13C metabolic flux analysis of microbial and mammalian systems is enhanced with GC-MS measurements of glycogen and RNA labeling

Metabolic Engineering

Volumn 38, Issue , 2016, Pages 65-72

  Long, Christopher P ^a   Au, Jennifer ^a   Gonzalez, Jacqueline E ^a   Antoniewicz, Maciek R ^a  

^a UNIVERSITY OF DELAWARE   (United States)

Author keywords

Flux estimation; Glucose and xylose co utilization; Metabolism; Pentose phosphate pathway; Stable isotope labeling

Indexed keywords

ESCHERICHIA COLI; GAS CHROMATOGRAPHY; GLUCOSE; ISOTOPES; MAMMALS; MASS SPECTROMETRY; METABOLISM; PHYSIOLOGY; RNA;

CO-UTILIZATION; FLUX ESTIMATION; GAS CHROMATOGRAPHY-MASS SPECTROMETRIES (GC-MS); INTRACELLULAR METABOLITES; METABOLIC FLUX ANALYSIS; PENTOSE PHOSPHATE PATHWAY; PRACTICAL IMPORTANCE; STABLE-ISOTOPE LABELING;

METABOLIC ENGINEERING;

CARBON 13; GLUCOSE; GLYCOGEN; RIBOSE; RNA; CARBON; RADIOPHARMACEUTICAL AGENT;

ANIMAL CELL; ARTICLE; CHO CELL LINE; ESCHERICHIA COLI; ISOTOPE LABELING; MASS FRAGMENTOGRAPHY; METABOLIC FLUX ANALYSIS; MICROBIAL METABOLISM; NONHUMAN; PENTOSE PHOSPHATE CYCLE; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; SAMPLE SIZE; ANIMAL; BIOLOGICAL MODEL; CARBON NUCLEAR MAGNETIC RESONANCE; CRICETULUS; METABOLISM; METABOLOME; PHYSIOLOGY; PROCEDURES;

ANIMALS; CARBON ISOTOPES; CARBON-13 MAGNETIC RESONANCE SPECTROSCOPY; CHO CELLS; CRICETULUS; ESCHERICHIA COLI; GAS CHROMATOGRAPHY-MASS SPECTROMETRY; GLYCOGEN; ISOTOPE LABELING; METABOLIC FLUX ANALYSIS; METABOLOME; MODELS, BIOLOGICAL; PENTOSE PHOSPHATE PATHWAY; RADIOPHARMACEUTICALS; RNA;

EID: 84978249216     PISSN: 10967176     EISSN: 10967184     Source Type: Journal    
DOI: 10.1016/j.ymben.2016.06.007     Document Type: Article

References (37)

1. Ahn, W.S., Antoniewicz, M.R., Metabolic flux analysis of CHO cells at growth and non-growth phases using isotopic tracers and mass spectrometry. Metab. Eng. 13 (2011), 598–609.
2. 13C]glutamine provide new insights into CHO cell metabolism. Metab. Eng. 15 (2013), 34–47.
3. 13C-metabolic flux analysis. Metab. Eng. 37 (2016), 72–78.
4. Antoniewicz, M.R., Tandem mass spectrometry for measuring stable-isotope labeling. Curr. Opin. Biotechnol. 24 (2013), 48–53.
5. 13C metabolic flux analysis: optimal design of isotopic labeling experiments. Curr. Opin. Biotechnol. 24 (2013), 1116–1121.
6. 13C metabolic flux analysis. Curr. Opin. Biotechnol. 36 (2015), 91–97.
7. Antoniewicz, M.R., Methods and advances in metabolic flux analysis: a mini-review. J. Ind. Microbiol. Biotechnol. 42 (2015), 317–325.
8. Antoniewicz, M.R., Kelleher, J.K., Stephanopoulos, G., Determination of confidence intervals of metabolic fluxes estimated from stable isotope measurements. Metab. Eng. 8 (2006), 324–337.
9. Antoniewicz, M.R., Kelleher, J.K., Stephanopoulos, G., Accurate assessment of amino acid mass isotopomer distributions for metabolic flux analysis. Anal. Chem. 79 (2007), 7554–7559.
10. Antoniewicz, M.R., Kelleher, J.K., Stephanopoulos, G., Elementary metabolite units (EMU): a novel framework for modeling isotopic distributions. Metab. Eng. 9 (2007), 68–86.
11. Antoniewicz, M.R., Kelleher, J.K., Stephanopoulos, G., Measuring deuterium enrichment of glucose hydrogen atoms by gas chromatography/mass spectrometry. Anal. Chem. 83 (2011), 3211–3216.
12. Aristilde, L., Lewis, I.A., Park, J.O., Rabinowitz, J.D., Hierarchy in pentose sugar metabolism in Clostridium acetobutylicum. Appl. Environ. Microbiol. 81 (2015), 1452–1462.
13. 13C metabolic flux analysis. Metab. Eng. 26 (2014), 23–33.
14. Badur, M.G., Zhang, H., Metallo, C.M., Enzymatic passaging of human embryonic stem cells alters central carbon metabolism and glycan abundance. Biotechnol. J. 10 (2015), 1600–1611.
15. Chiang, C., Lee, H.M., Guo, H.J., Wang, Z.W., Lin, L., Systematic approach to engineer Escherichia coli pathways for co-utilization of a glucose-xylose mixture. J. Agric. Food Chem. 61 (2013), 7583–7590.
16. 13C metabolic flux analysis of the extremely thermophilic, fast growing, xylose-utilizing Geobacillus strain LC300. Metab. Eng. 33 (2016), 148–157.
17. 13C-metabolic flux analysis using elementary metabolite units (EMU) basis vector methodology. Metab. Eng. 14 (2012), 150–161.
18. 13C-metabolic flux analysis of 14 parallel labeling experiments in Escherichia coli. Metab. Eng. 28 (2015), 151–158.
19. 13C metabolic flux analysis: a new precision and synergy scoring system. Metab. Eng. 37 (2016), 102–113.
20. 13C mass isotopomer distributions for natural stable isotope abundance. J. Mass. Spectrom. 31 (1996), 255–262.
21. 13C metabolic flux analysis shows that resistin impairs the metabolic response to insulin in L6E9 myotubes. BMC Syst. Biol., 8, 2014, 109.
22. Hanke, T., Nöh, K., Noack, S., Polen, T., Bringer, S., Sahm, H., Wiechert, W., Bott, M., Combined fluxomics and transcriptomics analysis of glucose catabolism via a partially cyclic pentose phosphate pathway in Gluconobacter oxydans 621H. Appl. Environ. Microbiol. 79 (2013), 2336–2348.
23. 13C metabolic flux analysis. Metab. Eng. 14 (2012), 533–541.
24. Leighty, R.W., Antoniewicz, M.R., COMPLETE-MFA: complementary parallel labeling experiments technique for metabolic flux analysis. Metab. Eng. 20 (2013), 49–55.
25. Li, R., Chen, Q., Wang, P.G., Qi, Q., A novel-designed Escherichia coli for the production of various polyhydroxyalkanoates from inexpensive substrate mixture. Appl. Microbiol. Biotechnol. 75 (2007), 1103–1109.
26. Long, C.P., Antoniewicz, M.R., Quantifying biomass composition by gas chromatography/mass spectrometry. Anal. Chem. 86 (2014), 9423–9427.
27. Long, C.P., Gonzalez, J.E., Sandoval, N.R., Antoniewicz, M.R., Characterization of physiological responses to 22 gene knockouts in Escherichia coli central carbon metabolism. Metab. Eng., 2016, 10.1016/j.ymben.2016.05.006.
28. 13C enrichments and isotopomer abundances for metabolic flux analysis using 1D NMR spectroscopy. Methods Mol. Biol. 1090 (2014), 73–86.
29. McConnell, B.O., Antoniewicz, M.R., Measuring the composition and stable-isotope labeling of algal biomass carbohydrates via gas chromatography/mass spectrometry. Anal. Chem. 88:9 (2016), 4624–4628.
30. Miranda-Santos, I., Gramacho, S., Pineiro, M., Martinez-Gomez, K., Fritz, M., Hollemeyer, K., Salvador, A., Heinzle, E., Mass isotopomer analysis of nucleosides isolated from RNA and DNA using GC/MS. Anal. Chem. 87 (2015), 617–623.
31. 13C flux analysis of Myc-induced metabolic reprogramming in B-cells. Metab. Eng. 15 (2013), 206–217.
32. 13C metabolic flux analysis. Biotechnol. Bioeng. 109 (2012), 763–771.
33. 13C]Glucose reveals a negligible isotopic influence on metabolism and physiology. PLoS One, 11, 2016, e0151130.
34. Truong, Q.X., Yoon, J.M., Shanks, J.V., Isotopomer measurement techniques in metabolic flux analysis I: nuclear magnetic resonance. Methods Mol. Biol. 1083 (2014), 65–83.
35. Valente, K.N., Lenhoff, A.M., Lee, K.H., Expression of difficult-to-remove host cell protein impurities during extended Chinese hamster ovary cell culture and their impact on continuous bioprocessing. Biotechnol. Bioeng. 112 (2015), 1232–1242.
36. Yoo, H., Antoniewicz, M.R., Stephanopoulos, G., Kelleher, J.K., Quantifying reductive carboxylation flux of glutamine to lipid in a brown adipocyte cell line. J. Biol. Chem. 283 (2008), 20621–20627.
37. 13C metabolic flux analysis of recombinant expression hosts. Curr. Opin. Biotechnol. 30 (2014), 238–245.