Biotechnology Second Edition David P. Clark Department of Microbiology Southern Illinois University Carbondale, Illinois, USA Nanette J. Pazdernik Washington University School of Medicine St. Louis, Missouri, USA AMSTERDAM • BOSTON • HEIDELBERG • LONDON NEW YORK • OXFORD • PARIS • SAN DIEGO SAN FRANCISCO • SINGAPORE • SYDNEY • TOKYO Academic Cell is an imprint of Elsevier Academic Cell is an imprint of Elsevier 125 London Wall, London EC2Y 5AS, UK 525 B Street, Suite 1800, San Diego, CA 92101-4495, USA 225 Wyman Street, Waltham, MA 02451, USA The Boulevard, Langford Lane, Kidlington, Oxford OX5 1GB, UK Copyright © 2016 Elsevier Inc. All rights reserved. No part of this publication may be reproduced or transmitted in any form or by any means, electronic or mechanical, including photocopying, recording, or any information storage and retrieval system, without permission in writing from the publisher. 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To the fullest extent of the law, neither the Publisher nor the authors, contributors, or editors, assume any liability for any injury and/or damage to persons or property as a matter of products liability, negligence or otherwise, or from any use or operation of any methods, products, instructions, or ideas contained in the material herein. ISBN: 978-0-12-385015-7 British Library Cataloguing-in-Publication Data A catalogue record for this book is available from the British Library Library of Congress Cataloging-in-Publication Data A catalog record for this book is available from the Library of Congress For information on all Academic Cell publications visit our website at http://store.elsevier.com/ Typeset by TNQ Books and Journals www.tnq.co.in Printed and bound in the United States of America ONLINE STUDY GUIDE Academic An Online Study Guide is now available with your textbook, containing a relevant journal article with a case study to focus understanding and discussion about each chapter. 1. To access the Online Study Guide, as well as other online resources for the book, please visit: http://booksite.elsevier. com/9780123850157 2. For instructor-only materials, please visit: http://textbooks.elsevier.com/web/Manuals.aspx?isbn= 9780123850157 This book is dedicated to Donna. —DPC This book is dedicated to my children and husband. Their patience and understanding have given me the time and inspiration to research and write this text. —NJP ACADEMIC CELL HOW WE GOT HERE In speaking with professors across the biological sciences and going to conferences, we, the editors at Academic Press and Cell Press, saw how often journal content was being incorporated in the classroom. We understood the benefits students were receiving by being exposed to journal articles early: to add perspective, improve analytical skills, and bring the most current content into the classroom. We also learned how much additional preparation time was required on the part of instructors finding the articles, then obtaining the images for presentations and providing additional assessment. So we collaborated to offer instructors and students a solution, and Academic Cell was born. We offer the benefits of a traditional textbook (to serve as a reference to students and a framework to instructors), but we also offer much more. With the purchase of every copy of an Academic Cell book, students can access an online study guide containing relevant, recent Cell Press articles and providing bridge material in the form of a case study to help ease them into the articles. In addition, the images from the articles are available as zipped .jpg files and we have optional test bank questions. We plan to expand this initiative, as future editions will be further integrated with unique pedagogical features incorporating current research from the pages of Cell Press journals into the textbook itself. vii PREFACE From the simple acts of brewing beer and baking bread has emerged a field now known as bio- technology. Over the ages the meaning of the word biotechnology has evolved along with our growing technical knowledge. Biotechnology began by using cultured microorganisms to create a variety of food and drinks, despite its early practitioners not even knowing of the existence of the microbial world. Today, biotechnology is still defined as any application of living organ- isms or bioprocesses to create new products. Although the underlying idea is unchanged, the use of genetic engineering and other modern scientific techniques has revolutionized the area. The fields of genetics, molecular biology, microbiology, and biochemistry are merging their respective discoveries into the expanding applied field of biotechnology, and advances are occurring at a record pace. Two or three years of research can dramatically alter the approaches that are of practical use. For example, the simple discovery that double-stranded RNA can block expression of any gene with a matching sequence has revolutionized how we study and apply genetic interactions in less than a ten-year period. This rapid increase in knowledge is very hard to incorporate into a textbook format, and often instructors who teach advanced molecular biology classes rely on the primary research to teach students novel concepts and applications. This type of teaching is difficult and requires many hours to plan and organize. The new partnership between Academic Press and Cell Press has adopted a solution to teach- ing advanced molecular biology and biotechnology courses. The partnership combines years xi of textbook publishing experience with the most relevant and high impact research. What has emerged is a new teaching paradigm. In Biotechnology, the basic ideas and methodologies are explained using very clear and concise language. These techniques are supplemented with a wide variety of diagrams and illustrations to simplify the complex biotechnology processes. These basics are then supported with a Biotechnology online study guide that not only tests the student’s knowledge of the textbook chapter, but also contains primary research articles. The articles are chosen from the Cell Press family of journals, which includes such high- impact journals as Cell, Molecular Cell, and Current Biology. The articles expand upon a topic presented in each chapter or provide an exemplary research paper for that particular chapter. The entire full-color research article is included online. In addition to the article itself, the Biotechnology study guide includes a synopsis of the research paper. The synopsis includes a thorough discussion of the relevant background information. This material is often absent from primary research articles because their authors assume that readers are also experts. Then each synopsis breaks the paper into sections, explaining each individual experiment separately. Each experiment is explained by defining the underlying hypothesis or question, the methods used to study the question, and the results. The final sec- tion of the synopsis provides the overall conclusions for the paper. This approach reinforces the basic scientific method. The instructor does not have to find an article, create a presentation on the background, and then work with the student to explain each of the methods and results. The study guide synopsis provides all of this information already. The online format ensures that only the most recent papers are associated with the chapter. The combination of the online study guide with the newest relevant research and a solid basic textbook provides the instructor with the best of both worlds. You can teach students the basic concepts using the textbook, and then use the relevant research paper to stretch the student’s knowledge of current research in the field of biotechnology. ACKNOWLEDGMENTS We would like to thank the following individuals for their help in providing information, suggestions for improvement, and encouragement: Laurie Achenbach, Rubina Ahsan, Phil Cunningham, Donna Mueller, Dan Nickrent, Holly Simmonds, and Dave Pazdernik. Special thanks go to Marshall Spector for helping us understand bioethics, to Michelle McGehee for writing the questions and online supplements and to Karen Fiorino for creating most of the original artwork for the first edition. Alex Berezow was responsible for writing a major part of the following chapters: Chapter 16, Transgenic animals, Chapter 22, Biowarfare and bioterrorism, and Chapter 24, Bioethics in biotechnology. xiii INTRODUCTION MODERN BIOTECHNOLOGY RELIES ON ADVANCES IN MOLECULAR BIOLOGY AND COMPUTER TECHNOLOGY Traditional biotechnology goes back thousands of years. It includes the selective breeding of livestock and crop plants as well as the invention of alcoholic beverages, dairy products, paper, silk, and other natural products. Only in the past couple of centuries has genetics emerged as a field of scientific study. Recent rapid advances in this area have in turn allowed the breeding of crops and livestock by deliberate genetic manipulation rather than trial and error. The so-called green revolution of the period from 1960 to 1980 applied genetic knowledge to natural breeding and had a massive impact on crop productivity in particular. Today, plants and animals are being directly altered by genetic engineering. New varieties of several plants and animals have already been made, and some are in agricultural use. Animals and plants used as human food sources are being engineered to adapt them to conditions that were previously unfavorable. Farm animals that are resistant to disease and crop plants that are resistant to pests are being developed in order to increase yields and reduce costs. The impact of these genetically modified organisms on other species and on the environment is presently a controversial issue. Modern biotechnology applies not only modern genetics but also advances in other sciences. For example, dealing with vast amounts of genetic information depends on advances in computing power. Indeed, the sequencing of the human genome would have xv been impossible without the development of ever more sophisticated computers and software. It is sometimes claimed that we are in the middle of two scientific revolutions, one in information technology and the other in molecular biology. Both involve handling large amounts of encoded information. In one case the information is human made, or at any rate man-encoded, and the mechanisms are artificial; the other case deals with the genetic information that underlies life. However, there is a third revolution that is just emerging—nanotechnology. The develop- ment of techniques to visualize and manipulate atoms individually or in small clusters is opening the way to an ever-finer analysis of living systems. Nanoscale techniques are now beginning to play significant roles in many areas of biotechnology. This raises the question of what exactly defines biotechnology. To this there is no real answer. A generation ago, brewing and baking would have been viewed as biotechnology. Today, the application of modern genetics or other equivalent modern technology is usually seen as necessary for a process to count as “biotechnology.” Thus, the definition of biotechnology has become partly a matter of fashion. In this book, we regard (modern) biotechnology as resulting in a broad manner from the merger of classical biotechnology with modern genetics, molecular biology, computer technology, and nanotechnology. The resulting field is of necessity large and poorly defined. It includes more than just agriculture: it also affects many aspects of human health and medicine, such as vaccine development and gene therapy. We have attempted to provide a unified approach that is based on genetic information, while at the same time indicate how biotechnology has begun to sprawl, often rather erratically, into many related fields of human endeavor. 1 CHAPTER Basics of Biotechnology Advent of the Biotechnology Revolution Chemical Structure of Nucleic Acids Packaging of Nucleic Acids Bacteria as the Workhorses of Biotechnology Escherichia coli Is the Model Bacterium Many Bacteria Contain Plasmids Other Bacteria in Biotechnology Basic Genetics of Eukaryotic Cells Yeast and Filamentous Fungi in Biotechnology Yeast Mating Types and Cell Cycle Multicellular Organisms as Research Models Caenorhabditis elegans, a Small Roundworm 1 Drosophila melanogaster, the Common Fruit Fly Zebrafish Are Models for Developmental Genetics Mus musculus, the Mouse, Is Genetically Similar to Humans Animal Cell Culture In Vitro Arabidopsis thaliana, a Model Flowering Plant Viruses Used in Genetics Research Subviral Infectious Agents and Other Gene Creatures Biotechnology Copyright © 2016 Elsevier Inc. All rights reserved. http://dx.doi.org/10.1016/B978-0-12-385015-7.00001-6 Basics of Biotechnology ADVENT OF THE BIOTECHNOLOGY REVOLUTION Biotechnology involves the use of living organisms in industrial processes—particularly in agriculture, food processing, and medicine. Biotechnology has been around ever since humans began manipulating the natural environment to improve their food supply, hous- ing, and health. Biotechnology is not limited to humankind. Beavers cut up trees to build homes. Elephants deliberately drink fermented fruit to get an alcohol buzz. People have been making wine, beer, cheese, and bread for centuries (Fig. 1.1). For wine, the earliest evidence of wine production has been dated to c. 6000 BC. All these processes rely on microorganisms to modify the original ingredients. Ever since the beginning of human civilization, farmers have chosen higher yielding crops by trial and error, so that many modern crop plants have much larger fruit or seeds than their ancestors (Fig. 1.2). 2 FIGURE 1.1 Traditional Biotechnology We think of biotechnology as modern because of recent advances in molecular biology and Products genetic engineering. Huge strides have been made in our understanding of microorganisms, Bread, cheese, wine, and beer plants, livestock, as well as the human body and the natural environment. This has caused have been made worldwide an explosion in the number and variety of biotechnology products. Face creams contain using microorganisms such as antioxidants—supposedly to fight the aging process. Genetically modified plants have genes yeast. Photo taken by Karen inserted to protect them from insects, thus increasing the crop yield while decreasing the Fiorino, Clay Lick Creek Pottery, IL, USA. amount of insecticides used. Medicines are becoming more specific and compatible with our physiology. For example, insulin for diabetics is now genuine human insulin, although FIGURE 1.2 produced by genetically modified bacteria. Almost everyone has been affected by the recent Teosinte versus advances in genetics and biochemistry. Modern Corn Since early civilization, people Mendel’s early work that described how genetic characteristics are inherited from one have improved many plants generation to the next was the beginning of modern genetics (see Box 1.1). Next came the for higher yields. Teosinte discovery of the chemical material of which genes are made—DNA (deoxyribonucleic (smaller cob and green seeds) acid). This in turn led to the central dogma of genetics: the concept that genes made of is considered the ancestor of DNA are expressed as an RNA (ribonucleic acid) intermediary that is then decoded to commercial corn (larger cob; a make proteins. These three steps are universal, applying to every type of living organism blue-seeded variety is shown). Courtesy of Wayne Campbell, on earth. Yet these three steps are so malleable that life is found in almost every available Hila Science Camp. niche on our planet. Biotechnology affects all of our lives and has altered everything we encounter in life.