Bacterial Stress Responses

524 Pages·2010·16.461 MB·English

by  Gisela Storz, Regine Hengge

BACTERIAL STRESS RESPONSES
Second Edition
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BACTERIAL STRESS RESPONSES
Second Edition
Edited by
Gisela Storz
Eunice Kennedy Shriver Institute of Child Health
and Human Development
Bethesda, Maryland
and
Regine Hengge
Freie Universität Berlin
Berlin, Germany
Washington, DC
Copyright © 2011 ASM Press
American Society for Microbiology
1752 N St., N.W.
Washington, DC 20036-2904
Library of Congress Cataloging-in-Publication Data
Bacterial stress responses / edited by Gisela Storz and Regine Hengge. — 2nd ed.
p. ; cm.
Includes bibliographical references and index.
ISBN-13: 978-1-55581-621-6 (hardcover : alk. paper)
ISBN-10: 1-55581-621-5 (hardcover : alk. paper) 1. Microorganisms—Physiology. 2.
Stress (Physiology) 3. Adaptation (Physiology) I. Storz, Gisela. II. Hengge, Regine.
III. American Society for Microbiology.
[DNLM: 1. Bacterial Physiological Phenomena. 2. Bacteria—genetics. 3. Bacteria
metabolism. 4. Environmental Microbiology. QW 52]

QR97.A1B33 2011
571.2'93—dc22
2010035452
10 9 8 7 6 5 4 3 2 1
All Rights Reserved
Printed in the United States of America
Address editorial correspondence to ASM Press, 1752 N St., N.W., Washington,
DC 20036-2904, USA.
Send orders to ASM Press, P.O. Box 605, Herndon, VA 20172, USA.
Phone: [phone]
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Online: http://estore.asm.org
Cover image: The two panels show the same area of false-color fluorescence images of a single microarray spot-
ted with 50-nucleotide oligomers specific for all open reading frames in the E. coli K-12 genome that was hybrid-
ized with a mixture of Cy3-/Cy5-labeled cDNA obtained with RNA extracted from strain W3110. The cells were
grown in defined rich medium and harvested for RNA preparation during growth (at an OD of 1.0) at 37°C
578
or 5 min after a shift from 37°C to 42°C (preparations labeled with Cy3 or Cy5, respectively). These cells were
treated exactly as the cells used by Roth van Bogelen and Fred Neidhardt for the “historic” proteomic analysis of
heat-shocked E. coli cells shown on the cover of the first edition of Bacterial Stress Responses in 2000. The upper
panel shows fluorescent signals derived from non-heat-shocked cells. The lower panel shows fluorescent signals
derived from heat-shocked cells. Spots representing heat-shock-inducible genes are circled, and gene designations
are given. Microarray analysis was performed by Nicole Sommerfeldt and R. Hengge.
To Ella, Toby, Felix, Lisa-Maria, and Manolis
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CONTENTS
Contributors • ix 8. Envelope Stress • 115
Preface • xiii Sarah E. Ades, Jennifer D. Hayden, and
Acknowledgments • xv Mary E. Laubacher
9. Osmotic Stress • 133
I. General Principles
Janet M. Wood
1. Structure and Evolution of Transcriptional 10. Sensing and Responding to Reactive Oxygen
Regulatory Networks • 3 and Nitrogen Species • 157
Guilhem Chalancon and M. Madan Babu Gisela Storz and Stephen Spiro
2. Architecture and Dynamics of Transcriptional
11. Global Responses of Bacteria to
Networks • 17 Oxygen Deprivation • 175
Anat Bren and Uri Alon
Patricia J. Kiley and Timothy J. Donohue
3. Regulation by Alternative Sigma
12. Sensing Metals: the Versatility
Factors • 31
John D. Helmann of Fur • 191
Sun-Shin Cha, Jung-Ho Shin, and Jung-Hye Roe
4. The Role of Two-Component Transduction
Systems in Bacterial Stress Responses • 45 13. The DNA Damage Response • 205
Michael T. Laub Susan T. Lovett
5. Roles of mRNA Stability, Translational
III. General Stress Responses
Regulation, and Small RNAs in Stress Response
Regulation • 59
Susan Gottesman
14. The Stringent Response • 231
Emmanuelle Bouveret and Aurélia Battesti
6. Role of Proteolysis and Chaperones in Stress
Response and Regulation • 75
15. The General Stress Response in
Kürs¸ad Turgay
Gram-Negative Bacteria • 251
Regine Hengge
II. Specific Stress Responses
16. The General Stress Response in
7. Cellular Response to Heat Shock and Cold Alphaproteobacteria • 291
Shock • 93 Anne Francez-Charlot, Julia Frunzke, and
Bentley Lim and Carol A. Gross Julia A. Vorholt
vii
viii CONTENTS
17. The General Stress Response in V. Bacteria Thriving in Stressful Environments
Bacillus subtilis and Related Gram-Positive
Bacteria • 301
25. Metamicrobiology: Analyzing Microbial
Chester W. Price
Behavior at the Community Level • 419
Jo Handelsman
18. Resistance of Bacterial Spores • 319
Peter Setlow
26. Life at the Extremes of
Temperature • 425
19. Protection against Foreign DNA • 333 Charles Gerday
Philippe Horvath and Rodolphe Barrangou
27. Comparative Genomics of Stress Response
20. More than Just a Quorum: Systems in Deinococcus Bacteria • 445
Integration of Stress and Other Kira S. Makarova and Michael J. Daly
Environmental Cues in Acyl-H omoserine
Lactone Signaling • 349
Brett Mellbye and Martin Schuster VI. Applications of Stress Response Studies
21. Biofilms • 365 28. Redox Mechanisms and Reactive
Hera Vlamakis and Roberto Kolter Oxygen Species in Antibiotic Action and
Resistance • 461
22. Persister Bacteria • 375 Inas J. Radhi and Gerard D. Wright
Nathalie Q. Balaban
29. Applications of Stress Response Studies:
Biofuel Production • 473
IV. Pathogenic Responses
James B. McKinlay and Caroline S. Harwood
23. Bacterial Responses to the 30. Microbial Bioremediation of Chemical
Host Cell • 385 Pollutants: How Bacteria Cope with Multi-Stress
Alfonso Felipe-López and Michael Hensel Environmental Scenarios • 481
Victor de Lorenzo and Herminia Loza-Tavera
24. Phase Variation • 399
Marjan W. van der Woude and
Sarah E. Broadbent Index • 493
CONTRIBUTORS
Sarah E. Ades Sarah E. Broadbent
Department of Biochemistry and Molecular Biology Department of Biology and the
Pennsylvania State University Hull York Medical School
University Park, PA 16802 University of York
York Y010 5YW, United Kingdom
Uri Alon
Department of Molecular Cell Biology Sun-Shin Cha
Weizmann Institute of Science Marine Biotechnology Research Center
Rehovot 76100, Israel Korea Ocean Research & Development Institute
Ansan P.O. Box 29
M. Madan Babu Seoul 425-600, Korea
MRC Laboratory of Molecular Biology
Hills Road Guilhem Chalancon
Cambridge CB2 0QH, United Kingdom MRC Laboratory of Molecular Biology
Hills Road
Nathalie Q. Balaban Cambridge CB2 0QH, United Kingdom
Racah Institute of Physics and The Sudarsky Center
for Computational Biology Michael J. Daly
Hebrew University Department of Pathology
Jerusalem 91904, Israel Uniformed Services University of the
Health Sciences
Rodolphe Barrangou Bethesda, MD 20814
Danisco USA Inc.
Madison, WI 53716 Victor de Lorenzo
Systems Biology Program
Aurélia Battesti Centro Nacional de Biotecnología-GSIC
NIH/NCI Campus de Cantoblanco
9000 Rockville Pike Madrid 28049, Spain
Bethesda, MD 20892
Timothy J. Donohue
Emmanuelle Bouveret Department of Bacteriology and Great Lakes
CNRS Bioenergy Research Center
University Aix-Marseille, LISM, UPR9027 University of Wisconsin—Madison
31 chemin Joseph Aiguier Madison, WI 53706
13009 Marseille, France
Alfonso Felipe-López
Anat Bren Abteilung Mikrobiologie
Department of Molecular Cell Biology Fachbereich Biologie/Chemie
Weizmann Institute of Science Universität Osnabrück
Rehovot 76100, Israel 49076 Osnabrück, Germany
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