Intracellular Amino Acid Research Articles

Antitumoral Activity and Metabolic Signatures of Dichloroacetate, 6-Aminonicotinamide and Etomoxir in Breast-Tumor-Educated Macrophages.

Pharmacological targeting of metabolic pathways represents an appealing strategy to selectively kill cancer cells while promoting antitumor functions of stromal cells. In this study, we assessed the effectiveness of 13 metabolic drugs (MDs) in steering in vitro generated breast tumor-educated macrophages (TEMs) toward an antitumoral phenotype. For that, the production of vascular endothelial growth factor (VEGF) and tumor necrosis factor α (TNF-α), two important regulators of tumor progression, was evaluated. Notably, dichloroacetate (DCA), 6-aminonicotinamide (6-AN), and etomoxir decreased VEGF production and enhanced TNF-α release. Hence, we further clarified their impact on TEM metabolism using an untargeted NMR-based metabolomics approach. DCA downregulated glycolysis and enhanced the utilization of extracellular substrates like lactate while reconfiguring lipid metabolism. Several DCA-induced changes significantly correlated with heightened TNF-α production in response to pro-inflammatory stimulation. The inhibition of the pentose phosphate pathway by 6-AN was accompanied by enhanced glutaminolysis, which correlated with a decreased level of VEGF production. In etomoxir-treated TEM, inhibition of fatty acid oxidation was compensated through upregulation of glycolysis, catabolism of intracellular amino acids, and consumption of extracellular branched chain alpha-ketoacids (BCKA) and citrate. Overall, our results offer a comprehensive view of the metabolic signature of each MD in breast TEM and highlight putative correlations with phenotypic effects.

Targeted and Untargeted Amine Metabolite Quantitation in Single Cells with Isobaric Multiplexing.

We developed a single cell amine analysis approach utilizing isobarically multiplexed samples of 6 individual cells along with analyte abundant carrier. This methodology was applied for absolute quantitation of amino acids and untargeted relative quantitation of amines in a total of 108 individual cells using nanoflow LC with high-resolution mass spectrometry. Together with individually determined cell sizes, this provides quantification of intracellularconcentrations within individual cells. The targeted method was partially validated for 10 amino acids with limits of detection in low attomoles, linear calibration range covering analyte amounts typically from 30 amol to 120 fmol, and correlation coefficients (R) above 0.99. This was applied with cell sizes recorded during dispensing to determine millimolar intracellular amino acid concentrations. The untargeted approach yielded 249 features that were detected in at least 25% of the single cells, providing modest cell type separation on principal component analysis. Using Greedy forward selection with regularized least squares, a sub-selection of 100 features explaining most of the difference was determined. These features were annotated using MS2 from analyte standards and accurate mass with library search. The approach provides accessible, sensitive, and high-throughput method with the potential to be expanded also to other forms of ultrasensitive analysis.

Mechanistic insight into assimilation capture: Implication for high-efficiency nitrogen removal from mature landfill leachate

The AO (Anoxic/oxic) process for treating high-strength ammonia in landfill leachate requires external carbon source and alkalinity. Alternatively, the processes of partial nitrification-Anammox (PNA) and partial denitrification-Anammox (PDA) with less or no carbon source have been developed, but enabled modulation difficulty due to nitrogen valence transformation. Ammonia assimilation for nitrogen removal immobilize ammonia (NH4+-N) as organic nitrogen, without nitrogen valence conversion and reducing greenhouse gases emission. This study offers a novel approach for nitrogen removal from low chemical oxygen demand (COD) to nitrogen (C/N) ratio leachate. The nitrogen removal response of biomass to ammonia assimilation in landfill leachate was established. Results demonstrated that the nitrogen removal contribution of ammonia assimilation and organics utilization by microorganisms significantly increased with biomass. When the initial mixed liquor suspended solid (MLSS) was 11200 mg/L, the removal efficiency of total nitrogen (TN) and COD in the landfill leachate achieved 98.42 ± 0.12 % and 80.60 ± 0.35 % after 30 days of operation, respectively. The corresponding assimilation contributions for TN and COD removals were 82.00 ± 0.96 % and 52.24 ± 0.82 %, respectively. Cell protein analysis showed that higher biomass significantly increased the production of intracellular and extracellular proteins or amino acids. The enrichment of bacterial genera such as Defluviicoccus, Aequorivita, Truepera, and Proteiniphilum played a crucial role in organics removal and NH4+-N assimilation. Functional gene analysis further demonstrated that most NH4+-N and organics were removed through bacterial assimilation. This research offered a green, efficient, and economical solution for the treatment of low C/N ratio landfill leachate.

Determination of Taurine in Infant Formula and Adult/Pediatric Nutritionals by Ultra High-Performance Liquid Chromatography with Multiple Reaction Monitoring-Mass Spectrometry: Single-Laboratory Validation, First Action 2022.08.

Taurine (2-aminoethanesulfonic acid) is an essential β-amino acid, which is one of the most abundant intracellular amino acid component in humans. The level of free taurine in human milk is higher than in bovine milk. Since taurine is considered important for the development of a newborn, fortification of infant nutrition with taurine is common. This publication describes a rapid method for the determination of taurine in infant formula and adult/pediatric nutritionals. This publication demonstrates the suitability and applicability of the method to determine taurine content in infant formula and adult/pediatric nutritionals. Test portions are deproteinized by acid in an aqueous environment prior to analysis. The level of taurine is analyzed by hydrophilic interaction chromatography (HILIC) coupled with multiple reaction monitoring MS (MRM-MS). Quantitation is accomplished using a stable isotope-labeled internal standard (SILS) for taurine. The accuracy of the method was validated using standard reference materials and spike recovery studies. The average recoveries ranged between 92% and 105%. The relative standard deviation repeatability (RSDr) and relative standard deviation intermediate precision (RSDiR) were in the range of 0.7-4.6% (RSDr) and 1.3-6.7% (RSDiR). The limit of quantitation (LOQ) was below the requirement of 0.5 mg/100 g. The single-laboratory validation (SLV) of the method for determination of taurine content in infant formula and adult/pediatric nutritionals demonstrates that it meets the requirements per AOAC INTERNATIONAL Standard Method Performance Requirements (SMPR) 2014.013. A fast method to selectively determine the content of taurine in infant formula and adult/pediatric nutritionals was evaluated and found to be fit for purpose for routine product compliance testing. Based on the results of this SLV, the method was approved by the AOAC Stakeholder Program on Infant Formula and Adult Nutritionals (SPIFAN) Expert Review Panel for SPIFAN Nutrient Methods for First Action Official MethodsSM status.

Exploring the stress response mechanisms to 2-phenylethanol conferred by Pdr1p mutation in Saccharomyces cerevisiae

BackgroundThe 2-phenylethanol (2-PE) tolerance phenotype is crucial to the production of 2-PE, and Pdr1p mutation can significantly increase the tolerance of 2-PE in Saccharomyces cerevisiae. However, its underlying molecular mechanisms are still unclear, hindering the rational design of superior 2-PE tolerance performance.ResultsHere, the physiology and biochemistry of the PDR1_862 and 5D strains were analyzed. At 3.5 g/L 2-PE, the ethanol concentration of PDR1_862 decreased by 21%, and the 2-PE production of PDR1_862 increased by 16% than those of 5D strain. Transcriptome analysis showed that at 2-PE stress, Pdr1p mutation increased the expression of genes involved in the Ehrlich pathway. In addition, Pdr1p mutation attenuated sulfur metabolism and enhanced the one-carbon pool by folate to resist 2-PE stress. These metabolic pathways were closely associated with amino acids metabolism. Furthermore, at 3.5 g/L 2-PE, the free amino acids content of PDR1_862 decreased by 31% than that of 5D strain, among the free amino acids, cysteine was key amino acid for the enhancement of 2-PE stress tolerance conferred by Pdr1p mutation.ConclusionsThe above results indicated that Pdr1p mutation enhanced the Ehrlich pathway to improve 2-PE production of S. cerevisiae, and Pdr1p mutation altered the intracellular amino acids contents, in which cysteine might be a biomarker in response to Pdr1p mutation under 2-PE stress. The findings help to elucidate the molecular mechanisms for 2-PE stress tolerance by Pdr1p mutation in S. cerevisiae, identify key metabolic pathway responsible for 2-PE stress tolerance.

ABCC2 induces metabolic vulnerability and cellular ferroptosis via enhanced glutathione efflux in gastric cancer.

Although it is traditionally believed that ATP binding cassette subfamily C member 2 (ABCC2) is a multidrug resistance-associated protein correlated with a worse prognosis, our previous and several other studies demonstrated the contrary to be true in gastric cancer (GC). We aim to explore the underlying mechanism of this discovery. Our study utilized whole-exome sequencing (WES), RNA sequencing, and droplet digital PCR (ddPCR) analysis of 80 gastric cancer samples, along with comprehensive immunohistochemical (IHC) analysis of 1044 human GC tissue samples.By utilizing CRISPRCas9 to genetically modify cell lines with the ABCC2-24C > T (rs717620) point mutation and conducting dual-luciferase reporter assays, we identified that transcription factors SOX9 and ETS1 serve as negative regulators of ABCC2 expression. Seahorse assay and mass spectrometry were used to discover altered metabolic patterns. Gain and loss-of-function experiments in GC cell lines and preclinical models were carried out to validate ABCC2 biological function. ABCC2 high expression correlated with better prognosis, and rs717620 can influence ABCC2 expression by disrupting the binding of ETS1 and SOX9. Gain and loss-of-function experiments in GC cell lines demonstrated amino acid deprivation reduces proliferation, migration, and drug resistance in ABCC2-high GC cells. ABCC2 leads to reduced intracellular amino acid pools and disruption of cellular energy metabolism. This phenomenon depended on ABCC2-mediated GSH extrusion, resulting in alterations in redox status, thereby increasing the cell's susceptibility to ferroptosis. Furthermore, patient-derived organoids and patient-derived tumor-like cell clusters were used to observe impact of ABCC2 on therapeutic effect. In the xenograft model with high ABCC2 expression, we observed that constricting amino acid intake in conjunction with GPX4 inactivation resulted in notable tumor regression. Our findings demonstrate a significant role of ABCC2 in amino acid metabolism and ferroptosis by mediating GSH efflux in GC. This discovery underlines the potential of combining multiple ferroptosis targets as a promising therapeutic strategy for GC with high ABCC2 expression. ABCC2 plays a crucial role in inducing metabolic vulnerability and ferroptosis in gastric cancer through enhanced glutathione efflux. The ABCC2 24C > T polymorphism is a key factor influencing its expression. These results highlight the potential of ABCC2 as a predictive biomarker and therapeutic target in gastric cancer.

Antibacterial mechanism of the methanol extract of Thamnolia subuliformis (Ehrh.) W. Culb against Staphylococcus aureus.

Thamnolia subuliformis (Ehrh.) W. Culb is a species of lichen with edible and medicinal applications in China. Our previous studies demonstrated that the methanol extract of Thamnolia subuliformis (METS) exhibits broad antibacterial activity and stability against foodborne pathogens. This study aimed to investigate the antibacterial mechanism of METS against Staphylococcus aureus using nontargeted metabolomics, focusing on cell wall and membrane damage. The results revealed that the minimum inhibitory concentration (MIC) was 0.625mg ml-1 and that METS had good biosafety at this concentration. METS caused significant damage to the cell wall and membrane integrity, based on both morphological observation by electron microscopy and the leakage of alkaline phosphatase, protein, and nucleic acid in the cell cultures. Treatment with METS at the MIC disrupted the lipid metabolism of S. aureus, causing a decrease in the metabolism of various phospholipids and sphingolipids in the cell membrane and an increase in the ratio of saturated fatty acids to unsaturated fatty acids. Moreover, it influenced intracellular amino acid and energy metabolism. These results shed light on the antibacterial mechanism of METS against S. aureus while also serving as a reference for the further development of natural antibacterial compounds derived from Thamnolia subuliformis.

Combined clinical, structural, and cellular studies discriminate pathogenic and benign TRPV4 variants.

Dominant mutations in the calcium-permeable ion channel TRPV4 (transient receptor potential vanilloid 4) cause diverse and largely distinct channelopathies, including inherited forms of neuromuscular disease, skeletal dysplasias, and arthropathy. Pathogenic TRPV4 mutations cause gain of ion channel function and toxicity that can be rescued by small molecule TRPV4 antagonists in cellular and animal models, suggesting that TRPV4 antagonism could be therapeutic for patients. Numerous variants in TRPV4 have been detected with targeted and whole exome/genome sequencing, but for the vast majority, their pathogenicity remains unclear. Here, we used a combination of clinical information and experimental structure-function analyses to evaluate 30 TRPV4 variants across various functional protein domains. We report clinical features of seven patients with TRPV4 variants of unknown significance and provide extensive functional characterization of these and an additional 17 variants, including structural position, ion channel function, subcellular localization, expression level, cytotoxicity, and protein-protein interactions. We find that gain-of-function mutations within the TRPV4 intracellular ankyrin repeat domain target charged amino acid residues important for RhoA interaction, whereas ankyrin repeat domain residues outside of the RhoA interface have normal or reduced ion channel activity. We further identify a cluster of gain-of-function variants within the intracellular intrinsically disordered region that may cause toxicity via altered interactions with membrane lipids. In contrast, assessed variants in the transmembrane domain and other regions of the intrinsically disordered region do not cause gain of function and are likely benign. Clinical features associated with gain of function and cytotoxicity include congenital onset of disease, vocal cord weakness, and motor predominant disease, whereas patients with likely benign variants often demonstrated late-onset and sensory-predominant disease. These results provide a framework for assessing additional TRPV4 variants with respect to likely pathogenicity, which will yield critical information to inform patient selection for future clinical trials for TRPV4 channelopathies.

Amino acids trigger MDC-dependent mitochondrial remodeling by altering mitochondrial function.

Cells utilize numerous pathways to maintain mitochondrial homeostasis, including a recently identified mechanism that adjusts the content of the outer mitochondrial membrane (OMM) through formation of OMM-derived multilamellar domains called mitochondrial-derived compartments, or MDCs. MDCs are triggered by perturbations in mitochondrial lipid and protein content, as well as increases in intracellular amino acids. Here, we sought to understand how amino acids trigger MDCs. We show that amino acid-activation of MDCs is dependent on the functional state of mitochondria. While amino acid excess triggers MDC formation when cells are grown on fermentable carbon sources, stimulating mitochondrial biogenesis blocks MDC formation. Moreover, amino acid elevation depletes TCA cycle metabolites in yeast, and preventing consumption of TCA cycle intermediates for amino acid catabolism suppresses MDC formation. Finally, we show that directly impairing the TCA cycle is sufficient to trigger MDC formation in the absence of amino acid stress. These results demonstrate that amino acids stimulate MDC formation by perturbing mitochondrial metabolism.

Glutamine enhances pneumococcal growth under methionine semi-starvation by elevating intracellular pH.

Bacteria frequently encounter nutrient limitation in nature. The ability of living in this nutrient shortage environment is vital for bacteria to preserve their population and important for some pathogenic bacteria to cause infectious diseases. Usually, we study how bacteria survive after nutrient depletion, a total starvation condition when bacteria almost cease growth and try to survive. However, nutrient limitation may not always lead to total starvation. Bacterial adaptation to nutrient shortage was studied by determining bacterial growth curves, intracellular pH, intracellular amino acid contents, gene transcription, protein expression, enzyme activity, and translation and replication activities. No exogenous supply of methionine results in growth attenuation of Streptococcus pneumoniae, a human pathogen. In this paper, we refer to this inhibited growth state between ceased growth under total starvation and full-speed growth with full nutrients as semi-starvation. Similar to total starvation, methionine semi-starvation also leads to intracellular acidification. Surprisingly, it is intracellular acidification but not insufficient methionine synthesis that causes growth attenuation under methionine semi-starvation. With excessive glutamine supply in the medium, intracellular methionine level was not changed, while bacterial intracellular pH was elevated to ~ 7.6 (the optimal intracellular pH for pneumococcal growth) by glutamine deamination, and bacterial growth under semi-starvation was restored fully. Our data suggest that intracellular acidification decreases translation level and glutamine supply increases intracellular pH to restore translation level, thus restoring bacterial growth. This growth with intracellular pH adjustment by glutamine is a novel strategy we found for bacterial adaptation to nutrient shortage, which may provide new drug targets to inhibit growth of pathogenic bacteria under semi-starvation.

Carboxylesterase 1 directs the metabolic profile of dendritic cells to a reduced inflammatory phenotype.

The metabolic profile of dendritic cells (DCs) shapes their phenotype and functions. The carboxylesterase 1 (CES1) enzyme is highly expressed in mononuclear myeloid cells; however, its exact role in DCs is elusive. We used a CES1 inhibitor (WWL113) and genetic overexpression to explore the role of CES1 in DC differentiation in inflammatory models. CES1 expression was analyzed during CD14+ monocytes differentiation to DCs (MoDCs) using quantitative polymerase chain reaction. A CES1 inhibitor (WWL113) was applied during MoDC differentiation. Surface markers, secreted cytokines, lactic acid production, and phagocytic and T cell polarization capacity were analyzed. The transcriptomic and metabolic profiles were assessed with RNA sequencing and mass spectrometry, respectively. Cellular respiration was assessed using seahorse respirometry. Transgenic mice were used to assess the effect of CES1 overexpression in DCs in inflammatory models. CES1 expression peaked early during MoDC differentiation. Pharmacological inhibition of CES1 led to higher expression of CD209, CD86 and MHCII. WWL113 treated MoDCs secreted higher quantities of interleukin (IL)-6, IL-8, tumor necrosis factor, and IL-10 and demonstrated stronger phagocytic ability and a higher capacity to polarize T helper 17 differentiation in an autologous DC-T cell coculture model. Transcriptomic profiling revealed enrichment of multiple inflammatory and metabolic pathways. Functional metabolic analysis showed impaired maximal mitochondrial respiration capacity, increased lactate production, and decreased intracellular amino acids and tricarboxylic acid cycle intermediates. Transgenic human CES1 overexpression in murine DCs generated a less inflammatory phenotype and increased resistance to T cell-mediated colitis. In conclusion, CES1 inhibition directs DC differentiation toward a more inflammatory phenotype that shows a stronger phagocytic capacity and supports T helper 17 skewing. This is associated with a disrupted mitochondrial respiration and amino acid depletion.

Overexpression of arginase gene CAR1 renders yeast Saccharomyces cerevisiae acetic acid tolerance

Acetic acid is a common inhibitor present in lignocellulose hydrolysate, which inhibits the ethanol production by yeast strains. Therefore, the cellulosic ethanol industry requires yeast strains that can tolerate acetic acid stress. Here we demonstrate that overexpressing a yeast native arginase-encoding gene, CAR1, renders Saccharomyces cerevisiae acetic acid tolerance. Specifically, ethanol yield increased by 27.3% in the CAR1-overexpressing strain compared to the control strain under 5.0 g/L acetic acid stress. The global intracellular amino acid level and compositions were further analyzed, and we found that CAR1 overexpression reduced the total amino acid content in response to acetic acid stress. Moreover, the CAR1 overexpressing strain showed increased ATP level and improved cell membrane integrity. Notably, we demonstrated that the effect of CAR1 overexpression was independent of the spermidine and proline metabolism, which indicates novel mechanisms for enhancing yeast stress tolerance. Our studies also suggest that CAR1 is a novel genetic element to be used in synthetic biology of yeast for efficient production of fuel ethanol.

Antimicrobial mechanism of morusin against Bacillus cereus and its potential as an antimicrobial agent

Bacillus cereus, a food-borne pathogen, threatens human health and food safety. The quest for biologically active substances from natural sources acting as antimicrobial agents for the replacement of antibiotics and chemical additives has received increasing attention. In this study, the antimicrobial mechanism of morusin against B. cereus was outlined, as well as its function as a food supplement to extend the shelf-life of skimmed milk was assessed. Our findings demonstrated that the minimum inhibitory concentration (MIC) value of morusin against B. cereus was 2.25 μg/mL, inhibiting biofilm formation and reducing intracellular ATP and membrane depolarization by disturbing the permeability of the B. cereus cytoplasmic membrane. Damage or collapse of B. cereus cell membranes produced by morusin was identified using the field gun scanning electron microscope (FEG-SEM). Transcriptomic assessment indicated that the two-component system of B. cereus (narG, narH, narI, phoP, phoR, motA) responded positively to morusin within an adverse environment. Moreover, several genes associated with cell membrane and cell wall generation (murA, murB, ddlB) and amino acid metabolism (argF, argH, BCN_RS02850) were significantly downregulated, potentially accelerating the death of B. cereus. In addition, metabolomic investigation suggested that morusin restricted pyruvate metabolism, cysteine and methionine metabolic pathways, and disturbed the intracellular amino acid metabolism of B. cereus. Ultimately, 4.5 μg/mL of morusin was determined to significantly inhibit the growth of B. cereus within skimmed milk. Overall, morusin can be utilized as a natural antimicrobial agent for regulating B. cereus contamination in skimmed milk.

The Integrated Stress Response Regulates Diurnal Rhythms in Liver Metabolism

Disruptions in biological rhythms are associated with the development of metabolic diseases. General control nonderepressible 2 (GCN2), a primary sensor of amino acid insuffciency and activator of the integrated stress response (ISR), plays an integral role in liver metabolism. The objective of this work was to examine the impact of feeding a low protein quality (LPQ) diet on diurnal rhythms in liver metabolism. We hypothesized that activation of the ISR by GCN2 maintains metabolic rhythms within the liver during LPQ feeding. To address our objective, wild type (WT) and whole body Gcn2 knockout (GCN2KO) mice were housed in total darkness and provided free access to either a Control or a LPQ diet (devoid of leucine) for 8-days and then killed at 2 circadian time (CT) points 12-hours apart (CT3, CT15). WT mice fed a Control diet showed oscillations in hepatic ISR activation that were lost in the livers of GCN2KO mice. Diurnal patterns in the liver transcriptome including genes regulating triglyceride metabolism were also dampened in GCN2KO mice. WT mice fed LPQ showed increased hepatic ISR activation and greater abundance of ISR target genes relative to Control only at CT15 (p<0.05 by two factor ANOVA). GCN2KO mice fed LPQ failed to show oscillations in ISR activation and instead displayed reductions in liver intracellular amino acids alongside significant upregulation of genes encoding gluconeogenesis and amino acid catabolism at CT15 (q<0.05, Log2FC>1). In conclusion, GCN2 is required for diurnal ISR activation and execution in the liver. LPQ feeding increases hepatic ISR activation in a time dependent manner. Sensing of LPQ by GCN2 is necessary for the maintenance of rhythms in liver macronutrient metabolism. NIH DK109714, Pilot award from the NJ IFNH Center for Human Nutrition, Exercise, and Metabolism (NExT). This is the full abstract presented at the American Physiology Summit 2024 meeting and is only available in HTML format. There are no additional versions or additional content available for this abstract. Physiology was not involved in the peer review process.

Concentration Recognition-Based Auto-Dynamic Regulation System (CRUISE) Enabling Efficient Production of Higher Alcohols.

Microbial factories lacking the ability of dynamically regulating the pathway enzymes overexpression, according to in situ metabolite concentrations, are suboptimal, especially when the metabolic intermediates are competed by growth and chemical production. The production of higher alcohols (HAs), which hijacks the amino acids (AAs) from protein biosynthesis, minimizes the intracellular concentration of AAs and thus inhibits the host growth. To balance the resource allocation and maintain stable AA flux, this work utilizes AA-responsive transcriptional attenuator ivbL and HA-responsive transcriptional activator BmoR to establish a concentration recognition-based auto-dynamic regulation system (CRUISE). This system ultimately maintains the intracellular homeostasisof AA and maximizes the production of HA. It is demonstrated that ivbL-driven enzymes overexpression can dynamically regulate the AA-to-HA conversion while BmoR-driven enzymes overexpression can accelerate the AA biosynthesis during the HA production in a feedback activation mode. The AA flux in biosynthesis and conversion pathways is balanced via the intracellular AA concentration, which is vice versa stabilized by the competition between AA biosynthesis and conversion. The CRUISE, further aided by scaffold-based self-assembly, enables 40.4gL-1 of isobutanol production in a bioreactor. Taken together, CRUISE realizes robust HA production and sheds new light on the dynamic flux control during the process of chemical production.

Global growth phase response of the gut bacterium Phocaeicola vulgatus (phylum Bacteroidota).

Phocaeicola vulgatus belongs to the intestinal microbiome, where it fermentatively breaks down of food-derived biopolymers , thereby, contributing to the gut metabolome. Moreover, due to its product range, P. vulgatus is a potential nonstandard platform organism for sustainable production of basic organic chemicals. Complementing a recent physiologic-proteomic report deciphering the strain's versatile fermentation network [1], the present study focuses on the global growth phase-dependent response. P. vulgatus was anaerobically cultivated with glucose in process-controlled bioreactors. Close sampling was conducted to measure growth parameters (OD, CDW, ATP content, substrate/product profiles) to determine growth stoichiometry. A coarser sampling (½ODmax, ODmax, and ODstat) served the molecular analysis of the global growth phase-dependent response, applying proteomics (soluble and membrane fractions, nanoLC-ESI-MS/MS) and targeted/untargeted metabolome analyses. The determined growth performance of features 1.74 h doubling time, 0.06 gCDW/mmolGlc biomass yield, 0.36 (succinate) and 0.61 (acetate) mmolP/mmolGlc as predominant fermentation product yields, and 0.43 mmolATP/mmolC as theoretically calculated ATP yield. The fermentation pathway displayed growth phase-dependent dynamics: the levels of proteins and their accompanying metabolites constituting the upper part of glycolysis peaked at ½ODmax, whereas those of the lower part of glycolysis and of the fermentation routes in particular towards predominant acetate and succinate were highest at ODmax and ODstat. While identified proteins of monomer biosynthesis displayed rather unspecific profiles, most of the intracellular amino acids peaked at ODmax. By contrast, proteins and metabolites related to stress response and quorum sensing showed increased abundances at ODmax and ODstat. The composition of the exometabolome expanded from 2,317 molecular formulas at ½ODmax via 4,258 at ODmax to 4,501 at ODstat, with growth phase-specific subsets increasing in parallel. The present study provides insights into the distinct growth phase-dependent behavior of P. vulgatus during cultivation in bioreactors. This could serve as a valuable knowledge base for further developing P. vulgatus as a non-conventional platform organism for biotechnological applications. In addition, the findings shed new light on the potential growth phase-dependent imprints of P. vulgatus on the gut microbiome environment, e.g. by indicating interactions via quorum sensing and by unraveling the complex exometabolic background against which fermentation products and secondary metabolites are formed.

Unveiling the mechanism of efficient β-phenylethyl alcohol conversion in wild-type Saccharomyces cerevisiae WY319 through multi-omics analysis.

β-Phenylethanol (2-PE), as an important flavor component in wine, is widely used in the fields of flavor chemistry and food health. 2-PE can be sustainably produced through Saccharomyces cerevisiae. Although significant progress has been made in obtaining high-yield strains, as well as improving the synthesis pathways of 2-PE, there still lies a gap between these two fields to unpin. In this study, the macroscopic metabolic characteristics of high-yield and low-yield 2-PE strains were systematically compared and analyzed. The results indicated that the production potential of the high-yield strain might be contributed to the enhancement of respiratory metabolism and the high tolerance to 2-PE. Furthermore, this hypothesis was confirmed through comparative genomics. Meanwhile, transcriptome analysis at key specific growth rates revealed that the collective upregulation of mitochondrial functional gene clusters plays a more prominent role in the production process of 2-PE. Finally, findings from untargeted metabolomics suggested that by enhancing respiratory metabolism and reducing the Crabtree effect, the accumulation of metabolites resisting high 2-PE stress was observed, such as intracellular amino acids and purines. Hence, this strategy provided a richer supply of precursors and cofactors, effectively promoting the synthesis of 2-PE. In short, this study provides a bridge for studying the metabolic mechanism of high-yield 2-PE strains with the subsequent targeted strengthening of relevant synthetic pathways. It also provides insights for the synthesis of nonalcoholic products in S. cerevisiae.

Temporal dynamics of stress response in Halomonas elongata to NaCl shock: physiological, metabolomic, and transcriptomic insights

BackgroundThe halophilic bacterium Halomonas elongata is an industrially important strain for ectoine production, with high value and intense research focus. While existing studies primarily delve into the adaptive mechanisms of this bacterium under fixed salt concentrations, there is a notable dearth of attention regarding its response to fluctuating saline environments. Consequently, the stress response of H. elongata to salt shock remains inadequately understood.ResultsThis study investigated the stress response mechanism of H. elongata when exposed to NaCl shock at short- and long-time scales. Results showed that NaCl shock induced two major stresses, namely osmotic stress and oxidative stress. In response to the former, within the cell’s tolerable range (1–8% NaCl shock), H. elongata urgently balanced the surging osmotic pressure by uptaking sodium and potassium ions and augmenting intracellular amino acid pools, particularly glutamate and glutamine. However, ectoine content started to increase until 20 min post-shock, rapidly becoming the dominant osmoprotectant, and reaching the maximum productivity (1450 ± 99 mg/L/h). Transcriptomic data also confirmed the delayed response in ectoine biosynthesis, and we speculate that this might be attributed to an intracellular energy crisis caused by NaCl shock. In response to oxidative stress, transcription factor cysB was significantly upregulated, positively regulating the sulfur metabolism and cysteine biosynthesis. Furthermore, the upregulation of the crucial peroxidase gene (HELO_RS18165) and the simultaneous enhancement of peroxidase (POD) and catalase (CAT) activities collectively constitute the antioxidant defense in H. elongata following shock. When exceeding the tolerance threshold of H. elongata (1–13% NaCl shock), the sustained compromised energy status, resulting from the pronounced inhibition of the respiratory chain and ATP synthase, may be a crucial factor leading to the stagnation of both cell growth and ectoine biosynthesis.ConclusionsThis study conducted a comprehensive analysis of H. elongata’s stress response to NaCl shock at multiple scales. It extends the understanding of stress response of halophilic bacteria to NaCl shock and provides promising theoretical insights to guide future improvements in optimizing industrial ectoine production.

Knock-out of dipeptidase CN2 in human proximal tubular cells disrupts dipeptide and amino acid homeostasis and para- and transcellular solute transport.

Although of potential biomedical relevance, dipeptide metabolism has hardly been studied. We found the dipeptidase carnosinase-2 (CN2) to be abundant in human proximal tubules, which regulate water and solute homeostasis. We therefore hypothesized, that CN2 has a key metabolic role, impacting proximal tubular transport function. A knockout of the CN2 gene (CNDP2-KO) was generated in human proximal tubule cells and characterized by metabolomics, RNA-seq analysis, paracellular permeability analysis and ion transport. CNDP2-KO in human proximal tubule cells resulted in the accumulation of cellular dipeptides, reduction of amino acids and imbalance of related metabolic pathways, and of energy supply. RNA-seq analyses indicated altered protein metabolism and ion transport. Detailed functional studies demonstrated lower CNDP2-KO cell viability and proliferation, and altered ion and macromolecule transport via trans- and paracellular pathways. Regulatory and transport protein abundance was disturbed, either as a consequence of the metabolic imbalance or the resulting functional disequilibrium. CN2 function has a major impact on intracellular amino acid and dipeptide metabolism and is essential for key metabolic and regulatory functions of proximal tubular cells. These findings deserve invivo analysis of the relevance of CN2 for nephron function and regulation of body homeostasis.

Abstract 3067: SLC7A5/LAT1 promotes the Warburg Effect for TNBC progression through Trp/QPRT/NAD+ pathway

Abstract SLC7A5/LAT1 is a cross-membrane transporter that functions in uptake of large neutral amino acids into cells. Many pathological studies have shown that LAT1 is highly expressed in cancer tissue from various origins such as lung, biliary tract, breast, prostate, bone, and their metastatic legions. High LAT1 expression has been recognized as a significant prognostic marker in various cancers. Our TCGA data analysis showed that the expression level of LAT1 is higher in TNBC tumors compared with normal breast tissues. The higher expression level of LAT1 is linked with poor overall and progression-free survival. Dysregulation of amino acid transporters lead to metabolic reprogramming, which changes intracellular amino acid levels, contributing to the pathogenesis of cancer. However, it remains elusive whether and how LAT1 re-wires the cellular metabolic programs to promote TNBC tumor proliferation. In this study, we showed that inhibition of SLC7A5/LAT1 significantly reduced TNBC cell proliferation, viability, migration capability while promoting apoptosis. Mechanistically, we found significant positive correlations of LAT1 with PKM2 and LDHA in breast cancer tissues, which are key enzymes in mediating glycolysis and lactate fermentation or the Warburg Effect. Knock down LAT1 via siRNA decreased the expression levels of p-PKM2 and p-LDHA in TNBC cells. Tryptophan, a major substrate amino acid transported into cytosol by LAT1, is the precursor for the de novo synthesis of nicotinamide adenine dinucleotide (NAD+). The enzyme quinolinic acid phosphoribosyltransferase (QPRT) catalyzes the conversion from quinolinate, a product of tryptophan degradation, to NAD+. We showed LAT1 inhibition reduced the expression level of QPRT, cytosolic NAD+/NADH ratio as well as lactate production. Addition of L-Tryptophan increased the levels of p-PKM2 and p-LDHA while knockdown of LAT1 reversed tryptophan-mediated increase of PKM2 and LDHA activities, suggesting that LAT1 may regulate PKM2/LDHA through Trp/QPRT/NAD+ pathway for promoting the Warburg Effect. Additionally, we found upregulations of SLC7A5/LAT1, p-PKM2 and p-LDHA in doxorubicin-resistant cells and PDX mouse model compared with their corresponding controls. Collectively, these results provide evidence that overexpression of LAT1 in TNBC drives cancer progression and drug resistance by reinforcing the Warburg Effect, suggesting LAT1 as a promising therapeutic target for addressing TNBC. Our ongoing work will evaluate whether inhibiting LAT1 genetically or pharmacologically reduces xenograft tumor growth and enhances the sensitivities of TNBC resistant cells to chemotherapy in vivo. Our investigation will elucidate the underlying mechanisms involved in these processes. Citation Format: Margot Y. Fedoroff, Lei Zhao, Leili Saeednejad Zanjani, Jun He. SLC7A5/LAT1 promotes the Warburg Effect for TNBC progression through Trp/QPRT/NAD+ pathway [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3067.