Handbook Ofof Industrialindustrial Cellcell Cultureculture Mammalian,Mammalian, Microbial,Microbial, Andand Plantplant Cellscells
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HandbookHandbook ofof IndustrialIndustrial CellCell CultureCulture Mammalian,Mammalian, Microbial,Microbial, andand PlantPlant CellsCells EditedEdited byby VVictorictor A.A. VinciVinci SaradSarad R.R. ParekhParekh Humana Press Handbook of Industrial Cell Culture Handbook of Industrial Cell Culture Mammalian, Microbial, and Plant Cells Edited by Victor A. Vinci, PhD Eli Lilly and Company, Indianapolis, IN and Sarad R. Parekh, PhD Dow AgroSciences, Indianapolis, IN Humana Press Totowa, New Jersey © 2003 Humana Press Inc. 999 Riverview Drive, Suite 208 Totowa, New Jersey 07512 humanapress.com All rights reserved. No part of this book 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. All authored papers, comments, opinions, conclusions, or recommendations are those of the author(s), and do not necessarily reflect the views of the publisher. This publication is printed on acid-free paper. ' ANSI Z39.48-1984 (American Standards Institute) Permanence of Paper for Printed Library Materials. Production Editor: Mark J. Breaugh. Cover illustration: Map of the tobacco plastid genome and sites of foreign gene insertions. See Fig. 1 on page 262. Maternal inheritance of plastid transgenes. See Fig. 3 on page 265. Cover design: Patricia Cleary. 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Printed in the United States of America. 10 9 8 7 6 5 4 3 2 1 Library of Congress Cataloging in Publication Data Handbook of industrial cell culture : mammalian, microbial, and plant cells / edited by Victor A. Vinci and Sarad R. Parekh. p. cm. Includes bibliographical references and index. ISBN 1-58829-032-8 (alk. paper); 1-59259-346-1 (ebook) 1. Cell culture--Handbooks, manuals, etc. 2. Biotechnology--Handbooks, manuals, etc. I. Parekh, Sarad R., 1953– II. Vinci, Victor. TP248.25.C44 H36 2003 660.6--dc21 2002068470 Preface The essential and determining feature of an industrial bioprocess is the culturing of cells that yield a desired product. Mammalian, microbial, and plant cells are traditionally used for the manufacture of products derived directly or semisynthetically from cellular metabolites. These cells are increasingly used as the cellular machinery to express recom- binant proteins of considerable economic and therapeutic value. The choice of cell cul- ture type determines the degree of success in obtaining a clinically useful product, as well as in achieving an economical process, by facilitating acceptable yield and purity. Each of the major classes of industrially relevant cultures is manipulated by a variety of means, selected for desired phenotypes, and is exploited either in bioreactors or in the field by functionally similar approaches. The knowledge of how best to achieve this utility has its roots in empirical learning that reaches back many thousands of years. Much later, Pasteur, Koch, and others dramati- cally advanced our knowledge of the underlying cellular nature of bioprocesses during classical studies in the 19th century using modern scientific methods. Following World War II, the advent of modern industrial production methods, inspired by the discovery and isolation of penicillin, brought the first boom in natural product biotechnology. More recently, the dramatic acceleration in identifying protein biopharmaceutical candidates, as well as the current rebirth in natural product discovery, have been driven by molecular genetics. Likewise, plant cell culture and engineered crops have already impacted agri- culture and are poised to revolutionize biotechnology. The progression of transgenic animal and plant methodologies from laboratory to industrial scale production has resulted in the most recent, and perhaps most dramatic, step in using cells to make products. Supporting the production of novel therapeutics in mammalian, microbial, and plant cells is an impressive array of new methodologies from the fields of molecular genetics, proteomics, genomics, analytical biochemistry, and screening. For an industrial bioprocess, manipulation and propagation of cells in order to elicit expression of a product is followed by the recovery, analysis, and identification of these products. The methodology for successfully developing a commercial process is functionally similar across the spectrum of cell types. Handbook of Industrial Cell Culture: Mammalian, Microbial, and Plant Cells attempts to link these common approaches, while also delineating those specific aspects of cell types, to give the reader not only an overview of the best current practices, but also of today’s evolving technologies, with examples of both their practical applications and their future potential. Many scientists currently in the field find their careers transitioning across work with mammalian, microbial, and plant bioprocesses; thus they are very much in need of a book linking these disciplines in a single format. Moreover, the next generation of scientists and engineers will interface across these disciplines and likely see even more dramatic enhancements in technology. Our hope is that this Handbook will prove espe- cially useful not only to those involved in biotechnology as a broad discipline, but also assist experienced practitioners in perfecting the special art of industrial cell culture. Victor A. Vinci Sarad R. Parekh v • Contents Preface ............................................................................................................................ v Contributors .................................................................................................................. ix PART I. MAMMALIAN CELL CULTURE 1 Analysis and Manipulation of Recombinant Glycoproteins Manufactured in Mammalian Cell Culture...................................................... 3 Nigel Jenkins 2 • Genetic Approaches to Recombinant Protein Production in Mammalian Cells........................................................................................ 21 Peter P. Mueller, Dagmar Wirth, Jacqueline Unsinger, and Hansjörg Hauser 3 • Protein Expression Using Transgenic Animals ................................................. 51 William H. Velander and Kevin E. van Cott 4 • Mammalian Cell Culture: Process Development Considerations .................... 69 Steven Rose, Thomas Black, and Divakar Ramakrishnan PART II. MICROBIAL CELL CULTURE 5 • Natural Products: Discovery and Screening .................................................... 107 Matthew D. Hilton 6 • Genetic Engineering Solutions for Natural Products in Actinomycetes .......................................................................................... 137 Richard H. Baltz 7 • Culture Medium Optimization and Scale-Up for Microbial Fermentations ........................................................................ 171 Neal C. Connors PART III. PLANT CELL CULTURE 8 • Functional Genomics for Plant Trait Discovery .............................................. 197 Sam Reddy, Ignacio M. Larrinua, Max O. Ruegger, Vipula K. Shukla, and Yuejin Sun 9 • Molecular Tools for Engineering Plant Cells .................................................. 217 Donald J. Merlo 10 • Plant Cell Culture: A Critical Tool for Agricultural Biotechnology ..............243 Joseph F. Petolino, Jean L. Roberts, and Ponsamuel Jayakumar 11 • Expression of Recombinant Proteins via the Plastid Genome ........................ 259 Jeffrey M. Staub 12 • Oleosin Partitioning Technology for Production of Recombinant Proteins in Oil Seeds .......................................................279 Maurice M. Moloney vii viii Contents PART IV. CRITICAL TOOLS FOR BIOTECHNOLOGY 13 • Genome Sequencing and Genomic Techniques in Drug Discovery and Development .......................................................................................... 299 Lawrence M. Gelbert 14 • Proteomics .........................................................................................................321 Gerald W. Becker, Michael D. Knierman, Pavel Shiyanov, and John E. Hale 15 • Metabolic Flux Analysis, Modeling, and Engineering Solutions ................... 349 Walter M. van Gulik, Wouter A. van Winden, and Joseph J. Heijnen 16 • Advances in Analytical Chemistry for Biotechnology: Mass Spectrometry of Peptides, Proteins, and Glycoproteins ................... 393 Jeffrey S. Patrick 17 • DNA Shuffling for Whole Cell Engineering ...................................................465 Steve del Cardayre and Keith Powell 18 • Cell Culture Preservation and Storage for Industrial Bioprocesses ............... 483 James R. Moldenhauer Index ..........................................................................................................................515