120 Advances in Biochemical Engineering/Biotechnology - Springer

120 Advances in Biochemical Engineering/Biotechnology Series Editor: T. Scheper

Editorial Board: S. Belkin I. Endo S.-O. Enfors W.-S. Hu B. Mattiasson J. Nielsen G. Stephanopoulos G. T. Tsao R. Ulber A.-P. Zeng J.-J. Zhong W. Zhou l

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Advances in Biochemical Engineering/Biotechnology Series Editor: T. Scheper Recently Published and Forthcoming Volumes

Biosystems Engineering I Volume Editors: Wittmann, C., Krull, R. Vol. 120, 2010

Biosensing for the 21st Century Volume Editors: Renneberg, R., Lisdat, F. Vol. 109, 2007

Whole Cell Sensing Systems II Volume Editors: Belkin, S., Gu, M.B. Vol. 118, 2010

Biofuels Volume Editor: Olsson, L. Vol. 108, 2007

Whole Cell Sensing Systems I Volume Editors: Belkin, S., Gu, M.B. Vol. 117, 2010 Optical Sensor Systems in Biotechnology Volume Editor: Rao, G. Vol. 116, 2009 Disposable Bioreactors Volume Editor: Eibl, R., Eibl, D. Vol. 115, 2009 Engineering of Stem Cells Volume Editor: Martin, U. Vol. 114, 2009 Biotechnology in China I From Bioreaction to Bioseparation and Bioremediation Volume Editors: Zhong, J.J., Bai, F.-W., Zhang, W. Vol. 113, 2009 Bioreactor Systems for Tissue Engineering Volume Editors: Kasper, C., van Griensven, M., Poertner, R. Vol. 112, 2008

Green Gene Technology Research in an Area of Social Conflict Volume Editors: Fiechter, A., Sautter, C. Vol. 107, 2007 White Biotechnology Volume Editors: Ulber, R., Sell, D. Vol. 105, 2007 Analytics of Protein-DNA Interactions Volume Editor: Seitz, H. Vol. 104, 2007 Tissue Engineering II Basics of Tissue Engineering and Tissue Applications Volume Editors: Lee, K., Kaplan, D. Vol. 103, 2007 Tissue Engineering I Scaffold Systems for Tissue Engineering Volume Editors: Lee, K., Kaplan, D. Vol. 102, 2006 Cell Culture Engineering Volume Editor: Hu, W.-S. Vol. 101, 2006

Food Biotechnology Volume Editors: Stahl, U., Donalies, U. E. B., Nevoigt, E. Vol. 111, 2008

Biotechnology for the Future Volume Editor: Nielsen, J. Vol. 100, 2005

Protein – Protein Interaction Volume Editors: Seitz, H., Werther, M. Vol. 110, 2008

Gene Therapy and Gene Delivery Systems Volume Editors: Schaffer, D.V., Zhou, W. Vol. 99, 2005

Biosystems Engineering I Creating Superior Biocatalysts

Volume Editors: Christoph Wittmann
Rainer Krull

With contributions by R. Biedendieck
K. Buchholz
B. Bunk
E. Franco-Lara
T. Fu¨rch
A. Ghaderi
H. Gro¨ger
W. Hummel
D. Jahn
M. Jahn
H.-J. Jo¨rdening
D. Klein-Marcuschamer
S.Y. Lee
J. Nielsen
M. Papini
J.H. Park
M. Salazar
J. Seibel
G.N. Stephanopoulos
A. Weckbecker
C. Wittmann
V.G. Yadav

Editors Prof. Dr. Christoph Wittmann Technische Universita¨t Braunschweig Biochemical Engineering Institute Gaußstraße 17 38106 Braunschweig Germany [email protected]

Prof. Dr. Rainer Krull Technische Universita¨t Braunschweig Biochemical Engineering Institute Gaußstraße 17 38106 Braunschweig Germany [email protected]

ISSN 0724-6145 e-ISSN 1616-8542 ISBN 978-3-642-14230-7 e-ISBN 978-3-642-14231-4 DOI 10.1007/978-3-642-14231-4 Springer Heidelberg Dordrecht London New York Library of Congress Control Number: 2010933955 # Springer-Verlag Berlin Heidelberg 2010 This work is subject to copyright. All rights are reserved, whether the whole or part of the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfilm or in any other way, and storage in data banks. Duplication of this publication or parts thereof is permitted only under the provisions of the German Copyright Law of September 9, 1965, in its current version, and permission for use must always be obtained from Springer. Violations are liable to prosecution under the German Copyright Law. The use of general descriptive names, registered names, trademarks, etc. in this publication does not imply, even in the absence of a specific statement, that such names are exempt from the relevant protective laws and regulations and therefore free for general use. Cover design: WMXDesign GmbH, Heidelberg, Germany Printed on acid-free paper Springer is part of Springer Science+Business Media (www.springer.com)

Series Editor Prof. Dr. T. Scheper Institute of Technical Chemistry University of Hannover Callinstraße 3 30167 Hannover, Germany [email protected]

Volume Editors Prof. Dr. Christoph Wittmann

Prof. Dr. Rainer Krull

Technische Universita¨t Braunschweig Biochemical Engineering Institute Gaußstraße 17 38106 Braunschweig Germany [email protected]

Technische Universita¨t Braunschweig Biochemical Engineering Institute Gaußstraße 17 38106 Braunschweig Germany [email protected]

Editorial Board Prof. Dr. S. Belkin

Prof. Dr. W.-S. Hu

Interfaculty Biotechnology Program Institute of Life Sciences The Hebrew University of Jerusalem Jerusalem 91904, Israel [email protected]

Chemical Engineering and Materials Science University of Minnesota 421Washington Avenue SE Minneapolis, MN 55455-0132, USA [email protected]

Prof. Dr. I. Endo Saitama Industrial Technology Center 3-12-18, Kamiaoki Kawaguchi-shi Saitama, 333-0844, Japan [email protected]

Prof. Dr. B. Mattiasson Department of Biotechnology Chemical Center, Lund University P.O. Box 124, 221 00 Lund, Sweden [email protected]

Prof. Dr. S.-O. Enfors Department of Biochemistry and Biotechnology Royal Institute of Technology Teknikringen 34, 100 44 Stockholm, Sweden [email protected]

Prof. Dr. J. Nielsen Center for Process Biotechnology Technical University of Denmark Building 223 2800 Lyngby, Denmark [email protected]

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Editorial Board

Prof. Dr. G. Stephanopoulos

Prof. Dr. J.-J. Zhong

Department of Chemical Engineering Massachusetts Institute of Technology Cambridge, MA 02139-4307, USA [email protected]

Bio-Building #3-311 College of Life Science & Biotechnology Key Laboratory of Microbial Metabolism, Ministry of Education Shanghai Jiao Tong University 800 Dong-Chuan Road Minhang, Shanghai 200240, China [email protected]

Prof. Dr. G. T. Tsao Professor Emeritus Purdue University West Lafayette, IN 47907, USA [email protected] [email protected] Prof. Dr. Roland Ulber FB Maschinenbau und Verfahrenstechnik Technische Universita¨t Kaiserslautern Gottlieb-Daimler-Straße 67663 Kaiserslautern, Germany [email protected]

Dr. W. Zhou Sr. Director, BioProcess Engineering Technology Development Genzyme Corporation 45 New York Avenue Framingham, MA 01701-9322, USA [email protected]

Prof. Dr. A.-P. Zeng Technische Universita¨t Hamburg-Harburg Institut fu¨r Bioprozess- und Biosystemtechnik Denickestrasse 1 21073 Hamburg, Germany [email protected]

Honorary Editors Prof. Dr. A. Fiechter

Prof. Dr. K. Schu¨gerl

Institute of Biotechnology Eidgeno¨ssische Technische Hochschule ETH-Ho¨nggerberg 8093 Zu¨rich, Switzerland [email protected]

Institute of Technical Chemistry University of Hannover, Callinstraße 3 30167 Hannover, Germany [email protected]

Advances in Biochemical Engineering/ Biotechnology Also Available Electronically

Advances in Biochemical Engineering/Biotechnology is included in Springer’s eBook package Chemistry and Materials Science. If a library does not opt for the whole package the book series may be bought on a subscription basis. Also, all back volumes are available electronically. For all customers who have a standing order to the print version of Advances in Biochemical Engineering/Biotechnology, we offer the electronic version via SpringerLink free of charge. If you do not have access, you can still view the table of contents of each volume and the abstract of each article by going to the SpringerLink homepage, clicking on “Chemistry and Materials Science,” under Subject Collection, then “Book Series,” under Content Type and finally by selecting Advances in Biochemical Bioengineering/Biotechnology You will find information about the – Editorial Board – Aims and Scope – Instructions for Authors – Sample Contribution at springer.com using the search function by typing in Advances in Biochemical Engineering/Biotechnology. Color figures are published in full color in the electronic version on SpringerLink.

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Advances in Biochemical Engineering/Biotechnology

Aims and Scope Advances in Biochemical Engineering/Biotechnology reviews actual trends in modern biotechnology. Its aim is to cover all aspects of this interdisciplinary technology where knowledge, methods and expertise are required for chemistry, biochemistry, microbiology, genetics, chemical engineering and computer science. Special volumes are dedicated to selected topics which focus on new biotechnological products and new processes for their synthesis and purification. They give the state-of-the-art of a topic in a comprehensive way thus being a valuable source for the next 3-5 years. It also discusses new discoveries and applications. In general, special volumes are edited by well known guest editors. The series editor and publisher will however always be pleased to receive suggestions and supplementary information. Manuscripts are accepted in English. In references Advances in Biochemical Engineering/Biotechnology is abbreviated as Adv. Biochem. Engin./Biotechnol. and is cited as a journal. Special volumes are edited by well known guest editors who invite reputed authors for the review articles in their volumes. Impact Factor in 2009: 4.165; Section “Biotechnology and Applied Microbiology”: Rank 23 of 150

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Save 15% We recommend a standing order for the series to ensure you automatically receive all volumes and all supplements and save 15% on the list price.

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Laudatio

This special volume “Biosystems Engineering” is dedicated to Professor Dr.-Ing. Dietmar Christian Hempel on the occasion of his 65th birthday, whereby the different contributions display an excellent reflection of his research during the past 30 years, bridging engineering and life sciences. Prof. Hempel, born in Ko¨nigsberg, studied Construction and Process Engineering in Dortmund and Berlin (1963–1971). After his PhD work on “Heterogeneous catalytic fixed bed reactors” he became the head for “Reaction and Biochemical Engineering” at the Bayer AG in Leverkusen, where he started to apply chemical engineering principles to biological systems (1975–1980). This was obviously stimulating his later research as Professor of Technical Chemistry and Chemical Engineering at the University of Paderborn (1980–1994) and as Professor and Director of the Institute of Biochemical Engineering at the Technische Universita¨t Braunschweig (1994–2009) where he kept his research interest on biological systems in technical applications – covering various aspects process engineering of biological and biochemical processes. As impressive outcome of his career, Dietmar Christian Hempel authored and co-authored about 300 publications and supervised 70 PhD students as a “Doktorvater”. From 2001 to 2008 he was head and speaker of the still successfully continued interdisciplinary DFG-collaborate research centre SFB 578 “Development of biotechnological processes by integrating genetic and engineering methods – From gene to product”. This collaborate research centre displays a landmark in the German biochemical engineering community and serves as important link between cellular biology and bioprocess engineering.

Preface

The special volume “Biosystems Engineering” reflects an emerging field of applied research that aims at a system-level understanding of biological systems toward their targeted design and improvement. To obtain system-wide insight, interdisciplinary approaches are applied, which integrate expertise from biologists, engineers, and computer scientists, who have developed powerful analytical methods, modelling concepts, and information technologies for this challenging task. With the increasing need for sustainable production of fuels and chemicals from renewable resources, a major focus in this area is on the optimization of biotechnological production strains and processes. Of specific importance hereby is the consideration of the microorganism as a part of the bioprocess in its entirety. In this regard, the different contributions of this volume provide an outstanding review of novel tools, methods, and concepts in the field of biosystems engineering, a still young, but yet powerful direction of interdisciplinary research. Part I “Creating Superior biocatalysts” of this volume highlights how system-wide analysis, modelling and understanding of gene regulation, metabolic networks, and fluxes open a new era for rational design and optimization of superior production strains, one of the key pre-requisites for bio-based production of pharmaceuticals, chemicals, materials, and fuels. This includes the introduction of systems and synthetic metabolic engineering approaches as well as industrial application examples. Part II “Linking Cellular Networks and Bioprocesses” illustrates concepts and tools which are based on models and experiments to investigate metabolic networks in correlation with the cell environment. In addition to the introduction of fundamental strategies introducing thermodynamic principles as well as different modelling approaches to metabolic network simulation, different examples directly address the link of cells and bioreactors providing fascinating and valuable insights into the interaction between cellular metabolism and process environment.

Braunschweig, Summer 2010

Christoph Wittmann Rainer Krull

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Contents

Integration of Systems Biology with Bioprocess Engineering: L-Threonine Production by Systems Metabolic Engineering of Escherichia Coli . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 Sang Yup Lee and Jin Hwan Park Analysis and Engineering of Metabolic Pathway Fluxes in Corynebacterium glutamicum . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21 Christoph Wittmann Systems Biology of Industrial Microorganisms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51 Marta Papini, Margarita Salazar, and Jens Nielsen De Novo Metabolic Engineering and the Promise of Synthetic DNA . . . . 101 Daniel Klein-Marcuschamer, Vikramaditya G. Yadav, Adel Ghaderi, and Gregory N. Stephanopoulos Systems Biology of Recombinant Protein Production in Bacillus megaterium . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 133 Rebekka Biedendieck, Boyke Bunk, Tobias Fu¨rch, Ezequiel Franco-Lara, Martina Jahn, and Dieter Jahn Extending Synthetic Routes for Oligosaccharides by Enzyme, Substrate and Reaction Engineering . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 163 Ju¨rgen Seibel, Hans-Joachim Jo¨rdening, and Klaus Buchholz Regeneration of Nicotinamide Coenzymes: Principles and Applications for the Synthesis of Chiral Compounds . . . . . . . . . . . . . . . . . . . . . 195 Andrea Weckbecker, Harald Gro¨ger, and Werner Hummel Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 243

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