Molecular Microbiology

329 Pages·1998·19.853 MB·English

by  Steven E. Finkel, Erik Zinser, Srishti Gupta, Roberto Kolter (auth.), Stephen J. W. Busby, Christopher M. Thomas, Nigel L. Brown (eds.)

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Series H: Cell Biology, Vol. 103
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Molecular Microbiology
Edited by
Stephen J. W. Busby
The University of Birmingham, School of Biochemistry
P.O. Box 363, Birmingham, B15 2TI, U.K.
Christopher M. Thomas
Nigel L. Brown
The University of Birmingham, School of Biological Sciences
P.O. Box 363, Birmingham, B15 2TI, U.K.
With 78 Figures
Springer
Published in cooperation with NATO Scientific Affairs Division
Proceedings of the NATO Advanced Study Institute "Molecular Microbiology".
held at Chamberlain Hall. The University of Birmingham. Birmingham. U.K.,
April 7-17. 1997
Library of Congress Cataloging-in-Publication Data
Molecular microbiology / edited by Stephen J. W. Busby, Christopher M. Thomas, Nigel L. Brown.
p. cm. - (NATO ASI series. Series H, Cell biology; vol. 103)
Includes bibliographical references and index.
ISBN-13:978-3-642-72073-4
1. Molecular microbiology. I. Busby, Stephen J. W., 1951-. II. Thomas, Christopher M.
III. Brown, Nigel., 1948-. IV. Series.
QR74.M653 1998 527.8'29-dc21 97-32739 CIP
ISSN 1010-8793
ISBN-13:978-3-642-72073-4 e-ISBN-13:978-3-642-72071-0
001: 10.1007/978-3-642-72071-0
This work is subject to copyright. All rights are reserved, whether the whole or part of the material is
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© Springer-Verlag Berlin Heidelberg 1998
Softcover reprint of the hardcover 1st edition 1998
Typesetting: Camera ready by authors/editors
Printed on acid-free paper
SPIN 10531516 31/3137 -5 4 3 210
PREFACE
Molecular Microbiology is a rapidly expanding area of contemporary
science: the application of molecular biology has opened up the
microbial world in many remarkable ways. The attraction of microbes
is that they are self contained and that they offer complete solutions to
understanding the phenomenon of life .. Perhaps the clearest index of
this growth is the number of doctoral students and young postdoctoral
workers currently engaged in this research area. The NATO Advanced
Study Institute, reported in this volume, was organised in order to cater
for the needs of these research workers. The aim was to provide a
course that would provide essential background information for anyone
recently recruited to (or about to enter) Molecular Microbiology. Thus
the Advanced Study Institute united nearly 100 students and
postdoctoral workers who enjoyed a gourmet guide to the subject.
Contributors were urged to focus on the background and the principles
of the subject rather than the detail and, for this reason, we believe that
the Advanced Study Institute and the ensuing book are unique. Clearly
the main defect is that neither the taught course nor the book is
comprehensive and concentrates on four rather arbitrarily chosen
research themes. However we believe that, despite this shortcoming,
this book will have lasting value as an introductory text to this exciting
research area.
Birmingham, England
Steve Busby
Chris Thomas
Nigel Brown
CONTENTS
Part 1 Bacterial Biochemistry
Life and Death in Stationary Phase
SE. Finkel, E. Zinser, S Gupta, R. Kolter ........................................... 3
The Citric Acid Cycle and Oxygen-Regulated Gene Expression
in Escherichia coli
J Green, JR. Guest .............................................................................. 17
Part 2 Genomes and their Survival
Gene Transfer by Bacterial Conjugation:
Establishment of the Immigrant Plasmid in the Recipient Cell
B.M Wilkins, S. Bates .......................................................................... 43
Bacteriophage Mu
MM Howe ..................................................................... 65
Regulation of Bacteriophage A Replication
K. Taylor, G. Wegrzyn ........................................................ 81
Replication and Maintenance of Bacterial Plasmids
CM Thomas, G. Jagura-Burdzy, K. Kostelidou .......................... 99
P. Thorsted, M Zatyka
Part 3 Expression
Bacterial Gene Regulatory Proteins:
Organisation and Mechanism of Action
G. Lloyd, T Belyaeva, V Rhodius, N Savery, S Busby ................ 123
Bacterial Two-Component Regulatory Systems
V Stewart ..................................................................... 141
VIII
Metal Regulation of Gene Expression in Bacterial Systems
N.L. Brown, K.R. Brocklehurst, B. Lawley, JL. Hobman .............. 159
Regulation of Prespore-Specific Transcription
During Sporulation in Bacillus subtilis
J Errington, R. Daniel, A. Feucht, P. Lewis, L.J Wu .................. 175
Quorum Sensing: Bacterial Cell-Cell Signalling
from Bioluminescence to Pathogenicity
S. Swift, J Throup, B. Bycrojt, P. Williams, G. Stewart ............... 185
Studying Protein Synthesis Factors in Yeast:
Structure, Function and Regulation
MF. Tuite ..................................................................... 209
Part 4 Microbial Cell Biology
The Roles of Molecular Chaperones in the Bacterial Cell
P.A. Lund. ..................................................................... 229
Protein Traffic in Bacteria
A.P. Pugsley .................................................................. 245
Oxygen Toxicity, Oxygen Starvation and the Assembly of Cytochrome
c-Dependent Electron Transfer Chains in Escherichia coli
J. Cole, H Crooke ........................................................... 265
Aspects of the Molecular Genetics of Antibiotics
J. Davies ....................................................................... 285
Interactions of the Bacterial Pathogen Listeria monocytogenes
with Mammalian Cells
P. Cossart .................................................................... 301
The Behaviour of Bacterial Pathogens in vivo
H Smith ....................................................................... 319
Part 1
Bacterial Biochemistry
Life and Death in Stationary Phase
Steven E. Finkel, Erik Zinser, Srishti Gupta, and Roberto Kolter
Department of Microbiology and Molecular Genetics, Harvard Medical School,
200 Longwood Avenue, Boston, MA 02115, USA
Introduction
Bacteria are remarkable for their ability to occupy virtually all environmental niches.
In addition, many bacterial organisms transit from one environment to another as part
of their normal lifestyle. From the bacterial point of view most of these
environments are nutrient poor; more often than not, bacteria find themselves growing
under conditions where nutrients are scarce and competition for those nutrients is
fierce. Therefore, most bacteria spend much of their lives in a state of starvation,
only occasionally finding themselves in a nutrient-rich environment where balanced
growth can be achieved. II). order to survive within these disparate and changing
environments bacterial populations have developed mechanisms to protect both their
cellular and genetic integrity. These mechanisms involve changes in cellular
properties and morphology, the production of protective enzymes and agents, and, in
some cases, entry into developmental programs resulting in sporulation, dormancy
and programmed cell death.
The well-characterized gram-negative bacterium Escherichia coli is an ideal model
organism for the study of bacterial responses to starvation. It occupies many
environmental niches, including fresh water, soil, and the gut of many higher
organisms. It can transit between all of these environments and has developed
mechanisms to survive and reproduce within each of them.
The E. coli Life Cycle
E. coli llildergoes a well-characterized cycle of growth llilder standard laboratory
conditions (Fig. 1). These conditions typically consist of growth at a constant
temperature, with or without aeration, in complex or minimal media. Under these
batch culture conditions cells freshly inoculated into culture medium will sustain a
"lag period" where cell division has not yet begun, followed by a period of
"exponential" or "log-phase" growth where all readily available nutrients are rapidly
NATO ASI Series, Vol. H 103
Molecular Microbiology
Edited by Stephen 1. W. Busby,
Christopher M. Thomas and Nigel L. Brown
© Springer-Verlag Berlin Heidelberg 1998
4
metabolized. As nutrients become exhausted the population begins to starve and
enters "stationary phase." Stationary phase is defmed as the period when increases in
population size, as assayed by cell density or colony forming units (CFU) within the
culture, are no longer observed (Kolter et al., 1993). Cells grown under these batch
culture conditions can reach densities of 109_1010 CFU/ml upon entry into stationary
phase.
10
~J
8
E
.......
=> 6
LL
U
C) 4
.S!
2
,
0 , l i i j i i i I I I
8 15 30 3 6 9 12
Hours Days Months
FIG. 1 Long-tenn incubation of E. coli. E. coli remains viable for long periods of time
without the addition of nutrients. Sterile, distilled water is added periodically to maintain
constant volume.
Responses to Starvation
Bacteria have developed different responses to starvation. Some organisms, such as
Bacillus subtilis, form spores in response to nutrient deprivation (Losick and
Youngman, 1984). These spores are highly resistant to desiccation, heat, and
radiation and can remain dormant until a nutrient source is encountered. A more
complex response to starvation occurs in Myxococcus xanthus (Kaiser, 1984). These
bacteria normally function as individual cells, however, in response to starvation
conditions, millions of bacterial cells will coalesce to form a fruiting body and release
spores. Individual cells within the fruiting body enter different developmental
programs to enable a sub-population of the cells to survive as spores.
E. coli does not form spores in response to starvation, although a stereotypical
pattern of gene expression and morphological changes does occur as cells begin to
starve (Huisman et al., 1996). Stationary phase in E. coli can be thought of as