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ACS Infectious Diseases Apr 2024New antimicrobial strategies are needed to address pathogen resistance to currently used antibiotics. Bacterial central metabolism is a promising target space for the...
New antimicrobial strategies are needed to address pathogen resistance to currently used antibiotics. Bacterial central metabolism is a promising target space for the development of agents that selectively target bacterial pathogens. 1-Deoxy-d-xylulose 5-phosphate synthase (DXPS) converts pyruvate and d-glyceraldehyde 3-phosphate (d-GAP) to DXP, which is required for synthesis of essential vitamins and isoprenoids in bacterial pathogens. Thus, DXPS is a promising antimicrobial target. Toward this goal, our lab has demonstrated selective inhibition of DXPS by alkyl acetylphosphonate (alkylAP)-based bisubstrate analogs that exploit the requirement for ternary complex formation in the DXPS mechanism. Here, we present the first DXPS structure with a bisubstrate analog bound in the active site. Insights gained from this cocrystal structure guided structure-activity relationship studies of the bisubstrate scaffold. A low nanomolar inhibitor (compound ) bearing a -dibenzyl glycine moiety conjugated to the acetylphosphonate pyruvate mimic via a triazole-based linker emerged from this study. Compound was found to exhibit slow, tight-binding inhibition, with contacts to DXPS residues R99 and R478 demonstrated to be important for this behavior. This work has discovered the most potent DXPS inhibitor to date and highlights a new role of R99 that can be exploited in future inhibitor designs toward the development of a novel class of antimicrobial agents.
Topics: Escherichia coli; Bacteria; Anti-Bacterial Agents; Pyruvates; Acetaldehyde; Transferases
PubMed: 38513073
DOI: 10.1021/acsinfecdis.3c00734 -
Microbial Biotechnology Mar 2024Pseudomonas putida is a soil bacterium with multiple uses in fermentation and biotransformation processes. P. putida ATCC 12633 can biotransform benzaldehyde and other...
Pseudomonas putida is a soil bacterium with multiple uses in fermentation and biotransformation processes. P. putida ATCC 12633 can biotransform benzaldehyde and other aldehydes into valuable α-hydroxyketones, such as (S)-2-hydroxypropiophenone. However, poor tolerance of this strain toward chaotropic aldehydes hampers efficient biotransformation processes. To circumvent this problem, we expressed the gene encoding the global regulator PprI from Deinococcus radiodurans, an inducer of pleiotropic proteins promoting DNA repair, in P. putida. Fine-tuned gene expression was achieved using an expression plasmid under the control of the LacI /P system, and the cross-protective role of PprI was assessed against multiple stress treatments. Moreover, the stress-tolerant P. putida strain was tested for 2-hydroxypropiophenone production using whole resting cells in the presence of relevant aldehyde substrates. P. putida cells harbouring the global transcriptional regulator exhibited high tolerance toward benzaldehyde, acetaldehyde, ethanol, butanol, NaCl, H O and thermal stress, thereby reflecting the multistress protection profile conferred by PprI. Additionally, the engineered cells converted aldehydes to 2-hydroxypropiophenone more efficiently than the parental P. putida strain. 2-Hydroxypropiophenone concentration reached 1.6 g L upon a 3-h incubation under optimized conditions, at a cell concentration of 0.033 g wet cell weight mL in the presence of 20 mM benzaldehyde and 600 mM acetaldehyde. Product yield and productivity were 0.74 g 2-HPP g benzaldehyde and 0.089 g 2-HPP g cell dry weight h , respectively, 35% higher than the control experiments. Taken together, these results demonstrate that introducing PprI from D. radiodurans enhances chaotrope tolerance and 2-HPP production in P. putida ATCC 12633.
Topics: Benzaldehydes; Pseudomonas putida; Deinococcus; Hydroxypropiophenone; Acetaldehyde
PubMed: 38498302
DOI: 10.1111/1751-7915.14448 -
Cytotechnology Apr 2024is a lactic-acid bacterium recently identified in fructose-rich environments. is also known to exhibit unusual growth characteristics due to an incomplete gene...
is a lactic-acid bacterium recently identified in fructose-rich environments. is also known to exhibit unusual growth characteristics due to an incomplete gene encoding alcohol/acetaldehyde hydrogenase, which results in an imbalance in the nicotinamide adenine mononucleotide (NAD)/NADN levels. Recently, the addition of d-fructose to the culture medium of strains increased the intracellular nicotinamide mononucleotide (NMN) content. In the present study, we evaluated the functionality of that produces high levels of NMN, using one substrain ( OS-1010). Therefore, in this study, we examined its functionality in the interaction between intestinal cells and muscle cells. The results showed that supernatant derived from intestinal epithelial cells (Caco-2 cells) treated with OS-1010 activated muscle cells (C2C12 cells). Further analysis revealed that Caco-2 cells treated with OS-1010 secreted exosomes known as extracellular vesicles, which activated the muscle cells. Furthermore, pathway analysis of the target genes of miRNA in exosomes revealed that pathways involved in muscle cell activation, including insulin signaling and cardiac muscle regulation, neurotrophic factors, longevity, and anti-aging, can be activated by exosomes. In other words, OS-1010 could activate various cells such as the skin and muscle cells, by secreting functional exosomes from the intestinal tract.
PubMed: 38495295
DOI: 10.1007/s10616-023-00610-1 -
AMB Express Mar 2024This study aimed to identify substances including Lactobacillus rhamnosus vitaP1 (KACC 92054P) that alleviate hangover-induced emotional anxiety and liver damage. The...
This study aimed to identify substances including Lactobacillus rhamnosus vitaP1 (KACC 92054P) that alleviate hangover-induced emotional anxiety and liver damage. The association between emotional anxiety caused by hangover and the genes P2X4, P2X7, SLC6A4 was investigated. In vitro and in vivo analyses were conducted to assess the influence of free-panica on alcohol-induced upregulated gene expression. Additionally, the concentration of AST, ALT, alcohol, and acetaldehyde in blood was measured. Free-panica, consisting of five natural products (Phyllanthus amarus, Phoenix dactylifera, Vitis vinifera, Zingiber officinale, and Lactobacillus rhamnosus), were evaluated for their regulatory effects on genes involved in alcohol-induced emotional anxiety and liver damage. The combination of these natural products in free-panica successfully restored emotional anxiety, and the concentration of AST, ALT, alcohol, and acetaldehyde in blood to those of the normal control group. These findings support the potential development of free-panica as a health functional food or medicinal intervention for relieving hangover symptoms and protecting liver from alcohol consumption.
PubMed: 38491208
DOI: 10.1186/s13568-024-01685-5 -
Translational Vision Science &... Mar 2024The purpose of this study was to search for contaminants in silicone oil tamponades removed from eyes treated for retinal detachment, and to correlate chemical results...
PURPOSE
The purpose of this study was to search for contaminants in silicone oil tamponades removed from eyes treated for retinal detachment, and to correlate chemical results with some clinical/functional parameters of the considered eyes.
METHODS
We examined a sequential cohort of eyes grouped according to the tamponade received: (1) Siluron2000 (S2), (2) RS-OIL ECS5000 (S5), and (3) Densiron Xtra (DX). Samples were collected at the beginning of the scheduled removal and analyzed by untargeted headspace gas-chromatography mass spectrometry (HS-GC-MS). Visual acuity and optic coherence tomography assessments were obtained before and after the tamponade removal.
RESULTS
Forty-one samples were analyzed: 22 belonging to the DX group, 13 to the S2 group, and 6 to the S5 group. For each group, a mixture of uninjected commercial preparation was analyzed as the reference. Different siloxanes and fluorinated compounds including perfluorodecalin (PFCL) were the most prevalent chemicals, found in 55% to 100% of the intraocular samples of the 3 groups. Some siloxanes were present also in the control matrices, whereas PFCL was only in the extracted tamponades. In the DX group, the concentration of hexamethylcyclotrisiloxane showed an inverse correlation trend with the duration of its permanence inside the eye (P = 0.054). Different alkanes, propanol, and acetaldehyde were identified only in the control matrices.
CONCLUSIONS
Several contaminants including siloxanes were identified in the intraocular samples and in the control matrices. A time-related ocular uptake of some of these is conceivable. PFCL was also highly present but only in intraocular samples.
TRANSLATIONAL RELEVANCE
After intraocular permanence silicone oils (SOs) have various unlabeled contaminants with some relevant differences with the commercial formulation chemical profile.
Topics: Humans; Retinal Detachment; Silicone Oils; Siloxanes; Eye; Fluorocarbons
PubMed: 38466299
DOI: 10.1167/tvst.13.3.4 -
Microbiology Spectrum Apr 2024All organisms utilize -adenosyl-l-methionine (SAM) as a key co-substrate for the methylation of biological molecules, the synthesis of polyamines, and radical SAM...
UNLABELLED
All organisms utilize -adenosyl-l-methionine (SAM) as a key co-substrate for the methylation of biological molecules, the synthesis of polyamines, and radical SAM reactions. When these processes occur, 5'-deoxy-nucleosides are formed as byproducts such as -adenosyl-l-homocysteine, 5'-methylthioadenosine (MTA), and 5'-deoxyadenosine (5dAdo). A prevalent pathway found in bacteria for the metabolism of MTA and 5dAdo is the dihydroxyacetone phosphate (DHAP) shunt, which converts these compounds into dihydroxyacetone phosphate and 2-methylthioacetaldehyde or acetaldehyde, respectively. Previous work in other organisms has shown that the DHAP shunt can enable methionine synthesis from MTA or serve as an MTA and 5dAdo detoxification pathway. Rather, the DHAP shunt in ATCC 25922, when introduced into K-12, enables the use of 5dAdo and MTA as a carbon source for growth. When MTA is the substrate, the sulfur component is not significantly recycled back to methionine but rather accumulates as 2-methylthioethanol, which is slowly oxidized non-enzymatically under aerobic conditions. The DHAP shunt in ATCC 25922 is active under oxic and anoxic conditions. Growth using 5-deoxy-d-ribose was observed during aerobic respiration and anaerobic respiration with Trimethylamine N-oxide (TMAO), but not during fermentation or respiration with nitrate. This suggests the DHAP shunt may only be relevant for extraintestinal pathogenic lineages with the DHAP shunt that inhabit oxic or TMAO-rich extraintestinal environments. This reveals a heretofore overlooked role of the DHAP shunt in carbon and energy metabolism from ubiquitous SAM utilization byproducts and suggests a similar role may occur in other pathogenic and non-pathogenic bacteria with the DHAP shunt.
IMPORTANCE
The acquisition and utilization of organic compounds that serve as growth substrates are essential for to grow and multiply. Ubiquitous enzymatic reactions involving S-adenosyl-l-methionine as a co-substrate by all organisms result in the formation of the 5'-deoxy-nucleoside byproducts, 5'-methylthioadenosine and 5'-deoxyadenosine. All possess a conserved nucleosidase that cleaves these 5'-deoxy-nucleosides into 5-deoxy-pentose sugars for adenine salvage. The DHAP shunt pathway is found in some extraintestinal pathogenic , but its function in possessing it has remained unknown. This study reveals that the DHAP shunt enables the utilization of 5'-deoxy-nucleosides and 5-deoxy-pentose sugars as growth substrates in strains with the pathway during aerobic respiration and anaerobic respiration with TMAO, but not fermentative growth. This provides an insight into the diversity of sugar compounds accessible by with the DHAP shunt and suggests that the DHAP shunt is primarily relevant in oxic or TMAO-rich extraintestinal environments.
Topics: S-Adenosylmethionine; Escherichia coli; Dihydroxyacetone Phosphate; Methionine; Bacteria; Pentoses; Carbon; Sugars; Deoxyadenosines; Methylamines; Thionucleosides
PubMed: 38441472
DOI: 10.1128/spectrum.03086-23 -
Polish Journal of Microbiology Mar 2024Hydrocarbon constituents of petroleum are persistent, bioaccumulated, and bio-magnified in living tissues, transported to longer distances, and exert hazardous effects...
Hydrocarbon constituents of petroleum are persistent, bioaccumulated, and bio-magnified in living tissues, transported to longer distances, and exert hazardous effects on human health and the ecosystem. Bioaugmentation with microorganisms like bacteria is an emerging approach that can mitigate the toxins from environmental sources. The present study was initiated to target the petroleum-contaminated soil of gasoline stations situated in Lahore. Petroleum degrading bacteria were isolated by serial dilution method followed by growth analysis, biochemical and molecular characterization, removal efficiency estimation, metabolites extraction, and GC-MS of the metabolites. Molecular analysis identified the bacterium as Bacillus cereus, which exhibited maximum growth at 72 hours and removed 75% petroleum. Biochemical characterization via the Remel RapID ONE panel system showed positive results for arginine dehydrolase (ADH), ornithine decarboxylase (ODC), lysine decarboxylase (LDC), -nitrophenyl-β-D-galactosidase (ONPG), -nitrophenyl-β-D-glucosidase (βGLU), -nitrophenyl-N-acetyl-β-D-glucosaminidase (NAG), malonate (MAL), adonitol fermentation (ADON), and tryptophane utilization (IND). GC-MS-based metabolic profiling identified alcohols (methyl alcohol, -, - and -cresols, catechol, and 3-methyl catechol), aldehydes (methanone, acetaldehyde, and -tolualdehyde), carboxylic acid (methanoic acid, -muconic acid, cyclohexane carboxylic acid and benzoic acid), conjugate bases of carboxylic acids (benzoate, -muconate, 4-hydroxybenzoate, and pyruvate) and cycloalkane (cyclohexene). It suggested the presence of methane, methylcyclohexane, toluene, xylene, and benzene degradation pathways in .
Topics: Humans; Bacillus cereus; Ecosystem; Hydrocarbons; Methane; Carboxylic Acids
PubMed: 38437466
DOI: 10.33073/pjm-2024-012 -
The Journal of Physical Chemistry. A Mar 2024Though there is a growing body of literature on the kinetics of CIs with simple carbonyls, CI reactions with functionalized carbonyls such as hydroxyketones remain...
Though there is a growing body of literature on the kinetics of CIs with simple carbonyls, CI reactions with functionalized carbonyls such as hydroxyketones remain unexplored. In this work, the temperature-dependent kinetics of the reactions of CHOO with two hydroxyketones, hydroxyacetone (AcOH) and 4-hydroxy-2-butanone (4H2B), have been studied using a laser flash photolysis transient absorption spectroscopy technique and complementary quantum chemistry calculations. Bimolecular rate constants were determined from CHOO loss rates observed under pseudo-first-order conditions across the temperature range 275-335 K. Arrhenius plots were linear and yielded -dependent bimolecular rate constants: () = (4.3 ± 1.7) × 10 exp[(1630 ± 120)/] and () = (3.5 ± 2.6) × 10 exp[(1700 ± 200)/]. Both reactions show negative temperature dependences and overall very similar rate constants. Stationary points on the reaction energy surfaces were characterized using the composite CBS-QB3 method. Transition states were identified for both 1,3-dipolar cycloaddition reactions across the carbonyl and 1,2-insertion/addition at the hydroxyl group. The free-energy barriers for the latter reaction pathways are higher by ∼4-5 kcal mol, and their contributions are presumed to be negligible for both AcOH and 4H2B. The cycloaddition reactions are highly exothermic and form cyclic secondary ozonides that are the typical primary products of Criegee intermediate reactions with carbonyl compounds. The reactivity of the hydroxyketones toward CHOO appears to be similar to that of acetaldehyde, which can be rationalized by consideration of the energies of the frontier molecular orbitals involved in the cycloaddition. The CHOO + hydroxyketone reactions are likely too slow to be of significance in the atmosphere, except at very low temperatures.
PubMed: 38428028
DOI: 10.1021/acs.jpca.4c00156 -
Environmental Science & Technology Mar 2024-Nitrosamines are potential human carcinogens frequently detected in natural and engineered aquatic systems. This study sheds light on the role of carbonyl compounds in...
-Nitrosamines are potential human carcinogens frequently detected in natural and engineered aquatic systems. This study sheds light on the role of carbonyl compounds in the formation of -nitrosamines by nitrosation of five secondary amines via different pathways. The results showed that compared to a control system, the presence of formaldehyde enhances the formation of -nitrosamines by a factor of 5-152 at pH 7, depending on the structure of the secondary amines. Acetaldehyde showed a slight enhancement effect on -nitrosamine formation, while acetone and benzaldehyde did not promote nitrosation reactions. For neutral and basic conditions, the iminium ion was the dominant intermediate for -nitrosamine formation, while carbinolamine became the major contributor under acidic conditions. Negative free energy changes (<-19 kcal mol) and relatively low activation energies (<18 kcal mol) of the reactions of secondary amines with NO, iminium ions with nitrite and carbinolamines with NO from quantum chemical computations further support the proposed reaction pathways. This highlights the roles of the iminium ion and carbinolamine in the formation of -nitrosamines during nitrosation in the presence of carbonyl compounds, especially in the context of industrial wastewater.
Topics: Humans; Nitrosamines; Nitrosation; Amines; Carcinogens; Nitrites
PubMed: 38427382
DOI: 10.1021/acs.est.3c07461 -
Frontiers in Cellular and Infection... 2024The aim of the work was to analyze the metabolites of the intestinal microbiota from the patients with mild cognitive impairment (MCI) and progressive MCI due to...
PURPOSE
The aim of the work was to analyze the metabolites of the intestinal microbiota from the patients with mild cognitive impairment (MCI) and progressive MCI due to Alzheimer's disease (AD).
METHOD
Two cohorts were established. The first one included 87 subjects with 30 healthy controls (NC), 22 patients with MCI due to AD, and 35 patients with AD. The second cohort included 87 patients with MCI due to AD, who were followed up for 2 years and finally were divided into progressive MCI due to AD group (P-G) and unprogressive MCI due to AD group (U-G) according their cognitive levels. Fecal samples were collected to all patients at the baseline time point. Differential metabolites were subjected to pathway analysis by MetaboAnalyst.
RESULTS
In the first cohort, we found 21 different metabolites among the three groups (AD, MCI, and NC). In the second cohort, we identified 19 differential metabolites between the P-G and U-G groups. By machine learning analysis, we found that seven characteristic metabolites [Erythrodiol, alpha-Curcumene, Synephrine, o-Hydroxylaminobenzoate, 3-Amino-4-hydroxybenzoic acid, 2-Deoxystreptamine, and 9(S] were of characteristic significance for the diagnosis of MCI due to AD, and six metabolites (Indolelactate, Indole-3-acetaldehyde, L-Proline, Perillyl, Mesaconate, and Sphingosine) were the characteristic metabolites of early warning for the progression of MCI due to AD. D-Glucuronic acid was negatively correlated with Apolipoprotein E4 (APOE4). Perillyl alcohol was negatively correlated with all of the five biomarkers [P-tau181, Neurofilament light chain (NF-light), Aβ1-42, Aβ1-40, and glial fibrillary acidic protein (GFAP)], but Indoleacetaldehyde was positively correlated with three biomarkers (P-tau181, Aβ1-42, and GFAP). Three characteristic metabolites (3-Amino-4-hydroxybenzoate, 2-Deoxystreptamine, and p-Synephrine) were positively correlated with Aβ1-42. 2-Deoxystreptamine, 9(S)-HPOT, and Indoleacetaldehyde were positively correlated with GFAP. L-Proline and Indoleacetaldehyde were positively correlated with NF-light.
CONCLUSION
Specific metabolites of intestinal fora can be used as diagnostic and progressive markers for MCI.
Topics: Humans; Amyloid beta-Peptides; tau Proteins; Synephrine; Alzheimer Disease; Cognitive Dysfunction; Biomarkers; Proline
PubMed: 38404286
DOI: 10.3389/fcimb.2024.1351523