Systems Biology and Biotechnology of Escherichia coli
Systems biology is changing the way biological systems are studied by allowing us to examine the cell and organism as a whole. Systems biotechnology allows optimal design and development of upstream to downstream bioprocesses by taking a systems-approach.
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Sang Yup Lee Editor
Systems Biology and Biotechnology of Escherichia coli
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Editor Prof. Dr. Sang Yup Lee Korea Advanced Institute of Science and Technology (KAIST) Dept. of Chemical and Biomolecular Engineering 335 Gwahangno Yuseong-gu Daejeon 305-701 Republic of Korea (South Korea) [email protected]
ISBN 978-1-4020-9393-7
e-ISBN 978-1-4020-9394-4
DOI 10.1007/978-1-4020-9394-4 Library of Congress Control Number: 2008942030 c Springer Science+Business Media B.V. 2009 No part of this work may be reproduced, stored in a retrieval system, or transmitted in any form or by any means, electronic, mechanical, photocopying, microfilming, recording or otherwise, without written permission from the Publisher, with the exception of any material supplied specifically for the purpose of being entered and executed on a computer system, for exclusive use by the purchaser of the work. Printed on acid-free paper 9 8 7 6 5 4 3 2 1 springer.com
To Hyejean and Gina, with love
Preface
Escherichia coli has been a workhorse not only in fundamental biological and microbiological studies, but also in various biotechnological applications. Recent advances in systems biology have been changing the way biological studies are performed – we are hoping to move towards system-wide understanding of the cell and organism; however, we are still far from truly doing so due to the lack of thorough understanding on complex metabolic, gene regulatory and signaling networks and their interactions. E. coli, being a much simpler organism compared with higher organisms, can be a good model system in systems biological studies. The strategies, methods, and tools developed through the systems biological studies on E. coli can be extended to other organisms, just like recombinant DNA techniques and other molecular biological tools did. Also, biotechnological applications developed using E. coli can be extended to other organisms, in particular other microorganisms, by taking similar metabolic and cellular engineering strategies. Significant advances have been made during the last several years on the systems biology and biotechnology of E. coli. In this book, the worldwide experts in the field provide us with the state-of-the-art reviews on the systems-level analyses and applications of E. coli. In Chapter 1, Dr. Kim and his colleagues present the genome project of E. coli B. They performed comprehensive functional genomic studies after finishing the genome sequencing. This will be an important addition to the literature as we now have the complete picture of another E. coli workhorse, B strain, in addition to the K12 strains. In Chapter 2, Professor Kim and his colleagues present the stateof-the-art strategies and applications of genome minimization. Impressive genome engineering strategies are presented with the practical applications of E. coli strains with reduced genomes. In Chapter 3, Professor Tomita and his colleagues review the systems biology of E. coli based on multi-omics analyses. Strategies for the combined analyses of transcrip
