Bacterial Physiology: A Molecular Approach

376 Pages·2008·2.08 MB·English

by  Peter J. Lewis (auth.), Walid El-Sharoud (eds.)

Bacterial Physiology
A Molecular Approach
Walid El-Sharoud
Editor
Bacterial
Physiology
A Molecular Approach
Dr. Walid M. El-Sharoud
Faculty of Agriculture
Mansoura University
Mansoura
Egypt
[email protected]
Cover Illustration: Image shows exponentially growing Bacillus subtilis cells expressing GFP-MreB
(upper panel). Second panel shows DNA stain, third panel overlay of GFP-MreB (green) and membrane
stain (red, indicating the septa between cells, which grow in chains), lower panel overlay of GFP-MreB
(green) and DNA stain (blue). Image courtesy of Hervé Joël Defeu Soufo and Peter L. Graumann,
University of Freiburg, Germany.
ISBN: 978-3-540-74920-2 e-ISBN: 978-3-540-74921-9
Library of Congress Control Number: 2007934673
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Dedicated to my father, Mahmoud El-Sharoud,
who inspired my love for writing!!
W. M. El-Sharoud
Preface
How well do we understand bacteria? How true is the hypothesis of Jacques Monod
that if we understand Escherichia coli, we will be able to understand elephant? It is
striking that the more we learn regarding bacteria the less we can be convinced of
this hypothesis. For a long time, scientists thought that bacteria were just simple
single-celled organisms that could be used as model systems for higher, complex,
and multi-celled eukaryotic organisms. In a rather simplified view, bacteria were
considered as self-contained packets of enzymes that had little interaction with each
other or the surrounding environments. Conversely, it is now appreciated that
bacteria can show community features of communication between individual cells
and interaction with surrounding environments. As with higher organisms, a
community of bacteria can display individual phenotypic variations; this is the case
even within a clonal population of identical genetic composition (see Chap. 12).
Such individual diversity seems to promote communication between cells that aids
adaptation in the environment (see Chap. 9). The tremendous diversity between
different bacterial species is also striking; suffice it to say that the genetic distance
between two bacterial groups may be of a similar order to the average genetic
distance between plants and animals.
Although the significance of the early contributions of pioneering microbiologists
cannot be overemphasised, it is unquestionable that the study of bacteria has been
revolutionized by the application of molecular methodologies. These methods
allowed direct manipulation and monitoring of bacterial cells’ components rather
than hypothesizing on them. This was not an option for an old bacteriologist, given
the limitation of traditional methodology in microbiology, and it has been the
massive advancement in genetics, biochemistry, biophysics, bioinformatics, etc.
that made molecular techniques available. The use of molecular methods includ-
ing the “omics” (genomics, transcriptomics, proteomics) and fluorescence-based
techniques not only allowed new discoveries, but has also changed our way of
researching and thinking of bacteria. Modern bacteriologists do now adopt “a
molecular approach,” in which cell structure, function, and behaviour are inter-
preted on molecular basis. This approach has broadened and deepened the
level of study of bacterial cells, but also raised concerns regarding a number of
the past’s theories.
Within this context comes the present book, which presents the impact of applying
the molecular approach to the study of bacterial physiology. The first chapter
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viii Preface
discusses recent discoveries of subcellular organisation that have been made
possible by the use of molecular techniques. The author exploits such sophisticated
structural findings in reforming our ideas regarding the basic physiological proc-
esses of transcription, translation, cell division, etc. The second chapter reports on
the presence of cytoskeletal elements in bacteria, a structural property that was
thought to be restricted to eukaryotic cells. This is an interesting and significant
discovery, given the involvement of bacterial cytoskeleton in shaping cells, cell
division, chromosome segregation, and cell motility. The third chapter is also on
newly discovered structural phenomena related to the cytoplasmic membrane. The
authors provide comprehensive review of the presence of mechanosensitive
channels that form large pores in the cytoplasmic membrane that switch between
open and closed states, aiding cell survival during environmental stress. In relation
to this, the authors also describe recent findings showing the dynamic structural
nature of bacterial cell wall. The fourth chapter considers an interesting aspect of
one of the basic physiological processes: respiration. The author discusses the
phenomenon of respiratory flexibility in bacteria, where cells use a range of differ-
ent electron donors and acceptors in response to different environmental pressures.
Chapter 5 describes protein secretion systems, a novel research area with particularly
potential medical applications. Chapter 6 discusses the regulation of gene expres-
sion by DNA supercoiling. This is an unorthodox view of gene regulation, usually
thought to be mediated by primary DNA sequences, activators, repressors, etc.
Here, the author shows that DNA topology is significantly important for regulating
gene expression. Chapters 7 through 9 provide reports on different systems used by
bacteria to sense changes in the surrounding environment. These chapters empha-
size the ability of bacterial cells to interact with each other and with surrounding
environments, a trait that enables adaptation and survival under different environ-
mental conditions. Chapters 10 and 11 further describe other cellular mechanisms
to cope with environmental stress. Chapter 10 reports on ribosome modulation
factor, whose binding to bacterial ribosomes has been shown to aid cell survival
during stress, whereas Chapter 11 demonstrates diverse aspects of the so-called
“stress master regulator,” RpoS, which is a sigma factor protein mediating the tran-
scription of stress-responsive genes. Apart from structural and functional issues
discussed in the previous chapters, the last chapter explains the striking phenomena
of phenotypic switching and bistability in bacteria. The authors provide an account
of the molecular basis of these phenomena, in which individual cells with identical
genotypes may display different phenotypes under identical conditions within the
same clonal population.
As mentioned above, bacteria display a high degree of structural and functional
diversity. Since much of our knowledge of bacteria has been gained through the
study of relatively few species, such as E. coli and Bacillus subtilis, this raises the
question of how applicable our current understanding is to the physiology of the
rest of bacterial species. It is interesting to see in this book several examples of
knowledge generated with bacterial species other than the previous model ones.
This will certainly help provide better and thorough understanding of the physiology
of bacterial cells. As we will also see in most chapters, there is a concluding
Preface ix
section showing potential applications of the aspects discussed in each chapter.
It could be realized from these sections that significant applications in biotechnology
and drug discovery can be made effective using the wealth of basic knowledge in
bacterial physiology.
This book has been developed to suit readers of diverse backgrounds. While the
text serves as a reference for researchers pursuing work in areas highlighted by the
book chapters, it is also intended to be useful to undergraduates and postgraduates
majoring in microbiology and to microbiologists who wish to be familiar with
advances in other areas of microbiology. I am very grateful to the colleagues who
contributed chapters to this book, dedicating time and sincere effort for such a
project. I would also like to thank all of them for their patience with me during the
review process. My greatest appreciation to the following professors who kindly
contributed to reviewing the book chapters: Peter Graumann, Frank Mayer, Paul
Williams, Wolfgang Schumann, Regin Hengge, Eberhard Klauck, Tracy Palmer,
and Mattew Hicks. I would like also to thank Dr. Christina Eckey, Ms. Ursula
Gramm, Ms. Alice Blanck, and the rest of the editorial team at Springer for their
support and help during the development of this book.
Indeed, I am most appreciative to Dr. Gordon Niven for significantly contribut-
ing to my development as a scientist. My deepest thanks also to Dr. Bernard
Mackey, Prof. Robin Rowbury, Prof. Martin Adams, and Prof. David White for
their continued support and advice. Finally, all the kind words cannot express my
warmest gratitude to my mother and father, with whom I feel the joy of kindness
and tenderness. My love and sincere appreciation to my lovely wife, Sherine
Mostafa, who turned my life into enjoyable times. At last, and never at least, I am
writing this preface while awaiting the birth of my new daughter Merna, to whom
I also dedicate this book.
Aga, July 2007 Walid M. El-Sharoud
Contents
1 Subcellular Organisation in Bacteria . . . . . . . . . . . . . . . . . . . . . . . . . . 1
Peter J. Lewis
2 Molecular Components of the Bacterial Cytoskeleton . . . . . . . . . . . . 43
Katharine A. Michie
3 Mechanosensitive Channels: Their Mechanisms and Roles
in Preserving Bacterial Ultrastructure During Adaptation
to Environmental Changes. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73
Ian R. Booth, Samantha Miller, Akiko Rasmussen, Tim Rasmussen,
and Michelle D. Edwards
4 Structural and Functional Flexibility of Bacterial Respiromes . . . . . 97
David J. Richardson
5 Protein Secretion in Bacterial Cells . . . . . . . . . . . . . . . . . . . . . . . . . . . 129
Christos Stathopoulos, Yihfen T. Yen, Casey Tsang,
and Todd Cameron
6 Regulation of Transcription in Bacteria by DNA Supercoiling . . . . . 155
Charles J. Dorman
7 Quorum Sensing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 179
Simon Swift, Maria C. Rowe, and Malavika Kamath
8 Environmental Sensing and the Role of Extracytoplasmic
Function Sigma Factors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 233
Bronwyn G. Butcher, Thorsten Mascher, and John D. Helmann
9 Extracellular Sensors and Extracellular Induction Components
in Stress Tolerance Induction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 263
Robin J. Rowbury
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xii Contents
10 Ribosome Modulation Factor. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 293
Gordon W. Niven and Walid M. El-Sharoud
11 The Role of RpoS in Bacterial Adaptation . . . . . . . . . . . . . . . . . . . . . 313
Tao Dong, Charlie Joyce, and Herb E. Schellhorn
12 Phenotypic Variation and Bistable Switching in Bacteria. . . . . . . . . 339
Wiep Klaas Smits, Jan-Willem Veening, and Oscar P. Kuipers
Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 367
Contributors
Ian R. Booth
School of Medical Sciences, Institute of Medical Sciences, University of
Aberdeen, Aberdeen AB25 2ZD, UK
Bronwyn G. Butcher
Department of Microbiology, Cornell University, Ithaca, NY 14853-8101, USA
Todd Cameron
Biological Sciences Department, California State Polytechnic University, USA
Tao Dong
Department of Biology, McMaster University, Canada
Charles J Dorman
Department of Microbiology, Moyne Institute of Preventive Medicine, Trinity
College Dublin, Dublin 2, Ireland, [email protected]
Michelle D. Edwards
School of Medical Sciences, Institute of Medical Sciences, University of
Aberdeen, Aberdeen AB25 2ZD, UK, [email protected]
Walid M. El-Sharoud
Food Safety and Microbial Physiology (FSMP) Laboratory, Mansoura University,
Egypt
John D. Helmann
Department of Microbiology, Cornell University, Ithaca, NY 14853-8101, USA,
[email protected]
Charlie Joyce
Department of Biology, McMaster University, Canada
Malavika Kamath
Department of Molecular Medicine and Pathology, University of Auckland,
Auckland, New Zealand
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