Luisi / Stano The Minimal Cell

The Biophysics of Cell Compartment and the Origin of Cell Functionality
1. Auflage 2010
ISBN: 978-90-481-9944-0
Verlag: Springer Netherlands
Format: PDF
Kopierschutz: 1 - PDF Watermark

E-Book, Englisch, 298 Seiten

Reihe: Biomedical and Life Sciences

In the last ten years there has been a considerable increase of interest on the notion of the minimal cell. With this term we usually mean a cell-like structure containing the minimal and sufficient number of components to be defined as alive, or at least capable of displaying some of the fundamental functions of a living cell. In fact, when we look at extant living cells we realize that thousands of molecules are organized spatially and functionally in order to realize what we call cellular life. This fact elicits the question whether such huge complexity is a necessary condition for life, or a simpler molecular system can also be defined as alive. Obviously, the concept of minimal cell encompasses entire families of cells, from totally synthetic cells, to semi-synthetic ones, to primitive cell models, to simple biomimetic cellular systems. Typically, in the experimental approach to the construction of minimal the main ingredient is the compartment. Lipid vesicles (liposomes) are used to host simple and complex molecular transformations, from single or multiple enzymic reactions, to polymerase chain reactions, to gene expression. Today this research is seen as part of the broader scenario of synthetic biology but it is rooted in origins of life studies, because the construction of a minimal cell might provide biophysical insights into the origins of primitive cells, and the emergence of life on earth. The volume provides an overview of physical, biochemical and functional studies on minimal cells, with emphasis to experimental approaches. 15 International experts report on their innovative contributions to the construction of minimal cells.

Autoren/Hrsg.

Luisi, Pier Luigi

Stano, Pasquale

Inhaltsverzeichnis

1;Preface;6
1.1;References;8
2;Contents;10
3;Part I The Physical Aspects;12
3.1;Chapter 1: Towards a Minimal Cytoplasm;13
3.1.1;1.1 Cytoplasm;14
3.1.1.1;1.1.1 Macromolecular Crowding;14
3.1.1.2;1.1.2 Microvolumes;16
3.1.1.3;1.1.3 Compartmentation;16
3.1.2;1.2 Experimental Models for the Intracellular Environment;18
3.1.2.1;1.2.1 Bulk Cytoplasm Models;19
3.1.2.1.1;1.2.1.1 Polymer Solutions Can Provide Volume Exclusion;19
3.1.2.1.2;1.2.1.2 Enzyme Assemblies Can Provide Colocalization;20
3.1.2.2;1.2.2 “Cell-Sized” Volumes;24
3.1.3;1.3 Incorporation of Model Cytoplasm into the Minimal Cell;25
3.1.3.1;1.3.1 Macromolecules and Macromolecular Crowding in Model Cells;25
3.1.3.2;1.3.2 Compartments in Model Cells;27
3.1.3.2.1;1.3.2.1 Compartments Formed by Interior Vesicles;28
3.1.3.2.2;1.3.2.2 Compartments Formed by Hydrogels;28
3.1.3.2.3;1.3.2.3 Compartments Formed by Aqueous Phase Separation;30
3.1.4;1.4 The Role of Cytoplasm in the Evolution of the Cell;34
3.1.5;1.5 Conclusions;35
3.1.6;References;35
3.2;Chapter 2: Evolution of the Cell’s Mechanical Design;41
3.2.1;2.1 Introduction;41
3.2.2;2.2 Mechanical Features of a Simple Cell;43
3.2.2.1;2.2.1 Bending Resistance of a Membrane;43
3.2.2.2;2.2.2 Edge Tension of a Bilayer;43
3.2.2.3;2.2.3 Minimal Cell Size to Close a Bilayer into a Sphere;44
3.2.2.4;2.2.4 Maximal Size for Wall-Less Cells Under Pressure;44
3.2.2.5;2.2.5 Bending and Packaging of DNA;45
3.2.3;2.3 Structural Evolution of Filamentous Cells;46
3.2.4;2.4 Models for the Cell Division Cycle;51
3.2.5;2.5 Evolution of the Division Cycle of Rod-Like Cells and Diplococci;55
3.2.6;2.6 Summary;58
3.2.7;References;59
3.3;Chapter 3: On the Minimal Requirements for the Emergence of Cellular Crowding;61
3.3.1;3.1 Introduction;61
3.3.2;3.2 Minimal Bacterial Model;63
3.3.3;3.3 Minimal Protocellular Model;67
3.3.4;3.4 Final Remarks;69
3.3.5;References;72
3.4;Chapter 4: How Small is Small?;75
3.4.1;4.1 Introduction;75
3.4.2;4.2 What is an Organism?;76
3.4.3;4.3 On the Sizes of Extant Bacteria;76
3.4.4;4.4 Expedients for Reducing Cell Size;79
3.4.5;References;80
3.5;Chapter 5: Biochemical Reactions in the Crowded and Confined Physiological Environment: Physical Chemistry Meets Synthetic Biology;82
3.5.1;FOREWORD;82
3.5.2;HOW CAN BIOCHEMICAL REACTIONS WITHIN CELLS DIFFER FROM THOSE IN TEST TUBES?1;83
3.5.3;5.1 Introduction;83
3.5.4;5.2 Types of Background and Background Interactions;84
3.5.4.1;5.3 Macromolecular Crowding;84
3.5.4.2;5.2.2 Macromolecular Confinement;85
3.5.4.3;5.2.3 Macromolecular Adsorption;86
3.5.4.4;5.2.4 Influence of Background Interactions upon Reaction Equilibria and Rates;86
3.5.5;5.3 A Common Energetic Formalism;88
3.5.6;5.4 Predictions and Observations;89
3.5.7;5.5 Relevance to Cell Biology;90
3.5.8;References;95
4;Part II Steps Towards Functionality;99
4.1;Chapter 6: The Influence of Environment and Metabolic Capacity on the Size of a Microorganism;100
4.1.1;6.1 Introduction;100
4.1.2;6.2 Organisms with Low Biosynthetic Capacity;103
4.1.3;6.3 The Most Slowly Evolving Microorganisms;103
4.1.4;6.4 Organisms with High Biosynthetic Capacity;105
4.1.5;6.5 The Smallest Cell;105
4.1.6;6.6 DNA Content Determines Minimal Cell Size;106
4.1.7;References;109
4.2;Chapter 7: The Minimal Cell and Life’s Origin: Role of Water and Aqueous Interfaces;111
4.2.1;7.1 Introduction;111
4.2.2;7.2 Problems with the Aqueous-Solution-Based Paradigm;112
4.2.2.1;7.2.1 Does this Really Happen?;113
4.2.3;7.3 Cells as Gels;114
4.2.3.1;7.3.1 Is There an Escape?;114
4.2.4;7.4 Cells, Gels and Water;115
4.2.5;7.5 Interfacial Water and Exclusion Zones;119
4.2.6;7.6 Charge Separation and Energy;119
4.2.7;7.7 Exclusion Zones and Protons;121
4.2.8;7.8 Like-Likes-Like;121
4.2.9;7.9 Biological Coalescence and Origin of Life;123
4.2.10;7.10 Conclusion: Is Life’s Origin a One-Time Event?;124
4.2.11;References;125
4.3;Chapter 8: Membrane Self-Assembly Processes: Steps Toward the First Cellular Life*;128
4.3.1;8.1 Introduction;128
4.3.2;8.2 Models of Protocellular Compartments;130
4.3.3;8.3 Stability and Permeability of Amphiphile Vesicles;130
4.3.4;8.4 Lipid Bilayer Membranes;138
4.3.5;8.5 Mixed Amphiphile Systems;138
4.3.6;8.6 Prebiotic Plausibility of Various Model Membranes;140
4.3.7;8.7 Mineral Surfaces and Compartments;141
4.3.8;8.8 Compartmentalization of Catalytic Molecules;142
4.3.9;8.9 Transfer of Encapsulated “Genetic” Information;145
4.3.10;8.10 Self-Reproducing Compartments;148
4.3.11;8.11 Conclusions and Future Directions;151
4.3.12;References;152
4.4;Chapter 9: Approaches to Building Chemical Cells/Chells: Examples of Relevant Mechanistic ‘Couples’;157
4.4.1;9.1 Introduction: Grounds for Focusing on Container, Metabolism and Information;157
4.4.2;9.2 The ‘Turing Test’ for Artificial Life;160
4.4.3;9.3 Paired Couplings of Components for Life;163
4.4.4;9.4 Container and Metabolism Coupling (C–M);163
4.4.5;9.5 C–I;165
4.4.6;9.6 M–I;168
4.4.7;9.7 Future Directions: Towards the Union of CMI;170
4.4.8;References;171
5;Part III Steps Towards Minimal Life;175
5.1;Chapter 10: Construction of an In Vitro Model of a Living Cellular System;176
5.1.1;10.1 General Introduction;177
5.1.2;10.2 Construction of the Structure and Function of a Model Cell;177
5.1.3;10.3 Recombinant Proteoliposomes;182
5.1.4;10.4 Efficient Construction of Giant Vesicles;185
5.1.5;10.5 Construction of a Model for Studying Changes in Cell Morphology;187
5.1.6;10.6 Conclusion;193
5.1.7;References;193
5.2;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
5.2.1;11.1 Minimal Cells and Synthetic Biology;198
5.2.2;11.2 The Minimal Size of Cells;199
5.2.3;11.3 In Vitro Protein Expression with a Minimal Set of Enzymes;200
5.2.4;11.4 Results;201
5.2.4.1;11.4.1 Protein Expression in Small Liposomes;202
5.2.5;11.5 The Conundrum of the Multiple Entrapment and the Hypothesis of “Superconcentration”;207
5.2.6;11.6 Investigating Protein Entrapment into Vesicles;210
5.2.7;11.7 Concluding Remarks;213
5.2.8;11.8 Experimental Section;214
5.2.9;Appendix;215
5.2.10;References;216
5.3;Chapter 12: Liposomes Mediated Synthesis of Membrane Proteins;219
5.3.1;12.1 Introduction;220
5.3.2;12.2 Construction of Minimal Cells by Synthetic Approaches;221
5.3.2.1;12.2.1 Minimal Cells;221
5.3.2.2;12.2.2 Minimal Genome;221
5.3.3;12.3 Protein Synthesis Inside Liposomes;222
5.3.3.1;12.3.1 Cell-Free Translation Systems;222
5.3.3.2;12.3.2 Liposomes;223
5.3.3.3;12.3.3 Model Proteins;225
5.3.4;12.4 Liposome-Mediated Membrane Protein Synthesis;225
5.3.4.1;12.4.1 a-Hemolysin;226
5.3.4.2;12.4.2 Membrane Enzymes Involved in Lipid Biosynthesis;227
5.3.5;12.5 Future Developments;228
5.3.6;12.6 Conclusions and Remarks;229
5.3.7;References;230
5.4;Chapter 13: Giant Unilamellar Vesicles: From Minimal Membrane Systems to Minimal Cells?;232
5.4.1;13.1 Short History of the GUV Model System;233
5.4.2;13.2 How to Make GUVs?;234
5.4.2.1;13.2.1 Electroswelling on Wires;234
5.4.2.2;13.2.2 Electroswelling Between ITO-Coated Coverslips;235
5.4.2.3;13.2.3 GUV Production at Physiological Conditions;236
5.4.2.4;13.2.4 Reverse Emulsion;236
5.4.2.5;13.2.5 Jetting;237
5.4.3;13.3 GUVs with Membrane Domains: A Success Story;237
5.4.4;13.4 GUVs Being Transformed by Proteins;239
5.4.5;13.5 Splitting GUVs;241
5.4.6;13.6 More Than Membrane: GUVs with a Cytoskeleton/Cortex;243
5.4.6.1;13.6.1 General Actin Cortex Assembly;243
5.4.6.2;13.6.2 Stable Filament Anchoring;244
5.4.6.2.1;13.6.2.1 GUVs Containing Functional Ion Channels;245
5.4.6.2.2;13.6.2.2 Attachment of Actin Filaments;246
5.4.7;13.7 GUVs as Containers;247
5.4.7.1;13.7.1 Cell Free Protein Expression in Vesicles;247
5.4.8;13.8 Perspective: Bacterial Cell Division Realized in GUVs?;248
5.4.9;13.9 Conclusion and Outlook;251
5.4.10;References;251
5.5;Chapter 14: Theoretical Approaches to Ribocell Modeling;255
5.5.1;14.1 Introduction;255
5.5.2;14.2 In Silico Ribocell;258
5.5.2.1;14.2.1 Reacting Vesicle Dynamics;258
5.5.2.1.1;14.2.1.1 Membrane Stability;260
5.5.2.2;14.2.2 Internal Metabolism;261
5.5.2.3;14.2.3 Kinetic Parameters and Assumptions;261
5.5.3;14.3 Theoretical Approaches;263
5.5.3.1;14.3.1 Deterministic Analysis;263
5.5.3.2;14.3.2 Stochastic Simulations;264
5.5.4;14.4 Results and Discussion;265
5.5.4.1;14.4.1 Deterministic Curves;265
5.5.4.2;14.4.2 Simulation Data;269
5.5.5;14.5 Conclusions;271
5.5.6;References;272
5.6;Chapter 15: Evolvability and Self-Replication of Genetic Information in Liposomes;274
5.6.1;15.1 Top-Down and Bottom-Up Approaches Toward Minimal Cell Synthesis;274
5.6.2;15.2 Achievements by the Bottom-Up Approach Toward Minimal Cell Synthesis;276
5.6.3;15.3 Replication of Genetic Information in Liposomes;276
5.6.4;15.4 Effects of Compartmentalization of the Self-Replication Reaction;278
5.6.5;15.5 Evolvability in Liposomes;280
5.6.6;15.6 Future Prospects;282
5.6.7;References;284
6;Index;287