Search Results (427)

Probiotics, due to their multifaceted benefits to the host, are essential in medicine, agriculture, and aquaculture. The mechanisms of their action at the molecular level are complex and less explored. Both previous research and our own investigations have highlighted that incorporating probiotics into the feed of commercial fish can increase growth and influence the expression of genes related to stress and immunity. Additionally, probiotics with antioxidant properties often exert systemic effects. The aim of this work was to explore possible mechanisms of probiotic effects on stress-related proteins in African catfish C. gariepinus using molecular docking and dynamics approaches. Stress biomarker proteins such as catalase, cytochrome P450, HSP70, metallothionein 1, and superoxide dismutase were evaluated for possible interactions with bioactive non-ribosomal peptides (NRPs) from Bacillus subtilis R5, used as ligands. The study involved molecular docking and dynamics interactions between proteins and NRPs. The results of molecular docking and dynamics reveal multiple bindings between proteins and ligands, forming stable complexes, which may explain the mechanisms of action of probiotics and their particularly positive effects, such as the reduction in stress levels, which was demonstrated in the clarium catfish model in our previous work. Non-ribosomal peptides synthesized by probiotics may influence key signalling pathways underlying antioxidant and antimutagenic properties. Full article

Environmental pollution from metal toxicity is a widespread concern. Certain bacteria hold promise for bioremediation via the conversion of toxic chromium compounds into less harmful forms, promoting environmental cleanup. In this study, we report the isolation and detailed characterization of a highly chromium-tolerant bacterium, Bacillus tropicus CRB14. The isolate is capable of growing on 5000 mg/L Cr (VI) in an LB (Luria Bertani) agar plate while on 900 mg/L Cr (VI) in LB broth. It shows an 86.57% reduction ability in 96 h of culture. It can also tolerate high levels of As, Cd, Co, Fe, Zn, and Pb. The isolate also shows plant growth-promoting potential as demonstrated by a significant activity of nitrogen fixation, phosphate solubilization, IAA (indole acetic acid), and siderophore production. Whole-genome sequencing revealed that the isolate lacks Cr resistance genes in their plasmids and are located on its chromosome. The presence of the chrA gene points towards Cr(VI) transport, while the absence of ycnD suggests alternative reduction pathways. The genome harbors features like genomic islands and CRISPR-Cas systems, potentially aiding adaptation and defense. Analysis suggests robust metabolic pathways, potentially involved in Cr detoxification. Notably, genes for siderophore and NRP-metallophore production were identified. Whole-genome sequencing data also provides the basis for molecular validation of various genes. Findings from this study highlight the potential application of Bacillus tropicus CRB14 for bioremediation while plant growth promotion can be utilized as an added benefit. Full article

Structural variations in the duck genome significantly impact the environmental adaptability and phenotypic diversity of duck populations. Characterizing these SVs in local domestic duck breeds from Shandong province offers valuable insights for breed selection and the development of new breeds. This study aimed to profile the genomic SVs in three local duck breeds (Matahu duck, Weishan partridge duck, and Wendeng black duck) and explore their differential distributions. A total of 21,673 SVs were detected using LUMPY (v0.2.13) and DELLY (v1.0.3) software, with 46% located in intergenic regions, 33% in intronic regions, and frameshift deletions being the most prevalent in exonic regions (3%). SVs distribution showed a decreasing trend with shorter chromosome lengths. Population structure analysis revealed distinct genetic profiles, with Matahu and Weishan partridge ducks showing closer affinities and the Wendeng black duck having a more homogeneous genetic background, likely due to geographic isolation. Functional annotation identified genes related to nervous system development, mitosis, spindle assembly, and energy metabolism. Notable genes included PLXNA4, NRP2, SEMA3A, PTEN, MYBL2, ADK, and COX4I1. Additionally, genes such as PRKG1, GABRA2, and FSHR were linked to energy metabolism and reproductive activity. The study provides a comprehensive analysis of SVs, revealing significant genetic differentiation and identifying genes associated with economically important traits, offering valuable resources for the genetic improvement and breeding of local duck breeds. Full article

Background: Despite extensive research on proteinuria’s impact on chronic kidney disease progression, there is no direct comparison of outcomes in biopsy-diagnosed glomerular disease (GD) patients with nephrotic syndrome (NS) or nephrotic range proteinuria (NRP). Our study addresses this gap, comparing long-term outcomes between NS and NRP. Methods: We conducted a retrospective study on 240 kidney biopsy-proven GD patients, tracked from 2010 to 2015 until end-stage kidney disease (ESKD), death, or the study end in January 2022. Results: The median follow-up was 8.8 years. Diagnoses were predominantly nonproliferative (53%), proliferative (25%) nephropathies, diabetic nephropathy (12%), and paraprotein diseases (10%). NS was observed in 141 (59%) patients, presenting more frequently with arterial hypertension, higher eGFR, increased proteinuria, and dyslipidemia than NRP patients. NRP patients often had proliferative GD and diabetic nephropathy; their renal chronicity score was higher. The ESKD endpoint occurred in 35% NS and 39% NRP patients (p 0.4). The cohort’s mean kidney survival time was 8.2 years. In a multivariate analysis, NS, lower eGFR, a higher renal chronicity score, and diabetic nephropathy were associated with ESKD. A total of 64 patients (27%) died, 73% post-kidney replacement therapy initiation, and mostly from cardiovascular disease (63%). Mortality between proteinuria forms showed no difference. The multivariate analysis found lower eGFR, a higher Charlson comorbidity score, and diabetic nephropathy associated with mortality. Conclusions: Our study found no difference in all-cause mortality between NS and NRP in glomerular diseases. However, an adjusted analysis revealed poorer kidney survival for NS patients, emphasizing the need for personalized management to improve renal prognoses. Full article

Irpex lacteus is an edible and medicinal macrofungus with significant biological activity and broad pharmaceutical prospects that has received increasing attention in recent years. Although it is an important resource for macrofungi, knowledge of it remains limited. In this study, we sequenced, de novo assembled, and annotated the whole genome of I. lacteus using a PacBio Sequel II sequencer. The assembled 41.83 Mb genome contains 13,135 predicted protein-coding genes, 83.44% of which have searchable sequence similarity to other genes available in public databases. Using genome-based bioinformatics analysis, we identified 556 enzymes involved in carbohydrate metabolism and 103 cytochrome P450 proteins. Genome annotation revealed genes for key enzymes responsible for the biosynthesis of secondary metabolites, such as terpenoids and polyketides. Among them, we identified 14 terpene synthases, 8 NRPS-like enzymes, and 4 polyketide synthases (PKS), as well as 2 clusters of biosynthetic genes presumably related to terpene synthesis in I. lacteus. Gene family analysis revealed that the MYB transcription factor gene family plays an important role in the growth and development of I. lacteus. This study further enriches the genomic content of I. lacteus, provides genomic information for further research on the molecular mechanism of I. lacteus, and promotes the development of I. lacteus in the fields of drug research and functional food production. Full article

Recently, the use of click chemistry for localization of chemically modified cyanopeptides has been introduced, i.e., taking advantage of promiscuous adenylation (A) domains in non-ribosomal peptide synthesis (NRPS), allowing for the incorporation of clickable non-natural amino acids (non-AAs) into their peptide products. In this study, time-lapse experiments have been performed using pulsed feeding of three different non-AAs in order to observe the synthesis or decline of azide- or alkyne-modified microcystins (MCs) or anabaenopeptins (APs). The cyanobacteria Microcystis aeruginosa and Planktothrix agardhii were grown under maximum growth rate conditions (r = 0.35–0.6 and 0.2–0.4 (day⁻¹), respectively) in the presence of non-AAs for 12–168 h. The decline of the azide- or alkyne-modified MC or AP was observed via pulse-feeding. In general, the increase in clickable MC/AP in peptide content reached a plateau after 24–48 h and was related to growth rate, i.e., faster-growing cells also produced more clickable MC/AP. Overall, the proportion of clickable MC/AP in the intracellular fraction correlated with the proportion observed in the dissolved fraction. Conversely, the overall linear decrease in clickable MC/AP points to a rather constant decline via dilution by growth instead of a regulated or induced release in the course of the synthesis process. Full article

Neutrophil elastase (NE) has been reported to be a pro-inflammatory stimulus for macrophages. The aim of the present study was to determine the impact of NE exposure on the human macrophage proteome and evaluate its impact on pro-inflammatory signals. Human blood monocytes from healthy volunteers were differentiated to macrophages and then exposed to either 500 nM of NE or control vehicle for 2 h in triplicate. Label-free quantitative proteomics analysis identified 41 differentially expressed proteins in the NE versus control vehicle datasets. A total of 26 proteins were downregulated and of those, 21 were cell surface proteins. Importantly, four of the cell surface proteins were proteoglycans: neuropilin 1 (NRP1), syndecan 2 (SDC2), glypican 4 (GPC4), and CD99 antigen-like protein 2 (CD99L2) along with neuropilin 2 (NRP2), CD99 antigen (CD99), and endoglin (ENG) which are known interactors. Additional NE-targeted proteins related to macrophage function were also measured including CD40, CD48, SPINT1, ST14, and MSR1. Collectively, this study provides a comprehensive unbiased view of selective NE-targeted cell surface proteins in chronically inflamed lungs. Full article

Despite all the progress in treating SARS-CoV-2, escape mutants to current therapies remain a constant concern. Promising alternative treatments for current and future coronaviruses are those that limit escape mutants by inhibiting multiple pathogenic targets, analogous to the current strategies for treating HCV and HIV. With increasing popularity and ease of manufacturing of RNA technologies for vaccines and drugs, therapeutic microRNAs represent a promising option. In the present work, miR-24-3p was identified to inhibit SARS-CoV-2 entry, replication, and production; furthermore, this inhibition was retained against common mutations improving SARS-CoV-2 fitness. To determine the mechanism of action, bioinformatic tools were employed, identifying numerous potential effectors promoting infection targeted by miR-24-3p. Of these targets, several key host proteins for priming and facilitating SARS-CoV-2 entry were identified: furin, NRP1, NRP2, and SREBP2. With further experimental analysis, we show that miR-24-3p directly downregulates these viral entry factors to impede infection when producing virions and when infecting the target cell. Furthermore, we compare the findings with coronavirus, HCoV-229E, which relies on different factors strengthening the miR-24-3p mechanism. Taken together, the following work suggests that miR-24-3p could be an avenue to treat current coronaviruses and those likely to emerge. Full article

Fungal secondary metabolites (SMs) have broad applications in biomedicine, biocontrol, and the food industry. In this study, whole-genome sequencing and annotation of Taiwanofungus gaoligongensis were conducted, followed by comparative genomic analysis with 11 other species of Polyporales to examine genomic variations and secondary metabolite biosynthesis pathways. Additionally, transcriptome data were used to analyze the differential expression of polyketide synthase (PKS), terpene synthase (TPS) genes, and transcription factors (TFs) under different culture conditions. The results show that T. gaoligongensis differs from other fungal species in genome size (34.58 Mb) and GC content (50.72%). The antibiotics and Secondary Metabolites Analysis Shell (AntiSMASH) analysis reveals significant variation in the number of SM biosynthetic gene clusters (SMBGCs) across the 12 species (12–29), with T. gaoligongensis containing 25 SMBGCs: 4 PKS, 6 non-ribosomal peptide synthetase (NRPS), and 15 TPS clusters. The TgPKS1 gene is hypothesized to be involved in the biosynthesis of orsellinic acid or its derivatives, while TgPKS2 might catalyze the synthesis of 6-methylsalicylic acid (6MSA) and its derivatives. The TgTRI5 genes are suggested to synthesize tetracyclic sesquiterpene type B trichothecene compounds, while TgPentS may be involved in the synthesis of δ-cadinol, β-copaene, and α-murolene analogs or derivatives. Comparative genomic analysis shows that the genome size of T. gaoligongensis is similar to that of T. camphoratus, with comparable SMs. Both species share four types of PKS domains and five distinct types of TPS. Additionally, T. gaoligongensis exhibits a high degree of similarity to Laetiporus sulphureus, despite belonging to a different genus within the same family. Transcriptome analysis reveals significant variation in the expression levels of PKS and TPS genes across different cultivation conditions. The TgPKS1 and TgPKS4 genes, along with nine TgTFs, are significantly upregulated under three solid culture conditions. In contrast, under three different liquid culture conditions, the TgPKS3, TgTRI5-1, and TgTRI5-2 genes, along with twelve TgTFs, exhibit higher activity. Co-expression network analysis and TgTFs binding site prediction in the promoter regions of TgPKS and TgTPS genes suggest that TgMYB9 and TgFTD4 regulate TgPKS4 expression. TgHOX1, TgHSF2, TgHSF3, and TgZnF4 likely modulate TgPKS3 transcriptional activity. TgTRI5-1 and TgTRI5-5 expression is likely regulated by TgbZIP2 and TgZnF15, respectively. This study provides new insights into the regulatory mechanisms of SMs in T. gaoligongensis and offers potential strategies for enhancing the biosynthesis of target compounds through artificial intervention. Full article

In this paper, we present a novel class of hybrid polyketides, tenuazamines A–H (1–8), which exhibit a unique tautomeric equilibrium from Alternaria alternata FL7. The elucidation of the structures was achieved through a diverse combination of NMR, HR-ESIMS, and ECD methods, with a focus on extensive spectroscopic data analysis. Notably, compounds 1, 4, 8–9 exhibited potent toxic effects on the growth of Arabidopsis thaliana. This research expands the structural diversity of tenuazonic acid compounds derived from endophytic fungi and provides potential hit compounds for the development of herbicides. Full article

Surfactin, a potent biosurfactant produced by Bacillus subtilis, is synthesized using a non-ribosomal peptide synthetase (NRPS) encoded by the srfAA-AD operon. Despite its association with quorum sensing via the ComX pheromone, the dynamic behavior and in vivo quantification of the NRPS complex remain underexplored. This study established an in vivo quantification system using fluorescence labeling to monitor the availability of surfactin-forming NRPS subunits (SrfAA, SrfAB, SrfAC, and SrfAD) during bioprocesses. Four Bacillus subtilis sensor strains were constructed by fusing these subunits with the megfp gene, resulting in strains BMV25, BMV26, BMV27, and BMV28. These strains displayed growth and surfactin productivity similar to those of the parental strain, BMV9. Fluorescence signals indicated varying NRPS availability, with BMV27 showing the highest and BMV25 showing the lowest relative fluorescence units (RFUs). RFUs were converted to the relative number of NRPS molecules using open-source FPCountR package. During bioprocesses, NRPS availability peaked at the end of the exponential growth phase and declined in the stationary phase, suggesting reduced NRPS productivity under nutrient-limited conditions and potential post-translational regulation. This study provides a quantitative framework for monitoring NRPS dynamics in vivo, offering insights into optimizing surfactin production. The established sensor strains and quantification system enable the real-time monitoring of NRPS availability, aiding bioprocess optimization for industrial applications of surfactin and potentially other non-ribosomal peptides. Full article

Fusarium subglutinans and F. temperatum are widely distributed maize pathogens recognized as distinct species with a species-specific chemotype based on patterns of mycotoxins. Recent comparative genomic analysis revealed that genomes of both species carry a complete beauvericin (Bea) biosynthetic genes cluster, but the key gene Bea1 in F. subglutinans is not functional likely due to a large insertion (NRPS22ins) and multiple mutations (SNP298 and SNP528). We used the recently published genome sequences for these species to develop PCR markers for investigating the distribution of three main mutations in the Bea1 gene in a large collection of strains of both species from around the world. We also designed a PCR assay for a rapid and reliable discrimination of both species in the evaluation of crop exposure to mycotoxins. Overall, our results showed that SNP528 was the most common mutation, followed by NRPS22ins and SNP298. Moreover, phylogenetic analyses suggest that non-synonymous SNPs have occurred first, and that the resulting inactivation of BEA production has caused the accumulation of other polymorphisms, including the NRPS22ins, in the entire gene-coding region. The screening for genetic differences between these species could guide future crop management strategies. Full article

The general features of the shift to a dormant state in mycobacterial species include several phenotypic changes, reduced metabolic activities, and increased resistance to host and environmental stress conditions. In this study, we aimed to provide novel insights into the viability state and morphological changes in dormant M. smegmatis that contribute to its long-term survival under starvation or hypoxia. To this end, we conducted assays to evaluate cell viability, morphological changes and gene expression. During starvation, M. smegmatis exhibited a reduction in cell length, the presence of viable but non-culturable (VBNC) cells and the formation of anucleated small cells, potentially due to a phenomenon known as reductive cell division. Under hypoxia, a novel population of pleomorphic mycobacteria with a rough surface before the cells reached nonreplicating persistence 1 (NRP1) was identified. This population exhibited VBNC-like behaviour, with a loss of cell wall rigidity and the presence of lipid-body-like structures. Based on dosR and hspX expression, we suggest that M. smegmatis encounters reductive stress conditions during starvation, while lipid storage may induce oxidative stress during hypoxia. These insights into the heterogeneous populations presented here could offer valuable opportunities for developing new therapeutic strategies to control dormant mycobacterial populations. Full article

The nonribosomal peptide synthetase (NRPS) is a highly precise molecular assembly machinery for synthesizing structurally diverse peptides, which have broad medicinal applications. Withinthe NRPS, the condensation (C) domain is a core catalytic domain responsible for the formation of amide bonds between individual monomer residues during peptide elongation. This review summarizes various aspects of the C domain, including its structural characteristics, catalytic mechanisms, substrate specificity, substrate gating function, and auxiliary functions. Moreover, through case analyses of the NRPS engineering targeting the C domains, the vast potential of the C domain in the combinatorial biosynthesis of peptide natural product derivatives is demonstrated. Full article

Systemic lupus erythematosus (SLE) is an autoimmune disease affecting multiple organs, with lupus nephritis (LN) occurring in 40–50% of SLE patients. Despite advances in diagnosis and treatment, LN remains a major cause of morbidity and mortality, with 10–20% of patients progressing to end-stage renal disease (ESRD). While knowledge of LN’s pathogenesis has improved, mechanisms of renal recovery are still largely unexplored. Neuropilin-1 (NRP-1), a transmembrane receptor expressed in renal tissue, has emerged as a promising biomarker for assessing renal recovery in LN. This study evaluates and correlates longitudinal levels of NRP-1 with kidney histology using an NZB/W F1 mouse model of LN. A total of 30 mice were used, with 15 receiving intravenous cyclophosphamide (CYC) and 15 being untreated. NRP-1 levels were measured in urine and serum, and kidney samples were taken from a subgroup of mice for histological evaluation. The results demonstrated a progressive increase in renal and urinary NRP-1 expression, particularly notable at weeks 26 and 32. Urinary NRP-1 levels above 34.40 ng/mL were strong predictors of favorable renal response, showing 100% sensitivity and 88% specificity. These findings indicate a robust correlation between urinary NRP-1 levels and renal histological recovery, underscoring the potential of NRP-1 as a valuable biomarker for assessing renal response in LN. This study demonstrates that renal production of NRP-1 is linked to histological recovery and establishes a foundation for future research into the role of NRP-1 in lupus kidney recovery. Full article