Table Of ContentMobile Genetic Elements
EDITED BY
James A. Shapiro
Department of Microbiology
University of Chicago
Chicago, Illinois
1983
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Library of Congress Cataloging in Publication Data
Main entry under title:
Mobile genetic elements.
Includes index.
1. Extrachromosomal DNA. 2. Translocation (Genetics)
3. Cytoplasmic inheritance. I. Shapiro, James Allen,
Date
QHA62.T7M63 1982 57^.87'3282 82-11624
ISBN 0-12-638680-3
PRINTED IN THE UNITED STATES OF AMERICA
83 84 85 86 9 8 7 6 5 4 3 2 1
Contributors
Numbers in parentheses indicate the pages on which the authors' contributions begin.
WERNER ARBER (159), Department of Microbiology, Biozentrum, University of
Basel, Basel, Switzerland
P. BORST (621), Section for Medical Enzymology and Molecular Biology,
Laboratory of Biochemistry, Jan Swammerdam Institute, Amsterdam, The
Netherlands
JEAN-CLAUDE BREGLIANO (363), Laboratorie de Genetique, Universite de
Clermont-Ferrand II, Aubiere, France
ALLAN CAMPBELL (65), Department of Biological Sciences, Stanford Univer
sity, Stanford, California 94305
NINA V. FEDOROFF (1), Department of Embryology, Carnegie Institution of
Washington, Baltimore, Maryland 21210
GERALD R. FINK1 (299), Section of Biochemistry, Molecular and Cell Biology,
Cornell University, Ithaca, New York 14853
HOWARD Μ. GOODMAN (505), Department of Molecular Biology, Massachusetts
General Hospital, Boston, Massachusetts 02114
JAMES E. HABER (559), Department of Biology, Rosenstiel Basic Medical Scien
ces Research Center, Brandeis University, Waltham, Massachusetts 02254
FRED HEFFRON (223), Cold Spring Harbor Laboratory, Cold Spring Harbor, New
York 11724
SHIGERU IIDA (159), Department of Microbiology, Biozentrum, University of
Basel, Basel, Switzerland
MARGARET G. KIDWELL (363), Division of Biology and Medicine, Brown Uni
versity, Providence, Rhode Island 02912
NANCY KLECKNER (261) Department of Biochemistry and Molecular Biology,
Harvard University, Cambridge, Massachusetts 02138
JÜRG MEYER (159), Department of Microbiology, Biozentrum, University of
Basel, Basel, Switzerland
Present address: Department of Biology, Massachusetts Institute of Technology, Cambridge, Massa
chusetts 02139
ix
χ CONTRIBUTORS
ANNE RESIBOIS (105), Laboratoire d'Histologie, Universite Libre de Bruxelles,
Bruxelles, Belgium
G. SHIRLEEN ROEDER (299), Department of Biology, Yale University, New
Haven, Connecticut 06511
GERALD M. RUBIN (329), Department of Embryology, Carnegie Institution of
Washington, Baltimore, Maryland 21210
JEFF SCHELL (505), Max-Plank-Institut für Züchtungsforschung, Köln, Federal
Republic of Germany, and Laboratorium voor Genetika, Rijksuniversiteit
Gent, Gent, Belgium
MICHAEL SILVERMAN (537), Department of Biology, University of California at
San Diego, La Jolla, California 92093
MELVIN SIMON (537), Agouron Institute, La Jolla, California 92037
ARIANE TOUSSAINT (105), Laboratoire de Genetique, Universite Libre de
Bruxelles, Bruxelles, Belgium
MARC VAN MONTAGU (505), Laboratorium voor Genetische Virologie, Vrije
Universiteit Brüssel, Brüssel, Belgium
HAROLDE. VARMUS (411), Department of Microbiology and Immunology, Uni
versity of California, San Francisco, California 94143
PATRICIA ZAMBRYSKI1 (505), Department of Biochemistry and Biophysics, San
Francisco Medical School, University of California, San Francisco, Cali
fornia 94143
Present address: Laboratorium voor Genetika, Rijksuniversiteit Gent, Gent, Belgium
Genomic Reorganization in
Cell Lineages
The chapters of this book describe several well-studied cases in which genetic
determinants—often identified as specific nucleic acid sequences—repeatedly
change their positions within or between cellular genomes. Because their geno
mic positions are not fixed, these determinants may conveniently be classed
together under the rubric of mobile genetic elements. Because all genomic con
figurations change over evolutionary time, this term has no rigorous definition.
Nonetheless, certain identifiable components of cellular genomes (such as pro-
viruses and transposable elements) display marked variability when compared to
the Mendelian factors whose usually reliable behavior permits the construction of
genetic maps.
It is a great temptation to try to place the discovery of mobile elements in the
development of our concepts about heredity. Certainly, their complex recom-
binational activities and sometimes non-Mendelian behavior pose fundamental
problems in understanding the organization of chromosomes and extrachromo
somal hereditary nucleic acids. They also open many possible mechanisms lead
ing to the formation of novel genomic configurations. However, our knowledge
is still too immature to permit fruitful generalizations. There is no organism—
not even Escherichia coli, in which intriguing new phenomena appear almost
monthly—in which the mobile elements have been cataloged and their effects on
phenotype and karyotype described with any completeness, and we do not yet
understand in sufficient detail the relationship between mobile elements that are
amenable to genetic analysis and the multiple repetitive elements that comprise a
major fraction of eukaryotic nuclear DNA. I shall therefore simply describe the
rationales that underlie the following collection of chapters and mention a few
points that I find particularly thought-provoking.
From an editorial point of view, this book has two general objectives. The first
is to introduce the nonspecialist to the biology and genetics of mobile elements.
If we are successful, the chapters will make the biochemistry of DNA rearrange
ments more accessible to embryologists and evolutionists and illuminate the
related developmental cycles to the biochemist. The second objective is to show
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JAMES A. SHAPIRO
how natural the activity of mobile elements can be in diverse biological situa
tions. This is an effort to counter the tendency to regard mobile elements as
interesting curiosities in a background of genomic stability. Although a century
of cytogenetic literature has already shown that chromosomes are dynamic struc
tures, it is still useful to see the different ways that mobile elements can fit
specific adaptive needs and respond to elaborate control systems.
The copious illustrations in Chapter 1 by Fedoroff on maize controlling ele
ments show how well suited corn is to clonal analysis of genetic change. This
made it possible for McClintock and others to uncover several systems of nuclear
differentiation within plant tissues. These systems can alter chromosome struc
ture, change specific cellular phenotypes, and create new developmental pat
terns. They utilize intranuclear communication between related but often distinct
mobile elements and reveal a wealth of regulatory phenomena linked to plant
development and cell lineages. Controlling elements were the first mobile ele
ments to be described with precision, and they demonstrate best of all the power
of mobile elements to remodel hereditary programs. Perhaps the most remark
able property of controlling elements is their capacity for generating patterns, as
seen in the color illustrations of kernels that have developed during controlling
element activity.
Chapters 2 and 3 on bacteriophages λ and Mu by Campbell and by Toussaint
and Resibois discuss two prokaryotic mobile elements that have been analyzed in
considerable detail. In large measure, so much information is available because
they can be isolated in virus particles and are thus easier to study physically and
genetically than elements that are always incorporated into more complex geno
mic structures. More than two decades of attention by molecular biologists and
biochemists to the specific recombination system associated with λ insertion and
excision make it possible (1) to define the specific proteins and DNA-substrate
sequences involved and (2) to describe with considerable precision the sophisti
cated regulatory system that controls the specific recombination events. Interest
ingly, a part of this regulation depends on DNA structures, so the recombination
events are self-regulatory. For λ, insertion and excision are not essential for
reproduction as a virus, but this is not the case for phage Mu. Mu's reproduction
(including both replication and morphogenesis) is completely dependent on its
ability to move through the bacterial genome and recombine with many regions
of the host DNA. Thus Mu illustrates how genetic mobility can be totally
integrated into a biological cycle. In addition to their existence as viruses (which
still depend on cells for reproduction), λ and Mu form prophages and are capable
of incorporating and mobilizing nonviral genetic material intracellularly and
intercellularly. In this way the distinctions between host and viral genomes
become less rigid, and it is apparent that the hereditary determinants of one cell
can communicate directly with those of another cell (sometimes of a completely
different species).
GENOMIC REORGANIZATION IN CELL LINEAGES xiii
Three chapters deal with nonviral mobile elements in bacteria. Iida, Meyer,
and Arber (Chapter 4) review IS elements comprehensively, and Heffron (Chap
ter 5) and Kleckner (Chapter 6), focus, respectively, on the Tn3 family of trans-
posons and on TnlO, which have been objects of more detailed analysis.
Although there are certain basic similarities between all the transposable ele
ments discussed in these chapters—in particular, the use of recombination
mechanisms that involve DNA replication—they appear to be functionally dis
tinguishable into at least two classes. The distinction relates to the biochemical
pathways for transposition and other DNA rearrangements, the biological signifi
cance of each element, and the origins of related transposable elements within
each class. The Tn3 family of transposons uses biochemical and regulatory
mechanisms that limit DNA reorganizations almost entirely to the dispersal of
sequences that are internal to the element among the various replicons within a
bacterial cell. Thus we understand why Tn3 and its relatives are efficient agents
for the rapid spread of specific phenotypic determinants. What is not yet under
stood is how these determinants become associated with the recombination
sequences of this class of element. Many IS elements (including the IS10 extrem
ities of TnlO) present a contrast. They utilize replicative recombination pathways
which frequently lead to the stable reorganization of DNA sequences that are
external to the element. Because IS elements do not determine specific cellular
phenotypes, their role appears to reside chiefly in restructuring and recombining
bacterial replicons. It sometimes happens that these DNA reorganizations create
structures in which specific determinants are flanked by duplicate IS elements,
thereby creating a composite mobile element or transposon encoding a particular
phenotype. In other words, the genetic activity of this second class of transpos
able element means that any sequence can be part of a mobile element.
Recombinant DNA technology has made it possible to analyze genetic phe
nomena in eukaryotic cells with the same precision at the molecular level as in
bacteria. Chapter 7 on transposable Ty elements in brewer's yeast (Sacchar-
omyces cerevisiae) by Roeder and Fink illustrates how molecular analysis leads
to a clear understanding of the mobile element events underlying phenotypic
changes. Because Ty elements form a major proportion of the repeated DNA
sequences in yeast nuclei, it is possible to identify the role of repeat sequences in
chromosome reorganization. The results show that related but distinguishable Ty
elements are in physical communication with each other and that an important
source of variability results from recombination between different Ty elements.
Although Ty elements can move to new positions in the yeast genome by
mechanisms that may resemble those for prokaryotic transposable elements (and
thereby alter the regulation of coding-sequence expression), these events are
rare. The most frequent events are exchanges between repeated sequences at
particular locations, and this means that variability is channeled in certain direc
tions by the distribution of elements in the chromosome complement. It is also
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JAMES A. SHAPIRO
intriguing to note that Ty elements have never been observed to excise precisely
from a chromosomal site and leave it as it was before insertion. Thus transposi
tion of a Ty element to a particular site initiates a particular set of chromosome
genealogies.
The genome of Drosphila melanogaster is more complex than that of Sacchar-
omyces cerevisiae, and Drosophila contains a greater diversity of mobile ele
ments. The catalog of these elements is far from complete, but there is already a
sizable corpus of molecular and genetic data about them. The connections have
become much clearer between mobile elements that have been identified as
repeated DNA sequences and those identified by genetic analysis. The two
complementary aspects of this research are discussed in Chapter 8 by Rubin on
Drosophila transposable elements and in Chapter 9 by Bregliano and Kidwell on
hybrid dysgenesis. The phenomenology of hybrid dysgenesis (which is not yet
widely known by nonspecialists) has a great deal to teach us about several
fundamental aspects of mobile genetic element biology. These include (1) the
cellular and environmental controls that govern when mobile elements become
active, (2) the spread of mobile elements through large populations (on a global
scale in this case because D. melanogaster is a cosmopolitan species), and (3) the
role of mobile elements in creating reproductively isolated populations (in other
words, their role in speciation).
It is ironic that the most intensively studied of all groups of mobile genetic
elements—the vertebrate retroviruses described in Chapter 10 by Varmus—are
not generally considered genetic elements at all. The formation of a chromosom
al provirus by reverse transcription in retrovirus reproduction is most often
viewed as a curiosity of viral nucleic acid replication, to be explained and
understood in terms of virus adaptation rather than as a fundamental genetic
process. This situation is analogous to that of temperate bacteriophages like λ
and Mu, and it arises because we have not yet learned how to incorporate the
basic, ubiquitous phenomena of virus-cell and parasite-host interactions into a
more comprehensive picture of heredity. There are alternatives to the strictly
virological point of view, and these are increasingly compelling as the parallels
between retroviruses and other mobile and repeated elements come into sharper
focus. In their DNA form (as pro viruses), retroviruses display much the same
behavior (including insertional mutagenesis, alteration of developmental pro
grams, and mobilization of external chromosomal sequences) as mobile elements
in other organisms. Moreover, sequence analogies between retroviruses and
other repeated elements in vertebrates as well as the abundant transcription of
transposable elements in yeast and Drosophila have suggested that reverse trans
cription may be a rather widespread mechanism of genome reorganization.
Chapter 11 on Agrobacterium oncogenesis in plants by Zambryski et al.
describes the most thoroughly investigated situation in which mobile elements
play a role in intergeneric genome communication and host-parasite interaction.
GENOMIC REORGANIZATION IN CELL LINEAGES XV
There are several fascinating aspects to this phenomenon. First, it involves a
highly evolved mechanism to induce a particular type of neoplastic change.
Second, under the control of a transmissible hereditary element (a plasmid), one
organism (a bacterium) directly modifies for its own benefit the hereditary appar
atus of another organism (a plant) by directing the insertion of a specific DNA
sequence. Third, analysis of this system of natural genetic engineering may
eventually permit human modification of plant genomes by piggybacking speci
fic determinants onto the bacterial transforming DNA. Indeed, most techniques
of genetic engineering utilize or mimic processes that occur naturally with
mobile genetic elements, and it may be that these parallels can teach us a great
deal about the modification of hereditary programs during evolution.
Not all genomic changes are limited to the germ line or have significance only
in organismal lineages. It has been known since at least the 1890s that cellular
differentiation during embryonic development involves nuclear and chromo
somal changes. So it would be surprising if DNA reorganization did not play a
role in some of the highly programmed and specific changes that underlie differ
entiation. Chapter 12 by Silverman and Simon on flagellar phase variation in
Salmonella describes the first case in which the new science of molecular biology
revealed (in 1956) that a change in DNA structure could control the state of
cellular differentiation. One of the intriguing aspects of the site-specific recom
bination system that changes flagellar phases is its close biochemical relationship
to other prokaryotic recombination systems discussed in this book. One (the
inversion of host-range determinants in phage Mu) performs a similar regulatory
function, but the other (To? resolvase) has a different purpose. It seems that
bacterial cells have been able to adapt one basic biochemical recombination
mechanism to meet different needs in DNA metabolism. Two other cases from
lower eukaryotes are discussed in Chapter 13 by Haber on yeast mating type and
in Chapter 14 by Borst on surface antigenic variation in trypanosomes. In both
cases, predictable movements of coding sequences to new genomic locations
lead to particular changes in cellular phenotypes. At least three features of these
systems merit special emphasis. One is the importance of coding-sequence loca
tion for expression of the information it contains. In the yeast mating-type
system, in which the details of transcription are known, this change is more
complex than simply the placing of a protein-coding sequence downstream of
appropriate transcription signals; it must involve regulation by a higher order of
chromosome organization. Both systems, in fact, illustrate a situation com
plementary to that seen with other mobile elements in which the movement of
noncoding sequences alters the expression of specific phenotypes. A second
noteworthy feature of mating-type and surface antigen changes is the limitation
of DNA movement to the appropriate sequence. This means that the underlying
biochemistry—which, at least in yeast, involves general recombination func
tions—can be recruited for more specific changes. The third feature that should
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JAMES A. SHAPIRO
be highlighted is the connection between DNA reorganization and the history of
the cell in which a genetic switch is to occur. Not all cells of a particular
genotype have the same capacity for change. In order to switch mating type, a
homothallic yeast cell must have budded at least once; a trypanosome recently
introduced into a mammalian bloodstream from an insect vector has a potential
antigenic repertoire that is different from one transferred by injection from one
mammal to another. So there must exist regulatory mechanisms operating on
DNA reorganization with "memories" of the previous cell lineage.
In 1977 the Cold Spring Harbor Laboratory published the first book dedicated
to mobile genetic elements, DNA Insertion Elements, Plasmids, and Episomes.
Up to the time of the meeting that formed the basis for the volume, I think it is
fair to say that only a handful of geneticists perceived how various and wide
spread are the hereditary processes that involve mobile elements. Then the major
events in hereditary variation seemed to most of us to be changes in protein-
coding sequences or unexplained sudden rearrangements of chromosome struc
ture. Since that time, there has been tremendous progress in defining the molecu
lar parameters of genomic change and elucidating the complexities of chromo
some organization. Some of this progress is described in the pages that follow.
Nonetheless, I think it is true even today that a majority of geneticists would
argue that mobile elements are fascinating but only have significance as part of
the "background noise" of random variability needed to provide the raw mate
rial of evolutionary change. I will use the editor's privilege to express a different
view. In my opinion, we will only integrate mobile elements fully into our
picture of heredity when we have formulated entirely new mechanisms for cellu
lar differentiation in both development and evolution. When Barbara McClintock
demonstrated that specific heritable nuclear elements were responsible for chang
ing the structure of maize chromosomes, she made a discovery comparable to
observing spontaneous atomic decay. Like scientists in other fields at various
periods in the histories of their disciplines, we geneticists now have to come to
terms with unanticipated levels of structure and organization.
The following chapters represent extensive summaries of these fourteen
mobile element systems. Although each chapter contains current and until now
unpublished information, the authors have also taken great pains to place current
observations within the historical development of their systems. It is pleasing to
think that so many diverse phenomena can unexpectedly reveal common patterns
of genetic control. In my opinion, these thoughtful reviews will not quickly
become dated. Through their efforts, the authors have created a unique statement
of a particularly exciting stage in the history of genetics. I hope the reader will
share the exhilaration of our voyage toward a richer appreciation of heredity.
JAMES A. SHAPIRO
