Tricarboxylic acid cycle activity suppresses acetylation of mitochondrial proteins during early embryonic development in Caenorhabditis elegans

Elucidating the effective age for dietary restriction and the key metabolites involved

Dietary restriction (DR) extends lifespan in various species, but its effect at different ages, especially when started later, is unclear. This study used Caenorhabditis elegans to explore the impact of DR at different ages. Worms were divided into control and DR groups, with daily survival monitored. To confirm the occurrence of DR, the expression of DR-sensitive genes namely acdh-1, pyk-1, pck-2 and cts-1 were determined using RT-qPCR. Liquid chromatography mass spectrometry (LC-MS) was employed to observe the changes in metabolites affected by DR. The results indicated that young worms subjected to mild DR displayed the longest lifespan, highlighting the effectiveness of initiating DR at a young age. Increased expression of acdh-1 and pck-2 suggests activation of beta-oxidation and gluconeogenesis, while decreased cts-1 expression indicates a reduced citric acid cycle, further supporting the observed effects of DR in these worms. Metabolomic results indicated that DR decreased the activity of mechanistic Target of Rapamycin (mTOR) and the synthesis of amino acids namely leucine, tyrosine and tryptophan to conserve energy for cell repair and survival. DR also decreased levels of N-acetyl-L-methionine and S-adenosyl-methionine (SAM) in methionine metabolism, thereby promoting autophagy, reducing inflammation, and facilitating the removal of damaged cells and proteins. In conclusion, initiating dietary restriction early in life extends the lifespan by modulating amino acid metabolism and enhancing the autophagy pathway, thereby maintaining cellular wellbeing.

Synergistic anti-aging effect of Dendrobium officinale polysaccharide and spermidine: A metabolomics analysis focusing on the regulation of lipid, nucleotide and energy metabolism

The importance of synergy has been underscored in recent medical research for augmenting the efficacy of therapeutic interventions, targeting multiple biological pathways simultaneously. Our prior research elucidated that Dendrobium officinale polysaccharide (DOP) has the potential to prolong the lifespan of Caenorhabditis elegans (C. elegans) via regulating gut microbiota. Concurrently, spermidine (Spd), as a mimicking caloric restriction, facilitates autophagy and exerts a pronounced anti-aging effect. To enhance the anti-aging capabilities of DOP, we conducted a comprehensive study examining the combined effects of DOP and Spd in C. elegans, incorporating metabolomics analysis to investigate the underlying mechanisms. A combination of 250 mg/L DOP and 29.0 mg/L Spd yielded the most favorable outcomes in lifespan extension, evidencing a synergistic effect with a combination index (CI) of 0.65. In oxidative and heat stress tolerance assays, the observed CIs were 0.50 and 0.33, respectively. Metabolomic analysis highlighted significant alterations in metabolites related to lipid, nucleotide and energy metabolism, notably regulating glycerol 3-phosphate, linoleoyl glycerol, docosapentaenoic acid and β-nicotinamide mononucleotide, nicotinamide adenine dinucleotide. The effects of DS on lipid metabolism were further validated using Oil Red O staining and triglyceride level in C. elegans. The results indicated that DS may primarily be via modulating lipid metabolism. To further confirm these findings, a high-fat diet-induced mouse model was employed. Consequently, it can be inferred that the synergistic anti-aging impact of DOP and Spd is likely mediated primarily through alterations in lipid metabolic processes.

Omics analysis unveils changes in the metabolome and lipidome of Caenorhabditis elegans upon polydopamine exposure

Polydopamine (PDA) is an insoluble biopolymer with a dark brown-black color that forms through the autoxidation of dopamine. Because of its outstanding biocompatibility and durability, PDA holds enormous promise for various applications, both in the biomedical and non-medical domains. To ensure human safety, protect health, and minimize environmental impacts, the assessment of PDA toxicity is important. In this study, metabolomics and lipidomics assessed the impact of acute PDA exposure on Caenorhabditis elegans (C. elegans). The findings revealed a pronounced perturbation in the metabolome and lipidome of C. elegans at the L4 stage following 24 hours of exposure to 100 µg/mL PDA. The changes in lipid composition varied based on lipid classes. Increased lipid classes included lysophosphatidylethanolamine, triacylglycerides, and fatty acids, while decreased species involved in several sub-classes of glycerophospholipids and sphingolipids. Besides, we detected 37 significantly affected metabolites in the positive and 8 in the negative ion modes due to exposure to PDA in C. elegans. The metabolites most impacted by PDA exposure were associated with purine metabolism, biosynthesis of valine, leucine, and isoleucine; aminoacyl-tRNA biosynthesis; and cysteine and methionine metabolism, along with pantothenate and CoA biosynthesis; the citrate cycle (TCA cycle); and beta-alanine metabolism. In conclusion, PDA exposure may intricately influence the metabolome and lipidome of C. elegans. The combined application of metabolomics and lipidomics offers additional insights into the metabolic perturbations involved in PDA-induced biological effects and presents potential biomarkers for the assessment of PDA safety.

Acylspermidines are conserved mitochondrial sirtuin-dependent metabolites

Sirtuins are nicotinamide adenine dinucleotide (NAD+)-dependent protein lysine deacylases regulating metabolism and stress responses; however, characterization of the removed acyl groups and their downstream metabolic fates remains incomplete. Here we employed untargeted comparative metabolomics to reinvestigate mitochondrial sirtuin biochemistry. First, we identified N-glutarylspermidines as metabolites downstream of the mitochondrial sirtuin SIR-2.3 in Caenorhabditis elegans and demonstrated that SIR-2.3 functions as a lysine deglutarylase and that N-glutarylspermidines can be derived from O-glutaryl-ADP-ribose. Subsequent targeted analysis of C. elegans, mouse and human metabolomes revealed a chemically diverse range of N-acylspermidines, and formation of N-succinylspermidines and/or N-glutarylspermidines was observed downstream of mammalian mitochondrial sirtuin SIRT5 in two cell lines, consistent with annotated functions of SIRT5. Finally, N-glutarylspermidines were found to adversely affect C. elegans lifespan and mammalian cell proliferation. Our results indicate that N-acylspermidines are conserved metabolites downstream of mitochondrial sirtuins that facilitate annotation of sirtuin enzymatic activities in vivo and may contribute to sirtuin-dependent phenotypes.

Ultrasound-driven radical chain reaction and immunoregulation of piezoelectric-based hybrid coating for treating implant infection

The poor efficiency of US-responsive coatings on implants restricts their practical application. Immunotherapy that stimulates immune cells to enhance their antibacterial activity is expected to synergize with sonodynamic therapy for treating implant infection effectively and safely. Herein, US-responsive hybrid coatings composed of the oxygen-deficient BaTiO3 nanorod arrays and l-arginine (BaTiO3-x/LA) are designed and prepared on titanium implants for sonocatalytic therapy-cooperated immunotherapy to treat Methicillin-resistant Staphylococcus aureus (MRSA) infection. BaTiO3-x/LA can generate more oxidizing reactive oxygen species (ROS, hydroxyl radical (·OH)) and reactive nitrogen species (RNS, peroxynitrite anion (ONOO-)). The construction of nanorod arrays and oxygen defects balances the piezoelectric properties and sonocatalytic capability during US treatment. The generated piezoelectric electric field provides a sufficient driving force to separate electrons and holes, and the oxygen defects attenuate the electron-hole recombination efficiency, consequently increasing the yield of ROS during the US treatment. Moreover, nitric oxide (NO) released by l-arginine reacts with the superoxide radical (·O2-) to produce ONOO-. Since, this radical chain reaction improves the oxidizing ability between bacteria and radicals, the cell membrane (argB, secA2) and DNA (dnaBGXN) are destroyed. The bacterial self-repair mechanism indirectly accelerates bacterial death based on the transcriptome analysis. In addition to participating in the radical chain reaction, NO positively affects macrophage M1 polarization to yield potent phagocytosis to MRSA. As a result, without introducing an extra sonosensitizer, BaTiO3-x/LA exhibits excellent antibacterial activity against MRSA after the US treatment for 15 min. Furthermore, BaTiO3-x/LA facilitates macrophage M2 polarization after implantation and improves osteogenic differentiation. The combined effects of sonodynamic therapy and immunoregulation lead to an effective and safe treatment method for implant-associated infections.

Effects of polystyrene microplastics on the metabolic level of Pseudomonas aeruginosa

Given the widespread presence of Pseudomonas aeruginosa in water and its threat to human health, the metabolic changes in Pseudomonas aeruginosa when exposed to polystyrene microplastics (PS-MPs) exposure were studied, focusing on molecular level. Through non-targeted metabolomics, a total of 64 differential metabolites were screened out under positive ion mode and 44 under negative ion mode. The content of bacterial metabolites changed significantly, primarily involving lipids, nucleotides, amino acids, and organic acids. Heightened intracellular oxidative damage led to a decrease in lipid molecules and nucleotide-related metabolites. The down-regulation of amino acid metabolites, such as L-Glutamic and L-Proline, highlighted disruptions in cellular energy metabolism and the impaired ability to synthesize proteins as a defense against oxidation. The impact of PS-MPs on organic acid metabolism was evident in the inhibition of pyruvate and citrate, thereby disrupting the cells' normal participation in energy cycles. The integration of Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that PS-MPs mainly caused changes in metabolic pathways, including ABC transporters, Aminoacyl-tRNA biosynthesis, Purine metabolism, Glycerophospholipid metabolism and TCA cycle in Pseudomonas aeruginosa. Most of the differential metabolites enriched in these pathways were down-regulated, demonstrating that PS-MPs hindered the expression of metabolic pathways, ultimately impairing the ability of cells to synthesize proteins, DNA, and RNA. This disruption affected cell proliferation and information transduction, thus hampering energy circulation and inhibiting cell growth. Findings of this study supplemented the toxic effects of microplastics and the defense mechanisms of microorganisms, in turn safeguarding drinking water safety and human health.

Allantoic fluid metabolome reveals specific metabolic signatures in chicken lines different for their muscle glycogen content

Nutrient availability in eggs can affect early metabolic orientation in birds. In chickens divergently selected on the Pectoralis major ultimate pH, a proxy for muscle glycogen stores, characterization of the yolk and amniotic fluid revealed a different nutritional environment. The present study aimed to assess indicators of embryo metabolism in pHu lines (pHu+ and pHu-) using allantoic fluids (compartment storing nitrogenous waste products and metabolites), collected at days 10, 14 and 17 of embryogenesis and characterized by 1H-NMR spectroscopy. Analysis of metabolic profiles revealed a significant stage effect, with an enrichment in metabolites at the end of incubation, and an increase in interindividual variability during development. OPLS-DA analysis discriminated the two lines. The allantoic fluid of pHu- was richer in carbohydrates, intermediates of purine metabolism and derivatives of tryptophan-histidine metabolism, while formate, branched-chain amino acids, Krebs cycle intermediates and metabolites from different catabolic pathways were more abundant in pHu+. In conclusion, the characterization of the main nutrient sources for embryos and now allantoic fluids provided an overview of the in ovo nutritional environment of pHu lines. Moreover, this study revealed the establishment, as early as day 10 of embryo development, of specific metabolic signatures in the allantoic fluid of pHu+ and pHu- lines.

The growth toxicity and neurotoxicity mechanism of waterborne TBOEP to nematodes: Insights from transcriptomic and metabolomic profiles

Tris(2-butoxy) ethyl phosphate (TBOEP) is a typical organophosphorus flame retardant (OPFR), which has been detected in natural water bodies and drinking water and has reached a certain concentration. As a new type of organic pollutant, the environmental health risk of TBOEP needs to be assessed urgently. Here, Caenorhabditis elegans were exposed to 0, 50, 500, and 5000 ng/L TBOEP in water for 72 h. The results showed that TBOEP exposure caused concentration-dependent inhibition to the growth of nematodes, while exposure to 5000 ng/L TBOEP significantly inhibited the locomotor behavior of nematodes. Transcriptomic and metabolomic analysis showed that the disturbances in neurotransmitter transmission and amino acid, carbohydrate, and lipid metabolism were the reason for the neurotoxicity and growth toxicity of TBOEP to nematodes. These results provide basic data and a theoretical basis for evaluating the environmental health risks of organophosphorus flame retardants.

Effects of Fe2+ addition to sugarcane molasses on poly-γ-glutamic acid production in Bacillus licheniformis CGMCC NO. 23967

BACKGROUND

Poly-γ-glutamic acid (γ-PGA) is biodegradable, water-soluble, environment-friendly, and edible. Consequently, it has a variety of industrial applications. It is crucial to control production cost and increase output for industrial production γ-PGA.

RESULTS

Here γ-PGA production from sugarcane molasses by Bacillus licheniformis CGMCC NO. 23967 was studied in shake-flasks and bioreactors, the results indicate that the yield of γ-PGA could reach 40.668 g/L in a 5L stirred tank fermenter. Further study found that γ-PGA production reached 70.436 g/L, γ-PGA production and cell growth increased by 73.20% and 55.44%, respectively, after FeSO₄·7H₂O was added. Therefore, we investigated the metabolomic and transcriptomic changes following FeSO₄·7H₂O addition. This addition resulted in increased abundance of intracellular metabolites, including amino acids, organic acids, and key TCA cycle intermediates, as well as upregulation of the glycolysis pathway and TCA cycle.

CONCLUSIONS

These results compare favorably with those obtained from glucose and other forms of biomass feedstock, confirming that sugarcane molasses can be used as an economical substrate without any pretreatment. The addition of FeSO₄·7H₂O to sugarcane molasses may increase the efficiency of γ-PGA production in intracellular.

Polyol pathway and redox balance in diabetes

Diabetes is a major public health disease that is globally approaching epidemic proportions. One of the major causes of type 2 diabetes is either a defect in insulin secretion or insulin action which is usually caused by a combination of genetic and environmental factors. Not only these factors but others such as deregulation of various pathways, and oxidative stress are also known to trigger the redox imbalance in diabetics. Increasing evidences suggest that there are tight interactions between the development of diabetes and redox imbalance. An alternate pathway of glucose metabolism, the polyol pathway, becomes active in patients with diabetes that disturbs the balance between NADH and NAD+ . The occurrence of such redox imbalance supports other pathways that lead to oxidative damage to DNA, lipids, and proteins and consequently to oxidative stress which further ascend diabetes and its complications. However, the precise mechanism through which oxidative stress regulates diabetes progression remains to be elucidated. The understanding of how antioxidants and oxidants are controlled and impact the generation of oxidative stress and progression of diabetes is essential. The main focus of this review is to provide an overview of redox imbalance caused by oxidative stress through the polyol pathway. Understanding the pathological role of oxidative stress in diabetes will help to design potential therapeutic strategies against diabetes.

Aberrant methylmalonylation underlies methylmalonic acidemia and is attenuated by an engineered sirtuin

Organic acidemias such as methylmalonic acidemia (MMA) are a group of inborn errors of metabolism that typically arise from defects in the catabolism of amino and fatty acids. Accretion of acyl-CoA species is postulated to underlie disease pathophysiology, but the mechanism(s) remain unknown. Here, we surveyed hepatic explants from patients with MMA and unaffected donors, in parallel with samples from various mouse models of methylmalonyl-CoA mutase deficiency. We found a widespread posttranslational modification, methylmalonylation, that inhibited enzymes in the urea cycle and glycine cleavage pathway in MMA. Biochemical studies and mouse genetics established that sirtuin 5 (SIRT5) controlled the metabolism of MMA-related posttranslational modifications. SIRT5 was engineered to resist acylation-driven inhibition via lysine to arginine mutagenesis. The modified SIRT5 was used to create an adeno-associated viral 8 (AAV8) vector and systemically delivered to mutant and control mice. Gene therapy ameliorated hyperammonemia and reduced global methylmalonylation in the MMA mice.

Bone protein analysis via label-free quantitative proteomics in patients with periprosthetic joint infection

Periprosthetic joint infection (PJI) is a catastrophic complication of arthroplasty. The treatment of PJI often requires multiple operations and long-term use of antibiotics, making PJI a substantial health and economic burden for patients. Therefore, there is an urgent need to elucidate the pathological mechanism of PJI to explore new therapeutic methods. This study aimed to explore proteomics changes in bone tissue around the prosthesis during PJI development, to explain the pathological mechanism and to provide new treatment ideas. Ten patients who underwent revision surgery at our institution were included: 5 patients with Staphylococcus aureus PJI and 5 patients with aseptic failure. The proteomics changes in bone tissues after PJI were investigated by label-free quantitative proteomics, and the pathways affected by the differential proteins were analyzed by GO annotation, GO enrichment analysis, KEGG enrichment analysis and protein-protein interaction network analysis. We identified 435 differentially expressed proteins (DEPs), with 213 upregulated and 222 downregulated proteins. Analysis revealed activation of immune-related pathways, such as complement and coagulation cascades, phagocytosis, and neutrophil activation, and inhibition of energy metabolism pathways represented by the TCA cycle. We also observed an altered balance between osteoblasts and osteoclasts during S. aureus PJI. We hope that these processes will reveal new treatment ideas. SIGNIFICANCE: PJI is a catastrophic complication of arthroplasty. When infection occurs, bacteria may invade periprosthetic bone tissue to escape immunity and cause damage. So far, only few studies focused on the changes of proteomics associated to PJI. This is the first study to describe the proteomics changes of periprosthetic bone tissue of patients with PJI. We found that the pathological process of S. aureus PJI mainly involves activation of the immune system, decreased energy metabolism, and an altered balance of osteoblasts and osteoclasts.

Environmentally relevant concentrations of tralopyril affect carbohydrate metabolism and lipid metabolism of zebrafish (Danio rerio) by disrupting mitochondrial function

Tralopyril (TP), an antifouling biocide, is widely used to prevent heavy biofouling, and can have potential risks to aquatic organisms. However, there is little information available on the toxicity of tralopyril to aquatic organisms. In this study, the effect of TP on carbohydrate and lipid metabolism, and related mechanisms were evaluated in zebrafish (Danio rerio) larvae. Adverse modifications in carbohydrate metabolism were observed in larvae: hexokinase (HK) activity, succinate dehydrogenase (SDH) activity, and adenosine triphosphate (ATP) content were significantly decreased; and transcript expression of genes (GK, HK1, and PCK1) was also significantly changed. Changes of TG content, FAS activity and transcript expression of genes (ACO, ehhadh, and fas) indicate that TP disrupt lipid metabolism in zebrafish larvae. The change in expression of genes (ndufs4, Sdhα, and uqcrc2) involved in the mitochondrial respiratory complexes, and genes (polg1 and tk2) involved in the mitochondrial DNA replication and transcription indicates that these adverse effects on carbohydrate and lipid metabolism are caused by mitochondrial dysfunction.

Mitochondrial aconitase controls adipogenesis through mediation of cellular ATP production

Mitochondrial aconitase (Aco2) catalyzes the conversion of citrate to isocitrate in the TCA cycle, which produces NADH and FADH2, driving synthesis of ATP through OXPHOS. In this study, to explore the relationship between adipogenesis and mitochondrial energy metabolism, we hypothesize that Aco2 may play a key role in the lipid synthesis. Here, we show that overexpression of Aco2 in 3T3-L1 cells significantly increased lipogenesis and adipogenesis, accompanied by elevated mitochondrial biogenesis and ATP production. However, when ATP is depleted by rotenone, an inhibitor of the respiratory chain, the promotive role of Aco2 in adipogenesis is abolished. In contrast to Aco2 overexpression, deficiency of Aco2 markedly reduced lipogenesis and adipogenesis, along with the decreased mitochondrial biogenesis and ATP production. Supplementation of isocitrate efficiently rescued the inhibitory effect of Aco2 deficiency. Similarly, the restorative effect of isocitrate was abolished in the presence of rotenone. Together, these results show that Aco2 sustains normal adipogenesis through mediating ATP production, revealing a potential mechanistic link between TCA cycle enzyme and lipid synthesis. Our work suggest that regulation of adipose tissue mitochondria function may be a potential way for combating abnormal adipogenesis related diseases such as obesity and lipodystrophy.

Update on the role of Sirtuin 3 in cell differentiation: A major metabolic target that can be pharmacologically controlled

Cell differentiation is a fundamental biological event in which a precursor stem cell is turning into a specialized somatic cell. It is thus crucial for the development, tissue turnover and regeneration in mammals. Among the numerous changes taking place in a cell during a differentiation programme, the biology of mitochondria, the central organelle mainly responsible for energy homeostasis and stress adaptation, is deeply modified. These modifications are now well recognized as taking an active part to the completion of the differentiation programme. Indeed, mitochondrial biogenesis and metabolic shift are observed during cell differentiation, adapting many syntheses, calcium homeostasis, ATP and reactive oxygen species production, to the needs. These mitochondrial functions are substantially regulated by the post-translational modifications of the mitochondrial proteins among which lysine acetylation is essential. This mitoacetylome is then globally controlled by the balance between spontaneous/enzymatically-catalysed protein acetylation and the NAD⁺-dependent deacetylation mediated by Sirtuin 3. This enzyme is now considered as a major regulator of the function of the organelle. Regarding the requirement of these mitochondrial adaptations, the subsequent growing interest for this enzyme recently extended to the investigation of the mechanisms driving cell differentiation. This review summarizes the currently available information about the significance of SIRT3 in cell differentiation in physio-pathological contexts. We also suggest a control of the differentiation-activated autophagy by SIRT3, a hypothesis supported by recent findings establishing a causal link between SIRT3 and autophagy. Eventually, an update on the present pharmacological modulators of SIRT3 in a context of cell differentiation is discussed.

Investigation of Glutamate Dependence Mechanism for Poly-γ-glutamic Acid Production in Bacillus subtilis on the Basis of Transcriptome Analysis

The development of commercial poly-γ-glutamic acid (γ-PGA) production by glutamate-dependent strains requires understanding the glutamate dependence mechanism in the strains. Here, we first systematically analyzed the response pattern of Bacillus subtilis to glutamate addition by comparative transcriptomics. Glutamate addition induced great changes in intracellular metabolite concentrations and significantly upregulated genes involved in the central metabolic pathways. Subsequent gene overexpression experiments revealed that only the enhancement of glutamate synthesis pathway successfully led to γ-PGA accumulation without glutamate addition, indicating the key role of intracellular glutamate for γ-PGA synthesis in glutamate-dependent strains. Finally, by a combination of metabolic engineering targets, the γ-PGA titer reached 10.21 ± 0.42 g/L without glutamate addition. Exogenous glutamate further enhanced the γ-PGA yield (35.52 ± 0.26 g/L) and productivity (0.74 g/(L h)) in shake-flask fermentation. This work provides insights into the glutamate dependence mechanism in B. subtilis and reveals potential molecular targets for increasing economical γ-PGA production.