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World Journal of Microbiology &... Jun 2024This study explores the biosynthesis of silver nanoparticles (AgNPs) using the Streptomyces tuirus S16 strain, presenting an eco-friendly alternative to mitigate the...
Enhanced biosynthesis of coated silver nanoparticles using isolated bacteria from heavy metal soils and their photothermal-based antibacterial activity: integrating Response Surface Methodology (RSM) Hybrid Artificial Neural Network (ANN)-Genetic Algorithm (GA) strategies.
This study explores the biosynthesis of silver nanoparticles (AgNPs) using the Streptomyces tuirus S16 strain, presenting an eco-friendly alternative to mitigate the environmental and health risks of chemical synthesis methods. It focuses on optimizing medium culture conditions, understanding their physicochemical properties, and investigating their potential photothermal-based antibacterial application. The S16 strain was selected from soils contaminated with heavy metals to exploit its ability to produce diverse bioactive compounds. By employing the combination of Response Surface Methodology (RSM) and Artificial Neural Network (ANN)-Genetic Algorithm (GA) strategies, we optimized AgNPs synthesis, achieving an improvement of nearly 2.45 times the initial yield under specific conditions (Bennet's medium supplemented with glycerol [5 g/L] and casamino-acid [3 g/L] at 30 °C for 72 h). A detailed physicochemical characterization was conducted. Notably, the AgNPs were well dispersed, and a carbonaceous coating layer on their surface was confirmed using energy-dispersive X-ray spectroscopy. Furthermore, functional groups were identified using Fourier-transform infrared spectroscopy, which helped enhance the AgNPs' stability and biocompatibility. AgNPs also demonstrated efficient photothermal conversion under light irradiation (0.2 W/cm), with temperatures increasing to 41.7 °C, after 30 min. In addition, treatment with light irradiation of E. coli K-12 model effectively reduced the concentration of AgNPs from 105 to 52.5 µg/mL, thereby enhancing the efficacy of silver nanoparticles in contact with the E. coli K-12.
Topics: Silver; Metal Nanoparticles; Anti-Bacterial Agents; Neural Networks, Computer; Soil Microbiology; Metals, Heavy; Algorithms; Streptomyces; Microbial Sensitivity Tests; Soil Pollutants; Escherichia coli; Spectroscopy, Fourier Transform Infrared
PubMed: 38913279
DOI: 10.1007/s11274-024-04048-1 -
AMB Express Jun 2024
PubMed: 38913277
DOI: 10.1186/s13568-024-01724-1 -
ACS Chemical Biology Jun 2024tRNA modifications help maintain tRNA structure and facilitate translation and stress response. Found in all three kingdoms of life, mA tRNA modification occurs in the T...
tRNA modifications help maintain tRNA structure and facilitate translation and stress response. Found in all three kingdoms of life, mA tRNA modification occurs in the T loop of many tRNAs, stabilizes tertiary tRNA structure, and impacts translation. MA in the T loop is reversible by three mammalian demethylase enzymes, which bypasses the need of turning over the tRNA molecule to adjust its mA levels in cells. However, no prokaryotic tRNA demethylase enzyme has been identified that acts on endogenous RNA modifications. Using as a model organism, we confirmed the presence and quantitative mA tRNA signatures using mass spectrometry and high-throughput tRNA sequencing. We identified two RNA demethylases that can remove mA in tRNA and validated the activity of a previously annotated tRNA mA writer. Using single-gene knockouts of these erasers and the mA writer, we found dynamic changes of mA levels in many tRNAs under stress conditions. Phenotypic characterization highlighted changes in their growth and altered antibiotic production. Our identification of the first prokaryotic tRNA demethylase enzyme paves the way for investigating new mechanisms of translational regulation in bacteria.
PubMed: 38912606
DOI: 10.1021/acschembio.4c00278 -
Journal of Hazardous Materials Jun 2024Phosphate-solubilizing bacteria (PSB) are important but often overlooked regulators of uranium (U) cycling in soil. However, the impact of PSB on uranate fixation...
Phosphate-solubilizing bacteria (PSB) are important but often overlooked regulators of uranium (U) cycling in soil. However, the impact of PSB on uranate fixation coupled with the decomposition of recalcitrant phosphorus (P) in mining land remains poorly understood. Here, we combined gene amplicon sequencing, metagenome and metatranscriptome sequencing analysis and strain isolation to explore the effects of PSB on the stabilization of uranate and P availability in U mining areas. We found that the content of available phosphorus (AP), carbonate-U and Fe-Mn-U oxides in tailings was significantly (P < 0.05) higher than their adjacent soils. Also, organic phosphate mineralizing (PhoD) bacteria (e.g., Streptomyces) and inorganic phosphate solubilizing (gcd) bacteria (e.g., Rhodococcus) were enriched in tailings and soils, but only organic phosphate mineralizing-bacteria substantially contributed to the AP. Notably, most genes involved in organophosphorus mineralization and uranate resistance were widely present in tailings rather than soil. Comparative genomics analyses supported that organophosphorus mineralizing-Streptomyces species could increase soil AP content and immobilize U(VI) through organophosphorus mineralization (e.g., PhoD, ugpBAEC) and U resistance related genes (e.g., petA). We further demonstrated that the isolated Streptomyces sp. PSBY1 could enhance the U(VI) immobilization mediated by the NADH-dependent ubiquinol-cytochrome c reductase (petA) through decomposing organophosphorous compounds. This study advances our understanding of the roles of PSB in regulating the fixation of uranate and P availability in U tailings.
PubMed: 38908177
DOI: 10.1016/j.jhazmat.2024.134975 -
Nucleic Acids Research Jun 2024Filamentous Actinobacteria, recently renamed Actinomycetia, are the most prolific source of microbial bioactive natural products. Studies on biosynthetic gene clusters...
Filamentous Actinobacteria, recently renamed Actinomycetia, are the most prolific source of microbial bioactive natural products. Studies on biosynthetic gene clusters benefit from or require chromosome-level assemblies. Here, we provide DNA sequences from >1000 isolates: 881 complete genomes and 153 near-complete genomes, representing 28 genera and 389 species, including 244 likely novel species. All genomes are from filamentous isolates of the class Actinomycetia from the NBC culture collection. The largest genus is Streptomyces with 886 genomes including 742 complete assemblies. We use this data to show that analysis of complete genomes can bring biological understanding not previously derived from more fragmented sequences or less systematic datasets. We document the central and structured location of core genes and distal location of specialized metabolite biosynthetic gene clusters and duplicate core genes on the linear Streptomyces chromosome, and analyze the content and length of the terminal inverted repeats which are characteristic for Streptomyces. We then analyze the diversity of trans-AT polyketide synthase biosynthetic gene clusters, which encodes the machinery of a biotechnologically highly interesting compound class. These insights have both ecological and biotechnological implications in understanding the importance of high quality genomic resources and the complex role synteny plays in Actinomycetia biology.
PubMed: 38908028
DOI: 10.1093/nar/gkae523 -
Biomolecular NMR Assignments Jun 2024Signalosomes are high-order protein machineries involved in complex mechanisms controlling regulated immune defense and cell death execution. The immune response is...
Signalosomes are high-order protein machineries involved in complex mechanisms controlling regulated immune defense and cell death execution. The immune response is initiated by the recognition of exogeneous or endogenous signals, triggering the signalosome assembly process. The final step of signalosome fate often involves membrane-targeting and activation of pore-forming execution domains, leading to membrane disruption and ultimately cell death. Such cell death-inducing domains have been thoroughly characterized in plants, mammals and fungi, notably for the fungal cell death execution protein domain HeLo. However, little is known on the mechanisms of signalosome-based immune response in bacteria, and the conformation of cell death executors in bacterial signalosomes is still poorly characterized. We recently uncovered the existence of NLR signalosomes in various multicellular bacteria and used genome mining approaches to identify putative cell death executors in Streptomyces olivochromogenes. These proteins contain a C-terminal amyloid domain involved in signal transmission and a N-terminal domain, termed BELL for Bacteria analogous to fungal HeLL (HeLo-like), presumably responsible for membrane-targeting, pore-forming and cell death execution. In the present study, we report the high yield expression of S. olivochromogenes BELL2 and its characterization by solution NMR spectroscopy. BELL is folded in solution and we report backbone and sidechain assignments. We identified five α-helical secondary structure elements and a folded core much smaller than its fungal homolog HeLo. This study constitutes the first step toward the NMR investigation of the full-length protein assembly and its membrane targeting.
PubMed: 38907837
DOI: 10.1007/s12104-024-10183-5 -
Microbial Pathogenesis Jun 2024The present study explores the bioinspired green synthesis of zinc oxide nanoparticles (ZnONPs) using marine Streptomyces plicatus and its potent antibacterial,...
The present study explores the bioinspired green synthesis of zinc oxide nanoparticles (ZnONPs) using marine Streptomyces plicatus and its potent antibacterial, antibiofilm activity against dental caries forming Streptococcus mutans MTCC and S. mutans clinical isolate (CI), cytotoxicity against oral KB cancer cells, hemolysis against blood erythrocytes and artemia toxicity. The bioinspired ZnONPs showed a distinctive absorption peak at 375 nm in UV-Vis spectra, the FT-IR spectra divulged the active functional groups, and XRD confirmed the crystalline nature of the nanoparticles with an average grain size of 41.76 nm. SEM analysis evidenced hexagonal morphology, and EDX spectra affirmed the presence of zinc. The ZnONPs exerted higher antagonistic activity against S. mutans MTCC (Inhibitory zone: 19 mm; MIC: 75 μg/ml) than S. mutans CI (Inhibitory zone: 17 mm; MIC: 100 μg/ml). Results of biofilm inhibitory activity showed a concentration-dependent reduction with S. mutans MTCC (15 %-95 %) more sensitive than S. mutans CI (13 %-89 %). The 50 % biofilm inhibitory concentration (BIC) of ZnONPs against S. mutans MTCC was considerably lower (71.76 μg/ml) than S. mutans CI (78.13 μg/ml). Confocal Laser Scanning Microscopic visuals clearly implied that ZnONPs effectively distorted the biofilm architecture of both S. mutans MTCC and S. mutans CI. This was further bolstered by a remarkable rise in protein leakage (19 %-85 %; 15 %-77 %) and a fall in exopolysaccharide production (34 mg-7 mg; 49 mg-12 mg). MTT cytotoxicity of ZnONPs recorded an IC value of 22.06 μg/ml against KB cells. Acridine orange/ethidium bromide staining showed an increasing incidence of apoptosis in KB cells. Brine shrimp cytotoxicity using Artemia salina larvae recorded an LC value of 78.41 μg/ml. Hemolysis assay substantiated the biocompatibility of the ZnONPs. This study underscores the multifaceted application of bioinspired ZnONPs in dentistry.
PubMed: 38906493
DOI: 10.1016/j.micpath.2024.106758 -
Environmental Pollution (Barking, Essex... Jun 2024Diazinon is an organophosphorus pesticide widely used in agriculture and household pest control, and its use also poses several environmental and health hazards. In this...
Diazinon is an organophosphorus pesticide widely used in agriculture and household pest control, and its use also poses several environmental and health hazards. In this study, we investigated the spatial and temporal distribution of diazinon in Baiyangdian, evaluated its potential ecological risk and toxicity to aquatic organisms based on RQ (Risk quotient) and TU (Toxic unit) analysis, and assessed the potential effects of diazinon accumulation on probiotics and pathogens based on statistical analysis of high-throughput sequencing data. The results showed that diazinon in Baiyangdian posed a low to moderate chronic risk to sediment-dwelling organisms and a low toxicity effect on aquatic invertebrates, which was mainly concentrated in October and human-intensive areas. Meanwhile, increases in sediment electrical conductivity (EC), amorphous iron oxides content and phenol oxidase activity favored diazinon accumulation in sediments, whereas the opposite was the case for sediment organic carbon, β-1,4-glucosidase, phosphatase, catalase and pH, suggesting that environmental indicators play a key role in the behavior and distribution of diazinon. In addition, diazinon in heavily contaminated areas seem to inhibit the rare probiotics (Bifidobacterium adolescentis and Serratia sp.), while promoted dominant pathogens (e.g., Burkholderia cenocepacia), which can lead to increased disease risk to humans and ecosystems, disruption of ecological balance and potential health problems. However, probiotic Streptomyces xiamenensis resist to diazinon would be a potential degrader for diazinon remove. In conclusion, this study unveiled the effects of diazinon pollution on wetland ecosystems, emphasizing ecological impacts and potential health concerns. In addition, the discovery of diazinon resistant probiotics provided new insights into wetland ecological restoration.
PubMed: 38906403
DOI: 10.1016/j.envpol.2024.124408 -
Applied and Environmental Microbiology Jun 2024Precursor supply plays a significant role in the production of secondary metabolites. In bacteria, propionyl-, malonyl-, and methylmalonyl-CoA are the most common...
UNLABELLED
Precursor supply plays a significant role in the production of secondary metabolites. In bacteria, propionyl-, malonyl-, and methylmalonyl-CoA are the most common precursors used for polyketide biosynthesis. Although propionyl-CoA synthetases participate in the propionate assimilation pathway and directly convert propionate into propionyl-CoA, malonyl- and methylmalonyl-CoA cannot be formed using common acyl-CoA synthetases. Therefore, both acetyl- and propionyl-CoA carboxylation, catalyzed by acyl-CoA carboxylases, should be considered when engineering a microorganism chassis to increase polyketide production. In this study, we identified a transcriptional regulator of the TetR family, BkdR, in B4, which binds directly to the promoter region of the neighboring operon. This operon encodes acetyl/propionyl-CoA carboxylase and negatively regulates its transcription. In addition to acetate and propionate, the binding of BkdR to is disrupted by acetyl- and propionyl-CoA ligands. We identified a 16-nucleotide palindromic BkdR-binding motif (GTTAg/CGGTCg/TTAAC) in the intergenic region between and . When was deleted, we found an enhanced supply of malonyl- and methylmalonyl-CoA precursors in B4. In this study, spinosad production was detected in the recombinant strain after introducing the entire artificial biosynthesized gene cluster into B4. When supplemented with propionate to provide propionyl-CoA, the novel -deleted strain produced 29.4% more spinosad than the initial strain in trypticase soy broth (TSB) medium.
IMPORTANCE
In this study, we describe a operon involved in short-chain acyl-CoA carboxylation in B4 chassis. The TetR family regulator, BkdR, represses this operon. Our results show that BkdR regulates the precursor supply needed for heterologous spinosad biosynthesis by controlling acetyl- and propionyl-CoA assimilation. The deletion of the BkdR-encoding gene exerts an increase in heterologous spinosad yield. Our research reveals a regulatory mechanism in short-chain acyl-CoA metabolism and suggests new possibilities for chassis engineering to enhance heterologous polyketide yield.
PubMed: 38904409
DOI: 10.1128/aem.00838-24 -
Chemical Science Jun 2024The thioether-connected bis-amino acid lanthionine (Lan) residues are class-defining residues of lanthipeptides. Typically, the cyclization step of lanthionine...
The thioether-connected bis-amino acid lanthionine (Lan) residues are class-defining residues of lanthipeptides. Typically, the cyclization step of lanthionine formation, which relies on the addition of a cysteine to an unsaturated dehydroamino acid, is directed either by a standalone cyclase LanC (class I) or by a cyclase domain (class II-IV). However, the pathways of characterized class V members often lack a known cyclase (domain), raising a question on the mechanism by which their multi-macrocycle systems are formed. Herein, we report a new RiPP gene cluster in TN 58, where it encodes the biosynthesis of 3 distinct class V lanthipeptides-termed triantimycins (TAMs). TAM A1∼A3 share an N-terminal ll-MeLan residue, and only TAM A1 contains an additional internal ll-Lan residue. TAM A1 also has a C-terminal (2, 3)--(()-2-aminovinyl)-3-methyl-d-cysteine (AviMeCys) residue, which is distinct from the previously reported (2, 3)-AviMeCys residue in other RiPPs. Gene deletion, heterologous coexpression, and structural elucidation demonstrated that the cyclization for an ll-MeLan formation occurs spontaneously and is independent of any known lanthionine cyclase. This study provides a new paradigm for lanthionine formation and facilitates genome mining and engineering efforts on RiPPs containing (Me)Lan and ()Avi(Me)Cys residues.
PubMed: 38903209
DOI: 10.1039/d4sc02302a