Cell Biology: A Comprehensive Treatise. The Structure and Replication of Genetic Material

494 Pages·1979·12.362 MB·English

by  David M. Prescott (Eds.)

CONTRIBUTORS
Friedrich Bonhoeffer R. F. Kimball
Jonathan O. Carlson Julie Korenberg
Cedric I. Davern Anthony W. Linnane
Ruth M. Hall W. J. Peacock
Roger Hand David E. Pettijohn
Leland H. Johnston Hans Ris
Burke H. Judd Peter Symmons
ADVISORY BOARD
Wolfgang Beermann Lee Peachey
Donald Brown Robert P. Perry
Joseph G. Gall Keith R. Porter
G. P. Georglev Frank H. Ruddle
Paul B. Green Robert T. Schimke
George Klein S. J. Singer
George Lefevre Tracy M. Sonneborn
A. W. Linnane Noboru Sueoka
Daniel Mazia Hewson Switt
Brian McCarthy George J. Todaro
Gordon Tom kins*
Deceased
CONTRIBUTORS
Friedrich Bonhoeffer R. F. Kimball
Jonathan O. Carlson Julie Korenberg
Cedric I. Davern Anthony W. Linnane
Ruth M. Hall W. J. Peacock
Roger Hand David E. Pettijohn
Leland H. Johnston Hans Ris
Burke H. Judd Peter Symmons
ADVISORY BOARD
Wolfgang Beermann Lee Peachey
Donald Brown Robert P. Perry
Joseph G. Gall Keith R. Porter
G. P. Georglev Frank H. Ruddle
Paul B. Green Robert T. Schimke
George Klein S. J. Singer
George Lefevre Tracy M. Sonneborn
A. W. Linnane Noboru Sueoka
Daniel Mazia Hewson Switt
Brian McCarthy George J. Todaro
Gordon Tom kins*
Deceased
CELL BIOLOGY
A Comprehensive Treatise
Volume 2
The Structure and Replication of
Genetic Material
Edited by
DAVID M. PRESCOTT
LESTER GOLDSTEIN
Department of Molecular, Cellular and Developmental Biology
University of Colorado
Boulder, Colorado
®
Academic Press New York San Francisco London 1979
A Subsidiary of Harcourt Brace Jovanovich, Publishers
COPYRIGHT © 1979, BY ACADEMIC PRESS, 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 PHOTOCOPY, RECORDING, OR ANY
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PERMISSION IN WRITING FROM THE PUBLISHER.
ACADEMIC PRESS, INC.
Ill Fifth Avenue, New York, New York 10003
United Kingdom Edition published by
ACADEMIC PRESS, INC. (LONDON) LTD.
24/28 Oval Road, London NW1 7DX
Library of Congress Cataloging in Publication Data
Main entry under title:
The Structure and replication of genetic material.
(Cell biology, a comprehensive treatise ; v. 2)
Includes bibliographies and index.
1. Chromosomes. 2. Chromosome replication.
3. Deoxyribonucleic acid repair. I. Prescott,
David M., Date II. Goldstein, Lester.
HI. Series.
QH574.C43 vol. 2 [QH600] 574.8'7s [574.8'732] 78-10457
ISBN 0-12-289502-9 (v. 2)
PRINTED IN THE UNITED STATES OF AMERICA
79 80 81 82 9 8 7 6 5 4 3 2 1
List of Contributors
Numbers in parentheses indicate the pages on which the authors' contributions begin.
Friedrich Bonhoefifer (59), Max-Planck-Institut für Virusforschung, 74
Tübingen, Spemannstr. 35, West Germany
Jonathan O. Carlson (1), Department of Biophysics and Genetics, Univer­
sity of Colorado Medical Center, Denver, Colorado 80262
Cedric I. Davern* (131), Department of Biology and Department of Mi­
crobiology, University of Utah, Salt Lake City, Utah 84132
Ruth M. Hall (171), Department of Biochemistry, Monash University,
Clayton, Victoria 3168, Australia
Roger Hand (389), Department of Microbiology, McGill University,
Montreal, Quebec H3A 2B4, Canada
Leland H. Johnston (59), Division of Microbiology, National Institute for
Medical Research, The Ridgeway, Mill Hill, London NW7 1AA,
England
Burke H. Judd (223), The University of Texas at Austin, Department of
Zoology, Austin, Texas 78712
R. F. Kimball (439), Biology Division, Oak Ridge National Laboratory,
Oak Ridge, Tennessee 37830
Julie Korenbergt (267), Department of Zoology, University of Wisconsin,
Madison, Wisconsin 53705
Anthony W. Linnane (171), Department of Biochemistry, Monash Univer­
sity, Clayton, Victoria 3168, Australia
W. J. Peacockt (363), Division of Plant Industry, Commonwealth Scien­
tific and Industrial Research Organization, Canberra, ACT, Australia
David E. Pettijohn (1), Department of Biophysics and Genetics, Univer­
sity of Colorado Medical Center, Denver, Colorado 80262
Hans Ris (267), Department of Zoology, University of Wisconsin, Madi­
son, Wisconsin 53705
Peter Symmons (59), Max-Planck-Institut für Virusforschung, 74 Tübin­
gen, Spemannstr. 35, West Germany
* Present address: University of Utah, Salt Lake City, Utah 84112.
t Present address: University of Miami School of Medicine, Miami, Florida.
Φ Present address: Division of Plant Industry, Commonwealth and Scientific Industrial
Research Organization, P.O. Box 1600, Canberra City, ACT 2601, Australia.
ix
Preface
Volume 1 of this treatise dealt with the genetic mechanisms of cells. A
logical extension of this topic is the consideration of genetics at the mo­
lecular level, and this volume, therefore, deals with the structure and
replication of the genetic material both in the nucleus (including bacterial
and viral nucleoids) and in cytoplasmic organelles. Volumes 3 and 4 will
be concerned with genetic expression, covering transcription and transla­
tion, respectively. These four volumes will complete the first part of the
treatise and establish a basis on which to deal with broad questions of cell
structure and function, such as cell reproduction, differentiation, and
cell-cell interactions, in subsequent volumes.
Continuing the objective presented in the Preface to Volume 1, we have
planned this and succeeding volumes to serve as primary sources of fun­
damental knowledge for graduate students, investigators working in
peripheral areas, and for anyone else in need of information on some par­
ticular phase of cell biology. Thus we asked authors to write chapters
emphasizing reasonably well established facts and concepts, but not to at­
tempt the more traditional up-to-the-minute reviews that investigators
working in specialized fields count on. A measure of the maturity of cell
biology also became evident from the fact that it has been a relatively
simple matter to construct each volume around a single, unified theme.
David M. Prescott
Lester Goldstein
XI
Titles of Other Volumes
Volume 1 Genetic Mechanisms of Cells
Volume 3 Genetic Expression: The Production of RNAs
Volume 4 Genetic Expression: Translation and the Behavior of
Proteins
Volume 5 Cell Growth and Reproduction
Volume 6 Cell Differentiation
Volume 7 Specialized Cells and Organelles
Volume 8 Cellular Interactions
Volume 9 The Plasma Membrane, the Cell Surface, and Exchanges
between the Cell and Its Environment
Volume 10 Energy Mobilization, Mechanical Work, and Cell
Movement
Volume 11 The Origin, Evolution, and Diversity of Cells
XIII
1
Chemical, Physical, and Genetic
Structure of Prokaryotic
Chromosomes
David E. Pettijohn and Jonathan O. Carlson
I. Introduction 2
II. Gross Organization of Prokaryotic Chromosomes 3
A. Structure of the Bacterial Nucleoid in Vivo 3
B. Gross Structure and Composition of Isolated
Nucleoids 5
C. Gross Structure of Bacteriophage Chromosomes 9
D. Interactions of Phage and Plasmid DNA's with
Bacterial Chromosomes 11
III. Long-Range Organization of DNA in Chromosomes 13
A. DNA Circularity and Supercoiling 13
B. Domains of Supercoiling in Isolated Bacterial
Chromosomes 15
C. Replication and Packaging of Bacteriophage λ DNA 22
D. Genetic Organization of Chromosomes 25
IV. Short-Range Structure of DNA in Chromosomes 39
A. Lac Control Region 39
B. λ Early Control Regions 42
C. Promotors 44
D. Other DNA Sequences That Interact with Specific
Proteins 45
E. Influence of DNA Secondary and Tertiary Structure on
Protein-DNA Interactions 45
References 48
1
CELL BIOLOGY, VOL. 2 Copyright © 1979 by Academic Press, Inc.
All rights of reproduction in any form reserved.
ISBN 0-12-289502-9
2 David E. Pettijohn and Jonathan 0. Carlson
I. INTRODUCTION
The word chromosome (colored body) was coined to describe the
darkly staining bodies that condense from components of the eukaryotic
nucleus as cells begin mitosis. We now know that these structures consist
of a very long DNA molecule (one per chromatid) and various other
molecules that are bound to the DNA. Some of the latter adducts are
probably involved in arranging the structure of the packaged DNA and in
organizing its replication, transcription, recombination, and other genetic
processes. In a prokaryotic cell, the genomic DNA is also condensed into
an easily recognized structure, although its shape and size are not as
regular as in a eukaryotic chromosome. In this chapter these prokaryotic
structures will be referred to as chromosomes. By analogy with the ter­
minology for eukaryotic chromosomes, molecules bound to the con­
densed prokaryotic DNA will be considered part of the chromosome. The
purpose of this chapter is to summarize the current state of knowledge of
the structure of prokaryotic chromosomes.
The chromosome can be described at several levels of organization. At
one extreme there have been extensive studies of the intracellular
morphology of bacterial chromosomes using various microscopy tech­
niques. At the other extreme, nucleotide sequences of limited regions of
the chromosomal DNA have been worked out to define the actual chemi­
cal structure of parts of the chromosome. In between these two levels
of study, other investigations have defined intermediate levels of
chromosomal organization, using genetic mapping techniques, biochemi­
cal dissection of isolated chromosomes, fine-structure microscopy, and
physicochemical approaches. In this chapter, we shall review these
developments. The order of discussion will be such that the gross struc­
ture is presented first, after which progressively finer levels of organiza­
tion will be introduced, finally extending down to DNA sequence studies.
By analogy with protein structure, the structure of DNA in a chromo­
some can be described from different points of reference. For example,
genetic mapping or DNA sequencing provides a one-dimensional repre­
sentation of the chromosomal DNA, analogous in some sense to the pri­
mary structure of an enzyme. The organization of the three-dimensional
structure of DNA in chromosomes, which has some analogy to tertiary
structure organization in enzymes, is just beginning to be elucidated. The
factors and structures that determine the positions of folds in the double-
helical DNA and organize superhelical turns as yet are not well defined. A
complete description of three-dimensional chromosome structure obvi­
ously will have implications for the mechanisms of DNA recombination,
replication, transcription, and their regulation. While the latter subjects
1. Chemical, Physical, and Genetic Structure of Prokaryotic Chromosomes 3
are covered in other chapters of these volumes, the subjects of these
chapters necessarily overlap with the present discussion. When more is
learned about the three-dimensional structure of the chromosome, one
would expect even greater complementarity among these subjects.
Chromosome structure has been studied in many different prokaryotic
systems. Space does not allow a survey of these; rather, we shall concen­
trate on the best-understood chromosomes of a few biological systems.
Specifically emphasized will be the chromosome of Escherichia coli and
the chromosomes of λ and T4 phages. Review of many other interesting
systems (for example, bacterial spores) will be restricted or omitted; be­
cause comparatively less is known about their chromosomes. In addition,
this chapter is not intended to be comprehensive. In an area as intensively
studied as prokaryotic chromosomes, it has been necessary to limit the
discussion to certain subjects and approaches.
II. GROSS ORGANIZATION OF PROKARYOTIC CHROMOSOMES
A. Structure of the Bacterial Nucleoid in Vivo
The bacterial chromosome (or nucleoid) can be visualized in the cell by
a variety of different microscopy techniques (for reviews, see Ryter, 1968;
Pettijohn, 1976). In all cases, the nucleoid is seen to occupy only a portion
of the intracellular volume; however, no nuclear membrane or other
structural components segregates it from the cytoplasm. Apparently, in­
teractions within the structure define its state of condensation. The size
and shape of the nucleoids vary when cells are grown in various media or
under different conditions (see Figure 1). When cells of E. coli are grown
in rich media, the apparent "surfaces" of the nucleoids appear more
uneven and convoluted than those seen in cells growing slowly in minimal
media (Ryter and Chang, 1975). When protein synthesis or RNA synthe­
sis is inhibited, the nucleoids can change in size and shape (Kellenberger
et al., 1958; Daneao-Moore and Higgins, 1972; Dworsky and Schaechter,
1973). It seems that the structure of the nucleoid is dynamic in the sense
that at least its gross organization is dependent on the physiological state
of the cell. Also, the gross appearance of the nucleoids varies among the
different bacterial strains. For example, in Bacillus subtilis the nucleoids
tend to be smaller and more compact than in E. coli.
It has been suggested that the intracellular nucleoids visualized by mi­
croscopy represent only the tightly condensed genetically inactive DNA
of the chromosome (Ryter and Chang, 1975) that perhaps is analogous to
heterochromatin. DNA sequences containing actively transcribed genes