Metabolic Flux Analysis Research Articles

LncRNA XIST Contributes to Cisplatin Resistance of Lung Cancer Cells by Promoting Cellular Glycolysis through Sponging miR-101-3p

Background: Non-small-cell lung carcinoma is one of the most frequently diagnosed cancers. Cisplatin (CDDP) is a currently applied standard anticancer agent for advanced lung cancers. Although effectively clinical response was achieved initially, a large fraction of lung cancer patients developed cisplatin resistance. Therefore, understanding the molecular mechanisms of chemoresistance is crucial for anti-lung cancer therapy. Long non-coding RNA (lncRNA)-X-inactive-specific transcript (XIST) has been reported to be positively associated with multiple cancers. Currently, the precise role and mechanism of XIST in cisplatin resistance of lung cancer have not been elucidated. Methods: The expression levels of miR-101-3p and lncRNA XIST were detected by qRT-PCR. Cisplatin-resistant lung cancer cell line was established by selecting the survival cells under gradually increased cisplatin treatments. The cell proliferation was detected by MTT assay, and the cellular glucose metabolism rate was evaluated by Seahorse metabolic flux analysis and glucose uptake and lactate product assays. Glycolysis-related protein expression levels were detected by Western blot. Dual luciferase reporter was constructed to determine the lncRNA-miRNA interaction. Results: Here, we report XIST is significantly upregulated in lung cancer tissues compared with normal lung tissues. In addition, cisplatin-resistant lung cancer cells displayed remarkably elevated XIST expression. We demonstrated that miR-101-3p functioned as a tumor suppressor in lung cancer and sensitized lung cancer cells to cisplatin. Bioinformatics analysis predicted miR-101-3p could be a potential target of XIST through direct binding with it as a competing endogenous RNA, which was further validated from lung tumor tissues and cell lines by luciferase assay. Intriguingly, XIST significantly promoted cellular glycolysis rate of lung cancer cells. The extracellular acidification rate, glucose uptake, and lactate product were elevated by XIST overexpression. On the contrary, miR-101-3p effectively suppressed glycolysis rate. Finally, we demonstrated silencing XIST significantly recovered miR-101-3p expression and downregulated expression of glycolysis key enzymes, a phenotype could be further overridden by miR-101-3p inhibition. Conclusions: This study reveals a new molecular mechanism for the lncRNA-XIST-promoted cisplatin resistance via sponging miR-101-3p, leading to de-repression of cellular glycolysis. Moreover, these findings warrant further in vivo investigations to study XIST as a potential target to overcome cisplatin resistance.

Subcellular Localizations of Catalase and Exogenously Added Fatty Acid in Chlamydomonas reinhardtii.

Fatty acids are important biological components, yet the metabolism of fatty acids in microalgae is not clearly understood. Previous studies found that Chlamydomonas reinhardtii, the model microalga, incorporates exogenously added fatty acids but metabolizes them differently from animals and yeast. Furthermore, a recent metabolic flux analysis found that the majority of lipid turnover in C. reinhardtii is the recycling of acyl chains from and to membranes, rather than β -oxidation. This indicates that for the alga, the maintenance of existing acyl chains may be more valuable than their breakdown for energy. To gain cell-biological knowledge of fatty acid metabolism in C. reinhardtii, we conducted microscopy analysis with fluorescent probes. First, we found that CAT1 (catalase isoform 1) is in the peroxisomes while CAT2 (catalase isoform 2) is localized in the endoplasmic reticulum, indicating the alga is capable of detoxifying hydrogen peroxide that would be produced during β-oxidation in the peroxisomes. Second, we compared the localization of exogenously added FL-C16 (fluorescently labelled palmitic acid) with fluorescently marked endosomes, mitochondria, peroxisomes, lysosomes, and lipid droplets. We found that exogenously added FL-C16 are incorporated and compartmentalized via a non-endocytic route within 10 min. However, the fluorescence signals from FL-C16 did not colocalize with any marked organelles, including peroxisomes. During triacylglycerol accumulation, the fluorescence signals from FL-C16 were localized in lipid droplets. These results support the idea that membrane turnover is favored over β-oxidation in C. reinhardtii. The knowledge gained in these analyses would aid further studies of the fatty acid metabolism.

Mfapy: An open-source Python package for 13C-based metabolic flux analysis

13C-based metabolic flux analysis (13C-MFA) is an essential tool for estimating intracellular metabolic flux levels in metabolic engineering and biology. In 13C-MFA, a metabolic flux distribution that explains the observed isotope labeling data was computationally estimated using a non-linear optimization method. Herein, we report the development of mfapy, an open-source Python package developed for more flexibility and extensibility for 13C-MFA. mfapy compels users to write a customized Python code by describing each step in the data analysis procedures of the isotope labeling experiments. The flexibility and extensibility provided by mfapy can support trial-and-error performance in the routine estimation of metabolic flux distributions, experimental design by computer simulations of 13C-MFA experiments, and development of new data analysis techniques for stable isotope labeling experiments. mfapy is available to the public from the Github repository (https://github.com/fumiomatsuda/mfapy).

Simultaneous 3-Nitrophenylhydrazine Derivatization Strategy of Carbonyl, Carboxyl and Phosphoryl Submetabolome for LC-MS/MS-Based Targeted Metabolomics with Improved Sensitivity and Coverage.

Metabolomics is a powerful and essential technology for profiling metabolic phenotypes and exploring metabolic reprogramming, which enables the identification of biomarkers and provides mechanistic insights into physiology and disease. However, its applications are still limited by the technical challenges particularly in its detection sensitivity for the analysis of biological samples with limited amount, necessitating the development of highly sensitive approaches. Here, we developed a highly sensitive liquid chromatography tandem mass spectrometry method based on a 3-nitrophenylhydrazine (3-NPH) derivatization strategy that simultaneously targets carbonyl, carboxyl, and phosphoryl groups for targeted metabolomic analysis (HSDccp-TM) in biological samples. By testing 130 endogenous metabolites including organic acids, amino acids, carbohydrates, nucleotides, carnitines, and vitamins, we showed that the derivatization strategy resulted in significantly improved detection sensitivity and chromatographic separation capability. Metabolic profiling of merely 60 oocytes and 5000 hematopoietic stem cells primarily isolated from mice demonstrated that this method enabled routine metabolomic analysis in trace amounts of biospecimens. Moreover, the derivatization strategy bypassed the tediousness of inferring the MS fragmentation patterns and simplified the complexity of monitoring ion pairs of metabolites, which greatly facilitated the metabolic flux analysis (MFA) for glycolysis, the tricarboxylic acid (TCA) cycle, and pentose phosphate pathway (PPP) in cell cultures. In summary, the novel 3-NPH derivatization-based method with high sensitivity, good chromatographic separation, and broad coverage showed great potential in promoting metabolomics and MFA, especially in trace amounts of biospecimens.

Dynamic membrane bioreactor for high rate continuous biohydrogen production from algal biomass

This study aimed to achieve continuous biohydrogen production from red algal biomass using a dynamic membrane bioreactor (DMBR). The DMBR was continuously fed with pretreated Echeuma spinosum containing 20 g/L hexose. The highest average hydrogen production rate (HPR) of 21.58 ± 1.59 L/L-d was observed at HRT 3 h, which was higher than previous reports for continuous H2 production from biomass feedstock. Metabolic flux analysis revealed that butyric acid and propionic acid were the major by-products of the H2-producing and H2-consuming pathways, respectively, of the algal biomass fermentation. Hydrogen consumption by propionic acid pathway could not be prevented completely by heat treatment. PICRUSt2 analysis predicted that Clostridium sp., Anaerostipes sp., and Caproiciproducens sp. might significantly contribute to the expression of both ferredoxin hydrogenase and propionate CoA-transferase. This study would provide the design and operational information on high-rate bioreactor for continuous hydrogen production using biomass.

Abstract 236: Genomic loss in cancers enable discovery of metabolic targets for precision cancer therapy via multiobjective flux analysis and machine learning

Abstract Large-scale chromosomal alterations, particularly chromosomal deletions in cancer genomes confer functional advantages to cancer cells via the loss of tumor suppressor genes (TSGs). However, due to the nature of these focal and arm-level deletions, essential house-keeping genes in the neighborhood of TSGs are potentially lost. We explore the emergence of metabolic adaptations and vulnerabilities that arise due to the collateral loss of essential metabolic genes. In our previous work, we showed that genomic loss in the locus containing SMAD4 and ME2 in pancreatic ductal adenocarcinomas forces these cells to rely on ME3 to compensate for the collateral loss of ME2; thereby revealing a highly selective metabolic target in these cells. Cancer cells can not only exploit such genetic redundancies but also rely on redundancies built into their complex metabolic network to compensate for the loss of metabolic function. Importantly, there is an unexplored landscape of these genomic loss events beyond well-characterized TSGs. To address these challenges, we have developed a platform to identify patient-specific metabolic vulnerabilities emerging due to distinct patterns of genomic loss events across tumors. Our platform presents opportunities for precision-based therapeutic intervention by targeting metabolic vulnerabilities in cancer patients. It uses genomic and clinical data available in cancer patient databases to obtain candidate metabolic genes that are lost to genomic deletions in an unbiased manner. To delineate metabolic redundances and tackle the complexity of genome-scale metabolic models, we employ an innovative multi-objective metabolic flux analysis approach. The utility of this platform is demonstrated via the discovery of a novel metabolic target in a cohort of ovarian cancer patients. The predicted collateral lethal target is validated in vitro using RNA interference and small-molecule inhibitors. Furthermore, we verify the metabolic mechanism of vulnerability predicted by the algorithm using deuterium tracing experiments. The target is also validated in vivo with mice containing ovarian tumors derived from cancer cells with and without the genomic deletion. Surprisingly, the collateral lethal metabolic target was also found to exist in a subset of aggressive endometrial cancers. Finally, we developed a multi-layer machine learning model to predict occurrence of the particular genomic deletion in ovarian and endometrial cancer patients with minimal molecular information to remove the need for whole-genome sequencing data. The model was trained and tested using the publicly-available molecular data from TCGA and AACR GENIE datasets. Citation Format: Abhinav Achreja, Tao Yu, Anjali Mittal, Srinadh Choppara, Noah Meurs, Olamide Animasahun, Jin Heon Jeon, Aradhana Mohan, Anusha Jayaraman, Reva Kulkarni, Justin Reinhold, Michele Cusato, Analisa Difeo, Xiongbin Lu, Deepak Nagrath. Genomic loss in cancers enable discovery of metabolic targets for precision cancer therapy via multiobjective flux analysis and machine learning [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 236.

Abstract 2409: The regulation of mitochondria metabolism is correlated with gemcitabine resistance in MIA-PaCa-2 cell line

Abstract We established gemcitabine (GEM)-resistant pancreatic ductal adenocarcinoma (PDAC) cell line, MIA-G cells from MIA-PaCa-2 (MIA-P) cells by continuous low-dose GEM treatment. MIA-G cells was also resistant to 5-fluorouracil in comparison with MIA-P. Metabolic flux analysis showed that oxygen consumption rate (OCR) in MIA-G cells was higher than MIA-P cells, however, OCR was suppressed by GEM treatment only in MIA-G cells. In MIA-P cells, GEM treatment generated elevation of mitochondrial membrane potential and mitochondrial ROS, but not MIA-G cells. In MIA-G cells, expression of mitochondrial transcription factor A was also decreased. Moreover, glutamine uptake and glutamine peroxidase level were elevated in MIA-G cells. These findings suggest that suppression of OXPHOS contributes to GEM resistance through reduction of ROS production. Citation Format: Rina Fujiwara-Tani, Shingo Kishi, Shiori Mori, Hiroki Kuniyasu. The regulation of mitochondria metabolism is correlated with gemcitabine resistance in MIA-PaCa-2 cell line [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2409.

Glutamine Catabolism Maintains MCL-1 Expression in Glucose-Deprived Multiple Myeloma

Multiple myeloma (MM) is a plasma cell malignancy accounting for 11,000 deaths annually in the US with the majority succumbing to disease due to the development of resistance. A key component to the development of resistance lies in ineffective engagement of the BCL-2 family of apoptosis regulators. We and others have demonstrated that glucose maintains levels of a key resistance-promoting BCL-2 family member, myeloid cell leukemia factor 1 (MCL-1). Expression of MCL-1 promotes resistance of MM to a wide range of therapeutics. MM, like other cancers, exhibits elevated glucose consumption associated with manifestation of the Warburg effect. We previously reported that myeloma cells maintain the glycolytic phenotype by achieving constitutive plasma membrane localization of GLUT4, and GLUT4 inhibition or glucose deprivation suppressed MCL-1 expression. In this study, we further investigated the mechanism underlying the suppression of MCL-1 expression upon glucose deprivation.L363 and KMS18 cell lines are sensitive to glucose deprivation, exhibiting significant cytotoxicity upon glucose deprivation and demonstrating rapid reduction of MCL-1 protein in contrast to JJN3 and KMS11 cells that are resistant to glucose deprivation. Knockdown of MCL-1 in JJN3 dramatically induced apoptosis while overexpression of MCL-1 in L363 significantly reversed cell death upon glucose deprivation, supporting a role for MCL-1 suppression in mediating glucose-deprivation elicited cell death. We next proceeded to investigate the metabolic pathways contributing to the persistence of MCL-1 in the glucose-insensitive lines. Since glutamine is an important carbon source that can compensate for glucose deprivation, we examined glutamine uptake in L363 and JJN3 cells. Evaluation of 3H-glutamine uptake revealed that JJN3 cells exhibit higher glutamine uptake than L363 cells. In addition, we performed 13C-based metabolic flux analysis in order to identify metabolites that may be contributing to the maintenance of MCL-1 in glucose-deprived cells. Interestingly the level of glutathione (GSH) was much higher in JJN3 than in L363 that was maintained even upon glucose deprivation. Since GSH is a major cellular reactive oxygen species (ROS) scavenger, we evaluated levels of ROS using a cyto-roGFP construct and found that it was significantly elevated upon glucose withdrawal in L363 but not in JJN3. In addition, treating glucose deprived L363 with cell-permeant GSH monoethyl ester (GSH-MEE) rescued MCL-1 expression, further supporting a role for ROS in suppressing MCL-1 expression.Glutamine uptake evaluation revealed that glutamine consumption was maintained upon glucose withdrawal in both JJN3 and L363, so we were then interested in the TCA cycle-related differences in glutamine metabolism between JJN3 and L363. The level of pyruvate dehydrogenase alpha 1 (PDHA1) phosphorylation decreased upon glucose deprivation only in JJN3 cells, which activates PDHA1 and allows pyruvate to flow into the TCA cycle. In accordance with this, treatment of JJN3 with dichloroacetate (DCA), which inhibits pyruvate dehydrogenase kinase and therefore activates PDHA1, restored MCL-1 expression and prevented cell death of L363 during glucose deprivation. To study how TCA cycle helps maintain the GSH level, glutamate dehydrogenase (GDH) knockdown cells were generated because GDH catalyzes the reversible inter-conversion of glutamate to α-ketoglutarate and glutamate is the precursor for GSH. Interestingly, in GDH knockdown L363 cells, treatment of DCA was not able to reverse MCL-1 protein level upon glucose deprivation. Taken together, our observations suggest that glucose-deprived resistant cells sustain higher levels of GSH via greater glutamine uptake, thereby scavenging ROS to sustain cell viability; while sensitive cells cannot make GSH effectively, leading to increased ROS level, decreased MCL-1 expression, and ultimately, apoptosis.In sum, we have discovered that targeting glucose entry elicits apoptosis via an induction of ROS leading to suppression of MCL-1. These observations provide further rationale for the development of GLUT4-specific biologics to target aberrant glucose metabolism in myeloma and the need to further understand how glutamine metabolism and the TCA cycle contribute to maintaining MCL-1 expression. DisclosuresNo relevant conflicts of interest to declare.

Robustifying Experimental Tracer Design for13C-Metabolic Flux Analysis.

13C metabolic flux analysis (MFA) has become an indispensable tool to measure metabolic reaction rates (fluxes) in living organisms, having an increasingly diverse range of applications. Here, the choice of the13C labeled tracer composition makes the difference between an information-rich experiment and an experiment with only limited insights. To improve the chances for an informative labeling experiment, optimal experimental design approaches have been devised for13C-MFA, all relying on some a priori knowledge about the actual fluxes. If such prior knowledge is unavailable, e.g., for research organisms and producer strains, existing methods are left with a chicken-and-egg problem. In this work, we present a general computational method, termed robustified experimental design (R-ED), to guide the decision making about suitable tracer choices when prior knowledge about the fluxes is lacking. Instead of focusing on one mixture, optimal for specific flux values, we pursue a sampling based approach and introduce a new design criterion, which characterizes the extent to which mixtures are informative in view of all possible flux values. The R-ED workflow enables the exploration of suitable tracer mixtures and provides full flexibility to trade off information and cost metrics. The potential of the R-ED workflow is showcased by applying the approach to the industrially relevant antibiotic producer Streptomyces clavuligerus, where we suggest informative, yet economic labeling strategies.

The next phase in the development of 13C isotopically non-stationary metabolic flux analysis.

This viewpoint devises recommendations for future studies utilizing 13C isotopically non-stationary metabolic flux analysis to characterize plant metabolism. Most importantly, it highlights the necessity for model validation.

Can offsetting the energetic cost of hibernation restore an active season phenotype in grizzly bears (Ursus arctos horribilis)?

Hibernation is characterized by depression of many physiological processes. To determine if this state is reversible in a non-food caching species, we fed hibernating grizzly bears (Ursus arctos horribilis) dextrose for 10 days to replace 53% or 100% of the estimated minimum daily energetic cost of hibernation. Feeding caused serum concentrations of glycerol and ketones (β-hydroxybutyrate) to return to active season levels irrespective of the amount of glucose fed. By contrast, free fatty acids (FFAs) and indices of metabolic rate, such as general activity, heart rate, strength of heart rate circadian rhythm, and insulin sensitivity were restored to approximately 50% of active season levels. Body temperature was unaffected by feeding. To determine the contribution of adipose to the metabolic effects observed after glucose feeding, we cultured bear adipocytes collected at the beginning and end of the feeding and performed metabolic flux analysis. We found a ∼33% increase in energy metabolism after feeding. Moreover, basal metabolism before feeding was 40% lower in hibernation cells compared with fed cells or active cells cultured at 37°C, thereby confirming the temperature independence of metabolic rate. The partial depression of circulating FFAs with feeding likely explains the incomplete restoration of insulin sensitivity and other metabolic parameters in hibernating bears. Further depression of metabolic function is likely to be an active process. Together, the results provide a highly controlled model to examine the relationship between nutrient availability and metabolism on the hibernation phenotype in bears.

Systematic metabolic tools reveal underlying mechanism of product biosynthesis in Chromochloris zofingiensis

This study comprehensively explored underlying mechanism of fed-batch culture on product biosynthesis in Chromochloris zofingiensis by dynamic model, targeted metabolite determination, enzyme activity analysis, and 13C tracer-based metabolic flux analysis. Based on dynamic models of cell growth and product formation, exponential fed-batch culture and fed-batch culture based on pH changes were established to increase biomass concentration by 20.05-fold and 18.28-fold, respectively. Exponential fed-batch culture exhibited great potentials in biodiesel and protein productions from microalgae. Systematic metabolic tools revealed fed-batch culture limited photosynthetic efficiency by inhibiting photosystem and Rubisco activity, while strengthened respiratory action to provide more substances and energy for product biosynthesis. Fed-batch culture elevated biosynthetic capability for carotenoid and lipid by promoting related metabolic flux and contents of pyruvate and ace-CoA. Finally, economic analysis revealed biomass cost was decreased to 1.99 $/kg from 2.39 $/kg, suggesting fed-batch culture was a cost-effective strategy to improve economic viability of microalgal production.

IGFBP-3 Mediates Metabolic Homeostasis During Hyperosmolar Stress in the Corneal Epithelium.

PurposeThe insulin-like growth factor binding protein-3 (IGFBP-3) is a multifunctional secretory protein with well-known roles in cell growth and survival. Data in our laboratory suggest that IGFBP-3 may be functioning as a stress response protein in the corneal epithelium. The purpose of this study is to determine the role of IGFBP-3 in mediating the corneal epithelial cell stress response to hyperosmolarity, a well-known pathophysiological event in the development of dry eye disease.MethodsTelomerase-immortalized human corneal epithelial (hTCEpi) cells were used in this study. Cells were cultured in serum-free media with (growth) or without (basal) supplements. Hyperosmolarity was achieved by increasing salt concentrations to 450 and 500 mOsM. Metabolic and mitochondrial changes were assessed using Seahorse metabolic flux analysis and assays for mitochondrial calcium, polarization and mtDNA. Levels of IGFBP-3 and inflammatory mediators were quantified using ELISA. Cytotoxicity was evaluated using a lactate dehydrogenase assay. In select experiments, cells were cotreated with 500 ng/mL recombinant human (rh)IGFBP-3.ResultsHyperosmolar stress altered metabolic activity, shifting cells towards a respiratory phenotype. Hyperosmolar stress further altered mitochondrial calcium levels, depolarized mitochondria, decreased levels of ATP, mtDNA, and expression of IGFBP-3. In contrast, hyperosmolar stress increased production of the proinflammatory cytokines IL-6 and IL-8. Supplementation with rhIGFBP-3 abrogated metabolic and mitochondrial changes with only marginal effects on IL-8.ConclusionsThese findings indicate that IGFBP-3 is a critical protein involved in hyperosmolar stress responses in the corneal epithelium. These data further support a new role for IGFBP-3 in the control of cellular metabolism.

Designing and Development of FRET-Based Nanosensor for Real Time Analysis of N-Acetyl-5-Neuraminic Acid in Living Cells

N-acetyl-5-neuraminic acid (NeuAc) plays crucial role in improving the growth, brain development, brain health maintenance, and immunity enhancement of infants. Commercially, it is used in the production of antiviral drugs, infant milk formulas, cosmetics, dietary supplements, and pharmaceutical products. Because of the rapidly increasing demand, metabolic engineering approach has attracted increasing attention for NeuAc biosynthesis. However, knowledge of metabolite flux in biosynthetic pathways is one of the major challenges in the practice of metabolic engineering. So, an understanding of the flux of NeuAc is needed to determine its cellular level at real time. The analysis of the flux can only be performed using a tool that has the capacity to measure metabolite level in cells without affecting other metabolic processes. A Fluorescence Resonance Energy Transfer (FRET)-based genetically-encoded nanosensor has been generated in this study to monitor the level of NeuAc in prokaryotic and eukaryotic cells. Sialic acid periplasmic binding protein (SiaP) from Haemophilus influenzae was exploited as a sensory element for the generation of nanosensor. The enhanced cyan fluorescent protein (ECFP) and Venus were used as Fluroscence Resonance Energy Transfer (FRET) pair. The nanosensor, which was termed fluorescent indicator protein for sialic acid (FLIP-SA), was successfully transformed into, and expressed in Escherichia coli BL21 (DE3) cells. The expressed protein of the nanosensor was isolated and purified. The purified nanosensor protein was characterized to assess the affinity, specificity, and stability in the pH range. The developed nanosensor exhibited FRET change after addition to NeuAc. The developed nanosensor was highly specific, exhibited pH stability, and detected NeuAc levels in the nanomolar to milimolar range. FLIP-SA was successfully introduced in bacterial and yeast cells and reported the real-time intracellular levels of NeuAc non-invasively. The FLIP-SA is an excellent tool for the metabolic flux analysis of the NeuAc biosynthetic pathway and, thus, may help unravel the regulatory mechanism of the metabolic pathway of NeuAc. Furthermore, FLIP-SA can be used for the high-throughput screening of E. coli mutant libraries for varied NeuAc production levels.

Thirty years development of ¹³C metabolic flux analysis: a review

¹³C metabolic flux analysis (¹³C-MFA) enables the precise quantification of intracellular metabolic reaction rates by analyzing the distribution of mass isotopomers of proteinogenic amino acids or intracellular metabolites through ¹³C labeling experiments. ¹³C-MFA has received much attention as it can help systematically understand cellular metabolic characteristics, guide metabolic engineering design and gain mechanistic insights into pathophysiology. This article reviews the advances of ¹³C-MFA in the past 30 years and discusses its potential and future perspective, with a focus on its application in industrial biotechnology and biomedicine.

Metabolic Flux Analysis of Simultaneous Production of Vitamin B12 and Propionic Acid in a Coupled Fermentation Process by Propionibacterium freudenreichii.

The metabolic processes involved in simultaneous production of vitamin B12 and propionic acid by Propionibacterium freudenreichii are very complicated. To further investigate the regulatory mechanism of this metabolism, a simplified metabolic network was established. The effects of glucose feeding, propionic acid removal, and 5,6-dimethylbenzimidazole (DMB) addition on the metabolic flux distribution were investigated. The results showed that synthesis of propionic acid can be increased by increasing the metabolic flux through the oxaloacetate and methylmalonyl-CoA branches in the early and middle stages of the coupled fermentation. After DMB addition, the synthesis of vitamin B12 was significantly enhanced via increased metabolic flux through the δ-aminolevulinate branch, which promoted the synthesis of uroporphyrinogen III, a precursor of vitamin B12. Therefore, the analysis of metabolic flux at key nodes can provide theoretical guidance for the optimization of P. freudenreichii fermentation processes. In an experimental coupled fermentation process, the concentrations of vitamin B12 and propionic acid reached 21.6 and 50.12 g/L respectively, increased by 105.71% and 73.91% compared with batch fermentation, which provides a new strategy for industrial production.

Saccharomyces cerevisiae Δ9‐desaturase Ole1 Interacts with Lipid Biosynthetic Enzymes that Produce Storage Lipid, Phospholipid, and Sterol‐esters

Lipids are essential both for integrity of membranes and energy storage in a variety of organisms, from yeast to humans. The chemical properties of membrane phospholipids and triacylglycerol are determined by the composition and organization of their acyl chain components. Acyl-CoA molecules are delivered to the enzymes involved in lipid biosynthesis in a specific order, as is evidenced by the high prevalence of unsaturated acyl chains in the second position of phosphatidic acid and triacylglycerol in Saccharomyces cerevisiae. The mechanism controlling the specific nature of these lipids is not yet known, but we have previously demonstrated that acyltransferases that produce both storage and membrane lipid interact with the Δ9-desaturase, Ole1, in a complex we have called the desaturasome. We propose that these interactions determine the incorporation of unsaturated acyl chains into phospholipid and triacylglycerol and thus control the composition of membrane and storage lipids. Yeast two-hybrid and coimmunoprecipitation studies have revealed novel protein-protein interactions between Ole1 and storage lipid, phospholipid, and sterol-ester biosynthesis enzymes. Notably, Ole1 has been found to interact with the acyl-CoA:sterol acyltransferases Are1 and Are2, phosphatidate cytidylyltransferase Cds1, phosphatidylserine synthase Cho1, phosphatidylinositol synthase Pis1, phosphatidylethanolamine methyltransferase Cho2, and the rate limiting step in sterol synthesis, HMG-CoA reductase Hmg1. This research has determined the composition of an interactome that may exist to regulate the order of acyl chain incorporation into phospholipid, triacylglycerol, and sterol-esters. Future research aims to determine exactly how these interactions control lipid synthesis and composition via metabolic flux analysis and gene deletion studies. Investigating this lipid biosynthesis complex will have implications for a wide variety of applied research, from treating lipid dysregulation in humans to biofuel production by microbes.

Metabolic fluxes for nutritional flexibility of Mycobacterium tuberculosis.

The co‐catabolism of multiple host‐derived carbon substrates is required by Mycobacterium tuberculosis (Mtb) to successfully sustain a tuberculosis infection. However, the metabolic plasticity of this pathogen and the complexity of the metabolic networks present a major obstacle in identifying those nodes most amenable to therapeutic interventions. It is therefore critical that we define the metabolic phenotypes of Mtb in different conditions. We applied metabolic flux analysis using stable isotopes and lipid fingerprinting to investigate the metabolic network of Mtb growing slowly in our steady‐state chemostat system. We demonstrate that Mtb efficiently co‐metabolises either cholesterol or glycerol, in combination with two‐carbon generating substrates without any compartmentalisation of metabolism. We discovered that partitioning of flux between the TCA cycle and the glyoxylate shunt combined with a reversible methyl citrate cycle is the critical metabolic nodes which underlie the nutritional flexibility of Mtb. These findings provide novel insights into the metabolic architecture that affords adaptability of bacteria to divergent carbon substrates and expand our fundamental knowledge about the methyl citrate cycle and the glyoxylate shunt.

In Vivo Estimation of Ketogenesis Using Metabolic Flux Analysis-Technical Aspects and Model Interpretation.

Ketogenesis occurs in liver mitochondria where acetyl-CoA molecules, derived from lipid oxidation, are condensed into acetoacetate (AcAc) and reduced to β-hydroxybutyrate (BHB). During carbohydrate scarcity, these two ketones are released into circulation at high rates and used as oxidative fuels in peripheral tissues. Despite their physiological relevance and emerging roles in a variety of diseases, endogenous ketone production is rarely measured in vivo using tracer approaches. Accurate determination of this flux requires a two-pool model, simultaneous BHB and AcAc tracers, and special consideration for the stability of the AcAc tracer and analyte. We describe the implementation of a two-pool model using a metabolic flux analysis (MFA) approach that simultaneously regresses liquid chromatography-tandem mass spectrometry (LC-MS/MS) ketone isotopologues and tracer infusion rates. Additionally, 1H NMR real-time reaction monitoring was used to evaluate AcAc tracer and analyte stability during infusion and sample analysis, which were critical for accurate flux calculations. The approach quantifies AcAc and BHB pool sizes and their rates of appearance, disposal, and exchange. Regression analysis provides confidence intervals and detects potential errors in experimental data. Complications for the physiological interpretation of individual ketone fluxes are discussed.

Engineering Clostridium cellulovorans for highly selective n-butanol production from cellulose in consolidated bioprocessing.

Cellulosic n-butanol from renewable lignocellulosic biomass has gained increased interest. Previously, we have engineered Clostridium cellulovorans, a cellulolytic acidogen, to overexpress the bifunctional butyraldehyde/butanol dehydrogenase gene adhE2 from C. acetobutylicum for n-butanol production from crystalline cellulose. However, butanol production by this engineered strain had a relatively low yield of approximately 0.22 g/g cellulose due to the coproduction of ethanol and acids. We hypothesized that strengthening the carbon flux through the central butyryl-CoA biosynthesis pathway and increasing intracellular NADH availability in C. cellulovorans adhE2 would enhance n-butanol production. In this study, thiolase (thlACA ) from C. acetobutylicum and 3-hydroxybutyryl-CoA dehydrogenase (hbdCT ) from C. tyrobutyricum were overexpressed in C. cellulovorans adhE2 to increase the flux from acetyl-CoA to butyryl-CoA. In addition, ferredoxin-NAD(P)+ oxidoreductase (fnr), which can regenerate the intracellular NAD(P)H and thus increase butanol biosynthesis, was also overexpressed. Metabolic flux analyses showed that mutants overexpressing these genes had a significantly increased carbon flux toward butyryl-CoA, which resulted in increased production of butyrate and butanol. The addition of methyl viologen as an electron carrier in batch fermentation further directed more carbon flux towards n-butanol biosynthesis due to increased reducing equivalent or NADH. The engineered strain C. cellulovorans adhE2-fnrCA -thlACA -hbdCT produced n-butanol from cellulose at a 50% higher yield (0.34 g/g), the highest ever obtained in batch fermentation by any known bacterial strain. The engineered C. cellulovorans is thus a promising host for n-butanol production from cellulosic biomass in consolidated bioprocessing.