Bacterial Cellular Metabolic Systems

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

Auteur

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.

Contenu

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Tables

About the author

Chapter 1: Main metabolism

Abstract:

1.1 Introduction

1.2 Energy generation in the cell

1.3 Carbohydrate metabolism

1.4 Respiratory chain pathways

1.5 Anaerobic metabolism

1.6 Anaerobic respiration

1.7 Photosynthesis

1.8 Amino acids synthesis

1.9 Nucleic acid synthesis and its control

1.10 Fatty acid metabolism and degradation

1.11 Phosphotransferase system (PTS)

1.12 Carbohydrate metabolism other than glucose

1.13 ATP generation under aerobic and anaerobic conditions

1.14 Metabolic regulation and futile cycle

Chapter 2: Brief overview of metabolic regulation of a bacterial cell

Abstract:

2.1 Introduction

2.2 Metabolic regulation analysis by protein expressions

2.3 Metabolic regulation during the time course of batch culture

2.4 Reduction of by-product (acetate) formation

Chapter 3: Metabolic regulation by global regulators in response to culture environment

Abstract:

3.1 Introduction

3.2 Carbon catabolite regulation

3.3 Nitrogen regulation

3.4 Phosphate regulation

3.5 Oxygen level regulation

3.6 Acid shock or the effect of pH

3.7 Heat shock response

3.8 Fatty acid metabolic regulation

3.9 Response to nutrient starvation

Chapter 4: Conventional flux balance analysis and its applications

Abstract:

4.1 Introduction

4.2 Basis for metabolic flux analysis

4.3 Application to photosynthetic bacteria

4.4 Metabolic flux analysis of a single gene knockout E. coli under anaerobic conditions

Chapter 5: 13C-metabolic flux analysis and its applications

Abstract:

5.1 Introduction

5.2 Basic principle for flux calculation based on 13C-labeling experiment

5.3 Simple example for flux calculation based on 13C-labeling experiment

5.4 Analytical approach for flux computation

5.5 13C metabolic flux analysis based on GC-MS

5.6 13C-MFA using NMR

5.7 13CMFA for cyanobacteria based on GC-MS and NMR

5.8 Appendix 5.A AP and bPEP in Equation 5.41

Chapter 6: Effect of a specific-gene knockout on metabolism

Abstract:

6.1 Introduction

6.2 Effect of ppc and pck gene knockout on metabolism

6.3 Effect of zwf and gnd genes knockout on metabolism

6.4 Effect of pyk gene knockout on metabolism

6.5 Effect of lpdA gene knockout on metabolism

6.6 Effect of sucA and sucC gene knockout on metabolism

6.7 Effect of icdA gene knockout on metabolism

6.8 Effect of pfl gene knockout on metabolism

6.9 Effect of ldhA gene knockout on metabolism

Appendices

Index