1. © 2015 H. Scott Hinton Lesson: E.coli Metabolic CoreBIE 5500/6500Utah State University Constraint-based Metabolic Reconstructions & Analysis E.coli CORE MODEL: METABOLIC CORE

2. © 2015 H. Scott Hinton Lesson: E.coli Metabolic CoreBIE 5500/6500Utah State University Constraint-based Metabolic Reconstructions & Analysis LEARNING OBJECTIVES Describe the glycolysis pathway in the core model. Describe the TCA cycle in the core model. Explain gluconeogenesis. Describe the pentose phosphate pathway in the core model. Describe the glycoxylate cycle and anapleurotic pathways in the core model. Describe the oxidative phosphorylation and electron transport chain pathways in the core model. Describe the fermentation pathways in the core model. Describe the nitrogen metabolism pathways in the core model. Each student should be able to:

3. © 2015 H. Scott Hinton Lesson: E.coli Metabolic CoreBIE 5500/6500Utah State University Constraint-based Metabolic Reconstructions & Analysis E.coli Core Model Component Parts of the E. coli Core Model Glycolysis Pentose Phosphate Shunt Tricarbonoxylic Acid (TCA) Cycle Glycoxylate Cycle, Gluconeogenesis, and Anapleurotic Reactions Oxidative Phosphorylation and Transfer of Reducing Equivalents Fermentation Nitrogen Metabolism

4. © 2015 H. Scott Hinton Lesson: E.coli Metabolic CoreBIE 5500/6500Utah State University Constraint-based Metabolic Reconstructions & Analysis Component Parts of the E. coli Core Model Reconstruction and Use of Microbial Metabolic Networks: the Core Escherichia coli Metabolic Model as an Educational Guide by Orth, Fleming, and Palsson (2010)

5. © 2015 H. Scott Hinton Lesson: E.coli Metabolic CoreBIE 5500/6500Utah State University Constraint-based Metabolic Reconstructions & Analysis E.coli Core Model Orth, J. D., I. Thiele, et al. (2010). "What is flux balance analysis?" Nature biotechnology 28(3): 245-248. http://systemsbiology.ucsd.edu/Downloads/E_coli_Core Ana TCA OxP PPP Glyc Ferm N N

6. © 2015 H. Scott Hinton Lesson: E.coli Metabolic CoreBIE 5500/6500Utah State University Constraint-based Metabolic Reconstructions & Analysis E.coli Precursor Metabolites Heptose in LPS 2-Keto-3-deoxyoctanate Pyruvate family Alanine Valine Leucine Isoleucine Isoprenoids Fatty Acids Murein Leucine Glutamate family Glutamate -> Hemes Glutamine Arginine -> Polyamines Proline Heme Aspartate family Asparagine Threonine Methionine -> Spermidine Aspartate -> Nicotinamide coenzymes -> Pyrimidine nucleotides Lysine Serine Family Serine -> Tryptophan -> Ethanolamine -> 1-C units Glycine -> Purine nucleotides Cysteine Amino sugars Nicotinamide coenzymes Glycerol-3-phosphate -> Phospholipids Sugar nucleotides Vitamins and cofactors Folates Riboflavin Coenzyme A Adenosylcobalamine Nicotinamide Purine nucleotides Pyrimidine nucleotides Phosphoribosyl pyrophosphate Histidine Tryptophan Aromatic Family Tyrosine Tryptophan Phenylalanine Chorismate Vitamins and cofactors Ubiquinone Menaquinone Folates

7. © 2015 H. Scott Hinton Lesson: E.coli Metabolic CoreBIE 5500/6500Utah State University Constraint-based Metabolic Reconstructions & Analysis E.coli Core Model Component Parts of the E. coli Core Model Glycolysis Pentose Phosphate Shunt Tricarbonoxylic Acid (TCA) Cycle Glycoxylate Cycle, Gluconeogenesis, and Anapleurotic Reactions Oxidative Phosphorylation and Transfer of Reducing Equivalents Fermentation Nitrogen Metabolism

8. © 2015 H. Scott Hinton Lesson: E.coli Metabolic CoreBIE 5500/6500Utah State University Constraint-based Metabolic Reconstructions & Analysis Glycolysis E.coli Core Model Orth, J. D., I. Thiele, et al. (2010). "What is flux balance analysis?" Nature biotechnology 28(3): 245-248. http://systemsbiology.ucsd.edu/Downloads/E_coli_Core Ana TCA OxP PPP Glyc Ferm N N

9. © 2015 H. Scott Hinton Lesson: E.coli Metabolic CoreBIE 5500/6500Utah State University Constraint-based Metabolic Reconstructions & Analysis Glycolysis http://en.wikipedia.org/wiki/Glycolysis Glycolysis is the metabolic pathway that converts glucose into pyruvate. The free energy released in this process is used to form the high-energy compounds of ATP and NADH.

10. © 2015 H. Scott Hinton Lesson: E.coli Metabolic CoreBIE 5500/6500Utah State University Constraint-based Metabolic Reconstructions & Analysis Glycolysis Reconstruction and Use of Microbial Metabolic Networks: the Core Escherichia coli Metabolic Model as an Educational Guide by Orth, Fleming, and Palsson (2010) Glycolysis is the metabolic pathway that converts glucose or fructose into a series of precursors for biosynthesis terminating with pyruvate. The free energy released in this process is used to form the high-energy compounds of ATP and NADH.

11. © 2015 H. Scott Hinton Lesson: E.coli Metabolic CoreBIE 5500/6500Utah State University Constraint-based Metabolic Reconstructions & Analysis Metabolites & Reactions Glycolysis Reconstruction and Use of Microbial Metabolic Networks: the Core Escherichia coli Metabolic Model as an Educational Guide by Orth, Fleming, and Palsson (2010)

12. © 2015 H. Scott Hinton Lesson: E.coli Metabolic CoreBIE 5500/6500Utah State University Constraint-based Metabolic Reconstructions & Analysis Biosynthetic Precursors (Glycolysis) Reconstruction and Use of Microbial Metabolic Networks: the Core Escherichia coli Metabolic Model as an Educational Guide by Orth, Fleming, and Palsson (2010) Cysteine Glycine Serine Tyrosine Tryptophan Phenylalanine Alanine Leucine Valine

13. © 2015 H. Scott Hinton Lesson: E.coli Metabolic CoreBIE 5500/6500Utah State University Constraint-based Metabolic Reconstructions & Analysis Glucose O2O2 Aerobic Conditions Carbon Source: Glucose Glycolysis NADH = NADPH = ATP =

14. © 2015 H. Scott Hinton Lesson: E.coli Metabolic CoreBIE 5500/6500Utah State University Constraint-based Metabolic Reconstructions & Analysis Glucose Anaerobic Conditions Carbon Source: Glucose Glycolysis NADH = NADPH = ATP =

15. © 2015 H. Scott Hinton Lesson: E.coli Metabolic CoreBIE 5500/6500Utah State University Constraint-based Metabolic Reconstructions & Analysis Fructose O2O2 Aerobic Conditions Carbon Source: Fructose Glycolysis NADH = NADPH = ATP =

16. © 2015 H. Scott Hinton Lesson: E.coli Metabolic CoreBIE 5500/6500Utah State University Constraint-based Metabolic Reconstructions & Analysis Anaerobic Conditions Carbon Source: Fructose Fructose Glycolysis NADH = NADPH = ATP =

17. © 2015 H. Scott Hinton Lesson: E.coli Metabolic CoreBIE 5500/6500Utah State University Constraint-based Metabolic Reconstructions & Analysis Pyruvate O2O2 Aerobic Conditions Carbon Source: Pyruvate Gluconeogenesis Does not grow in Anaerobic Conditions NADH = NADPH = ATP =

18. © 2015 H. Scott Hinton Lesson: E.coli Metabolic CoreBIE 5500/6500Utah State University Constraint-based Metabolic Reconstructions & Analysis E.coli Core Model Component Parts of the E. coli Core Model Glycolysis Pentose Phosphate Shunt Tricarbonoxylic Acid (TCA) Cycle Glycoxylate Cycle, Gluconeogenesis, and Anapleurotic Reactions Oxidative Phosphorylation and Transfer of Reducing Equivalents Fermentation Nitrogen Metabolism

19. © 2015 H. Scott Hinton Lesson: E.coli Metabolic CoreBIE 5500/6500Utah State University Constraint-based Metabolic Reconstructions & Analysis Pentose Phosphate Shunt E.coli Core Model Orth, J. D., I. Thiele, et al. (2010). "What is flux balance analysis?" Nature biotechnology 28(3): 245-248. http://systemsbiology.ucsd.edu/Downloads/E_coli_Core Ana TCA OxP PPP Glyc Ferm N N

20. © 2015 H. Scott Hinton Lesson: E.coli Metabolic CoreBIE 5500/6500Utah State University Constraint-based Metabolic Reconstructions & Analysis Pentose Phosphate Shunt (Pentose Phosphate Pathway) The pentose phosphate pathway generates NADPH and provides the 5-carbon (alpha-D- ribose-5-phosphate, “r5p”) and 4-carbon biosynthetic precursors (D-erythrose-4- phosphate, “e4p”). There are two distinct phases in the pathway. The first is the oxidative phase, in which NADPH is generated, and the second is the non-oxidative synthesis of 5-carbon and 4-carbon precursors. Reconstruction and Use of Microbial Metabolic Networks: the Core Escherichia coli Metabolic Model as an Educational Guide by Orth, Fleming, and Palsson (2010) Oxidative Pathway Non-oxidative Pathway

21. © 2015 H. Scott Hinton Lesson: E.coli Metabolic CoreBIE 5500/6500Utah State University Constraint-based Metabolic Reconstructions & Analysis Metabolites & Reactions Pentose Phosphate Pathway Reconstruction and Use of Microbial Metabolic Networks: the Core Escherichia coli Metabolic Model as an Educational Guide by Orth, Fleming, and Palsson (2010)

22. © 2015 H. Scott Hinton Lesson: E.coli Metabolic CoreBIE 5500/6500Utah State University Constraint-based Metabolic Reconstructions & Analysis Biosynthetic Precursors (Pentose Phosphate Pathway) Reconstruction and Use of Microbial Metabolic Networks: the Core Escherichia coli Metabolic Model as an Educational Guide by Orth, Fleming, and Palsson (2010) Histidine Purines (ATP, GTP,dATP, dGTP) Pyrimidines (UTP, CTP, dCTp, dTTP) Tryptophan Tyrosine Phenylalanine

23. © 2015 H. Scott Hinton Lesson: E.coli Metabolic CoreBIE 5500/6500Utah State University Constraint-based Metabolic Reconstructions & Analysis Glucose O2O2 Aerobic Conditions Carbon Source: Glucose Glycolysis Oxidative Pathway NADH = NADPH = ATP =

24. © 2015 H. Scott Hinton Lesson: E.coli Metabolic CoreBIE 5500/6500Utah State University Constraint-based Metabolic Reconstructions & Analysis Glucose Anaerobic Conditions Carbon Source: Glucose Glycolysis Non-oxidative Pathway NADH = NADPH = ATP =

25. © 2015 H. Scott Hinton Lesson: E.coli Metabolic CoreBIE 5500/6500Utah State University Constraint-based Metabolic Reconstructions & Analysis E.coli Core Model Component Parts of the E. coli Core Model Glycolysis Pentose Phosphate Shunt Tricarbonoxylic Acid (TCA) Cycle Glycoxylate Cycle, Gluconeogenesis, and Anapleurotic Reactions Oxidative Phosphorylation and Transfer of Reducing Equivalents Fermentation Nitrogen Metabolism

26. © 2015 H. Scott Hinton Lesson: E.coli Metabolic CoreBIE 5500/6500Utah State University Constraint-based Metabolic Reconstructions & Analysis Tricarbonoxylic Acid Cycle (TCA) E.coli Core Model Orth, J. D., I. Thiele, et al. (2010). "What is flux balance analysis?" Nature biotechnology 28(3): 245-248. http://systemsbiology.ucsd.edu/Downloads/E_coli_Core Ana TCA OxP PPP Glyc Ferm N N

27. © 2015 H. Scott Hinton Lesson: E.coli Metabolic CoreBIE 5500/6500Utah State University Constraint-based Metabolic Reconstructions & Analysis http://en.wikipedia.org/wiki/TCA_cycle The tricarboxylic acid cycle (TCA cycle), citric acid cycle — also known as the citric acid cycle, the Krebs cycle — is a series of chemical reactions used by all aerobic organisms to generate energy through the oxidization of acetate derived from carbohydrates, fats and proteins into carbon dioxide. In addition, the cycle provides precursors including certain amino acids as well as the reducing agent NADH. TCA Cycle

28. © 2015 H. Scott Hinton Lesson: E.coli Metabolic CoreBIE 5500/6500Utah State University Constraint-based Metabolic Reconstructions & Analysis TCA Cycle Reconstruction and Use of Microbial Metabolic Networks: the Core Escherichia coli Metabolic Model as an Educational Guide by Orth, Fleming, and Palsson (2010) The oxidative pathway of the TCA cycle runs counterclockwise in the lower part of the cycle, from oxaloacetate, oaa, through 2-oxoglutarate, akg. Continuing counterclockwise from 2-oxoglutarate, the full tricarboxylic acid cycle can totally oxidize acetyl-CoA, but is only functional during aerobic growth on acetate or fatty acids. Under anaerobic conditions, the TCA cycle functions not as a cycle, but as two separate pathways. The oxidative pathway, the counterclockwise lower part of the cycle, still forms the precursor 2-oxoglutarate. The reductive pathway, the clockwise upper part of the cycle, forms the precursor succinyl-CoA.

29. © 2015 H. Scott Hinton Lesson: E.coli Metabolic CoreBIE 5500/6500Utah State University Constraint-based Metabolic Reconstructions & Analysis Metabolites & Reactions TCA Cycle Reconstruction and Use of Microbial Metabolic Networks: the Core Escherichia coli Metabolic Model as an Educational Guide by Orth, Fleming, and Palsson (2010)

30. © 2015 H. Scott Hinton Lesson: E.coli Metabolic CoreBIE 5500/6500Utah State University Constraint-based Metabolic Reconstructions & Analysis Arginine Glutamine Glutamic acid Proline Asparagine Aspartic acid Isoleucine Lysine Methionine Threonine Biosynthetic Precursors (TCA Cycle) Reconstruction and Use of Microbial Metabolic Networks: the Core Escherichia coli Metabolic Model as an Educational Guide by Orth, Fleming, and Palsson (2010)

31. © 2015 H. Scott Hinton Lesson: E.coli Metabolic CoreBIE 5500/6500Utah State University Constraint-based Metabolic Reconstructions & Analysis Glucose O2O2 Aerobic Conditions Carbon Source: Glucose Oxidative Pathway NADH = NADPH = ATP =

32. © 2015 H. Scott Hinton Lesson: E.coli Metabolic CoreBIE 5500/6500Utah State University Constraint-based Metabolic Reconstructions & Analysis Glucose Anaerobic Conditions Carbon Source: Glucose Oxidative Pathway NADH = NADPH = ATP =

33. © 2015 H. Scott Hinton Lesson: E.coli Metabolic CoreBIE 5500/6500Utah State University Constraint-based Metabolic Reconstructions & Analysis E.coli Core Model Component Parts of the E. coli Core Model Glycolysis Pentose Phosphate Shunt Tricarbonoxylic Acid (TCA) Cycle Glycoxylate Cycle, Gluconeogenesis, and Anapleurotic Reactions Oxidative Phosphorylation and Transfer of Reducing Equivalents Fermentation Nitrogen Metabolism

34. © 2015 H. Scott Hinton Lesson: E.coli Metabolic CoreBIE 5500/6500Utah State University Constraint-based Metabolic Reconstructions & Analysis Glycoxylate Cycle, Gluconeogenesis, and Anapleurotic Reactions E.coli Core Model Orth, J. D., I. Thiele, et al. (2010). "What is flux balance analysis?" Nature biotechnology 28(3): 245-248. http://systemsbiology.ucsd.edu/Downloads/E_coli_Core Ana TCA OxP PPP Glyc Ferm The glycoxylate cycle and gluconeogenic reactions allow E. coli to grow on 3-carbon and 4-carbon compounds by avoiding the loss of carbon to carbon dioxide from the TCA cycle, providing a pathway for generation of glycolytic intermediates from TCA intermediates, and reversing the carbon flux through glycolysis to produce essential precursors for biosynthesis. N N

35. © 2015 H. Scott Hinton Lesson: E.coli Metabolic CoreBIE 5500/6500Utah State University Constraint-based Metabolic Reconstructions & Analysis Glycoxylate Cycle, Gluconeogenesis, and Anapleurotic Reactions Reconstruction and Use of Microbial Metabolic Networks: the Core Escherichia coli Metabolic Model as an Educational Guide by Orth, Fleming, and Palsson (2010)

36. © 2015 H. Scott Hinton Lesson: E.coli Metabolic CoreBIE 5500/6500Utah State University Constraint-based Metabolic Reconstructions & Analysis Metabolites & Reactions Glycoxylate Cycle, Gluconeogenesis, and Anapleurotic Reactions Reconstruction and Use of Microbial Metabolic Networks: the Core Escherichia coli Metabolic Model as an Educational Guide by Orth, Fleming, and Palsson (2010)

37. © 2015 H. Scott Hinton Lesson: E.coli Metabolic CoreBIE 5500/6500Utah State University Constraint-based Metabolic Reconstructions & Analysis Biosynthetic Precursors for Glycoxylate Cycle, Gluconeogenesis, and Anapleurotic Reactions Reconstruction and Use of Microbial Metabolic Networks: the Core Escherichia coli Metabolic Model as an Educational Guide by Orth, Fleming, and Palsson (2010) Asparagine Aspartic Acid Isoleucine Lysine Methionine Threonine Cysteine Glycine Serine Tyrosine Tryptophan Phenylalanine Alanine Leucine Valine

38. © 2015 H. Scott Hinton Lesson: E.coli Metabolic CoreBIE 5500/6500Utah State University Constraint-based Metabolic Reconstructions & Analysis Acetate O2O2 Aerobic Conditions Carbon Source: Acetate NADH = NADPH = ATP = Gluconeogenesis

39. © 2015 H. Scott Hinton Lesson: E.coli Metabolic CoreBIE 5500/6500Utah State University Constraint-based Metabolic Reconstructions & Analysis Acetaldehyde O2O2 Aerobic Conditions Carbon Source: Acetaldehyde NADH = NADPH = ATP = Gluconeogenesis

40. © 2015 H. Scott Hinton Lesson: E.coli Metabolic CoreBIE 5500/6500Utah State University Constraint-based Metabolic Reconstructions & Analysis Ethanol O2O2 Aerobic Conditions Carbon Source: Ethanol NADH = NADPH = ATP = Gluconeogenesis

41. © 2015 H. Scott Hinton Lesson: E.coli Metabolic CoreBIE 5500/6500Utah State University Constraint-based Metabolic Reconstructions & Analysis E.coli Core Model Component Parts of the E. coli Core Model Glycolysis Pentose Phosphate Shunt Tricarbonoxylic Acid (TCA) Cycle Glycoxylate Cycle, Gluconeogenesis, and Anapleurotic Reactions Oxidative Phosphorylation and Transfer of Reducing Equivalents Fermentation Nitrogen Metabolism

42. © 2015 H. Scott Hinton Lesson: E.coli Metabolic CoreBIE 5500/6500Utah State University Constraint-based Metabolic Reconstructions & Analysis Oxidative Phosphorylation and Transfer of Reducing Equivalents E.coli Core Model Orth, J. D., I. Thiele, et al. (2010). "What is flux balance analysis?" Nature biotechnology 28(3): 245-248. http://systemsbiology.ucsd.edu/Downloads/E_coli_Core Ana TCA OxP PPP Glyc Ferm N N

43. © 2015 H. Scott Hinton Lesson: E.coli Metabolic CoreBIE 5500/6500Utah State University Constraint-based Metabolic Reconstructions & Analysis Oxidative Phosphorylation and Transfer of Reducing Equivalents Energy is required to drive endergonic processes such as biosynthesis, polymerization, active transport of substrate into the cell against concentration gradients, maintaining internal pH, and motility. There are two main mechanisms for the production of energy, substrate level phosphorylation, and the electron transport chain. Substrate level phosphorylation is where ATP is formed by a reaction between ADP and a phosphorylated intermediate of a fueling pathway. Examples include: phosphoglycerate kinase, PGK, and pyruvate kinase, PYK, in glycolysis, and succinyl-CoA synthetase, SUCOAS, in the tricarboxylic acid cycle. Each molecule of glucose can potentially lead to the net generation of four molecules of ATP. The electron transport chain which produces the bulk of the cell's ATP under aerobic conditions. Mitchell's chemiosmotic theory describes the mechanism by which electron transport is coupled to the generation of ATP. The electron transport chain translocates protons, H +, from the cytoplasm, across the cytoplasmic membrane into the periplasmic space. Since the cytoplasmic membrane is effectively impermeable to protons and hydroxyl ions, OH -, this establishes a difference in concentration of protons, and a difference in electrical charge, across the cytoplasmic membrane. This thermodynamic potential difference gives rise to a proton motive force which can be utilized to drive a myriad of endergonic reactions, such as synthesis of high energy currency metabolites, such as ATP. Reconstruction and Use of Microbial Metabolic Networks: the Core Escherichia coli Metabolic Model as an Educational Guide by Orth, Fleming, and Palsson (2010)

44. © 2015 H. Scott Hinton Lesson: E.coli Metabolic CoreBIE 5500/6500Utah State University Constraint-based Metabolic Reconstructions & Analysis Oxidative Phosphorylation and Transfer of Reducing Equivalents Reconstruction and Use of Microbial Metabolic Networks: the Core Escherichia coli Metabolic Model as an Educational Guide by Orth, Fleming, and Palsson (2010)

45. © 2015 H. Scott Hinton Lesson: E.coli Metabolic CoreBIE 5500/6500Utah State University Constraint-based Metabolic Reconstructions & Analysis Metabolites & Reactions Reconstruction and Use of Microbial Metabolic Networks: the Core Escherichia coli Metabolic Model as an Educational Guide by Orth, Fleming, and Palsson (2010) Oxidative Phosphorylation and Transfer of Reducing Equivalents

46. © 2015 H. Scott Hinton Lesson: E.coli Metabolic CoreBIE 5500/6500Utah State University Constraint-based Metabolic Reconstructions & Analysis Glucose O2O2 Aerobic Conditions Carbon Source: Glucose NADH = NADPH = ATP =

47. © 2015 H. Scott Hinton Lesson: E.coli Metabolic CoreBIE 5500/6500Utah State University Constraint-based Metabolic Reconstructions & Analysis Glucose Anaerobic Conditions Carbon Source: Glucose NADH = NADPH = ATP =

48. © 2015 H. Scott Hinton Lesson: E.coli Metabolic CoreBIE 5500/6500Utah State University Constraint-based Metabolic Reconstructions & Analysis E.coli Core Model Component Parts of the E. coli Core Model Glycolysis Pentose Phosphate Shunt Tricarbonoxylic Acid (TCA) Cycle Glycoxylate Cycle, Gluconeogenesis, and Anapleurotic Reactions Oxidative Phosphorylation and Transfer of Reducing Equivalents Fermentation Nitrogen Metabolism

49. © 2015 H. Scott Hinton Lesson: E.coli Metabolic CoreBIE 5500/6500Utah State University Constraint-based Metabolic Reconstructions & Analysis Fermentation E.coli Core Model Orth, J. D., I. Thiele, et al. (2010). "What is flux balance analysis?" Nature biotechnology 28(3): 245-248. http://systemsbiology.ucsd.edu/Downloads/E_coli_Core Ana TCA OxP PPP Glyc Ferm Fermentation is the process of extracting energy from the oxidation of organic compounds, such as carbohydrates, using an endogenous electron acceptor (not oxygen), which is usually an organic compound. Glycolysis results in the net production of 2 ATP per glucose by substrate level phosphorylation, but this is low compared to 17.5 ATP per glucose for aerobic respiration. The substrates of fermentation are typically sugars, so during fermentative growth, each cell must maintain a large magnitude flux through glycolysis to generate sufficient ATP to drive the constitutive biosynthesis, polymerization, and assembly reactions required for growth. This necessitates a large magnitude effiux of fermentative end products since there is insufficient ATP to assimilate all carbon as biomass. Approximately 10% of carbon substrate is assimilated due to the poor energy yield of fermentation. N N

50. © 2015 H. Scott Hinton Lesson: E.coli Metabolic CoreBIE 5500/6500Utah State University Constraint-based Metabolic Reconstructions & Analysis Fermentation Reconstruction and Use of Microbial Metabolic Networks: the Core Escherichia coli Metabolic Model as an Educational Guide by Orth, Fleming, and Palsson (2010)

51. © 2015 H. Scott Hinton Lesson: E.coli Metabolic CoreBIE 5500/6500Utah State University Constraint-based Metabolic Reconstructions & Analysis Metabolites & Reactions Fermentation Reconstruction and Use of Microbial Metabolic Networks: the Core Escherichia coli Metabolic Model as an Educational Guide by Orth, Fleming, and Palsson (2010)

52. © 2015 H. Scott Hinton Lesson: E.coli Metabolic CoreBIE 5500/6500Utah State University Constraint-based Metabolic Reconstructions & Analysis Glucose O2O2 Mixed Acid Fermentation Anaerobic Conditions Carbon Source: Glucose NADH = NADPH = ATP = AcetateFormateEthanol

53. © 2015 H. Scott Hinton Lesson: E.coli Metabolic CoreBIE 5500/6500Utah State University Constraint-based Metabolic Reconstructions & Analysis E.coli Core Model Component Parts of the E. coli Core Model Glycolysis Pentose Phosphate Shunt Tricarbonoxylic Acid (TCA) Cycle Glycoxylate Cycle, Gluconeogenesis, and Anapleurotic Reactions Oxidative Phosphorylation and Transfer of Reducing Equivalents Fermentation Nitrogen Metabolism

54. © 2015 H. Scott Hinton Lesson: E.coli Metabolic CoreBIE 5500/6500Utah State University Constraint-based Metabolic Reconstructions & Analysis Nitrogen Metabolism E.coli Core Model Orth, J. D., I. Thiele, et al. (2010). "What is flux balance analysis?" Nature biotechnology 28(3): 245-248. http://systemsbiology.ucsd.edu/Downloads/E_coli_Core Ana TCA OxP PPP Glyc Ferm Nitrogen is the fourth most abundant atom in E. coli and enters the cell either by ammonium ion uptake, NH4t, or as a moiety within organic molecules, such as glutamine or glutamate. The E.coli core model covers the pathways between 2-oxoglutarate, L-glutamate, and L- glutamine. N N

55. © 2015 H. Scott Hinton Lesson: E.coli Metabolic CoreBIE 5500/6500Utah State University Constraint-based Metabolic Reconstructions & Analysis Nitrogen Metabolism Reconstruction and Use of Microbial Metabolic Networks: the Core Escherichia coli Metabolic Model as an Educational Guide by Orth, Fleming, and Palsson (2010)

56. © 2015 H. Scott Hinton Lesson: E.coli Metabolic CoreBIE 5500/6500Utah State University Constraint-based Metabolic Reconstructions & Analysis Biosynthetic Precursors (Nitrogen Metabolism) Reconstruction and Use of Microbial Metabolic Networks: the Core Escherichia coli Metabolic Model as an Educational Guide by Orth, Fleming, and Palsson (2010) Glutamine Proline Arginine Glutamate

57. © 2015 H. Scott Hinton Lesson: E.coli Metabolic CoreBIE 5500/6500Utah State University Constraint-based Metabolic Reconstructions & Analysis Metabolites & Reactions Nitrogen Metabolism Reconstruction and Use of Microbial Metabolic Networks: the Core Escherichia coli Metabolic Model as an Educational Guide by Orth, Fleming, and Palsson (2010)

58. © 2015 H. Scott Hinton Lesson: E.coli Metabolic CoreBIE 5500/6500Utah State University Constraint-based Metabolic Reconstructions & Analysis Glucose O2O2 Aerobic Conditions Carbon Source: Glucose NADH = NADPH = ATP =

59. © 2015 H. Scott Hinton Lesson: E.coli Metabolic CoreBIE 5500/6500Utah State University Constraint-based Metabolic Reconstructions & Analysis E.coli Core Model Component Parts of the E. coli Core Model Glycolysis Pentose Phosphate Shunt Tricarbonoxylic Acid (TCA) Cycle Glycoxylate Cycle, Gluconeogenesis, and Anapleurotic Reactions Oxidative Phosphorylation and Transfer of Reducing Equivalents Fermentation Nitrogen Metabolism

60. © 2015 H. Scott Hinton Lesson: E.coli Metabolic CoreBIE 5500/6500Utah State University Constraint-based Metabolic Reconstructions & Analysis EXTRA SLIDES

61. © 2015 H. Scott Hinton Lesson: E.coli Metabolic CoreBIE 5500/6500Utah State University Constraint-based Metabolic Reconstructions & Analysis Amino acid biosynthetic pathways in E. coli Pharkya, P., A. P. Burgard, et al. (2003). "Exploring the overproduction of amino acids using the bilevel optimization framework OptKnock." Biotechnology and bioengineering 84(7): 887-899.