The Minimal Cell (eBook)

Preface 6
References 8
Contents 10
Part I The Physical Aspects 12
Chapter 1: Towards a Minimal Cytoplasm 13
1.1 Cytoplasm 14
1.1.1 Macromolecular Crowding 14
1.1.2 Microvolumes 16
1.1.3 Compartmentation 16
1.2 Experimental Models for the Intracellular Environment 18
1.2.1 Bulk Cytoplasm Models 19
1.2.1.1 Polymer Solutions Can Provide Volume Exclusion 19
1.2.1.2 Enzyme Assemblies Can Provide Colocalization 20
1.2.2 “Cell-Sized” Volumes 24
1.3 Incorporation of Model Cytoplasm into the Minimal Cell 25
1.3.1 Macromolecules and Macromolecular Crowding in Model Cells 25
1.3.2 Compartments in Model Cells 27
1.3.2.1 Compartments Formed by Interior Vesicles 28
1.3.2.2 Compartments Formed by Hydrogels 28
1.3.2.3 Compartments Formed by Aqueous Phase Separation 30
1.4 The Role of Cytoplasm in the Evolution of the Cell 34
1.5 Conclusions 35
References 35
Chapter 2: Evolution of the Cell’s Mechanical Design 41
2.1 Introduction 41
2.2 Mechanical Features of a Simple Cell 43
2.2.1 Bending Resistance of a Membrane 43
2.2.2 Edge Tension of a Bilayer 43
2.2.3 Minimal Cell Size to Close a Bilayer into a Sphere 44
2.2.4 Maximal Size for Wall-Less Cells Under Pressure 44
2.2.5 Bending and Packaging of DNA 45
2.3 Structural Evolution of Filamentous Cells 46
2.4 Models for the Cell Division Cycle 51
2.5 Evolution of the Division Cycle of Rod-Like Cells and Diplococci 55
2.6 Summary 58
References 59
Chapter 3: On the Minimal Requirements for the Emergence of Cellular Crowding 61
3.1 Introduction 61
3.2 Minimal Bacterial Model 63
3.3 Minimal Protocellular Model 67
3.4 Final Remarks 69
References 72
Chapter 4: How Small is Small? 75
4.1 Introduction 75
4.2 What is an Organism? 76
4.3 On the Sizes of Extant Bacteria 76
4.4 Expedients for Reducing Cell Size 79
References 80
Chapter 5: Biochemical Reactions in the Crowded and Confined Physiological Environment: Physical Chemistry Meets Synthetic Biology 82
FOREWORD 82
HOW CAN BIOCHEMICAL REACTIONS WITHIN CELLS DIFFER FROM THOSE IN TEST TUBES?1 83
5.1 Introduction 83
5.2 Types of Background and Background Interactions 84
5.3 Macromolecular Crowding 84
5.2.2 Macromolecular Confinement 85
5.2.3 Macromolecular Adsorption 86
5.2.4 Influence of Background Interactions upon Reaction Equilibria and Rates 86
5.3 A Common Energetic Formalism 88
5.4 Predictions and Observations 89
5.5 Relevance to Cell Biology 90
References 95
Part II Steps Towards Functionality 99
Chapter 6: The Influence of Environment and Metabolic Capacity on the Size of a Microorganism 100
6.1 Introduction 100
6.2 Organisms with Low Biosynthetic Capacity 103
6.3 The Most Slowly Evolving Microorganisms 103
6.4 Organisms with High Biosynthetic Capacity 105
6.5 The Smallest Cell 105
6.6 DNA Content Determines Minimal Cell Size 106
References 109
Chapter 7: The Minimal Cell and Life’s Origin: Role of Water and Aqueous Interfaces 111
7.1 Introduction 111
7.2 Problems with the Aqueous-Solution-Based Paradigm 112
7.2.1 Does this Really Happen? 113
7.3 Cells as Gels 114
7.3.1 Is There an Escape? 114
7.4 Cells, Gels and Water 115
7.5 Interfacial Water and Exclusion Zones 119
7.6 Charge Separation and Energy 119
7.7 Exclusion Zones and Protons 121
7.8 Like-Likes-Like 121
7.9 Biological Coalescence and Origin of Life 123
7.10 Conclusion: Is Life’s Origin a One-Time Event? 124
References 125
Chapter 8: Membrane Self-Assembly Processes: Steps Toward the First Cellular Life* 128
8.1 Introduction 128
8.2 Models of Protocellular Compartments 130
8.3 Stability and Permeability of Amphiphile Vesicles 130
8.4 Lipid Bilayer Membranes 138
8.5 Mixed Amphiphile Systems 138
8.6 Prebiotic Plausibility of Various Model Membranes 140
8.7 Mineral Surfaces and Compartments 141
8.8 Compartmentalization of Catalytic Molecules 142
8.9 Transfer of Encapsulated “Genetic” Information 145
8.10 Self-Reproducing Compartments 148
8.11 Conclusions and Future Directions 151
References 152
Chapter 9: Approaches to Building Chemical Cells/Chells: Examples of Relevant Mechanistic ‘Couples’ 157
9.1 Introduction: Grounds for Focusing on Container, Metabolism and Information 157
9.2 The ‘Turing Test’ for Artificial Life 160
9.3 Paired Couplings of Components for Life 163
9.4 Container and Metabolism Coupling (C–M) 163
9.5 C–I 165
9.6 M–I 168
9.7 Future Directions: Towards the Union of CMI 170
References 171
Part III Steps Towards Minimal Life 175
Chapter 10: Construction of an In Vitro Model of a Living Cellular System 176
10.1 General Introduction 177
10.2 Construction of the Structure and Function of a Model Cell 177
10.3 Recombinant Proteoliposomes 182
10.4 Efficient Construction of Giant Vesicles 185
10.5 Construction of a Model for Studying Changes in Cell Morphology 187
10.6 Conclusion 193
References 193
Chapter 11: New and Unexpected Insights on the Formation of Protocells from a Synthetic Biology Approach: The Case of Entrapment of Biomacromoleculesand Protein Synthesis Inside Vesicles 197
11.1 Minimal Cells and Synthetic Biology 198
11.2 The Minimal Size of Cells 199
11.3 In Vitro Protein Expression with a Minimal Set of Enzymes 200
11.4 Results 201
11.4.1 Protein Expression in Small Liposomes 202
11.5 The Conundrum of the Multiple Entrapment and the Hypothesis of “Superconcentration” 207
11.6 Investigating Protein Entrapment into Vesicles 210
11.7 Concluding Remarks 213
11.8 Experimental Section 214
Appendix 215
References 216
Chapter 12: Liposomes Mediated Synthesis of Membrane Proteins 219
12.1 Introduction 220
12.2 Construction of Minimal Cells by Synthetic Approaches 221
12.2.1 Minimal Cells 221
12.2.2 Minimal Genome 221
12.3 Protein Synthesis Inside Liposomes 222
12.3.1 Cell-Free Translation Systems 222
12.3.2 Liposomes 223
12.3.3 Model Proteins 225
12.4 Liposome-Mediated Membrane Protein Synthesis 225
12.4.1 a-Hemolysin 226
12.4.2 Membrane Enzymes Involved in Lipid Biosynthesis 227
12.5 Future Developments 228
12.6 Conclusions and Remarks 229
References 230
Chapter 13: Giant Unilamellar Vesicles: From Minimal Membrane Systems to Minimal Cells? 232
13.1 Short History of the GUV Model System 233
13.2 How to Make GUVs? 234
13.2.1 Electroswelling on Wires 234
13.2.2 Electroswelling Between ITO-Coated Coverslips 235
13.2.3 GUV Production at Physiological Conditions 236
13.2.4 Reverse Emulsion 236
13.2.5 Jetting 237
13.3 GUVs with Membrane Domains: A Success Story 237
13.4 GUVs Being Transformed by Proteins 239
13.5 Splitting GUVs 241
13.6 More Than Membrane: GUVs with a Cytoskeleton/Cortex 243
13.6.1 General Actin Cortex Assembly 243
13.6.2 Stable Filament Anchoring 244
13.6.2.1 GUVs Containing Functional Ion Channels 245
13.6.2.2 Attachment of Actin Filaments 246
13.7 GUVs as Containers 247
13.7.1 Cell Free Protein Expression in Vesicles 247
13.8 Perspective: Bacterial Cell Division Realized in GUVs? 248
13.9 Conclusion and Outlook 251
References 251
Chapter 14: Theoretical Approaches to Ribocell Modeling 255
14.1 Introduction 255
14.2 In Silico Ribocell 258
14.2.1 Reacting Vesicle Dynamics 258
14.2.1.1 Membrane Stability 260
14.2.2 Internal Metabolism 261
14.2.3 Kinetic Parameters and Assumptions 261
14.3 Theoretical Approaches 263
14.3.1 Deterministic Analysis 263
14.3.2 Stochastic Simulations 264
14.4 Results and Discussion 265
14.4.1 Deterministic Curves 265
14.4.2 Simulation Data 269
14.5 Conclusions 271
References 272
Chapter 15: Evolvability and Self-Replication of Genetic Information in Liposomes 274
15.1 Top-Down and Bottom-Up Approaches Toward Minimal Cell Synthesis 274
15.2 Achievements by the Bottom-Up Approach Toward Minimal Cell Synthesis 276
15.3 Replication of Genetic Information in Liposomes 276
15.4 Effects of Compartmentalization of the Self-Replication Reaction 278
15.5 Evolvability in Liposomes 280
15.6 Future Prospects 282
References 284
Index 287