-
International Journal of Molecular... Oct 2023The healing properties of silver have been used since ancient times. The main aim of the study was to collect and review the literature on the clinical potential of... (Review)
Review
The healing properties of silver have been used since ancient times. The main aim of the study was to collect and review the literature on the clinical potential of silver, its salts and complex compounds. The second goal was to present an outline of the historical use of silver in medicine and pharmacy, taking into account the possibility of producing pharmaceutical drug forms on the premises of pharmacies. In the context of the growing resistance of microorganisms to available, widely used antibiotics, silver plays a key role. There is only one known case of bacterial resistance to silver-the strain, which naturally occurs in silver mines. The development of research in the field of coordination chemistry offers great opportunities in the design of new substances in which silver ions can be incorporated. These substances exhibit increased potency and often an extended antimicrobial spectrum. Silver-based compounds are, however, only limited to external applications, as opposed to their historic oral administration. Advanced studies of their physicochemical, microbiological, cytotoxic and genotoxic properties are ongoing and full of challenges. The improvement of the methods of synthesis gives the possibility of applying the newly synthesized compounds , as was the case with the complex of metronidazole with silver (I) nitrate. Some of these experimental efforts performed in vitro are followed with clinical trials. The third and final goal of this study was to present the possibility of obtaining an ointment under the conditions of an actual pharmacy using silver (I) salts and a ligand, both of which are active substances with antimicrobial properties.
Topics: Silver; Salts; Pharmacies; Anti-Infective Agents; Anti-Bacterial Agents; Silver Compounds; Pharmaceutical Preparations; Pharmacy
PubMed: 37958707
DOI: 10.3390/ijms242115723 -
Analytical Chemistry Aug 2023Small proteins of around 50 aa in length have been largely overlooked in genetic and biochemical assays due to the inherent challenges with detecting and characterizing...
Small proteins of around 50 aa in length have been largely overlooked in genetic and biochemical assays due to the inherent challenges with detecting and characterizing them. Recent discoveries of their critical roles in many biological processes have led to an increased recognition of the importance of small proteins for basic research and as potential new drug targets. One example is CcoM, a 36 aa subunit of the -type oxidase that plays an essential role in adaptation to oxygen-limited conditions in , a model for the clinically relevant, opportunistic pathogen . However, as no comprehensive data were available in , we devised an integrated, generic approach to study small proteins more systematically. Using the first complete genome as basis, we conducted bottom-up proteomics analyses and established a digest-free, direct-sequencing proteomics approach to study cells grown under aerobic and oxygen-limiting conditions. Finally, we also applied a proteogenomics pipeline to identify missed protein-coding genes. Overall, we identified 2921 known and 29 novel proteins, many of which were differentially regulated. Among 176 small proteins 16 were novel. Direct sequencing, featuring a specialized precursor acquisition scheme, exhibited advantages in the detection of small proteins with higher (up to 100%) sequence coverage and more spectral counts, including sequences with high proline content. Three novel small proteins, uniquely identified by direct sequencing and not conserved beyond , were predicted to form an operon with a conserved protein and may represent genes. These data demonstrate the power of this combined approach to study small proteins in and show its potential for other prokaryotes.
Topics: Pseudomonas stutzeri; Proteomics; Proteogenomics; Pseudomonas aeruginosa; Oxygen
PubMed: 37535005
DOI: 10.1021/acs.analchem.3c00676 -
Synthetic and Systems Biotechnology Dec 2023A1501 is a non-fluorescent denitrifying bacteria that belongs to the gram-negative bacterial group. As a prominent strain in the fields of agriculture and...
A1501 is a non-fluorescent denitrifying bacteria that belongs to the gram-negative bacterial group. As a prominent strain in the fields of agriculture and bioengineering, there is still a lack of comprehensive understanding regarding its metabolic capabilities, specifically in terms of central metabolism and substrate utilization. Therefore, further exploration and extensive studies are required to gain a detailed insight into these aspects. This study reconstructed a genome-scale metabolic network model for A1501 and conducted extensive curations, including correcting energy generation cycles, respiratory chains, and biomass composition. The final model, iQY1018, was successfully developed, covering more genes and reactions and having higher prediction accuracy compared with the previously published model iPB890. The substrate utilization ability of 71 carbon sources was investigated by BIOLOG experiment and was utilized to validate the model quality. The model prediction accuracy of substrate utilization for A1501 reached 90 %. The model analysis revealed its new ability in central metabolism and predicted that the strain is a suitable chassis for the production of Acetyl CoA-derived products. This work provides an updated, high-quality model of A1501for further research and will further enhance our understanding of the metabolic capabilities.
PubMed: 37927897
DOI: 10.1016/j.synbio.2023.10.001 -
Molecular Plant-microbe Interactions :... Sep 2023spp. make up 1.6% of the bacteria in the soil and are found throughout the world. More than 140 species of this genus have been identified, some beneficial to the...
spp. make up 1.6% of the bacteria in the soil and are found throughout the world. More than 140 species of this genus have been identified, some beneficial to the plant. Several species in the family Pseudomonadaceae, including AvOP, A1501, DSM4166, 6HT33bT, and sp. strain K1 can fix nitrogen from the air. The genes required for these reactions are organized in a nitrogen fixation island, obtained via horizontal gene transfer from , , and . Today, this island is conserved in spp. from different geographical locations, which, in turn, have evolved to deal with different geo-climatic conditions. Here, we summarize the molecular mechanisms behind -driven plant growth promotion, with particular focus on improving plant performance at limiting nitrogen (N) and improving plant N content. We describe -plant interaction strategies in the soil, noting that the mechanisms of denitrification, ammonification, and secondary metabolite signaling are only marginally explored. Plant growth promotion is dependent on the abiotic conditions and differs at sufficient and deficient N. The molecular controls behind different plant responses are not fully elucidated. We suggest that superposition of transcriptome, proteome, and metabolome data and their integration with plant phenotype development through time will help fill these gaps. The aim of this review is to summarize the knowledge behind -driven nitrogen fixation and to point to possible agricultural solutions. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
PubMed: 36989040
DOI: 10.1094/MPMI-10-22-0223-CR -
MSphere Jun 2024The RNA chaperone Hfq acts as a global regulator of numerous biological processes, such as carbon/nitrogen metabolism and environmental adaptation in plant-associated...
UNLABELLED
The RNA chaperone Hfq acts as a global regulator of numerous biological processes, such as carbon/nitrogen metabolism and environmental adaptation in plant-associated diazotrophs; however, its target RNAs and the mechanisms underlying nitrogen fixation remain largely unknown. Here, we used enhanced UV cross-linking immunoprecipitation coupled with high-throughput sequencing to identify hundreds of Hfq-binding RNAs probably involved in nitrogen fixation, carbon substrate utilization, biofilm formation, and other functions. Collectively, these processes endow strain A1501 with the requisite capabilities to thrive in the highly competitive rhizosphere. Our findings revealed a previously uncharted landscape of Hfq target genes. Notable among these is , encoding an isomerase necessary for nitrogenase reductase solubility; , encoding an ammonium transporter; , encoding a carbohydrate porin; and , encoding a chemotaxis protein. Furthermore, we identified more than 100 genes of unknown function, which expands the potential direct regulatory targets of Hfq in diazotrophs. Our data showed that Hfq directly interacts with the mRNA of regulatory proteins (RsmA, AlgU, and NifA), regulatory ncRNA RsmY, and other potential targets, thus revealing the mechanistic links in nitrogen fixation and other metabolic pathways.
IMPORTANCE
Numerous experimental approaches often face challenges in distinguishing between direct and indirect effects of Hfq-mediated regulation. New technologies based on high-throughput sequencing are increasingly providing insight into the global regulation of Hfq in gene expression. Here, enhanced UV cross-linking immunoprecipitation coupled with high-throughput sequencing was employed to identify the Hfq-binding sites and potential targets in the root-associated A1501 and identify hundreds of novel Hfq-binding RNAs that are predicted to be involved in metabolism, environmental adaptation, and nitrogen fixation. In particular, we have shown Hfq interactions with various regulatory proteins' mRNA and their potential targets at the posttranscriptional level. This study not only enhances our understanding of Hfq regulation but, importantly, also provides a framework for addressing integrated regulatory network underlying root-associated nitrogen fixation.
Topics: Pseudomonas stutzeri; Host Factor 1 Protein; Nitrogen Fixation; Gene Expression Regulation, Bacterial; Plant Roots; RNA, Bacterial; Gene Expression Profiling; Gene Regulatory Networks; Bacterial Proteins; High-Throughput Nucleotide Sequencing; Transcriptome; Rhizosphere
PubMed: 38747590
DOI: 10.1128/msphere.00762-23 -
Journal of Ophthalmic Inflammation and... Feb 2024To describe a puzzling case of endophthalmitis caused by three unusual bacteria after intravitreal injection, its outcome, and underlying questions.
PURPOSE
To describe a puzzling case of endophthalmitis caused by three unusual bacteria after intravitreal injection, its outcome, and underlying questions.
FINDINGS
A 70-year-old female patient was diagnosed with acute endophthalmitis following intravitreal aflibercept injection for age-related macular degeneration. A standard tap and inject procedure was performed. Microbiological analyses on the anterior chamber and vitreous samples yielded the presence of three non-fermenting Gram-negative rods: Pseudomonas stutzeri, Stenotrophomonas maltophilia, and Ochrobactrum anthropi. The outcome was favorable after intravitreal injections of vancomycin and ceftazidime, with an almost complete recovery of the visual acuity to its baseline level. No potential source of infection was identified.
CONCLUSION
Endophthalmitis following intravitreal injection can be caused by a wide variety of bacteria, including some rare Gram-negative species. They can sometimes co-exist in a single patient, but their virulence may vary greatly. Due to the variable antibiotic susceptibility and frequent multiresistance associated with non-fermenting Gram-negative rods, a prompt microbiological approach is required. Favorable outcome can be achieved with standard management.
PubMed: 38334879
DOI: 10.1186/s12348-023-00376-9 -
Applied and Environmental Microbiology Aug 2023Several microbial taxa have been associated with food processing facilities, and they might resist by attaching on tools and equipment even after sanitation procedures,...
Several microbial taxa have been associated with food processing facilities, and they might resist by attaching on tools and equipment even after sanitation procedures, producing biofilms that adhere to the surfaces and might embed other microorganisms, including spoilers and pathogens. There is increasing evidence that these communities can be transferred to the final product. To explore the microbial contamination routes in a facility producing ice creams, we collected foods and environmental swabs from industrial surfaces of equipment and tools and performed taxonomic and functional analyses of the microbial DNA extracted from the environmental samples. Our results suggest that complex communities dominated by psychrotrophic bacteria (e.g., Pseudomonas and Acinetobacter spp.) inhabit the food processing environment, and we demonstrate that these communities might be transferred from the surfaces to the products. Functional analysis performed on environmental samples highlighted the presence of several genes linked to antimicrobial resistance and adherence on abiotic surfaces; such genes were more abundant on food contact (FC) than on other surfaces. Metagenome-assembled genomes (MAGs) of Pseudomonas stutzeri showed genes linked with biofilm formation and motility, which are surely linked to colonizing capabilities in the processing lines. The study highlights clear potential advantages of applying microbiome mapping in the food industry for source tracking of microbial contamination and for planning appropriate sanitization strategies. Several microbial species might permanently establish in food processing facilities, thus contributing to food loss. In fact, food contact surfaces might transfer microorganisms to intermediates and products, potentially representing a hazard to human health. In this work, we provide evidence of the existence of complex microbial communities overcoming sanitation in an ice cream-producing facility. These communities harbored several genes that could potentially lead to attachment to surfaces and antimicrobial resistance. Also, prediction of routes of contamination showed that several potential spoilage taxa might end up in the final product. Importantly, in this work, we show that mapping the environmental microbiome is a high-resolution technique that might help food business operators ensure food quality and safety through detection of potentially hazardous microorganisms.
Topics: Humans; Ice Cream; Virulence; Bacteria; Food Handling; Biofilms; Anti-Infective Agents; Food Microbiology
PubMed: 37432121
DOI: 10.1128/aem.00765-23 -
Frontiers in Bioengineering and... 2023Acetate is a low-cost feedstock for the production of different bio-chemicals. Electrochemical reduction of CO into acetate and subsequent acetate fermentation is a...
Acetate is a low-cost feedstock for the production of different bio-chemicals. Electrochemical reduction of CO into acetate and subsequent acetate fermentation is a promising method for transforming CO into value-added chemicals. However, the significant inhibitory effect of acetate on microbial growth remains a barrier for acetate-based biorefinery. In this study, the deletion of genes involved in L-leucine degradation was found to be beneficial for the growth of A1501 in acetate. (Δ), in which the hydroxymethylglutaryl-CoA lyase catalyzing -hydroxy--methylglutaryl-CoA into acetyl-CoA and acetoacetate was deleted, grew faster than other mutants and exhibited increased tolerance to acetate. Then, the genes from H16 for poly-3-hydroxybutyrate (PHB) biosynthesis were overexpressed in (∆) and the recombinant strain (∆-) can accumulate 0.11 g L PHB from commercial acetate. Importantly, (∆-) can also use CO-derived acetate to produce PHB and the accumulated PHB accounted for 5.42% (w/w) of dried cell weight of (∆-).
PubMed: 38026858
DOI: 10.3389/fbioe.2023.1297431 -
Frontiers in Medicine 2023Although pre/pro/postbiotics have become more prevalent in dermatologic and cosmetic fields, the mode of action when topically applied is largely unknown. A multi-omic...
INTRODUCTION
Although pre/pro/postbiotics have become more prevalent in dermatologic and cosmetic fields, the mode of action when topically applied is largely unknown. A multi-omic approach was applied to decipher the impact of the skincare products with pre/postbiotics on skin microbiome and metabolome.
METHODS
Subjects with dry skin applied a body wash and body lotion with or without pre/postbiotics for 6 weeks. Skin hydration was measured at baseline, 3 and 6 weeks. Skin swabs were collected for 16S rRNA gene sequencing, metagenomics and metabolomics analysis.
RESULTS
Skin hydration significantly increased in both groups. The prebiotic group significantly reduced opportunistic pathogens, e.g., and , and increased the commensals, e.g., , . Bacterial sugar degradation pathways were enriched in the prebiotic group, while fatty acid biosynthesis pathways were reduced in control. The changes on skin metabolome profiles by the products were more prominent. The prebiotic group performed greater modulation on many clinically-relevant metabolites compared to control. Correlation analysis showed and positively correlated with skin hydration, and negatively correlated with the metabolites that are positively associated with skin hydration improvement.
CONCLUSION
This holistic study supported a hypothesis that the pre/postbiotics increased skin hydration through the modulation of skin microbiome, metabolic pathways and metabolome.
PubMed: 37534320
DOI: 10.3389/fmed.2023.1165980 -
Biofilm Dec 2023Biofilms are complex microbial communities embedded in extracellular matrix. Pathogens within the biofilm become more resistant to the antibiotics than planktonic...
Biofilms are complex microbial communities embedded in extracellular matrix. Pathogens within the biofilm become more resistant to the antibiotics than planktonic counterparts. Novel strategies are required to encounter biofilms. Exopolysaccharides are one of the major components of biofilm matrix and play a vital role in biofilm architecture. In previous studies, a glycosyl hydrolase, PslG, from was found to be able to inhibit biofilm formation by disintegrating exopolysaccharide in biofilms. Here, we investigate the potential spectrum of PslG homologous protein with anti-biofilm activity. One glycosyl hydrolase from , PslG, exhibits anti-biofilm activities and the key catalytic residues of PslG are conserved with those of PslG. PslG at concentrations as low as 50 nM efficiently inhibits the biofilm formation of and disassemble its preformed biofilm. Furthermore, PslG exhibits anti-biofilm activity on a series of , including and pv. . PslG stays active under various temperatures. Our findings suggest that glycosyl hydrolase PslG has potential to be a broad spectrum inhibitor on biofilm formation of a wide range of .
PubMed: 37928620
DOI: 10.1016/j.bioflm.2023.100155