Discovery of a Novel DNA Gyrase-Targeting Antibiotic through the Chemical Perturbation of Streptomyces venezuelae Sporulation

Catalytic evaluation and in vitro bacterial inactivation of graphitic carbon nitride/carbon sphere doped bismuth oxide quantum dots with evidential in silico analysis

Herein, Bi2O3 quantum dots (QDs) have been synthesized and doped with various concentrations of graphitic carbon nitride (g-C3N4) and a fixed amount of carbon spheres (CS) using a co-precipitation technique. XRD analysis confirmed the presence of monoclinic structure along the space group P21/c and C2/c. Various functional groups and characteristic peaks of (Bi-O) were identified using FTIR spectra. QDs morphology of Bi2O3 showed agglomeration with higher amounts of g-C3N4 by TEM analysis. HR-TEM determined the variation in the d-spacing which increased with increasing dopants. These doping agents were employed to reduce the exciting recombination rate of Bi2O3 QDs by providing more active sites which enhance antibacterial activity. Notably, (6 wt%) g-C3N4/CS-doped Bi2O3 exhibited considerable antimicrobial potential in opposition to E. coli at higher values of concentrations relative to ciprofloxacin. The (3 wt%) g-C3N4/CS-doped Bi2O3 exhibits the highest catalytic potential (97.67%) against RhB in a neutral medium. The compound g-C3N4/CS-Bi2O3 has been suggested as a potential inhibitor of β-lactamaseE. coli and DNA gyraseE. coli based on the findings of a molecular docking study that was in better agreement with in vitro bactericidal activity.

Enhancing the Antibiotic Production by Thermophilic Bacteria Isolated from Hot Spring Waters via Ethyl Methanesulfonate Mutagenesis

Antibiotic-resistant bacteria represent a serious public health threat. For that reason, the development of new and effective antibiotics to control pathogens has become necessary. The current study aims to search for new microorganisms expressing antibiotic production capacity. Fifteen sites covering a wide range of harsh environmental conditions in Egypt were investigated. Two hundred and eighty bacterial isolates were obtained and then tested against pathogenic bacteria using the agar disk diffusion technique. Fifty-two (18.6% of the total) of the isolates exhibited antagonistic properties, which affected one or more of the tested pathogens. The isolate 113 was identified as Bacillus licheniformis and isolate 10 was identified as Brevibacillus borstelensis using the 16S rRNA technique. The B. licheniformis strain was stronger in antibiotic production against S. typhi, M. luteus, and P. ariginosa, whereas the strain Br. borstelensis was more efficient against B. cereus, E. coli, and Klebs. sp. The sensitivity of the strains to commercial antibiotics showed that B. licheniformis was highly sensitive to seven commercial antibiotics, whereas Br. borstelensis was sensitive to nine antibiotics. The two strains were subjected to ethyl methanesulfonate (EMS) mutagenesis to obtain mutants with a higher antibiotic production. The total bacterial count was measured after treatment with EMS mutagen and showed a significant gradual increase in the antimicrobial activity, which was achieved via shaking in the presence of EMS for 60 min. High antimicrobial activities were noted with 17 and 14 mutants from the B. licheniformis and Br. borstelensis strains, respectively. The mutant B. licheniformis (M15/Amo) was more active than the parent strain against S. aureus (212.5%), while the mutant Br. borstelensis (B7/Neo) was more effective against S. typhi (83.3%). The present study demonstrates the possibility of obtaining potent antibiotic-producing bacteria in hot spring waters and further improving the indigenous bacterial capacity to produce antibiotics by using EMS mutagenesis.

La-Doped CeO2 Quantum Dots: Novel Dye Degrader, Antibacterial Activity, and In Silico Molecular Docking Analysis

The current work demonstrates a novel synthesis of different concentrations of La-doped (2, 4, and 6 wt %) CeO₂ quantum dots (QDs) using a hydrothermal approach. This research aimed to examine the dye degradation efficiency, antibacterial activity, and in silico molecular docking analysis of La-doped CeO₂ QDs. The structure, elemental composition, optical properties, d-spacing, and morphological features of QDs were examined using various methods. XRD spectra exhibited the cubic structure of CeO₂, and the crystallinity was suppressed upon La doping. TEM revealed the formation of cubic-shaped QDs of CeO₂, and the incorporation of La decreased agglomeration. UV-vis absorption spectra showed a red shift upon La doping, assigned to a decrease in band gap energy. 6% La-doped CeO₂ showed significant antibacterial activity against Escherichia coli at higher concentrations in comparison to ciprofloxacin. La-CeO₂ was proposed as a putative inhibitor of β-lactamase _E. coli and DNA gyrase _E. coli relying on the outcomes of a molecular docking analysis that was in improved accord with in vitro bactericidal activity. Moreover, the prepared QDs exhibited a remarkable photocatalytic degradation of methylene blue in a basic medium.

Streptomyces behavior and competition in the natural environment

Streptomyces are ubiquitous terrestrial bacteria that are renowned for their robust metabolic capabilities and their behavioral flexibility. In competing for environmental niches, these bacteria can employ novel growth and dispersal behaviors. They also wield their diverse metabolic repertoire for everything from maximizing nutrient uptake, to preventing phage replication or inhibiting bacterial and fungal growth. Increasingly, they are found to live in association with plants and insects, often conferring protective benefits to their host courtesy of their ability to produce pathogen-inhibitory antimicrobial compounds. Here, we highlight recent advances in understanding the competitive and cooperative interactions between Streptomyces and phage, microbes, and higher organisms in their environment.

Nb/Starch-Doped ZnO Nanostructures for Polluted Water Treatment and Antimicrobial Applications: Molecular Docking Analysis

Nb/starch-doped ZnO quantum dots (QDs) were prepared by a coprecipitation route. A fixed quantity of starch (st) and different concentrations (2 and 4%) of niobium (Nb) were doped in a ZnO lattice. To gain a better understanding of synthesized nanostructures, a systematic study was carried out utilizing several characterization methods. The goal of this research was to undertake methylene blue (MB) dye degradation with a synthetic material and also study its antibacterial properties. The phase structure, morphology, functional groups, optical properties, and elemental compositions of synthesized samples were investigated. Our study showed that ZnO QDs enhanced photocatalytic activity (PCA), resulting in effective MB degradation, in addition to showing good antimicrobial activity against Gram-negative relative to Gram-positive bacteria. Molecular docking study findings were in good agreement with the observed in vitro bactericidal potential and suggested ZnO, st-ZnO, and Nb/st-ZnO as possible inhibitors against dihydrofolate reductase (DHFR_E. coli) and DNA gyrase_E. coli.

Genome-Wide Identification of the LexA-Mediated DNA Damage Response in Streptomyces venezuelae

DNA damage triggers a widely conserved stress response in bacteria called the SOS response, which involves two key regulators, the activator RecA and the transcriptional repressor LexA. Despite the wide conservation of the SOS response, the number of genes controlled by LexA varies considerably between different organisms. The filamentous soil-dwelling bacteria of the genus Streptomyces contain LexA and RecA homologs, but their roles in Streptomyces have not been systematically studied. Here, we demonstrate that RecA and LexA are required for the survival of Streptomyces venezuelae during DNA-damaging conditions and for normal development during unperturbed growth. Monitoring the activity of a fluorescent recA promoter fusion and LexA protein levels revealed that the activation of the SOS response is delayed in S. venezuelae. By combining global transcriptional profiling and chromatin immunoprecipitation sequencing (ChIP-seq) analysis, we determined the LexA regulon and defined the core set of DNA damage repair genes that are expressed in response to treatment with the DNA-alkylating agent mitomycin C. Our results show that DNA damage-induced degradation of LexA results in the differential regulation of LexA target genes. Using surface plasmon resonance, we further confirmed the LexA DNA binding motif (SOS box) and demonstrated that LexA displays tight but distinct binding affinities to its target promoters, indicating a graded response to DNA damage.

IMPORTANCE The transcriptional regulator LexA functions as a repressor of the bacterial SOS response, which is induced under DNA-damaging conditions. This results in the expression of genes important for survival and adaptation. Here, we report the regulatory network controlled by LexA in the filamentous antibiotic-producing Streptomyces bacteria and establish the existence of the SOS response in Streptomyces. Collectively, our work reveals significant insights into the DNA damage response in Streptomyces that will promote further studies to understand how these important bacteria adapt to their environment.

DNA damage-induced block of sporulation in Streptomyces venezuelae involves downregulation of ssgB

DNA damage often causes an arrest of the cell cycle that provides time for genome integrity to be restored. In bacteria, the classical SOS DNA damage response leads to an inhibition of cell division resulting in temporarily filamentous growth. This raises the question as to whether such a response mechanism might similarly function in naturally filamentous bacteria such as Streptomyces. Streptomyces exhibit two functionally distinct forms of cell division: cross-wall formation in vegetative hyphae and sporulation septation in aerial hyphae. Here, we show that the genotoxic agent mitomycin C confers a block in sporulation septation in Streptomyces venezuelae in a mechanism that involves, at least in part, the downregulation of ssgB. Notably, this DNA damage response does not appear to block cross-wall formation and may be independent of canonical SOS and developmental regulators. We also show that the mitomycin C-induced block in sporulation can be partially bypassed by the constitutive expression of ssgB, though this appears to be largely limited to mitomycin C treatment and the resultant spore-like cells have reduced viability.

Effective Disposal of Methylene Blue and Bactericidal Benefits of Using GO-Doped MnO2 Nanorods Synthesized through One-Pot Synthesis

Graphene oxide (GO)-doped MnO2 nanorods loaded with 2, 4, and 6% GO were synthesized via the chemical precipitation route at room temperature. The aim of this work was to determine the catalytic and bactericidal activities of prepared nanocomposites. Structural, optical, and morphological properties as well as elemental composition of samples were investigated with advanced techniques such as X-ray diffraction (XRD), Fourier transform infrared (FTIR) spectroscopy, UV-visible (vis) spectroscopy, photoluminescence (PL), energy-dispersive spectrometry (EDS), and high-resolution transmission electron microscopy (HR-TEM). XRD measurements confirmed the monoclinic structure of MnO2. Vibrational mode and rotational mode of functional groups (O-H, C=C, C-O, and Mn-O) were evaluated using FTIR results. Band gap energy and blueshift in the absorption spectra of MnO2 and GO-doped MnO2 were identified with UV-vis spectroscopy. Emission spectra were attained using PL spectroscopy, whereas elemental composition of prepared materials was recorded with scanning electron microscopy (SEM)-EDS. Moreover, HR-TEM micrographs of doped and undoped MnO2 revealed elongated nanorod-like structure. Efficient degradation of methylene blue enhanced the catalytic activity in the presence of a reducing agent (NaBH4); this was attributed to the implantation of GO on MnO2 nanorods. Furthermore, substantial inhibition areas were measured for Escherichia coli (EC) ranging 2.10-2.85 mm and 2.50-3.15 mm at decreased and increased levels for doped MnO2 nanorods and 3.05-4.25 mm and 4.20-5.15 mm for both attentions against SA, respectively. In silico molecular docking studies suggested the inhibition of FabH and DNA gyrase of E. coli and Staphylococcus aureus as a possible mechanism behind the bactericidal activity of MnO2 and MnO2-doped GO nanoparticles (NPs).

Prodiginines Postpone the Onset of Sporulation in Streptomyces coelicolor

Bioactive natural products are typically secreted by the producer strain. Besides that, this allows the targeting of competitors, also filling a protective role, reducing the chance of self-killing. Surprisingly, DNA-degrading and membrane damaging prodiginines (PdGs) are only produced intracellularly, and are required for the onset of the second round of programmed cell death (PCD) in Streptomyces coelicolor. In this work, we investigated the influence of PdGs on the timing of the morphological differentiation of S. coelicolor. The deletion of the transcriptional activator gene redD that activates the red cluster for PdGs or nutrient-mediated reduction of PdG synthesis both resulted in the precocious appearance of mature spore chains. Transcriptional analysis revealed an accelerated expression of key developmental genes in the redD null mutant, including bldN for the developmental σ factor BldN which is essential for aerial mycelium formation. In contrast, PdG overproduction due to the enhanced copy number of redD resulted in a delay or block in sporulation. In addition, confocal fluorescence microscopy revealed that the earliest aerial hyphae do not produce PdGs. This suggests that filaments that eventually differentiate into spore chains and are hence required for survival of the colony, are excluded from the second round of PCD induced by PdGs. We propose that one of the roles of PdGs would be to delay the entrance of S. coelicolor into the dormancy state (sporulation) by inducing the leakage of the intracellular content of dying filaments thereby providing nutrients for the survivors.

Nonpathogenic Bacteria as Targets in Antimicrobial High-Throughput Screening

Antimicrobial screening usually analyses the effects of natural or synthetic molecules against pathogens. McAuley et al. changed this paradigm, testing the effect of synthetic compounds against the sporulation of the nonpathogenic bacterium Streptomyces venezuelae. They discovered a novel DNA-targeting antibiotic effective against pathogens.