Central Carbon Research Articles

Mechanism of action of persulfate activation based on humic acid modified sludge biochar: Enhancement of electron transfer mechanism

Humic acid (HA) was used to modify sludge biochar (SBC) in order to prepare HBC with higher defect structure and abundant oxygenated functional groups. The degradation of TC by HBC was up to 90 % much higher than that of SBC (30 %). HBC possessed a large number of defective structures and oxygenated functional groups, which contributed greatly to the activation of PMS. The co-regulation of highly exposed active sites such as CO, pyrrole N and pyridine N on HBC2, which played a key role in the activation of PMS. In addition, the results of electrochemical tests indicated that an active intermediate (Persistent free radicals PFRs). Oxygen-centered PFRs were implicated in the movement of electrons through conversion to carbon centers. The conductivity of the process was enhanced by the presence of graphite N. A large number of reactive radicals made sufficient preparations for the production of PFRs. Mutual electron transfer between the oxygen and carbon centers of PFRs was the main mechanism. In addition, the PFRs mechanism and the 1O2 mechanism were subjected, which yielded that both degrade TC by electrophilic addition attack and ring-opening reaction, respectively.

Coral larvae increase nitrogen assimilation to stabilize algal symbiosis and combat bleaching under increased temperature.

Rising sea surface temperatures are increasingly causing breakdown in the nutritional relationship between corals and algal endosymbionts (Symbiodiniaceae), threatening the basis of coral reef ecosystems and highlighting the critical role of coral reproduction in reef maintenance. The effects of thermal stress on metabolic exchange (i.e., transfer of fixed carbon photosynthates from symbiont to host) during sensitive early life stages, however, remains understudied. We exposed symbiotic Montipora capitata coral larvae in Hawai'i to high temperature (+2.5°C for 3 days), assessed rates of photosynthesis and respiration, and used stable isotope tracing (4 mM 13C sodium bicarbonate; 4.5 h) to quantify metabolite exchange. While larvae did not show any signs of bleaching and did not experience declines in survival and settlement, metabolic depression was significant under high temperature, indicated by a 19% reduction in respiration rates, but with no change in photosynthesis. Larvae exposed to high temperature showed evidence for maintained translocation of a major photosynthate, glucose, from the symbiont, but there was reduced metabolism of glucose through central carbon metabolism (i.e., glycolysis). The larval host invested in nitrogen cycling by increasing ammonium assimilation, urea metabolism, and sequestration of nitrogen into dipeptides, a mechanism that may support the maintenance of glucose translocation under thermal stress. Host nitrogen assimilation via dipeptide synthesis appears to be used for nitrogen limitation to the Symbiodiniaceae, and we hypothesize that nitrogen limitation contributes to retention of fixed carbon by favoring photosynthate translocation to the host. Collectively, our findings indicate that although these larvae are susceptible to metabolic stress under high temperature, diverting energy to nitrogen assimilation to maintain symbiont population density, photosynthesis, and carbon translocation may allow larvae to avoid bleaching and highlights potential life stage specific metabolic responses to stress.

Proteo-metabolomic insights for early dual physical and cognitive impairments: A search for biomarkers of healthy aging based on muscle-brain crosstalk.

We employed an untargeted proteo-metabolomic approach to profile circulating biomarkers in plasma samples from the I-Lan Longitudinal Aging Study, aiming to identify biomarkers and pathways associated with physio-cognitive decline syndrome (PCDS). In 115 propensity score-matched PCDS case-control pairs, pathway analyses implicated dysregulation of fatty acid metabolism and inflammation in PCDS pathogenesis. Sex-specific associations were observed, with disruptions in central carbon metabolism (elevated PKM, MDH1, and GAPDH; decreased MINPP1) and tyrosine metabolism (decreased MIF, DBH; increased thyroxine) characterizing in men. In contrast, perturbations in glutathione and phenylalanine metabolism, including increased ANPEP, GSTP1, and decreased pyroglutamic acid, were identified in women. Results suggest that dysregulated energy and redox homeostasis likely contribute to PCDS development. Notably, ANPEP, PKM, and MIF emerged as potential biomarkers, elucidating the muscle-brain crosstalk framework. Our findings provide insights into potential molecular mechanisms underlying PCDS and the muscle-brain crosstalk, marking progress toward elucidating biomarkers in the journey of healthy aging.

Sonophotocatalytic degradation of rhodamine B dye using Zr doped ZnO nanoparticles: Kinetic study and toxicity assessment

This study investigates sonophotocatalysis for the oxidation of Rhodamine B (RhB) dye using Zr doped ZnO nanoparticles. The synthesized nanoparticles were characterized by scanning electron microscope, Fourier-transform infrared, X-ray diffraction, Brunauer Emmett-Teller, thermogravimetric analysis, and photoluminescence. The hybrid sonophotocatalysis system achieved 98.73 ± 1.25% degradation of RhB under the conditions: RhB dye concentration = 10 ppm, 4 wt% of Zr doped ZnO = 0.1 g, reaction temperature = 30 °C, time = 60 min, pH = 7. A kinetic model was developed to predict the efficiency of RhB degradation through intrinsic elementary chemical reactions. The high coefficient of determination (R2 = 0.96) indicates the model's prediction accuracy in describing the degradation kinetics of RhB within sonophotocatalysis system. The electrical energy per order (EEO) analysis demonstrated that US + UVC + 4 wt% of Zr doped ZnO significantly reduced EEO (1055 kWh m−3 order−1). The synergy index for this combination was approximately 1.60, demonstrating a significant synergistic effect. Density Functional Theory (DFT) studies were utilized to propose the most probable degradation pathway, identifying reactive sites and potential byproducts. The simulations revealed the central carbon atom (1C site) as highly susceptible to radical attacks, indicating potential decolorization pathways such as N-de-ethylation, chromophore cleavage, and ring opening. Toxicity assessments of both the parent dye and its intermediates were conducted using ECOSAR (Ecological Structure Activity Relationship) to evaluate their ecological impacts. The combination of experimental results and kinetic modeling and simulations offers a deep understanding of RhB degradation complexities, driving advancements in sustainable water treatment technologies.

Synthesis and Structural Characterization of Carbazole‐Tailored Luminescent Triarylmethyl Radical and its Stable Cation

AbstractThe development of novel luminescent radicals, characterized by their unique doublet emission, endows a significant challenge. In this study, we reported the synthesis of a luminescent neutral radical, BCzAnM‐R, tailored by two carbazolyl groups and an anthryl group to achieve a nonalternant structure. It exhibited near‐infrared emission with a peak at 1020 nm in toluene. Interestingly, its corresponding cation, BCzAnM‐C, was synthesized through an unconventional SnCl2‐mediated reduction‐aromatization‐oxidation reaction in one‐pot and gram‐scale. The cation demonstrated remarkable stability for up to weeks in ambient conditions and facilitated the silica‐gel chromatography isolation as an organic salt with SnCl3− as the counter ion. The carbazolyl groups effectively modulate molecular structures, photophysical properties, and stabilities. Notably, BCzAnM‐R represents the first luminescent triarylmethyl radical with two carbazolyl groups directly attached to the central carbon.

“Boron Ylide” Enables Stereoselective Construction of gem‐Diborylcyclopropanes

AbstractThe stereoselective cyclopropanation of olefins with “boron ylide” is disclosed for the first time, providing a modular strategy for the synthesis of stereospecific diboryl‐functionalized cyclopropanes. The chiral gem‐diborylcyclopropanes are synthesized with excellent enantioselectivity with the aid of a chiral auxiliary. Based on the powerful transformable ability of boryl group, those challenging multi‐quaternary carbon centers in cyclopropane units have been facilely constructed with excellent stereoselectivity. Control experiments indicate that the boryl groups are necessary for both chemoselectivity and stereoselectivity control.

"Boron Ylide" Enables Stereoselective Construction of gem-Diborylcyclopropanes.

The stereoselective cyclopropanation of olefins with "boron ylide" is disclosed for the first time, providing a modular strategy for the synthesis of stereospecific diboryl-functionalized cyclopropanes. The chiral gem-diborylcyclopropanes are synthesized with excellent enantioselectivity with the aid of a chiral auxiliary. Based on the powerful transformable ability of boryl group, those challenging multi-quaternary carbon centers in cyclopropane units have been facilely constructed with excellent stereoselectivity. Control experiments indicate that the boryl groups are necessary for both chemoselectivity and stereoselectivity control.

Host dependent specialized metabolism of nitrogen export in actinorhizal nodules induced by Frankia cluster-2.

Frankia cluster-2 strains are diazotrophs that engage in root nodule symbiosis with actinorhizal plants of the Cucurbitales and the Rosales. Previous studies have shown that an assimilated nitrogen source, presumably arginine, is exported to the host in nodules of Datisca glomerata (Cucurbitales), while a different metabolite is exported in the nodules of Ceanothus thyrsiflorus (Rosales). To investigate if an assimilated nitrogen form is commonly exported to the host by cluster-2 strains, and which metabolite would be exported in Ceanothus, we analysed gene expression levels, metabolite profiles, and enzyme activities in nodules. We conclude that the export of assimilated nitrogen in symbiosis seems to be a common feature for Frankia cluster-2 strains, but which source is host-dependent. The export of assimilated ammonium to the host suggests that 2-oxoglutarate is drawn from the TCA cycle at a high rate. This specialised metabolism obviates the need for the reductive branch of the TCA cycle. We found several genes encoding enzymes of the central carbon and nitrogen metabolism were lacking in Frankia cluster-2 genomes: the glyoxylate shunt and succinate semialdehyde dehydrogenase. This led to a linearization of the TCA cycle, and we hypothesize this could explain the low saprotrophic potential of Frankia cluster-2.

Transcriptomics-guided optimization of vitamins to enhance erythromycin yield in saccharopolyspora erythraea

Comparative transcriptomics uncovered distinct expression patterns of genes associated with cofactor and vitamin metabolism in the high-yielding mutant strain Saccharopolyspora erythraea HL3168 E3, as compared to the wild-type NRRL 2338. An in-depth analysis was conducted on the effects of nine vitamins, and it was determined that thiamine pyrophosphate (TPP), vitamin B2, vitamin B6, vitamin B9, vitamin B12, and hemin are key enhancers in erythromycin production in E3, increasing the erythromycin titer by 7.96–12.66%. Then, the Plackett-Burman design and the path of steepest ascent were applied to further optimize the vitamin combination for maximum production efficiency, enhancing the erythromycin titer in shake flasks by 39.2%. Otherwise, targeted metabolomics and metabolic flux analysis illuminated how vitamin supplementation modulates the central carbon metabolism with notable effects on the TCA cycle and methionine synthesis to augment the provision of energy and precursors essential for erythromycin synthesis. This work highlights the capacity for precise vitamin supplementation to refine metabolic pathways, thereby boosting erythromycin production, and provides valuable directions for application on an industrial scale.Graphical

Unraveling Cecal Alterations in Clostridioides difficile Colonized Mice through Comprehensive Metabolic Profiling.

The disruption of gut microbiota caused by antibiotics favors the intestinal colonization of Clostridioides difficile - a Gram-positive, spore-forming anaerobic bacterium that causes potentially fatal gastrointestinal infections. In an endeavor to elucidate the complexities of the gut-brain axis in the context of Clostridium difficile infection (CDI), a murine model has been used to investigate the potential effects of antibiotic administration and subsequent colonization by C. difficile, as well as the impact of three different 10-day treatments (metronidazole, probiotics, and fecal microbiota transplantation), on the cecal metabolome for the first time. This follows our previous research which highlighted the metabolic effect of CDI and these treatments in the brain and employs the same four different metabolomics-based methods (targeted GC-MS/MS, targeted HILIC-MS/MS, untargeted RP-LC-HRMS/MS and untargeted GC-MS). A total of 286 unique metabolites have been identified in the mouse cecal profiles and statistical analysis revealed that CDI, as well as the subsequent treatments, significantly alters cecal metabolites and lipids implicated in various biochemical pathways centered around amino acid metabolism, glycerophospholipid metabolism, and central carbon metabolism. To our knowledge, this study represents the first exploration of the effects of C. difficile-induced colitis and potential treatments on the cecal tissue metabolome.

Enantioselective Preparation of Cyclopentene-Based Amino Acids with a Quaternary Carbon Center.

Azlactone is an important starting material for synthesizing amino acids containing a quaternary α-carbon. In this study, we have developed a sequential "one-pot" procedure involving an enantioselective spirocyclization reaction followed by acidic azlactone opening, which led to amino acid derivatives. The key step of this procedure is a spirocyclization between propargylated azlactones and enals by using a cooperative catalytic approach that combines chiral secondary amine and achiral Pd(0) complexes. The final acid opening of the azlactone motif allows isolation of the corresponding amino acid derivatives as major diastereoisomers in yields ranging from 37% to 70% with enantioselectivities of 85-97% ee. These synthesized amino acid derivatives hold great potential in the pharmaceutical and bioactive compound industries. Moreover, the final amino acid products with a cyclopentene moiety can be further derivatized, opening up even more possibilities for their application.

Diastereoselective Access to Ester-Substituted cis-Phenanthridinones via Hydrogen Atom Transfer-Involved 1,7-Enyne Bicyclization.

An organophotoredox-catalyzed 1,7-enyne bicyclization for the cis-diastereoselective synthesis of ester-substituted phenanthridinones has been achieved through radical cascade cyclization involving 1,6-hydrogen atom transfer. This transition-metal- and oxidant-free one-pot protocol generates three distinct C-C bonds and two quaternary carbon centers.

Understanding metabolic plasticity at single cell resolution.

It is increasingly clear that cellular metabolic function varies not just between cells of different tissues, but also within tissues and cell types. In this essay, we envision how differences in central carbon metabolism arise from multiple sources, including the cell cycle, circadian rhythms, intrinsic metabolic cycles, and others. We also discuss and compare methods that enable such variation to be detected, including single-cell metabolomics and RNA-sequencing. We pay particular attention to biosensors for AMPK and central carbon metabolites, which when used in combination with metabolic perturbations, provide clear evidence of cellular variance in metabolic function.

Engineering Halomonas bluephagenesis for synthesis of polyhydroxybutyrate (PHB) in the presence of high nitrogen containing media

The trade-offs exist between microbial growth and bioproduct synthesis including intracellular polyester polyhydroxybutyrate (PHB). Under nitrogen limitation, more carbon flux is directed to PHB synthesis while growth is inhibited with diminishing overall carbon utilization, similar to the suboptimal carbon utilization during glycolysis-derived pyruvate decarboxylation. This study reconfigured the central carbon network of Halomonas bluephagenesis to improve PHB yield theoretically and practically. It was found that the downregulation of glutamine synthetase (GS) activity led to a synchronous improvement on PHB accumulation and cell growth under nitrogen non-limitation condition, increasing the PHB yield from glucose (g/g) to 85% of theoretical yield, PHB titer from 7.6 g/L to 12.9 g/L, and from 51 g/L to 65 g/L when grown in shake flasks containing a rich N-source, and grown in a fed-batch cultivation conducted in a 7-L bioreactor also containing a rich N-source, respectively. Results offer better metabolic balance between glucose conversion efficiency and microbial growth for economic PHB production.

Regulating the metabolic flux of pyruvate dehydrogenase bypass to enhance lipid production in Saccharomyces cerevisiae

To achieve high efficiency in microbial cell factories, it is crucial to redesign central carbon fluxes to ensure an adequate supply of precursors for producing high-value compounds. In this study, we employed a multi-omics approach to rearrange the central carbon flux of the pyruvate dehydrogenase (PDH) bypass, thereby enhancing the supply of intermediate precursors, specifically acetyl-CoA. This enhancement aimed to improve the biosynthesis of acetyl-CoA-derived compounds, such as terpenoids and fatty acid-derived molecules, in Saccharomyces cerevisiae. Through transcriptomic and lipidomic analyses, we identified ALD4 as a key regulatory gene influencing lipid metabolism. Genetic validation demonstrated that overexpression of the mitochondrial acetaldehyde dehydrogenase (ALDH) gene ALD4 resulted in a 20.1% increase in lipid production. This study provides theoretical support for optimising the performance of S. cerevisiae as a “cell factory” for the production of commercial compounds.

Coordination of cell division and chromosome segregation by iron and a sRNA in Escherichia coli

Iron is a vital metal ion frequently present as a cofactor in metabolic enzymes involved in central carbon metabolism, respiratory chain, and DNA synthesis. Notably, iron starvation was previously shown to inhibit cell division, although the mechanism underlying this observation remained obscure. In bacteria, the sRNA RyhB has been intensively characterized to regulate genes involved in iron metabolism during iron starvation. While using the screening tool MAPS for new RyhB targets, we found that the mRNA zapB, a factor coordinating chromosome segregation and cell division (cytokinesis), was significantly enriched in association with RyhB. To confirm the interaction between RyhB and zapB mRNA, we conducted both in vitro and in vivo experiments, which showed that RyhB represses zapB translation by binding at two distinct sites. Microscopy and flow cytometry assays revealed that, in the absence of RyhB, cells become shorter and display impaired chromosome segregation during iron starvation. We hypothesized that RyhB might suppress ZapB expression and reduce cell division during iron starvation. Moreover, we observed that deleting zapB gene completely rescued the slow growth phenotype observed in ryhB mutant during strict iron starvation. Altogether, these results suggest that during growth in the absence of iron, RyhB sRNA downregulates zapB mRNA, which leads to longer cells containing extra chromosomes, potentially to optimize survival. Thus, the RyhB-zapB interaction demonstrates intricate regulatory mechanisms between cell division and chromosome segregation depending on iron availability in E. coli.

Tricyanomethane or Dicyanoketenimine-Silylation makes the Difference.

Pseudohalides such as tricyanomethanide, [C(CN)3]-, are well known in chemistry, biochemistry and industrial chemistry. The protonated species HC(CN)3, a classic hydrogen pseudohalide Brønsted acid, is a very strong acid with a pKa value of -5. However, HC(CN)3 is difficult to handle as it tends to decompose rapidly or, more precisely, to oligo- and polymerize. Therefore, silylated pseudohalide compounds with the [Me3Si]+ as the "big organometallic proton" have become interesting, exhibiting similar chemical properties but better kinetic protection. Here, the stepwise silylation of the pseudohalide anion [C(CN)3]- is reported, forming the heavier homologue of HC(CN)3, namely [Me3Si][C(CN)3], and in presence of two additional [Me3Si]+ cations even the dicationic species [(Me3Si-NC)3C]2+ as stable [B(C6F5)4]- salt. Surprisingly, in contrast to the protonated species HC(CN)3, in which the proton is bound to the central carbon atom of [C(CN)3]-, silylation of the [C(CN)3]- anion occurs at one of the three terminal nitrogen atoms, thus forming the long-sought dicyanoketenimine [Me3Si-NC-C(CN)2]. All further silylation steps take place exclusively on the terminal N atoms of the three CN groups and not on the central carbon atom, until the intriguing, highly symmetrical dication, [(Me3Si-NC)3C]2+, is finally generated. The experimental data are supported by quantum chemical calculations in terms of thermodynamics and chemical bonding.

Strain variation in Candida albicans glycolytic gene regulation.

Central carbon metabolism is vital for the proliferation of Candida albicans, a fungus that is prominent as a commensal and pathogen. Glycolytic genes are activated by overlapping activities of the transcription factors Tye7 and Gal4, as shown by studies in the SC5314 genetic background. However, regulatory relationships can vary among C. albicans isolates. Here, we analyzed Tye7- and Gal4-related phenotypes in five diverse clinical isolates of C. albicans. We tested growth properties and gene expression impact through Nanostring profiling and, for the two strains SC5314 and P87, RNA sequencing. Our results lead to three main conclusions. First, the functional redundancy of Tye7 and Gal4 for glycolytic gene activation is preserved among all strains tested. Second, at the gene expression level, strain P87 is an outlier with regard to tye7Δ/Δ impact, and strain SC5314 is an outlier with regard to gal4Δ/Δ impact. Third, while Gal4 is well known to be dispensable for induction of the GAL1, GAL7, and GAL10 galactose-specific metabolic genes, we find that gal4Δ/Δ mutants of several strains have a mild galactose fermentation defect, as assayed by growth on galactose with the respiration inhibitor antimycin A. Our findings indicate that even a central metabolic regulatory network is subject to strain variation and illustrates an unexpected genotype-phenotype relationship.The fungal commensal and pathogen Candida albicans rely upon metabolic flexibility to colonize and infect host niches. Central carbon metabolism is governed by two regulators, Tye7 and Gal4, as defined in the reference strain SC5314. Here, we have explored the impact of Tye7 and Gal4 on carbon utilization and gene expression across five diverse C. albicans clinical isolates. Novel aspects of this study are the finding that even a central metabolic regulatory network is subject to strain variation and the observation of an unexpected mutant phenotype.

Advancing Anticancer Drug Discovery: Leveraging Metabolomics and Machine Learning for Mode of Action Prediction by Pattern Recognition.

A bottleneck in the development of new anti-cancer drugs is the recognition of their mode of action (MoA). Metabolomics combined with machine learning allowed to predict MoAs of novel anti-proliferative drug candidates, focusing on human prostate cancer cells (PC-3). As proof of concept, 38 drugs are studied with known effects on 16 key processes of cancer metabolism, profiling low molecular weight intermediates of the central carbon and cellular energy metabolism (CCEM) by LC-MS/MS. These metabolic patterns unveiled distinct MoAs, enabling accurate MoA predictions for novel agents by machine learning. The transferability of MoA predictions based on PC-3 cell treatments is validated with two other cancer cell models, i.e., breast cancer and Ewing's sarcoma, and show that correct MoA predictions for alternative cancer cells are possible, but still at some expense of prediction quality. Furthermore, metabolic profiles of treated cells yield insights into intracellular processes, exemplified for drugs inducing different types of mitochondrial dysfunction. Specifically, it is predicted that pentacyclic triterpenes inhibit oxidative phosphorylation and affect phospholipid biosynthesis, as confirmed by respiration parameters, lipidomics, and molecular docking. Using biochemical insights from individual drug treatments, this approach offers new opportunities, including the optimization of combinatorial drug applications.

Fluxomic, Metabolomic, and Transcriptomic Analyses Reveal Metabolic Responses to Phenazine-1-carboxamide Synthesized in Pseudomonas chlororaphis.

Phenazine-1-carboxamide (PCN) has been exploited as a successful biopesticide due to its broad-spectrum antifungal activity. We engineered a PCN-overproducing Pseudomonas chlororaphis strain through overexpressing shikimate pathway genes (aroB, aroQ, aroE, and phzC) and deleting negative regulatory genes (relA, fleQ, and pykF). The optimized strain produced 1.92 g/L PCN with a yield of 0.11 g/g glycerol, the highest titer ever reported by using minimal media. To gain deeper insights into the underlying regulatory network, the final strain and the parental strain were examined using three distinct omic data sets. 13C-metabolic flux analysis revealed a substantial flux reconfiguration in the optimized strain, including the activation of the EDEMP cycle, the PP pathway, the glyoxylate shunt, and the shikimate pathway. Metabolomic results indicated that central carbon was rerouted to the shikimate pathway. Transcriptomic data identified global gene expression changes. This study forms the basis for further engineering of strains to achieve outstanding performance.