Heidelberg Science Library Plasmids of Eukaryotes Fundamentals und Applications By K. Esser U. Klick C. Lang-Hinrichs P. Lemke H. D. Osiewacz U. Stahl P. Tudzynski With 25 Figures Springer-Verlag Berlin Heidelberg New York Tokyo ISBN-13: 978-3-540-15798-4 e-ISBN-13: 978-3-642-82585-9 DOl: 10.1007/978-3-642-82585-9 Library of Congress Cataloging-in-Publication Data. Main entry under title: Plasmids of eukaryotes. (Heidelberg science library) Bibliography: p. Includes index. 1. Plasmids. 2. Eukaryotic cells. 3. Genetic engineering. I. Esser, Karl, 1924-. II. Series. QH452.6.P57 1986 574.87'328 85-27749 This work is subject to copyright. All rights are reserved, whether the whole or part of the material is concerned, specifically those of translation, reprinting, re-use of illustrations, broadcasting, reproduction by photocopying machine or similar means, and storage in data banks. Under § 54 of the German Copyright Law where copies are made for other than private use a fee is payable to "Verwertungsgesellschaft Wort", Munich. © by Springer-Verlag Berlin Heidelberg 1986 The use of 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. 2131/3130-543210 Dedicated to GEORGES RIZET the discoverer of Podospora anserina Preface The possession of plasmids was for a long time recognized only in the bacteria. It is now evident that plasmids, or replicative forms of DNA structurally and experimentally comparable to bacterial plasmids, exist in eukaryotic organisms as well. Such plasmids are in fact common among fungi and higher plants. The present review is undertaken to provide a comprehensive account of the data available on plasmids found in eukaryotic organisms. This review will not consider plasmids of prokaryotic origin, even though certain bacterial plasmids, such as the tumor-inducing (Ti) plasmids of Agrobacterium tumefaciens, may be intimately associated with transformation of the eukaryotic host. This book, moreover, does not consider transformation experiments in eukaryotic hosts involving viral DNA as vectors, although indeed such vectors have been developed for use in plant and animal systems. After a general introduction, providing historical perspective on the nature and role of plasmids, a list of eukaryotic plasmids will be presented according to their origin. This is followed by a detailed discussion of known structure and function. In subsequent chapters the practical implications of eukaryotic plasmids for molecular cloning and biotechnology will be discussed. This latter part traces the development of interest'in biotechnical genetics and gives special consideration to the use of eukaryotic systems for gene cloning. The terminology biotechni cal genetics is introduced to the reader and is used in a general sense as equivalent to genetic engineering. Biotechnical genetics includes, but is not limited to, gene cloning through recombinant DNA technology. Genetic manipUlations involving protoplast fusion, embryo transplanta tion or directed mutagenesis would also represent forms of biotechnical genetics. Since this booklet is intended as a general reference source, not only for scholars but for industrial scientists and engineers as well as others more generally interested in biotechnology, a concerted effort has been made to compile recently published scientific data along with relevant background information and experimental details. The authors invite constructive criticism from readers of this first edition concerning the selection and presentation of material in the text. During the preparation of the manuscript, friends and colleagues have assisted with critical advice. We would like to acknowledge also the assistance of Frau Ch. Konig and Frau D. Lenke in preparing the manuscript and of Herr H. J. Rathke for the excellent art work. Bochum, June 1985 The Authors Contents I. Introduction. 1 A. Definition. . 1 B. Historical Perspective 2 II. Fundamental Aspects 7 A. General Characteristics 7 B. Nuclear Plasmids ... 13 1. Saccharomyces cerevisiae - the 2,um Plasmid 13 2. Dictyostelium discoideum - a Cobalt Resistance Plasmid 21 3. Drosophila melanogaster - the Transposable Element Copia ....... 23 C. Mitochondrial Plasmids 27 1. Podospora anserina - the Senescence Plasmid 27 2. Neurospora crassa - the Stopper and Poky Plasmids 34 3. Neurospora crassa - the Mauriceville Plasmid; Neurospora intermedia-the Labelle and Fiji Plasmids 37 4. Claviceps purpurea 41 5. Other Fungi . . . . 44 6. Higher Plants . . . . 48 D. Unknown Association . 53 III. Practical Implications 57 A. Fundamentals for Eukaryotic Gene Cloning 58 1. Generalized Vector ....... . 59 2. Choice of an Appropriate Host Cell 64 B. Plasmids for Gene Cloning. . . . . . . 65 1. The 2,um Plasmid of Saccharomyces cerevisiae 65 2. RibosomalDNAPlasmids . . . . . . . . . . 68 3. The Senescence Plasmid of Podospora anserina . 69 4. The Labelle Plasmid of Neurospora intermedia 69 5. The Mitochondrial Plasmid of Cochliobolus heterostro- phus . . . . . . . . . . . . . . . . . . . . . . . . . . 70 6. The Transposable Elements of Drosophila melanogaster 70 C. Organellar DNA for Gene Cloning ............. 71 1. Vectors Based on Confirmed Replication Origins . . . .. 73 2. Vectors Based on Random DNA Segments as Origin of Replication. . . . . . . . . . . . . . . 74 D. Maintenance of Vector Transferred Genes . 79 1. Stabilization of Vectors in Host Cells . 79 2. Efficient Expression of Cloned Genes 80 E. Biotechnological Perspectives 87 References . . 89 Subject Index . 119 Authors Prof. Dr. Dr. h. c. KARL ESSER Lehrstuhl fur Allgemeine Botanik, Ruhr-UniversiHit, Postfach 102148, D-4630 Bochum Dr. ULRICH KOCK Lehrstuhl fur Allgemeine Botanik, Ruhr-Universitat, Postfach 102148, D-4630 Bochum Dr. CHRISTINE LANG-HINRICHS Technische Universitat Berlin, Pachgebiet Mikrobiologie, SeestraBe 13, D-1000 Berlin 65 Prof. Dr. PAUL LEMKE Molecular Genetics Program, Department of Botany and Microbiology, Auburn University, Alabama 36849, USA Dr. HEINZ DIETER OSIEWACZ Lehrstuhl fur Allgemeine Botanik, Ruhr-Universitat, Postfach 102148, D-4630 Bochum Prof. Dr. ULF STAHL Technische Universitat Berlin, Pachgebiet Mikrobiologie, SeestraBe 13, D-1000 Berlin 65 Priv. Doz. Dr. PAUL TUOZYNSKI Lehrstuhl fur Allgemeine Botanik, Ruhr-Universitat, Postfach 102148, D-4630 Bochum I. Introduction Concurrent with the development of bacterial genetics in the early 1950s was the discovery in Escherichia coli of genetic factors not lo calized routinely on the bacterial chromosome. These included: 1. The fertility (F +) factors responsible for bacterial conjugation; 2. Factors responsible for the production of the bacterial toxins of the colicin type; 3. Factors responsible for bacterial resistance to antibiotics. It be came evident in time that these factors, termed plasmids by Lederberg (1952), consisted of double-stranded DNA (dsDNA) and were able to propagate in either of two alternative modes: either autonomously in the bacterial cytoplasm (replicative plas mids) or as an integral part of the bacterial chromosome (inte grative plasmids). Before these dual modes of plasmid replication were understood, inserted factors were called episomes and considered to be fundamentally different from the extra chromosomal plasmids (see Bresch 1964). The autonomous or extrachromosomal mode of replication explains why bacterial cells may contain many copies of specific plasmids. Plas mids are found in a great variety of bacteria and vary considerably in size, ranging from 2.25kb to 500kb. A. Definition In short, one may define a plasmid as any genetic element which is supplemental to the normal genome of the cell (modified after Rieger et al. 1976). Details and further references may be taken from textbooks, such as Bukhari et al. (1977); Knippers (1982); Fincham (1983) and Kaudewitz (1983). Thus broadly defined, a plasmid may be either extragenomic (exoplasmid) or derived from· the cell's normal genome as a sequence brought to multicopy status by autonomous replication (endoplasmid). In this context it is necessary to discuss terminology related to plasmid replication. As early as 1963, Jacob and Brenner introduced the term repli con for the smallest unit of autonomous replication according to data obtained in prokaryotes. Subsequently, it was found that this unit starts with a specific sequence responsible for initiations of replica tion and ends with a terminator sequence. It was generally accepted to call the initiation sequence the origin of replication: its function consists in formation of the replication fork, visible either by electron microscopy or by fiber autoradiography (Kornberg 1980). Sometimes a proper identification of the origin of replication was not possible either due to a lack of material or to problems in technology. In these cases DNA sequence analysis can provide indicative evidence for its location. Then, the term putative origin of replication is used. Another technique to identify a putative origin of replication has been developed in yeast (p. 74 f.). By shot gun cloning experiments DNA sequences can be identified as putative origins after integration in nonreplicative vectors (Fig. 24) and are termed ars (autonomously replicating sequences). From more developed analysis it has become obvious that .some ars, although functional in yeast, fail to replicate in other eukaryotic systems. Therefore, the term ars is restricted to sequences tested in yeast. For reasons of simplification and to avoid confusion for our reader, in this booklet all sequences promoting au tonomous replication are called origins of replication (on), regardless of whether they function in yeast or in other systems. While struc turally the majority of known plasmids are covalently closed and cir cular double-stranded DNA (cee dsDNA) molecules, linear dsDNA plasmids are also recognized. Self-replicating forms of single-stranded RNA (ssRNA), such as the viroids of higher plants, and endogenous dsRNA molecules found in certain fungi might also be included in a broad conceptual definition of a plasmid. Since reviews are available on viroids (Diener 1984) and dsRNA plasmids of fungi (Tipper and Bostian 1984), these genetic elements will not be considered in the present review. B. Historical Perspective Aside from the role played by plasmids in bacterial recombination, early interest in bacterial plasmids was focused during the 1960s on antibiotic resistance and the practical implications for control of ac quired resistance. It was found that eoliplasmids were able to infect other bacteria, such as Salmonella typhosa, and were expressed in the new host, leading to interspecific transfer of antibiotic resistance. It also became clear that plasmids were not restricted to E. coli but rather common among bacteria (for rev. see Foster 1983). The field of plasmid research received new emphasis in the 1970s through the 2