Utilizing tandem mass spectrometry for metabolic flux analysis

Model validation and selection in metabolic flux analysis and flux balance analysis

13C-Metabolic Flux Analysis (13C-MFA) and Flux Balance Analysis (FBA) are widely used to investigate the operation of biochemical networks in both biological and biotechnological research. Both methods use metabolic reaction network models of metabolism operating at steady state so that reaction rates (fluxes) and the levels of metabolic intermediates are constrained to be invariant. They provide estimated (MFA) or predicted (FBA) values of the fluxes through the network in vivo, which cannot be measured directly. These fluxes can shed light on basic biology and have been successfully used to inform metabolic engineering strategies. Several approaches have been taken to test the reliability of estimates and predictions from constraint-based methods and to compare alternative model architectures. Despite advances in other areas of the statistical evaluation of metabolic models, such as the quantification of flux estimate uncertainty, validation and model selection methods have been underappreciated and underexplored. We review the history and state-of-the-art in constraint-based metabolic model validation and model selection. Applications and limitations of the χ2 -test of goodness-of-fit, the most widely used quantitative validation and selection approach in 13C-MFA, are discussed, and complementary and alternative forms of validation and selection are proposed. A combined model validation and selection framework for 13C-MFA incorporating metabolite pool size information that leverages new developments in the field is presented and advocated for. Finally, we discuss how adopting robust validation and selection procedures can enhance confidence in constraint-based modeling as a whole and ultimately facilitate more widespread use of FBA in biotechnology.

Improved 13C metabolic flux analysis in Escherichia coli metabolism: application of a high-resolution MS (GC-EI-QTOF) for comprehensive assessment of MS/MS fragments

Gas chromatography-tandem mass spectrometry with electron ionization (GC-EI-MS/MS) provides rich information on stable-isotope labeling for 13C-metabolic flux analysis (13C-MFA). To pave the way for the routine application of tandem MS data for metabolic flux quantification, we aimed to compile a comprehensive library of GC-EI-MS/MS fragments of tert-butyldimethylsilyl (TBDMS) derivatized proteinogenic amino acids. First, we established an analytical workflow that combines high-resolution gas chromatography-quadrupole time-of-flight mass spectrometry and fully 13C-labeled biomass to identify and structurally elucidate tandem MS amino acid fragments. Application of the high-mass accuracy MS procedure resulted into the identification of 129 validated precursor-product ion pairs of 13 amino acids with 30 fragments being accepted for 13C-MFA. The practical benefit of the novel tandem MS data was demonstrated by a proof-of-concept study, which confirmed the importance of the compiled library for high-resolution 13C-MFA.

ONE SENTENCE SUMMARY

An analytical workflow that combines high-resolution mass spectrometry (MS) and fully 13C-labeled biomass to identify and structurally elucidate tandem MS amino acid fragments, which provide positional information and therefore offering significant advantages over traditional MS to improve 13C-metabolic flux analysis.

Graphene quantum dots disturbed the energy homeostasis by influencing lipid metabolism of macrophages

To investigate the potential factors of graphene quantum dots (GQDs), the assessment impact on the innate immune system is one of the most important. As the innate immune cell, macrophages possess phagocytosis activity and affect immunomodulation. Higher oxygen consumption rates (OCR) are used to gain insight into GQDs' effects on macrophages. Metabolomics profiling also revealed that GQDs exposure provoked an increase in phosphoglycerides, sphingolipids, and oxidized lipids in macrophages. The molecular pathways disrupted by GQDs were associated with lipid and energy metabolisms. Metabolite flux analysis was used to evaluate changes in the lipid metabolism of macrophages exposed to 100 µg mL^-1 GQDs for 24 and 48 h. A combination of ¹³C-flux analysis and metabolomics revealed the regulation of lipid biosynthesis influenced the balance of energy metabolism. Integrated proteomics and metabolomics analyses showed that nicotinic acid adenine dinucleotide and coenzyme Q10 were significantly increased under GQDs treatment, alongside upregulated protein activity (e.g., Cox5b and Cd36). The experimental evidences were expected to be provided in this study to reveal the potential harmful effect from exposure to GQDs.

Mitochondrial Lipid Signaling and Adaptive Thermogenesis

Thermogenesis is an energy demanding process by which endotherms produce heat to maintain their body temperature in response to cold exposure. Mitochondria in the brown and beige adipocytes play a key role in thermogenesis, as the site for uncoupling protein 1 (UCP1), which allows for the diffusion of protons through the mitochondrial inner membrane to produce heat. To support this energy demanding process, the mitochondria in brown and beige adipocytes increase oxidation of glucose, amino acids, and lipids. This review article explores the various mitochondria-produced and processed lipids that regulate thermogenesis including cardiolipins, free fatty acids, and acylcarnitines. These lipids play a number of roles in thermogenic adipose tissue including structural support of UCP1, transcriptional regulation, fuel source, and activation of cell signaling cascades.