codons in pol1a were also positively selected. These findings suggest that even in an adapted host, IBV variability does not stabilize without immune pressure, indicating continuous molecular changes within its genome. Full article

Antarctic microorganisms have genomic characteristics and biological functions to ensure survival in complex habitats, potentially representing bioactive compounds of biotechnological interest. Pseudarthrobacter sp. So.54 is an Antarctic bacteria strain isolated from the rhizospheric soil of Colobanthus quitensis. Our work aimed to study its genomic characteristics and metabolic potential, linked to environmental adaptation and the production of secondary metabolites with possible biotechnological applications. Whole-genome sequencing, assembly, phylogenetic analysis, functional annotation, and genomic islands prediction were performed to determine the taxonomic affiliation and differential characteristics of the strain So.54. Additionally, Biosynthetic Gene Clusters (BGCs) responsible for secondary metabolites production were identified. The assembled genome of strain So.54 has 3,871,805 bp with 66.0% G + C content. Phylogenetic analysis confirmed that strain So.54 belongs to the Pseudarthrobacter genus; nevertheless, its nucleotide and amino acid identity values were below the species threshold. The main metabolic pathways and 64 genomic islands associated with stress defense and environmental adaptation, such as heavy metal resistance genes, were identified. AntiSMASH analysis predicted six BGCs with low or no similarity to known clusters, suggesting potential as novel natural products. These findings indicate that strain So.54 could be a novel Pseudarthrobacter species with significant environmental adaptation and biotechnological potential. Full article

Bioactive peptides, composed of amino acid chains, are fundamental to a wide range of biological functions. Their inherent multifunctionality, however, complicates accurate classification and prediction. To address these challenges, we present MFP-MFL, an advanced multi-feature, multi-label learning framework that integrates Graph Attention Networks (GAT) with leading protein language models, including ESM-2, ProtT5, and RoBERTa. By employing an ensemble learning strategy, MFP-MFL effectively utilizes deep sequence features and complex functional dependencies, ensuring highly accurate and robust predictions of multifunctional peptides. Comparative experiments demonstrate that MFP-MFL achieves precision, coverage, and accuracy scores of 0.799, 0.821, and 0.786, respectively. Additionally, it attains an Absolute true of 0.737 while maintaining a low Absolute false of 0.086. A comprehensive case study involving 86,970 mutations further highlights the model’s ability to predict functional changes resulting from sequence variations. These results establish MFP-MFL as a powerful tool for the discovery and application of multifunctional peptides, offering significant potential to advance research and biomedical applications. Full article

Wound healing incurs various challenges, making it an important topic in medicine. Short-chain peptides from fish protein hydrolysates possess wound healing properties that may represent a solution. In this study, perch hydrolysates were produced from perch side steams using a designed commercial complex enzyme via a proprietary pressure extraction technique. The average molecular weight of the perch peptides was 1289 kDa, and 62.60% of the peptides had a low molecular weight (≤1 kDa). Similarly to the beneficial amino acid sequence FPSIVGRP, FPSLVRGP accounted for 6.21% abundance may have a potential antihypertensive effect. The concentrations of collagen composition and branched-chain amino acids were 1183 and 1122 mg/100 g, respectively. In a fibroblast model, active perch peptides accelerated wound healing mainly by increasing the secretion of procollagen I, fibronectin, and hyaluronan. In an SD rat model established to mimic human wounds, orally administered perch hydrolysates with a molecular weight below 2.3 kDa accelerated wound healing, which mainly resulted from collagen-forming amino acids, branched-chain amino acids, and matrikine. Collectively, the residue of perch extract can be upcycled via a hydrolysis technique to produce not only bioactive sequences but also short-chain peptides. Considering the therapeutic potential to promote wound healing, such by-products are of great value and may be developed as dietary nutraceuticals. Full article

Enzyme-mediated protein degradation is a major concern in industrial fungal strain improvement, making low-proteolytic strains preferable for enhanced protein production. Here, we improved food-grade Aspergillus oryzae BCC7051 by manipulating the transcriptional regulation of protease-encoding genes. Genome mining of the transcription factor AoprtR and computational analysis confirmed its deduced amino acid sequence sharing evolutionary conservation across Aspergillus and Penicillium spp. The AoPrtR protein, which is classified into the Zn(II)2-Cys6-type transcription factor family, manipulates both intra- and extracellular proteolytic enzymes. Our transcriptional analysis indicated that the regulation of several protease-encoding genes was AoPrtR-dependent, with AoPrtR acting as a potent activator for extracellular acid-protease-encoding genes and a likely repressor for intracellular non-acid-protease-encoding genes. An indirect regulatory mechanism independent of PrtR may enhance proteolysis. Moreover, AoPrtR disruption increased extracellular esterase production by 2.55-fold, emphasizing its role in protein secretion. Our findings highlight the complexity of AoPrtR-mediated regulation by A. oryzae. Manipulation of regulatory processes through AoPrtR prevents secreted protein degradation and enhances the quantity of extracellular proteins, suggesting the low-proteolytic variant as a promising platform for the production of these proteins. This modified strain has biotechnological potential for further refinement and sustainable production of bio-based products in the food, feed, and nutraceutical industries. Full article

Maize (Zea mays L.) is highly sensitive to temperature during its growth and development stage. A 1 °C drop in temperature can delay maturity by 10 days, resulting in a yield reduction of over 10%. Low-temperature tolerance in maize is a complex quantitative trait, and different germplasms exhibit significant differences in their responses to low-temperature stress. To explore the differences in gene expression and metabolites between B144 (tolerant) and Q319 (susceptible) during germination under low-temperature stress and to identify key genes and metabolites that respond to this stress, high-throughput transcriptome sequencing was performed on the leaves of B144 and Q319 subjected to low-temperature stress for 24 h and their respective controls using Illumina HiSeq^TM 4000 high-throughput sequencing technology. Additionally, high-throughput metabolite sequencing was conducted on the samples using widely targeted metabolome sequencing technology. The results indicated that low-temperature stress triggered the accumulation of stress-related metabolites such as amino acids and their derivatives, lipids, phenolic acids, organic acids, flavonoids, lignin, coumarins, and alkaloids, suggesting their significant roles in the response to low temperature. This stress also promoted gene expression and metabolite accumulation involved in the flavonoid biosynthesis pathway. Notably, there were marked differences in gene expression and metabolites related to the glyoxylate and dicarboxylate metabolism pathways between B144 and Q319. This study, through multi-omics integrated analysis, provides valuable insights into the identification of metabolites, elucidation of metabolic pathways, and the biochemical and genetic basis of plant responses to stress, particularly under low-temperature conditions. Full article

Background: Newcastle disease virus (NDV) is a highly contagious and economically devastating pathogen affecting poultry worldwide, leading to significant losses in the poultry industry. Despite existing vaccines, outbreaks continue to occur, highlighting the need for more effective vaccination strategies. Developing a multi-epitopic peptide vaccine offers a promising approach to enhance protection against NDV. Objectives: Here, we aimed to design and evaluate a multi-epitopic vaccine against NDV using molecular dynamics (MD) simulation. Methodology: We retrieved NDV sequences for the fusion (F) protein and hemagglutinin–neuraminidase (HN) protein. Subsequently, B-cell and T-cell epitopes were predicted. The top potential epitopes were utilized to design the vaccine construct, which was subsequently docked against chicken TLR4 and MHC1 receptors to assess the immunological response. The resulting docked complex underwent a 1 microsecond (1000 ns) MD simulation. For experimental evaluation, the vaccine’s efficacy was assessed in mice and chickens using a controlled study design, where animals were randomly divided into groups receiving either a local ND vaccine or the peptide vaccine or a control treatment. Results: The 40 amino acid peptide vaccine demonstrated strong binding affinity and stability within the TLR4 and MHC1 receptor–peptide complexes. The root mean square deviation of peptide vaccine and TLR4 receptor showed rapid stabilization after an initial repositioning. The root mean square fluctuation revealed relatively low fluctuations (below 3 Å) for the TLR4 receptor, while the peptide exhibited higher fluctuations. The overall binding energy of the peptide vaccine with TLR4 and MHC1 receptors amounted to −15.7 kcal·mol⁻¹ and −36.8 kcal·mol⁻¹, respectively. For experimental evaluations in mice and chicken, the peptide vaccine was synthesized using services of GeneScript Biotech^® (Singapore) PTE Limited. Experimental evaluations showed a significant immune response in both mice and chickens, with the vaccine eliciting robust antibody production, as evidenced by increasing HI titers over time. Statistical analysis was performed using an independent t-test with Type-II error to compare the groups, calculating the p-values to determine the significance of the immune response between different groups. Conclusions: Multi-epitopic peptide vaccine has demonstrated a good immunological response in natural hosts. Full article

Mercury, a toxic heavy metal produced through both natural and anthropogenic processes, is found in all of Earth’s major systems. Mercury’s bioaccumulation characteristics in the human body have a significant impact on the liver, kidneys, brain, and muscles. In order to detect Hg²⁺ ions, a highly sensitive and specific fluorescent biosensor has been developed using a novel, modified seven amino acid peptide, FY7. The tyrosine ring in the FY7 peptide sequence forms a 2:1 complex with Hg²⁺ ions that are present in the water-based sample. As a result, the peptide’s fluorescence emission decreases with higher concentrations of Hg²⁺. The FY7 peptide’s performance was tested in the presence of Hg²⁺ ions and other metal ions, revealing its sensitivity and stability despite high concentrations. Conformational changes to the FY7 structure were confirmed by FTIR studies. Simultaneously, we designed a miniaturized setup to support an in-house-developed micro-volume capillary container for volume fluorometry measurements. We compared and verified the results from the micro-volume system with those from the commercial setup. The micro-volume capillary system accommodated only 2.9 µL of sample volume, allowing for rapid, sensitive, and selective detection of toxic mercury (II) ions as low as 0.02 µM. Full article

Multipartite genomes are thought to confer evolutionary advantages to bacteria by providing greater metabolic flexibility in fluctuating environments and enabling rapid adaptation to new ecological niches and stress conditions. This genome architecture is commonly found in plant symbionts, including nitrogen-fixing rhizobia, such as Rhizobium leguminosarum bv. trifolii TA1 (RtTA1), whose genome comprises a chromosome and four extrachromosomal replicons (ECRs). In this study, the transcriptomic responses of RtTA1 to partial nutrient limitation and low acidic pH were analyzed using high-throughput RNA sequencing. RtTA1 growth under these conditions resulted in the differential expression of 1035 to 1700 genes (DEGs), which were assigned to functional categories primarily related to amino acid and carbohydrate metabolism, ribosome and cell envelope biogenesis, signal transduction, and transcription. These results highlight the complexity of the bacterial response to stress. Notably, the distribution of DEGs among the replicons indicated that ECRs played a significant role in the stress response. The transcriptomic data align with the Rhizobium pangenome analysis, which revealed an over-representation of functional categories related to transport, metabolism, and regulatory functions on ECRs. These findings confirm that ECRs contribute substantially to the ability of rhizobia to adapt to challenging environmental conditions. Full article

This study aimed to assess the fermentation characteristics, bacterial community structure, co-occurrence networks, and their predicted functionality and pathogenic risk in high-moisture Italian ryegrass (IR; Lolium multiflorum Lam.) silage. The IR harvested at heading stage (208 g dry matter (DM)/kg fresh weight) was spontaneously ensiled in plastic silos (10 L scale). Triplicated silos were opened after 1, 3, 7, 15, 30, and 60 days of fermentation, respectively. The bacterial community structure on days 3 and 60 were investigated using high-throughput sequencing technology, and 16S rRNA-gene predicted functionality and phenotypes were determined by PICRUSt2 and BugBase tools, respectively. After 60 days, the IR silage exhibited good ensiling characteristics indicated by large amounts of acetic acid (~58.7 g/kg DM) and lactic acid (~91.5 g/kg DM), relatively low pH (~4.20), acceptable levels of ammonia nitrogen (~87.0 g/kg total nitrogen), and trace amounts of butyric acid (~1.59 g/kg DM). Psychrobacter was prevalent in fresh IR, and Lactobacillus became the most predominant genus after 3 and 60 days. The ensilage process reduced the complexity of the bacterial community networks in IR silage. The bacterial functional pathways in fresh and ensilaged IR are primarily characterized by the metabolism of carbohydrate and amino acid. The pyruvate kinase and 1-phosphofructokinase were critical in promoting lactic acid fermentation. A greater (p < 0.01) abundance of the “potentially pathogenic” label was noticed in the bacterial communities of ensiled IR than fresh IR. Altogether, the findings indicated that the high-moisture IR silage exhibited good ensiling characteristics, but the potential for microbial contamination and pathogens still remained after ensiling. Full article