Shene2020 - flux balance analysis of biomass and lipid production by Antarctic thraustochytrid Oblongichytrium
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ABSTRACT:
SUBMITTER: 
Carolina Shene
PROVIDER: MODEL2006010001 | BioModels | 2020-07-16
REPOSITORIES: BioModels
Similar Datasets
Project description:<p><strong>Background:</strong> Cell line specific, genome-scale metabolic models enable rigorous and systematic in silico investigation of cellular metabolism. Such models have recently become available for Chinese hamster ovary (CHO) too. However, a key ingredient, namely an experimentally validated biomass function that summarizes the cellular composition, was so far missing in all genome-scale metabolic models of CHO cell lines. Here, we close this gap by providing extensive experimental data on the biomass composition of 13 parental and producer CHO cell lines under various conditions.</p><p><strong>Results:</strong> We report protein, lipid, DNA, RNA and carbohydrate content, cell dry mass, and protein and lipid composition. Furthermore, we present meticulous data on exchange rates between cells and environment and provide detailed experimental protocols on how to determine all of the above. The biomass composition is converted into cell line and condition specific biomass functions for usage in cell line specific, genome-scale metabolic models of CHO. Finally, flux-balance analysis (FBA) is used to demonstrate consistency between in silico predictions and experimental analysis.</p><p><strong>Conclusions:</strong> Our study reveals a strong variability of the total protein content and cell dry mass across cell lines. Yet, the relative amino acid composition is independent of the cell lines and conditions and thus needs not be explicitly measured for each new cell line. In contrast, the lipid composition is strongly influenced by the growth media and needs to be determined for each case. These cell line specific variations in the biomass composition have a small impact on growth rate predictions with FBA, as inaccuracies in the predictions are typically dominated by inaccuracies in the exchange rate spectra. Cell specific biomass variations become only important if the experimental errors in the exchange rate spectra drop below twenty percent.</p><p><br></p><p><strong>Links:</strong></p><p>All data and code for data processing are available at <a href='http://dx.doi.org/10.17632/g3wz7spyc9.1' rel='noopener noreferrer' target='_blank'>Data Mendeley</a>.</p><p>Cell line specific metabolic models were deposited in <a href='https://www.ebi.ac.uk/biomodels/(Chelliah et al, 2014)' rel='noopener noreferrer' target='_blank'>BioModels</a>, identifiers are listed in the study sample table.</p>
2020-07-13 | MTBLS1210 | MetaboLights
Project description:Cellular lipid requirements are achieved through a combination of biosynthesis and import programs. Using isotope tracer analysis, we show that type I interferon (IFN) signaling rapidly shifts the balance of these programs by decreasing synthesis and increasing import of cholesterol and long chain fatty acids. Genetically enforcing this metabolic shift in macrophages is sufficient to render mice resistant to viral challenge, demonstrating the importance of reprogramming the balance of these two metabolic pathways in vivo. Unexpectedly, mechanistic studies reveal that limiting flux through the cholesterol biosynthetic pathway spontaneously engages a type I IFN response in a STING-dependent manner. The upregulation of type I IFNs was traced to a decrease in the pool size of synthesized cholesterol, and could be inhibited by replenishing cells with free cholesterol. Taken together, these studies delineate a metabolic-inflammatory circuit that links perturbations in cholesterol biosynthesis with activation of innate immunity. shRNA to SREBF1 (shSREBP1) or SREBF2 (shSREBP2) were stably introduced via 3rd generation lentivirus into human THP1 monocytic cells under puromycin selection. Non-targeting shRNA scramble was used for a control (shControl). shControl, shSREBP1 and shSREBP2 modified cell types were analyzed by RNA-seq in duplicate.
2015-12-10 | E-GEOD-73942 | biostudies-arrayexpress
Project description:This study predicted flux differences between brown and white adipocytes by integrating the results of extracellular flux analyzers, such as the Seahorse Analyzer, with metabolic modeling. The microarrays of the individuals' preadipocytes were used to support the predictions. These are the same individuals who were assayed by microarray in GSE68544.
2017-12-18 | GSE100003 | GEO
Project description:Cellular lipid requirements are achieved through a combination of biosynthesis and import programs. Using isotope tracer analysis, we show that type I interferon (IFN) signaling rapidly shifts the balance of these programs by decreasing synthesis and increasing import of cholesterol and long chain fatty acids. Genetically enforcing this metabolic shift in macrophages is sufficient to render mice resistant to viral challenge, demonstrating the importance of reprogramming the balance of these two metabolic pathways in vivo. Unexpectedly, mechanistic studies reveal that limiting flux through the cholesterol biosynthetic pathway spontaneously engages a type I IFN response in a STING-dependent manner. The upregulation of type I IFNs was traced to a decrease in the pool size of synthesized cholesterol, and could be inhibited by replenishing cells with free cholesterol. Taken together, these studies delineate a metabolic-inflammatory circuit that links perturbations in cholesterol biosynthesis with activation of innate immunity.
2015-12-10 | GSE73942 | GEO
Project description:In microbial production of non-catabolic products, a loss of production capacity upon long-term cultivation (for example, chemostat), a phenomenon called strain degeneration, is nearly always observed. In this study, a systems biology approach (monitoring changes from gene to produced flux) was used to study degeneration of penicillin production by Penicillium chrysogenum in ethanol-limited chemostat fermentations where the biomass specific penicillin production rate decreased 10-fold within 30 generations. Results showed that the copy number of penicillin gene clusters and expression levels of central metabolism showed little decrease. With respect to penicillin production, major changes were observed: a strong downregulation of the cysteine pathway in agreement with its nearly 10-fold flux reduction. Also, levels of ACVS and IPNS, two penicillin pathway enzymes, and the penicillin transport capacity decreased many fold. This indicates that degeneration is caused by changed regulation of post-translational modifications or an increased protein degradation rate of these proteins. Continued subcultivation of a degenerated culture resulted in partial recovery of the biomass specific penicillin production rate, however, it was still 5-fold lower than the peak biomass specific penicillin production rate.
2011-06-10 | GSE24212 | GEO
Project description:Desulfovibrio vulgaris Hildenborough is a gram-negative anaerobic bacterium belonging to the sulfate-reducing bacteria, a group of microbes that can perform dissimilatory sulfate reduction coupled to the oxidation of various substrates as carbon and energy sources. In the absence of sulfate, they can also ferment organic acids in syntrophy with methanogens. They exhibit high metabolic diversity switching from one energy mode to another depending on nutrients availability in the environments. Hence, they play a central role in shaping ecosystems. Despite, intensive efforts to study D. vulgaris energy metabolism at the genomic, biochemical and ecological level, bioenergetics in this microorganism remains far from being fully understood. Alternatively, few metabolic models were also proposed to explain D. vulgaris bioenergetics. However, they appeared to be not easily adaptable to various environmental conditions. To lift off these limitations, here we constructed a new transparent and robust metabolic model of D. vulgaris bioenergetics by combining whole-cell proteomic analysis with modeling approaches (Flux Balance Analysis). The iDvu71 model showed over 0.95 correlation with experimental data. Further simulations allowed a detailed description of D. vulgaris metabolism in various conditions of growth. Altogether, the simulations run in this study highlighted the sulfate-to-lactate consumption ratio as a pivotal factor in D. vulgaris energy metabolism. In particular, the impact on the hydrogen/formate balance and biomass synthesis is discussed. Overall, this study provides a novel insight into D. vulgaris metabolic flexibility.
2024-02-01 | PXD046638 | Pride
Project description:Miz1 is required to maintain autophagic flux
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Project description:Induction of cell death represents a primary goal of most anti-cancer treatments. Despite the efficacy of such approaches, a small population of “persisters” develop evasion strategies to therapy-induced cell death. While previous studies have identified mechanisms of resistance to apoptosis, the mechanisms by which persisters dampen other forms of cell death, such as pyroptosis, remain to be elucidated. Pyroptosis is a form of inflammatory cell death that involves formation of membrane pores, ion gradient imbalance, water inflow and membrane rupture. Herein, we investigate mechanisms by which cancer persisters resist pyroptosis, survive, then proliferate in the presence of tyrosine kinase inhibitors (TKI). Lung, prostate and esophageal cancer persister cells remaining after treatments exhibited several hallmarks indicative of pyroptosis resistance. The inflammatory attributes of persisters included chronic activation of inflammasome, STING, and type I interferons. Comprehensive metabolomic characterization uncovered that TKI-induced pyroptotic persisters display high methionine consumption and excessive taurine production. Elevated methionine flux or exogenous taurine maintained plasma membrane integrity via osmolyte-mediated effects. Increased dependency on methionine flux decreased the level of one carbon metabolism intermediate S-(5'-adenosyl)-L-homocysteine, a determinant of cell methylation capacity. The consequent increase in methylation potential induced DNA hypermethylation of genes regulating metal ion balance and intrinsic immune response. This enabled thwarting TKI resistance by using the hypomethylating agent decitabine. In summary, the evolution of resistance to pyroptosis can occur via a stepwise process of physical acclimation and epigenetic changes without existing or recurrent mutations.
2022-12-02 | GSE219044 | GEO
Project description:The ability to control the synthesis of products in the absence of cell division remains an attractive alternative for the optimization of microbial processes. If this could be achieved, it would dramatically expand the productivity of many microbial processes by increasing product synthesis in the absence of an increase in cell mass. In the present work we have looked at the factors involved in the design of a host where the fluxes would be channeled towards product formation rather than biomass synthesis. To identify the genes responsible for diverting the metabolic flux specifically towards product formation we have used for this study is quiescent-cell (Q-cell) expression system, in which a plasmid-encoded protein is expressed in nongrowing but metabolically active cells. These cells channel the metabolic flux towards recombinant protein production and therefore the specific product yield per unit biomass is significantly higher. Indole which is previously known to be a signalling molecule is here used as an inducer of Quiescence. E.coli L-Asparaginase is used as a model protein in this work.
2011-06-01 | GSE29486 | GEO
Project description:Mice have their lowest (basal) metabolic rate when housed at thermoneutrality, which starts above 29 degrees C. Although they eat less, and thus reduce their energy intake, their energy balance remains positive leading to an increased adiposity, especially when fed a high fat diet. However, almost all metabolic mouse studies are performed at standard room temperatures ranging between 20 and 22 degrees C. Previously, we showed that housing mice at thermoneutrality lead to massive increased adiposity, while metabolic dysfunction of white adipose tissue (WAT) was absent. Here, we studied whether an increased metabolic flux through WAT induces cellular stress and underlies tissue dysfunction leading to tissue inflammation. C57BL/6JOlaHsd wildtype male mice, aged 9 weeks, were fed purified low fat diet (BIOCLAIMS, Hoevenaars et al., Genes and Nutrition 2012) for 3 weeks to acclimatize, followed by 12 weeks a BIOCLAIMS high-fat diet (HFD), all at thermoneutrality (29 degrees C). Subsequently, mice were divided into different treatment groups: i) control group, which remained at thermoneutrality for 5 days, ii) 5 days normal housing temperature (22 C degrees) while housed continously in an indirect calorimetry system. At the end of the study, after 2 hours food removal at the start of the light phase, mice were killed immediately by decapitation after taking them out of the indirect calorimetry system. After sacrification, epididymal WAT was immediately dissected and snap frozen in liquid nitrogen. Total RNA was isolated, quantified and qualified, and subsequently used for global gene expression profiling using Agilent 8x60K microarrays.
2017-04-06 | GSE53804 | GEO