Shimizu Bacterial Cellular Metabolic Systems

Metabolic Regulation of a Cell System with 13C-Metabolic Flux Analysis
1. Auflage 2013
ISBN: 978-1-908818-20-1
Verlag: Elsevier Science & Techn.
Format: EPUB
Kopierschutz: 6 - ePub Watermark

E-Book, Englisch, 496 Seiten

Reihe: Woodhead Publishing Series in Biomedicine

The metabolic regulation of a cell system is of critical importance in systems biology, and a robust model of these mechanisms is essential in predicting the effects on the metabolism of both the culture environment and the knockout of specific genes. Bacterial cellular metabolic systems focuses on this highly topical subject in relation to culture environment and provides a detailed analysis from gene level to metabolic level regulation, as well as offering a discussion of the most recent modelling approaches. The book begins with an introduction to metabolic mechanisms and to the metabolic regulation of a cell, before moving on to discussing the action of global regulators in response to a specific culture environment. The second half of the book examines conventional flux balance analysis and its applications, 13C-metabolic flux analysis, and the effect of a specific gene knockout on the metabolism. - Comprehensive account of metabolic regulation via global regulators in response to changes in the culture environment - Basic formulation of 13C-metabolic flux analysis based on 13C-labelling experiments - Systems biology approach for the modelling and computer simulation of the main metabolic pathways of a cell system

Kazuyuki Shimizu is based at the Kyushu Institute of Technology and the Institute of Advanced Biosciences, Keio University, Japan. He has long been involved in research on 13C-metabolic flux analysis based on the 13C-labelling experiment and studies modelling and computer simulation with the aim of developing a virtual cell system.

Autoren/Hrsg.

Shimizu, K.

Leseproben

Figures
1.1. Main metabolic pathways 2 1.2. Metabolic pathways of glycolysis 4 1.3. Structure of ATP 5 1.4. Structure of NADH and NADPH 5 1.5. (a) Pentose phosphate pathway, and (b) the change in carbon numbers 11 1.6. Entner Doudoroff pathway 15 1.7. PDH and TCA cycle 16 1.8. Acetate producing pathways 21 1.9. Anaplerotic pathways 22 1.10. Gluconeogenetic pathways 24 1.11. Modularity of respiratory chains 26 1.12. Proton translocating values per electron in the respiratory chain 26 1.13. Schematic illustration for the electron transfer and proton translocation 28 1.14. Chemical structure of quinones 28 1.15. Pathway of UQ biosynthesis in E. coli 30 1.16. Anaerobic pathways 31 1.17. Nitrate respiration 33 1.18. Calvin-Benson cycle 35 1.19. Amino acid synthesis from their precursors 37 1.20. Alanine synthesis from PYR 38 1.21. Valine, leusine, and isoleusine biosynthesis 39 1.22. Glutamate and glutamine synthesis as well as aspartate and asparagine synthesis 39 1.23. Proline biosynthesis from glutamate 40 1.24. Arginine, ornitine, and citorline synthesis pathway 40 1.25. Lysine, threonine, and methionine biosynthesis 41 1.26. Aromatic amino acid synthesis pathways 43 1.27. Several control schemes for aromatic amino acid biosynthesis 44 1.28. Serine, glycine, and cystein synthesis pathways 44 1.29. Histisine synthesis pathways 45 1.30. Nucleic acids synthesis pathways 46 1.31. ß oxidation and biosynthesis of fatty acid 47 1.32. Phosphotransferase system (PTS) 49 1.33. Fructose metabolism 50 1.34. Xylose metabolism 51 1.35. ATP balance for aerobic and anaerobic conditions 52 2.1. Batch cultivations of E. coli K12 using different DO levels and different carbon sources 58 2.2. 2-DE gel maps of the total lysate of E. coli cells 63 2.3. The relative expression levels of E. coli K-12 proteins of central metabolic pathways under different conditions based on 2DE results 66 2.4. Comparison of the logarithmic protein expression ratios based on 2DE and the corresponding enzyme activity ratios 77 2.5. Growth curves of E. coli BW25113, which was grown in minimal media containing 10 g glucose/l as the sole carbon source 78 2.6. Relative gene expression of different global regulators and the metabolic pathway genes known to be regulated by those global regulators during different phases of growth 80 2.7. Concentration of different intracellular metabolites 83 2.8. Total and relative expression of iso-genes of E. coli metabolic pathways 84 2.9. Acetate metabolism 86 3.1. Overall metabolic regulation scheme 96 3.2. Outer and inner membrane and periplasm 98 3.3. Inducer exclusion and the activation of adenylate cyclase in the glucose-lactose system 101 3.4. The multiple regulations by Mlc and cAMP-Crp 103 3.5. Batch cultivation of (a) E. coli BW25113 and (b) its cra mutant 105 3.6. Comparison of enzyme activities of cra mutant as compared to the wild type (BW25113) 110 3.7. The effect of dilution rate on the gene transcript levels 113 3.8. Comparison of gene transcript levels of the wild type, crp knockout mutant, and crp+ mutant 116 3.9. Glucose PTS and fructose PTS 118 3.10. Central metabolic pathways and NH3-assimilation pathways 121 3.11. Ammonia assimilation under diffferent concentration 122 3.12. Effect of C/N ratio on the fermentation characteristics for the continuous culture at the dilution rate of 0.2 h-1 123 3.13. Schematic illustration of the interaction among several metabolic regulations. Comparison of the transcriptional mRNA levels of the wild type E.coli genes cultivated at 100% (C/N = 1.68), 40% (C/N = 4.21), 20% (C/N = 8.42) and 10% (C/N = 1.68) N- concentration: (a) global regulatory, (b) N- regulatory, (c) metabolic pathway, (d) respiratory chain 124 3.14. The interaction between nitrogen regulation and catabolite regulation 126 3.15. Overall mechanism of nitrogen assimilation in E. coli under C-limited (N-rich) and N-limited conditions 129 3.16. Molecular mechanism of phosphate regulation 131 3.17. Comparison of the transcript levels of the wild type E.coli cultivated with different P concentrations of the feed (100%, 55%, 10%) 134 3.18. Schematic illustration of the interaction among several metabolic regulation mechanisms 136 3.19. Comparison of some gene expressions for parent E. coli BW25113 and arcB mutant at 4 h of batch cultivation along with the gel picture 141 3.20. Comparison of specific enzyme activities of E. coli BW25113, its arcB and arcA mutant at 4 h of batch cultivation 141 3.21. Comparison of the transcript levels between wild type and fnr mutant under micro-aerobic continuous culture conditions 144 3.22. Comparison of enzymes activities during micro-aerobic batch culture 145 3.23. Metabolic flux distributions of wild type and fnr mutant under micro-aerobic conditions 147 3.24. Comparison of gene expressions 151 3.25. Specific enzyme activities in cell extracts 152 3.26. The role of glutamate decarboxylase for acid resistance 154 3.27. Acid resistance mechanism under acidic conditions 157 3.28. Effect of temperature up-shift on gene expressions in E. coli BW25113 under aerobic continuous culture at the dilution rate of 0.2 h-1 160 3.29. Effect of heat shock on gene and protein expressions and the fermentation characteristics 163 3.30. Metabolic pathways showing levels of enzymes (or proteins) and intracellular metabolite concentrations in the fadR mutant E. coli relative to those in the parent at the exponential phase grown in glucose minimal medium under aerobic conditions 171 3.31. Different kinds of sigma factor in E. coli 176 3.32. Schematic diagram on the function of sigma factor as a transcription factor 176 3.33. Various levels of ss regulation are differentially affected by various stress...