Chemical Synthetic Biology E-Book

• Herausgeber: John Wiley & Sons
• Kategorie: Wissenschaft und neue Technologien
• Sprache: Englisch

Seitenzahl: 560

Veröffentlichungsjahr: 2011

Beschreibung

Chemistry plays a very important role in the emerging field of synthetic biology. In particular, chemical synthetic biology is concerned with the synthesis of chemical structures, such as proteins, that do not exist in nature. With contributions from leading international experts, Chemical Synthetic Biology shows how chemistry underpins synthetic biology. The book is an essential guide to this fascinating new field, and will find a place on the bookshelves of researchers and students working in synthetic chemistry, synthetic and molecular biology, bioengineering, systems biology, computational genomics, and bioinformatics.

Leseprobe

Table of Contents

Cover

Table of Contents

Half title page

Title page

Copyright page

List of Contributors

Introduction

Part One: Nucleic Acids

1 Searching for Nucleic Acid Alternatives

2 Never-Born RNAs: Versatile Modules for Chemical Synthetic Biology

2.1 INTRODUCTION

2.2 RANDOM RNAS READILY ADOPT A COMPACT AND THERMOSTABLE SECONDARY STRUCTURE

2.3 RANDOM RNAS CAN BE EASILY DESIGNED AND ENGINEERED TO ACQUIRE NOVEL FUNCTIONS

2.4 RANDOM RNAS AS A MODULAR SCAFFOLD FOR SYNTHETIC BIOLOGY

2.5 CONCLUSIONS

ACKNOWLEDGMENTS

3 Synthetic Biology, Tinkering Biology, and Artificial Biology: A Perspective from Chemistry

3.1 INTRODUCTION

3.2 ATTEMPTING TO SYNTHESIZE AN ARTIFICIAL GENETIC SYSTEM

3.3 BUILDING GENETICS FROM THE ATOM UP

3.4 DOES SYNTHETIC BIOLOGY CARRY HAZARDS?

3.5 CONCLUSIONS

ACKNOWLEDGMENTS

STATEMENT OF CONFLICTS OF INTEREST

4 Peptide Nucleic Acids (PNAs) as a Tool in Chemical Biology

4.1 INTRODUCTION

4.2 CHEMISTRY

4.3 AN ASSAY FOR CELLULAR DELIVERY USING PNA ANTISENSE IN PLUC–HELA CELLS

4.4 DUPLEX DNA RECOGNITION

4.5 TARGETED GENE REPAIR

4.6 SEQUENCE INFORMATION TRANSFER

4.7 CONCLUDING REMARKS

Part Two: Peptides and Proteins

5 High Solubility of Random-Sequence Proteins Consisting of Five Kinds of Primitive Amino Acids

5.1 INTRODUCTION

5.2 MATERIALS AND METHODS

5.3 RESULTS

5.4 DISCUSSION

ACKNOWLEDGMENTS

6 Experimental Approach for Early Evolution of Protein Function

6.1 INTRODUCTION

6.2 EXPERIMENTAL EVOLUTION STARTING FROM RANDOM SEQUENCES

6.3 DISCUSSION

7 Searching for de novo Totally Random Amino Acid Sequences

7.1 INTRODUCTION

7.2 STRATEGIES FOR PEPTIDE LIBRARIES PRODUCTION

7.3 COMBINATORIAL CHEMISTRY

7.4 A MODEL FOR CHEMICAL EVOLUTION OF MACROMOLECULAR SEQUENCES

7.5 NEVER-BORN PROTEINS PROJECT

Part Three: Complex Systems

8 Synthetic Genetic Codes as the Basis of Synthetic Life

8.1 INTRODUCTION

8.2 NATURAL CODE EXPANSION

8.3 NATURAL CODE TURNOVER

8.4 THE DEEP FREEZE

8.5 SYNTHETIC CODE EXPANSION

8.6 SYNTHETIC CODE TURNOVER

8.7 USEFULNESS OF SYNTHETIC CODES

8.8 DISCUSSION

ACKNOWLEDGMENTS

9 Toward Safe Genetically Modified Organisms through the Chemical Diversification of Nucleic Acids

9.1 INTRODUCTION

9.2 SPECIFICATIONS FOR AN ORTHOGONAL EPISOME

9.3 DIVERSIFICATION OF THE BACKBONE MOTIF

9.4 DIVERSIFICATION OF THE LEAVING GROUP

9.5 DIVERSIFICATION OF NUCLEIC BASES

9.6 DIVERSIFICATION OF NUCLEIC ACID POLYMERASES

9.7 CONCLUSIONS

ACKNOWLEDGMENTS

10 The Minimal Ribosome

10.1 INTRODUCTION

10.2 A BRIEF DESCRIPTION OF THE RIBOSOMAL STRUCTURE AND FUNCTION

10.3 NON-ESSENTIAL RIBOSOMAL PROTEINS: MUTATIONAL APPROACH

10.4 A SURPRISING OBSERVATION: THE KASUGAMYCIN PARTICLE

10.5 A MINIMAL CORE OF THE LARGE RIBOSOMAL SUBUNIT STILL ACTIVE IN PEPTIDE-BOND FORMATION

10.6 CUTTING DOWN THE RRNAS

10.7 CONCLUSIONS

11 Semi-Synthetic Minimal Living Cells

11.1 THE NOTION OF MINIMAL CELL

11.2 THE MINIMAL GENOME

11.3 THE MINIMAL RNA CELL

11.4 THE MINIMAL SIZE OF CELLS

11.5 CURRENT EXPERIMENTAL APPROACHES FOR THE CONSTRUCTION OF MINIMAL CELLS

11.6 CONCLUDING REMARKS

ACKNOWLEDGMENTS

Part Four: General Problems

12 Replicators: Components for Systems Chemistry

12.1 THE NEED FOR SYSTEMS CHEMISTRY

12.2 SELF-REPLICATING REACTIONS

12.3 TOOLS FOR SYSTEMS CHEMISTRY

13 Dealing with the Outer Reaches of Synthetic Biology Biosafety, Biosecurity, IPR, and Ethical Challenges of Chemical Synthetic Biology

13.1 INTRODUCTION

13.2 SOCIETAL ISSUES IN CHEMICAL SYNTHETIC BIOLOGY

13.3 CONCLUSIONS

14 The Synthetic Approach in Biology: Epistemological Notes for Synthetic Biology

14.1 INTRODUCTION

14.2 SETTING THE FRAMEWORK

14.3 THE TWO SOULS OF SYNTHETIC BIOLOGY

14.4 LIFE AS EMERGENCE, AND AS A PROCESS OF COLLECTIVE INTEGRATION

14.5 THE WAY OF OPERATION OF BIOENGINEERINGSB

14.6 CONCLUDING REMARKS

ACKNOWLEDGMENTS

Index

Color Plates

Chemical Synthetic Biology

This edition first published 2011

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Library of Congress Cataloging-in-Publication Data

Chemical synthetic biology / editors, Pier Luigi Luisi and Cristiano Chiarabelli.

p. cm.

 Includes bibliographical references and index.

 ISBN 978-0-470-71397-6 (cloth)

 1. Biomolecules–Synthesis. I. Luisi, P. L. II. Chiarabelli, Cristiano.

 QD415.C47 2011

 572–dc22

2010045647

A catalogue record for this book is available from the British Library.

Print ISBN: 9780470713976

ePDF ISBN: 9780470977880

oBook ISBN: 9780470977873

ePub ISBN: 9781119990307

List of Contributors

Takuyo Aita, Department of Functional Materials Science, Saitama University, Saitama, Japan

Fabrizio Anella, Department of Biology, University of Rome Tre – V.le G. Marconi 446 – 00146 Rome, Italy

Steven A. Benner, Department of Chemistry, University of Florida, Gainesville, FL 32611-7200, USA

Fei Chen, Foundation for Applied Molecular Evolution and The Westheimer Institute for Science and Technology, PO Box 13174, Gainesville FL 32604, USA

Cristiano Chiarabelli, Department of Biology, University of Rome Tre – V.le G. Marconi 446 – 00146 Rome, Italy

Malcolm Dando, Department of Peace Studies, Pemberton Building, University of Bradford, Bradford, West Yorkshire, BD7 1DP, UK

Anna Deplazes, UFSP Ethik, Universität Zürich, Klosbachstr. 107, 8032 Zürich, Switzerland; ETH Zürich, Institute of Biochemistry, Schafmattstrasse 18, 8093 Zurich, Switzerland

Nobuhide Doi, Department of Biosciences and Informatics, Keio University, 3–14–1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan

Albert Eschenmoser, Laboratory of Organic Chemistry ETH Hönggerberg, HCI-H309 CH-8093 Zürich, Switzerland

Francesca Ferri, Neuroscience Department, University of Parma, Via Volturno 39, 43100 Parma, Italy

Yuuki Hayashi, Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan

Piet Herdewijn, Laboratory For Medicinal Chemistry, Rega Institute for Medical Research, Minderbroedersstraat 10, Leuven-3000, Belgium

Koichi Kakukawa, Department of Biosciences and Informatics, Keio University, 3–14–1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan

Günter von Kiedrowski, Department of Organic Chemistry I – Bioorganic Chemistry, Faculty of Chemistry, Ruhr University Bochum, Universitätstrasse 150, 44801 Bochum, Germany

Davide De Lucrezia, European Centre for Living Technology, University Ca’ Foscari of Venice. Venice, Italy

Pier Luigi Luisi, Department of Biology, University of Rome Tre – V.le G. Marconi 446 – 00146 Rome, Italy

Philippe Marliere, Isthmus Sarl, 31 rue Saint Amand, F75015 Paris, France

Isabella Moll, Max F. Perutz Laboratories, Department of Microbiology, Immunobiology, and Genetics, Center for Molecular Biology, Dr. Bohrgasse 9/4, 1030 Vienna, Austria

Peter E. Nielsen, Department of Cellular and Molecular Medicine, Faculty of Health Sciences, The Panum Institute, University of Copenhagen, Blegdamsvej 3c, DK-2200, Copenhagen N, Denmark; Faculty of Pharmaceutical Sciences, Department of Medicinal Chemistry, Universitetsparken 2, DK-2100 Copenhagen Denmark

Knud H. Nierhaus, Max-Planck-Institut für Molekulare Genetik, AG Ribosomen, Ihnestr. 73, D-14195 Berlin, Germany

Yuko Oishi, Department of Biosciences and Informatics, Keio University, 3–14–1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan

Markus Pech, Max-Planck-Institut für Molekulare Genetik, AG Ribosomen, Ihnestr. 73, D-14195 Berlin, Germany

Cecilia Portela Pallares, Department of Biology, University of Rome Tre – V.le G. Marconi 446 – 00146 Rome, Italy

Anna Quintarelli, Department of Biology, University of Rome Tre – V.le G. Marconi 446 – 00146 Rome, Italy

Markus Schmidt, Organisation for International Dialogue and Conflict Management (IDC), Biosafety Working Group, Kaiserstr. 50/6, 1070 Vienna, Austria

Pasquale Stano, Biology Department, University of RomaTre, Viale G. Marconi 446, 00146 Roma, Italy

Olga Taran, Department of Organic Chemistry I – Bioorganic Chemistry, Faculty of Chemistry, Ruhr University Bochum, Universitätstrasse 150, 44801 Bochum, Germany

Hitoshi Toyota, Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan

Daniela Wittek, Max-Planck-Institut für Molekulare Genetik, AG Ribosomen, Ihnestr. 73, D-14195 Berlin, Germany

J. Tze-Fei Wong, Fok Ying Tung Graduate School and Department of Biochemistry, Hong Kong University of Science and Technology, Hong Kong, China

Hong Xue, Fok Ying Tung Graduate School and Department of Biochemistry, Hong Kong University of Science and Technology, Hong Kong, China

Hiroshi Yamamoto, Max-Planck-Institut für Molekulare Genetik, AG Ribosomen, Ihnestr. 73, D-14195 Berlin, Germany

Asao Yamauchi, Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan

Hiroshi Yanagawa, Department of Biosciences and Informatics, Keio University, 3–14–1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan

Zunyi Yang, Foundation for Applied Molecular Evolution and The Westheimer Institute for Science and Technology, PO Box 13174, Gainesville FL 32604, USA

Tetsuya Yomo, Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan; Graduate School of Frontier Science, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan; ERATO, JST, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan

Introduction

Pier Luigi Luisi

University of Roma 3, Biology Department, Viale G. Marconi 446, 00146 Roma, Italy

The novel and fashionable term synthetic biology (SB) is now used mostly to indicate a field aimed at synthesizing biological structures or life forms in the laboratory which do not exist in nature. Generally, existing microbial life forms are modified and the genomic content redirected towards novel modified organisms; for example, bacterial life that does not exist on Earth. First, important examples of these techniques can be found in recent issues in Nature [1] and Science [2]. This approach is the one which appears to have the greatest potentialities to do something socially useful; for example, novel bacteria for the production of hydrogen or methane to help our energy needs, or novel bacteria for the production of drugs and/or enzymes which are otherwise difficult to reach. All this is based on the hard hand of the bioengineering approach that thrives from classic DNA molecular biology. This is the major, most popular form of SB.

This book has a different slant, in the sense that it concerns work on SB which is not based on genetic manipulation, emphasizing instead a chemical approach, one which aims at the synthesis of molecular structures and/or multi-molecular organized biological systems that do not exist in nature. These man-made biological molecular or supramolecular structures that do not exist in nature can be obtained either by chemical or biochemical syntheses. For this, the term “chemical synthetic biology” has been coined [3]. This book deals with this aspect of SB and is based on original contributions, as well as on a couple of papers taken from the literature with suggestions and permissions from the authors.

One of the most beautiful examples of chemical SB, is the work by Albert Eschenmoser and coworkers at the ETH Zürich – presented in our book – on DNA having pyranose instead of ribose in the main chain. The basic question underlying this kind of work is: why this and not that? Why did nature choose that particular sugar and not another one? And this question impinges on a greater philosophical problem, that of the relation between determinism and contingency: is the way of nature the only possible one, as a kind of obligatory pathway? Or is it instead so that the choice of nature has been based on “chance” – and we have ribose instead of pyranose simply due to the vagaries of contingency? Or, looking at the work by Yanagawa in this book, why 20 amino acids to build proteins instead of, say, nine?

And the same question can be drawn for the work of Benner (why not different chemical modifications of nucleic acid?). Concerning nucleic acid, there is the approach by Henderwijn and Marliere, who argue that nucleic proliferation could be extended so as to enable the propagation in vivo of additional types of nucleic acid whose polymerization would not interfere with DNA and RNA biosynthesis.

In fact, chemical SB permits one to tackle the question “why this and not that?” by synthesizing in the laboratory the alternative forms – forms that do not exist in nature. And then by comparison with the natural forms, we can learn a lot on why nature had to proceed in one way instead of another one.

The question “why this and not that?” is particularly apparent in the project never-born proteins (NBPs), aimed at preparing families of totally random proteins which do not exist in nature and have never been subjected to evolution – with the important question: how and why have the “few” proteins which constitute our life been selected out? Such a project has been initiated at the Federal Institute of Technology in Zurich, Switzerland, to be pursued by my group transferred to the University of “Roma Tre”, Italy, in particular, by Cristiano Chiarabelli and Davide de Lucrezia.

In this sense, it is clear that chemical SB is more naturally inclined towards basic science more than towards the engineering approach, which is rather devoted to making things to achieve a predetermined scope. Of course, the difference between the two approaches is often not so in a black-and-white form. One can also add that the bio-ethical problems, often connected to the genetic manipulation approach, are generally not so relevant in the chemical SB approach. These two important aspects of the field, namely the philosophical implications of SB and the bio-ethical aspects, are duly represented in this book (the last two chapters).

Also, the approach pioneered by Craig Venter and coworkers, aimed at synthesizing an entire genome by chemical methods [4], can be considered as one of the clearest examples of chemical SB. This contribution is missing in this book, not out of negligence of the editors, but because we were unable to get a contribution from this group. The very last, recent contribution of Venter [5] has caused much press clamor. It is, indeed, a Cyclopic work from the experimental point of view. From the conceptual point of view, it is no surprise of course that a synthetic DNA can replace the natural one. The clamor, I believe, is mostly due to the misconception, still so present in the simplistic press, that life is DNA. This equation, equating life and DNA, has been instrumental in a lot of misconception about the big question: “what is life?” Life is much more than DNA, as it is due to the dynamic interaction of thousands of molecular components – even in the bacterium of Venter – of which DNA is only one.

We also could not receive a contribution on another subject we really wanted, the chemical synthesis of a virus [6].

We were lucky enough to obtain a contribution by ProfessorNielsen on his famous PNA chemistry – another example of chemical structures not existing in nature, and one may wonder why.

Thus, there is a part of this book on proteic structures and one on nucleic acids.

After that, it is the time to address the interaction between the two classes of biopolymers. There is first of all the question of the genetic code, and Wong’s school tackles the subject, whereas Nierhaus is asking whether ribosomes should really be so complex as they are in order to function, or whether one can construct some form of simpler ribosome; for example, one with a lower number of structural proteins.

The next part of this book is devoted to even more complex systems. And here the notion of a minimal cell is central. The procedure is based on the preparation and physico-chemical characterization of vesicles of given dimensions, and the entrapment of enzymes and DNA of known composition and concentration in their water pool, thus constituting a model for a biochemical cell. The main question here is what is the minimal and sufficient number of macromolecules which can endow the vesicle with cell-like functions? In particular, at which degree of complexity can cellular life arise? This kind of research is also important to show that life is an emergent property, which can arise “simply” from the interaction of nonliving chemical compounds. This project started in my laboratory in Zurich in the mid 1980s – the term “minimal cell” applied to liposomes appeared in a 1985 paper with Thomas Oberholzer and today around 10 groups around the world deal with this subject. Two chapters, those by Stano et al. and by Yomo and coworkers, are devoted to this subject.

The last part of the book is devoted to more general subjects. Thus, Schmidt and collaborators raise social questions in connection with SB in general, and in particular dwelling on bio-safety and bio-ethical issues. My own contribution is on epistemic aspects of SB, and tries to clarify the conceptual basis of the various approaches of SB, and also the difference between SB and other related fields, like artificial intelligence. Finally, the contribution of von Kiedrowski is an attempt to form a merger between chemical SB and system chemistry. The replicators as chemical systems which emulate the behavior of self-replication of nucleic acids offer a beautiful example of this endeavor. This merging is necessary and even inevitable when chemistry is moving topwards biology and where biology has to use the tools of chemistry to advance.

More generally, we believe that this book on chemical SB offers a space at the interface between chemistry, biology, and philosophy which is timely and useful.

REFERENCES

1. Church, G. (2005) Let us go forth and safely multiply. Nature, 438, 423 and all articles in this special issue.

2. Ferber, D. (2004) Microbes made to order. Science, 303, 158–161 and all articles in this special issue.

3. Luisi, P.L. (2007) Chemical aspects of synthetic biology. Chemistry & Biodiversity, 4, 603–621.

4. Gibson, D.G., Benders, G.A., Andrews-Pfannkoch, C. et al. (2008) Complete chemical synthesis, assembly, and cloning of a Mycoplasma genitalium genome. Science, 319 (5867), 1215–1220. Epub 2008 Jan 24.

5. Gibson, D.G., Glass, J.I., Lartigue, C. et al. (2010) Creation of a bacterial cell controlled by a chemically synthesized genome. Science, 329, 52–56.

6. Cello, J., Paul, A.V., and Wimmer, E. (2002) Chemical synthesis of poliovirus cDNA: generation of infectious virus in the absence of natural template. Science, 297 (5583), 1016–1018. Epub 2002 Jul 11.